101
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Wang X, Zhu Y, Zhao Q, Lu W, Xu Y, Hu H, Lu X. Chemical Space Profiling of SARS-CoV-2 PL pro Using DNA-Encoded Focused Libraries. ACS Med Chem Lett 2024; 15:555-564. [PMID: 38628804 PMCID: PMC11017295 DOI: 10.1021/acsmedchemlett.4c00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
DNA-encoded library (DEL) technology is gaining attention for its rapid construction and deconvolution capabilities. Our study explored a novel strategy using rational DELs tailored for the SARS-CoV-2 papain-like protease, which revealed new fragments. Structural changes post-DEL screening mimic traditional medicinal chemistry lead optimization. We unveiled unique aromatic structures offering an alternative optimization path. Notably, we identified superior binding fragments targeting the BL2 groove. Derivative 16 emerged as the most promising by exhibiting IC50 values of 0.25 μM. Derivative 6, which features an aromatic fragment capped with a naphthalene moiety, showed IC50 values of 2.91 μM. Molecular modeling revealed hydrogen bond interactions with Lys157 residue and potential covalent interactions with nearby amino acid residues. This research underscored DEL's potential for fragment-based drug discovery against SARS-CoV-2 protease.
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Affiliation(s)
- Xudong Wang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ying Zhu
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Qingyi Zhao
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Weiwei Lu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Yechun Xu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Hangchen Hu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- School
of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced
Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Xiaojie Lu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
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102
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Panda SK, Karmakar S, Sen Gupta PS, Rana MK. Can Duvelisib and Eganelisib work for both cancer and COVID-19? Molecular-level insights from MD simulations and enhanced samplings. Phys Chem Chem Phys 2024; 26:10961-10973. [PMID: 38526354 DOI: 10.1039/d3cp05934k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
SARS-CoV-2 has caused severe illness and anxiety worldwide, evolving into more dreadful variants capable of evading the host's immunity. Cytokine storms, led by PI3Kγ, are common in cancer and SARS-CoV-2. Naturally, there is a yearning to see whether any drugs could alleviate cytokine storms for both. Upon investigation, we identified two anticancer drugs, Duvelisib and Eganelisib, that could also work against SARS-CoV-2. This report is the first to decipher their synergic therapeutic effectiveness against COVID-19 and cancer with molecular insights from atomistic simulations. In addition to PI3Kγ, these drugs exhibit specificity for the main protease among all SARS-CoV-2 targets, with significant negative binding free energies and small time-dependent conformational changes of the complexes. Complexation makes active sites and secondary structures highly mechanically stiff, with barely any deformation. Replica simulations estimated large pulling forces in enhanced sampling to dissociate the drugs from Mpro's active site. Furthermore, the radial distribution function (RDF) demonstrated that the therapeutic molecules were closest to the His41 and Cys145 catalytic dyad residues. Finally, analyses implied Duvelisib and Eganelisib as promising dual-purposed anti-COVID and anticancer drugs, potentially targeting Mpro and PI3Kγ to stop virus replication and cytokine storms concomitantly. We also distinguished hotspot residues imparting significant interactions.
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Affiliation(s)
- Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Shaswata Karmakar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, Pune, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
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103
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Zhang Y, Guo J, Liu Y, Qu Y, Li YQ, Mu Y, Li W. An allosteric mechanism for potent inhibition of SARS-CoV-2 main proteinase. Int J Biol Macromol 2024; 265:130644. [PMID: 38462102 DOI: 10.1016/j.ijbiomac.2024.130644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
The main proteinase (Mpro) of SARS-CoV-2 plays a critical role in cleaving viral polyproteins into functional proteins required for viral replication and assembly, making it a prime drug target for COVID-19. It is well known that noncompetitive inhibition offers potential therapeutic options for treating COVID-19, which can effectively reduce the likelihood of cross-reactivity with other proteins and increase the selectivity of the drug. Therefore, the discovery of allosteric sites of Mpro has both scientific and practical significance. In this study, we explored the binding characteristics and inhibiting process of Mpro activity by two recently reported allosteric inhibitors, pelitinib and AT7519 which were obtained by the X-ray screening experiments, to probe the allosteric mechanism via molecular dynamic (MD) simulations. We found that pelitinib and AT7519 can stably bind to Mpro far from the active site. The binding affinity is estimated to be -24.37 ± 4.14 and - 26.96 ± 4.05 kcal/mol for pelitinib and AT7519, respectively, which is considerably stable compared with orthosteric drugs. Furthermore, the strong binding caused clear changes in the catalytic site of Mpro, thus decreasing the substrate accessibility. The community network analysis also validated that pelitinib and AT7519 strengthened intra- and inter-domain communication of Mpro dimer, resulting in a rigid Mpro, which could negatively impact substrate binding. In summary, our findings provide the detailed working mechanism for the two experimentally observed allosteric sites of Mpro. These allosteric sites greatly enhance the 'druggability' of Mpro and represent attractive targets for the development of new Mpro inhibitors.
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Affiliation(s)
- Yunju Zhang
- School of Physics, Shandong University, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
| | - Yang Liu
- School of Physics, Shandong University, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, China
| | | | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Weifeng Li
- School of Physics, Shandong University, China.
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104
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Wang H, Chi B, Li C, Tian Z, Liu Y. Isolation, characterization and SARS-CoV-2 3CL protease inhibitory activity of a new methylsulfinyl-butanyl derivative from Raphani Semen. Nat Prod Res 2024:1-6. [PMID: 38557255 DOI: 10.1080/14786419.2024.2335668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
A new compound named raphanised A (1), along with two known methylsulfinyl -butanyl derivatives (2-3) and seven known indole derivatives (4-10), were isolated from the Raphani Semen. Among the indole derivatives, 5 was identified as a new natural product, and 4, 6, 7, 8, 9, 10 were isolated from the genus of Raphanus for the first time. Their structures were elucidated based on the NMR and HR-EI-MS analysis. Additionally, the inhibitory activity of methylsulfinyl-butanyl derivatives 1-3 on SARS CoV-2 3CL protease was evaluated. The results showed that 1-3 exhibited inhibition of SARS-CoV-2 3CL protease activity at concentrations ranging from 3.3 to 30 µM.
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Affiliation(s)
- Huanjun Wang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Bingqing Chi
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Caiyu Li
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhenhua Tian
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuecheng Liu
- Shandong Academy of Chinese Medicine, Jinan, China
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105
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Abdel-Sattar E, Kutkat O, El-Shiekh RA, El-Ashrey MK, El Kerdawy AM. In Silico and In Vitro Screening of Some Pregnane Glycosides Isolated from Certain Caralluma Species as SARS-COV-2 Main Protease Inhibitors. Chem Biodivers 2024; 21:e202301786. [PMID: 38466126 DOI: 10.1002/cbdv.202301786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
SARS-CoV-2 caused pandemic represented a major risk for the worldwide human health, animal health and economy, forcing extraordinary efforts to discover drugs for its prevention and cure. Considering the extensive interest in the pregnane glycosides because of their diverse structures and excellent biological activities, we investigated them as antiviral agents against SARS-COV-2. We selected 21 pregnane glycosides previously isolated from the genus Caralluma from Asclepiadaceae family to be tested through virtual screening molecular docking simulations for their potential inhibition of SARS-CoV-2 Mpro. Almost all target compounds showed a more or equally negative docking energy score relative to the co-crystallized inhibitor X77 (S=-12.53 kcal/mol) with docking score range of (-12.55 to -19.76 kcal/mol) and so with a potent predicted binding affinity to the target enzyme. The activity of the most promising candidates was validated by in vitro testing. Arabincoside C showed the highest activity (IC50=35.42 μg/ml) and the highest selectivity index (SI=9.9) followed by Russelioside B (IC50=50.80 μg/ml), and Arabincoside B (IC50=53.31 μg/ml).
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Affiliation(s)
- Essam Abdel-Sattar
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
| | - Omnia Kutkat
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, 12622, Giza, Egypt
- Department of microbiology, Faculty of pharmacy, Ahram Canadian University, 6 th of October, Giza, 12566, Egypt
| | - Riham A El-Shiekh
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
| | - Mohamed K El-Ashrey
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
- Medicinal Chemistry Department, Faculty of Pharmacy, King Salman International University (KSIU), 46612, South Sinai, Egypt
| | - Ahmed M El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, 11562, Cairo, Egypt
- School of Pharmacy, College of Health and Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, LN6 7DL, Lincoln, Lincolnshire, United Kingdom
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106
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Nguyen TH, Thai QM, Pham MQ, Minh PTH, Phung HTT. Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds. Mol Divers 2024; 28:553-561. [PMID: 36823394 PMCID: PMC9950021 DOI: 10.1007/s11030-023-10601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 02/25/2023]
Abstract
To date, the COVID-19 pandemic has still been infectious around the world, continuously causing social and economic damage on a global scale. One of the most important therapeutic targets for the treatment of COVID-19 is the main protease (Mpro) of SARS-CoV-2. In this study, we combined machine-learning (ML) model with atomistic simulations to computationally search for highly promising SARS-CoV-2 Mpro inhibitors from the representative natural compounds of the National Cancer Institute (NCI) Database. First, the trained ML model was used to scan the library quickly and reliably for possible Mpro inhibitors. The ML output was then confirmed using atomistic simulations integrating molecular docking and molecular dynamic simulations with the linear interaction energy scheme. The results turned out to show that there was evidently good agreement between ML and atomistic simulations. Ten substances were proposed to be able to inhibit SARS-CoV-2 Mpro. Seven of them have high-nanomolar affinity and are very potential inhibitors. The strategy has been proven to be reliable and appropriate for fast prediction of SARS-CoV-2 Mpro inhibitors, benefiting for new emerging SARS-CoV-2 variants in the future accordingly.
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Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Quynh Mai Thai
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pham Thi Hong Minh
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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107
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Roney M, Singh G, Huq AKMM, Forid MS, Ishak WMBW, Rullah K, Aluwi MFFM, Tajuddin SN. Identification of Pyrazole Derivatives of Usnic Acid as Novel Inhibitor of SARS-CoV-2 Main Protease Through Virtual Screening Approaches. Mol Biotechnol 2024; 66:696-706. [PMID: 36752937 PMCID: PMC9907211 DOI: 10.1007/s12033-023-00667-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/12/2023] [Indexed: 02/09/2023]
Abstract
The infection produced by the SARS-CoV-2 virus remains a significant health crisis worldwide. The lack of specific medications for COVID-19 necessitates a concerted effort to find the much-desired therapies for this condition. The main protease (Mpro) of SARS-CoV-2 is a promising target, vital for virus replication and transcription. In this study, fifty pyrazole derivatives were tested for their pharmacokinetics and drugability, resulting in eight hit compounds. Subsequent molecular docking simulations on SARS-CoV-2 main protease afforded two lead compounds with strong affinity at the active site. Additionally, the molecular dynamics (MD) simulations of lead compounds (17 and 39), along with binding free energy calculations, were accomplished to validate the stability of the docked complexes and the binding poses achieved in docking experiments. Based on these findings, compound 17 and 39, with their favorable projected pharmacokinetics and pharmacological characteristics, are the proposed potential antiviral candidates which require further investigation to be used as anti-SARS-CoV-2 medication.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Gagandeep Singh
- Section of Microbiology, Central Ayurveda Research Institute, Jhansi, Uttar Pradesh, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - A K M Moyeenul Huq
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
- School of Medicine, Department of Pharmacy, University of Asia Pacific, 74/A, Green Road, Dhaka, 1205, Bangladesh.
| | - Md Shaekh Forid
- Faculty of Chemical and Processing Engineering Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Wan Maznah Binti Wan Ishak
- Faculty of Chemical and Processing Engineering Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Kamal Rullah
- Kulliyyah of Pharmacy, International Islamic University Malaysia (IIUM), Jalan Sultan Ahmad Shah, 25200, Kuantan, Pahang, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia.
| | - Saiful Nizam Tajuddin
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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108
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Chen X, Huang X, Ma Q, Kuzmič P, Zhou B, Zhang S, Chen J, Xu J, Liu B, Jiang H, Zhang W, Yang C, Wu S, Huang J, Li H, Long C, Zhao X, Xu H, Sheng Y, Guo Y, Niu C, Xue L, Xu Y, Liu J, Zhang T, Spencer J, Zhu Z, Deng W, Chen X, Chen SH, Zhong N, Xiong X, Yang Z. Preclinical evaluation of the SARS-CoV-2 M pro inhibitor RAY1216 shows improved pharmacokinetics compared with nirmatrelvir. Nat Microbiol 2024; 9:1075-1088. [PMID: 38553607 PMCID: PMC10994847 DOI: 10.1038/s41564-024-01618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 01/22/2024] [Indexed: 04/06/2024]
Abstract
Although vaccines are available for SARS-CoV-2, antiviral drugs such as nirmatrelvir are still needed, particularly for individuals in whom vaccines are less effective, such as the immunocompromised, to prevent severe COVID-19. Here we report an α-ketoamide-based peptidomimetic inhibitor of the SARS-CoV-2 main protease (Mpro), designated RAY1216. Enzyme inhibition kinetic analysis shows that RAY1216 has an inhibition constant of 8.4 nM and suggests that it dissociates about 12 times slower from Mpro compared with nirmatrelvir. The crystal structure of the SARS-CoV-2 Mpro:RAY1216 complex shows that RAY1216 covalently binds to the catalytic Cys145 through the α-ketoamide group. In vitro and using human ACE2 transgenic mouse models, RAY1216 shows antiviral activities against SARS-CoV-2 variants comparable to those of nirmatrelvir. It also shows improved pharmacokinetics in mice and rats, suggesting that RAY1216 could be used without ritonavir, which is co-administered with nirmatrelvir. RAY1216 has been approved as a single-component drug named 'leritrelvir' for COVID-19 treatment in China.
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Affiliation(s)
- Xiaoxin Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xiaodong Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qinhai Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Biao Zhou
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou National Laboratory, Guangzhou, China
| | - Sai Zhang
- Guangzhou National Laboratory, Guangzhou, China
| | | | - Jinxin Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Bin Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haiming Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenjie Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunguang Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shiguan Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | - Haijun Li
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Chaofeng Long
- Guangdong Raynovent Biotech Co., Ltd, Guangzhou, China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), Guangzhou, China
| | - Hongrui Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanan Sheng
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yaoting Guo
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Chuanying Niu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lu Xue
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Xu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | | | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xinwen Chen
- Guangzhou National Laboratory, Guangzhou, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | | | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China.
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109
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Mendonça SC, Gomes BA, Campos MF, da Fonseca TS, Esteves MEA, Andriolo BV, Cheohen CFDAR, Constant LEC, da Silva Costa S, Calil PT, Tucci AR, de Oliveira TKF, Rosa ADS, Ferreira VNDS, Lima JNH, Miranda MD, da Costa LJ, da Silva ML, Scotti MT, Allonso D, Leitão GG, Leitão SG. Myrtucommulones and Related Acylphloroglucinols from Myrtaceae as a Promising Source of Multitarget SARS-CoV-2 Cycle Inhibitors. Pharmaceuticals (Basel) 2024; 17:436. [PMID: 38675398 PMCID: PMC11054083 DOI: 10.3390/ph17040436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The LABEXTRACT plant extract bank, featuring diverse members of the Myrtaceae family from Brazilian hot spot regions, provides a promising avenue for bioprospection. Given the pivotal roles of the Spike protein and 3CLpro and PLpro proteases in SARS-CoV-2 infection, this study delves into the correlations between the Myrtaceae species from the Atlantic Forest and these targets, as well as an antiviral activity through both in vitro and in silico analyses. The results uncovered notable inhibitory effects, with Eugenia prasina and E. mosenii standing out, while E. mosenii proved to be multitarget, presenting inhibition values above 72% in the three targets analyzed. All extracts inhibited viral replication in Calu-3 cells (EC50 was lower than 8.3 µg·mL-1). Chemometric analyses, through LC-MS/MS, encompassing prediction models and molecular networking, identified potential active compounds, such as myrtucommulones, described in the literature for their antiviral activity. Docking analyses showed that one undescribed myrtucommulone (m/z 841 [M - H]-) had a higher fitness score when interacting with the targets of this study, including ACE2, Spike, PLpro and 3CLpro of SARS-CoV-2. Also, the study concludes that Myrtaceae extracts, particularly from E. mosenii and E. prasina, exhibit promising inhibitory effects against crucial stages in SARS-CoV-2 infection. Compounds like myrtucommulones emerge as potential anti-SARS-CoV-2 agents, warranting further exploration.
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Affiliation(s)
- Simony Carvalho Mendonça
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (S.C.M.); (B.A.G.); (M.F.C.)
| | - Brendo Araujo Gomes
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (S.C.M.); (B.A.G.); (M.F.C.)
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Mariana Freire Campos
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (S.C.M.); (B.A.G.); (M.F.C.)
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Thamirys Silva da Fonseca
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil;
| | - Maria Eduarda Alves Esteves
- Programa de Pós-Graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.A.E.); (M.L.d.S.)
| | - Bruce Veiga Andriolo
- Programa de Pós-Graduação em Biotecnologia, Instituto Nacional de Metrologia, Qualidade e Tecnologia, Duque de Caxias 25250-020, RJ, Brazil;
| | - Caio Felipe de Araujo Ribas Cheohen
- Programa de Pós-Graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé 27965-045, RJ, Brazil;
| | - Larissa Esteves Carvalho Constant
- Programa de Pós-Graduação em Ciências Biológicas, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (L.E.C.C.); (S.d.S.C.); (D.A.)
| | - Stephany da Silva Costa
- Programa de Pós-Graduação em Ciências Biológicas, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (L.E.C.C.); (S.d.S.C.); (D.A.)
| | - Pedro Telles Calil
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (P.T.C.); (L.J.d.C.)
| | - Amanda Resende Tucci
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Thamara Kelcya Fonseca de Oliveira
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Alice dos Santos Rosa
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Vivian Neuza dos Santos Ferreira
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
| | - Julia Nilo Henrique Lima
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
| | - Milene Dias Miranda
- Laboratory of Morphology and Viral Morphogenesis, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (T.K.F.d.O.); (A.d.S.R.); (V.N.d.S.F.); (J.N.H.L.); (M.D.M.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Luciana Jesus da Costa
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (P.T.C.); (L.J.d.C.)
| | - Manuela Leal da Silva
- Programa de Pós-Graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil; (M.E.A.E.); (M.L.d.S.)
- Programa de Pós-Graduação em Biotecnologia, Instituto Nacional de Metrologia, Qualidade e Tecnologia, Duque de Caxias 25250-020, RJ, Brazil;
- Programa de Pós-Graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé 27965-045, RJ, Brazil;
| | - Marcus Tullius Scotti
- Departamento de Química, Universidade Federal da Paraíba, João Pessoa 58033-455, PB, Brazil;
| | - Diego Allonso
- Programa de Pós-Graduação em Ciências Biológicas, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil; (L.E.C.C.); (S.d.S.C.); (D.A.)
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Gilda Guimarães Leitão
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Suzana Guimarães Leitão
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (S.C.M.); (B.A.G.); (M.F.C.)
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil;
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110
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Zengin IN, Koca MS, Tayfuroglu O, Yildiz M, Kocak A. Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 M pro. J Comput Aided Mol Des 2024; 38:15. [PMID: 38532176 DOI: 10.1007/s10822-024-00554-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024]
Abstract
Here, we introduce the use of ANI-ML potentials as a rescoring function in the host-guest interaction in molecular docking. Our results show that the "docking power" of ANI potentials can compete with the current scoring functions at the same level of computational cost. Benchmarking studies on CASF-2016 dataset showed that ANI is ranked in the top 5 scoring functions among the other 34 tested. In particular, the ANI predicted interaction energies when used in conjunction with GOLD-PLP scoring function can boost the top ranked solution to be the closest to the x-ray structure. Rapid and accurate calculation of interaction energies between ligand and protein also enables screening of millions of drug candidates/docking poses. Using a unique protocol in which docking by GOLD-PLP, rescoring by ANI-ML potentials and extensive MD simulations along with end state free energy methods are combined, we have screened FDA approved drugs against the SARS-CoV-2 main protease (Mpro). The top six drug molecules suggested by the consensus of these free energy methods have already been in clinical trials or proposed as potential drug molecules in previous theoretical and experimental studies, approving the validity and the power of accuracy in our screening method.
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Affiliation(s)
- Irem N Zengin
- Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - M Serdar Koca
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
- Pfizer - Universidad de Granada - Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), 18016, Granada, Spain
| | - Omer Tayfuroglu
- Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Muslum Yildiz
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Abdulkadir Kocak
- Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey.
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111
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Kumar A, Vashisth H. Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface. J Chem Inf Model 2024; 64:2068-2076. [PMID: 38460144 PMCID: PMC10966652 DOI: 10.1021/acs.jcim.3c01933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024]
Abstract
The highly conserved protease enzyme from SARS-CoV-2 (MPro) is crucial for viral replication and is an attractive target for the design of novel inhibitory compounds. MPro is known to be conformationally flexible and has been stabilized in an extended conformation in a complex with a novel nanobody (NB2B4), which inhibits the dimerization of the enzyme via binding to an allosteric site. However, the energetic contributions of the nanobody residues stabilizing the MPro/nanobody interface remain unresolved. We probed these residues using all-atom MD simulations in combination with alchemical free energy calculations by studying the physical residue-residue interactions and discovered the role of hydrophobic and electrostatic interactions in stabilizing the complex. Specifically, we found via mutational analysis that three interfacial nanobody residues (Y59, R106, and L109) contributed significantly, two residues (L107 and P110) contributed moderately, and two residues (H112 and T113) contributed minimally to the overall binding affinity of the nanobody. We also discovered that the nanobody affinity could be enhanced via a charge-reversal mutation (D62R) that alters the local interfacial electrostatic environment of this residue in the complex. These findings are potentially useful in designing novel synthetic nanobodies as allosteric inhibitors of MPro.
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Affiliation(s)
- Amit Kumar
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Harish Vashisth
- Department
of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, New Hampshire 03824, United States
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112
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Desantis J, Bazzacco A, Eleuteri M, Tuci S, Bianconi E, Macchiarulo A, Mercorelli B, Loregian A, Goracci L. Design, synthesis, and biological evaluation of first-in-class indomethacin-based PROTACs degrading SARS-CoV-2 main protease and with broad-spectrum antiviral activity. Eur J Med Chem 2024; 268:116202. [PMID: 38394929 DOI: 10.1016/j.ejmech.2024.116202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
To date, Proteolysis Targeting Chimera (PROTAC) technology has been successfully applied to mediate proteasomal-induced degradation of several pharmaceutical targets mainly related to oncology, immune disorders, and neurodegenerative diseases. On the other hand, its exploitation in the field of antiviral drug discovery is still in its infancy. Recently, we described two indomethacin (INM)-based PROTACs displaying broad-spectrum antiviral activity against coronaviruses. Here, we report the design, synthesis, and characterization of a novel series of INM-based PROTACs that recruit either Von-Hippel Lindau (VHL) or cereblon (CRBN) E3 ligases. The panel of INM-based PROTACs was also enlarged by varying the linker moiety. The antiviral activity resulted very susceptible to this modification, particularly for PROTACs hijacking VHL as E3 ligase, with one piperazine-based compound (PROTAC 6) showing potent anti-SARS-CoV-2 activity in infected human lung cells. Interestingly, degradation assays in both uninfected and virus-infected cells with the most promising PROTACs emerged so far (PROTACs 5 and 6) demonstrated that INM-PROTACs do not degrade human PGES-2 protein, as initially hypothesized, but induce the concentration-dependent degradation of SARS-CoV-2 main protease (Mpro) both in Mpro-transfected and in SARS-CoV-2-infected cells. Importantly, thanks to the target degradation, INM-PROTACs exhibited a considerable enhancement in antiviral activity with respect to indomethacin, with EC50 values in the low-micromolar/nanomolar range. Finally, kinetic solubility as well as metabolic and chemical stability were measured for PROTACs 5 and 6. Altogether, the identification of INM-based PROTACs as the first class of SARS-CoV-2 Mpro degraders demonstrating activity also in SARS-CoV-2-infected cells represents a significant advance in the development of effective, broad-spectrum anti-coronavirus strategies.
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Affiliation(s)
- Jenny Desantis
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy
| | | | - Michela Eleuteri
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy
| | - Sara Tuci
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Elisa Bianconi
- Department of Pharmaceutical Science, University of Perugia, Italy
| | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, Padua, Italy.
| | - Laura Goracci
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy.
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113
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Amblard F, LeCher JC, De R, Zhou S, Liu P, Goh SL, Tao S, Patel D, Downs-Bowen J, Zandi K, Zhang H, Chaudhry G, McBrayer T, Muczynski M, Al-Homoudi A, Engel J, Lan S, Sarafianos SG, Kovari LC, Schinazi RF. Synthesis and biological evaluation of novel peptidomimetic inhibitors of the coronavirus 3C-like protease. Eur J Med Chem 2024; 268:116263. [PMID: 38432056 PMCID: PMC11188152 DOI: 10.1016/j.ejmech.2024.116263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and related variants, are responsible for the devastating coronavirus disease 2019 (COVID-19) pandemic. The SARS-CoV-2 main protease (Mpro) plays a central role in the replication of the virus and represents an attractive drug target. Herein, we report the discovery of novel SARS-CoV-2 Mpro covalent inhibitors, including highly effective compound NIP-22c which displays high potency against several key variants and clinically relevant nirmatrelvir Mpro E166V mutants.
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Affiliation(s)
- Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
| | - Julia C LeCher
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ramyani De
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shaoman Zhou
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Peng Liu
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shu Ling Goh
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Dharmeshkumar Patel
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Jessica Downs-Bowen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Keivan Zandi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Huanchun Zhang
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Gitika Chaudhry
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Tamara McBrayer
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Michael Muczynski
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Abdullah Al-Homoudi
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Joseph Engel
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Shuiyun Lan
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
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114
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Shurtleff VW, Layton ME, Parish CA, Perkins JJ, Schreier JD, Wang Y, Adam GC, Alvarez N, Bahmanjah S, Bahnck-Teets CM, Boyce CW, Burlein C, Cabalu TD, Campbell BT, Carroll SS, Chang W, de Lera Ruiz M, Dolgov E, Fay JF, Fox NG, Goh SL, Hartingh TJ, Hurzy DM, Kelly MJ, Klein DJ, Klingler FM, Krishnamurthy H, Kudalkar S, Mayhood TW, McKenna PM, Murray EM, Nahas D, Nawrat CC, Park S, Qian D, Roecker AJ, Sharma V, Shipe WD, Su J, Taggart RV, Truong Q, Wu Y, Zhou X, Zhuang N, Perlin DS, Olsen DB, Howe JA, McCauley JA. Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic. J Med Chem 2024; 67:3935-3958. [PMID: 38365209 DOI: 10.1021/acs.jmedchem.3c02248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
As SARS-CoV-2 continues to circulate, antiviral treatments are needed to complement vaccines. The virus's main protease, 3CLPro, is an attractive drug target in part because it recognizes a unique cleavage site, which features a glutamine residue at the P1 position and is not utilized by human proteases. Herein, we report the invention of MK-7845, a novel reversible covalent 3CLPro inhibitor. While most covalent inhibitors of SARS-CoV-2 3CLPro reported to date contain an amide as a Gln mimic at P1, MK-7845 bears a difluorobutyl substituent at this position. SAR analysis and X-ray crystallographic studies indicate that this group interacts with His163, the same residue that forms a hydrogen bond with the amide substituents typically found at P1. In addition to promising in vivo efficacy and an acceptable projected human dose with unboosted pharmacokinetics, MK-7845 exhibits favorable properties for both solubility and absorption that may be attributable to the unusual difluorobutyl substituent.
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Affiliation(s)
| | - Mark E Layton
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Craig A Parish
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - James J Perkins
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John D Schreier
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yunyi Wang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Gregory C Adam
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nadine Alvarez
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | | | | | | | | | - Tamara D Cabalu
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Brian T Campbell
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Steven S Carroll
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Wonsuk Chang
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Enriko Dolgov
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - John F Fay
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Nicholas G Fox
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shih Lin Goh
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Danielle M Hurzy
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Michael J Kelly
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel J Klein
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | | | - Shalley Kudalkar
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Todd W Mayhood
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Philip M McKenna
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Edward M Murray
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Debbie Nahas
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Steven Park
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | | | | | - Vijeta Sharma
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - William D Shipe
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jing Su
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Robert V Taggart
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Quang Truong
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yin Wu
- Viva Biotech Ltd., Shanghai 201318, China
| | - Xiaoyan Zhou
- Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - David B Olsen
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John A Howe
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John A McCauley
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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115
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Westberg M, Su Y, Zou X, Huang P, Rustagi A, Garhyan J, Patel PB, Fernandez D, Wu Y, Hao C, Lo CW, Karim M, Ning L, Beck A, Saenkham-Huntsinger P, Tat V, Drelich A, Peng BH, Einav S, Tseng CTK, Blish C, Lin MZ. An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Sci Transl Med 2024; 16:eadi0979. [PMID: 38478629 PMCID: PMC11193659 DOI: 10.1126/scitranslmed.adi0979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/21/2024] [Indexed: 05/09/2024]
Abstract
Inhibitors of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) such as nirmatrelvir (NTV) and ensitrelvir (ETV) have proven effective in reducing the severity of COVID-19, but the presence of resistance-conferring mutations in sequenced viral genomes raises concerns about future drug resistance. Second-generation oral drugs that retain function against these mutants are thus urgently needed. We hypothesized that the covalent hepatitis C virus protease inhibitor boceprevir (BPV) could serve as the basis for orally bioavailable drugs that inhibit SARS-CoV-2 Mpro more efficiently than existing drugs. Performing structure-guided modifications of BPV, we developed a picomolar-affinity inhibitor, ML2006a4, with antiviral activity, oral pharmacokinetics, and therapeutic efficacy similar or superior to those of NTV. A crucial feature of ML2006a4 is a derivatization of the ketoamide reactive group that improves cell permeability and oral bioavailability. Last, ML2006a4 was found to be less sensitive to several mutations that cause resistance to NTV or ETV and occur in the natural SARS-CoV-2 population. Thus, anticipatory design can preemptively address potential resistance mechanisms to expand future treatment options against coronavirus variants.
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Affiliation(s)
- Michael Westberg
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
- Department of Chemistry, Aarhus University; 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University; 8000 Aarhus C, Denmark
| | - Yichi Su
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Xinzhi Zou
- Department of Bioengineering, Stanford University; Stanford, CA 94305, USA
| | - Pinghan Huang
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | - Jaishree Garhyan
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University; Stanford, CA 94305, USA
| | - Puja Bhavesh Patel
- Stanford In Vitro Biosafety Level 3 Service Center, Stanford University; Stanford, CA 94305, USA
| | - Daniel Fernandez
- Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University; Stanford, CA 94305, USA
- Sarafan ChEM-H, Macromolecular Structure Knowledge Center, Stanford University; Stanford, CA 94305, USA
| | - Yan Wu
- Department of Bioengineering, Stanford University; Stanford, CA 94305, USA
| | - Chenzhou Hao
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
| | - Chieh-Wen Lo
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | - Marwah Karim
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | - Lin Ning
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
| | - Aimee Beck
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
| | | | - Vivian Tat
- Department of Pathology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Bi-Hung Peng
- Department of Neuroscience, Cell Biology, and Anatomy, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Shirit Einav
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University; Stanford, CA 94305, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, The University of Texas Medical Branch; Galveston, TX 77555, USA
- Department of Pathology, The University of Texas Medical Branch; Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology, and Anatomy, The University of Texas Medical Branch; Galveston, TX 77555, USA
| | - Catherine Blish
- Department of Medicine, Stanford University; Stanford, CA 94305, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Michael Z. Lin
- Department of Neurobiology, Stanford University; Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University; Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford University; Stanford, CA 94305, USA
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116
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Nguyen HH, Tufts J, Minh DDL. On Inactivation of the Coronavirus Main Protease. J Chem Inf Model 2024; 64:1644-1656. [PMID: 38423522 PMCID: PMC10936523 DOI: 10.1021/acs.jcim.3c01518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
A deeper understanding of the inactive conformations of the coronavirus main protease (MPro) could inform the design of allosteric drugs. Based on extensive molecular dynamics simulations, we built a Markov State Model to investigate structural changes that can inactivate the SARS-CoV-2 MPro. In a subset of structures, one subunit of the homodimer assumes an inactive conformation that resembles an inactive crystal structure. However, contradicting the widely held half-of-sites activity hypothesis, the most populated enzyme structures have two active subunits. We then used transition path theory (TPT) and the Jensen-Shannon Divergence (JSD) to pinpoint residues involved in the inactivation process. A π stack between Phe140 and His163 is a key feature that can distinguish active and inactive conformations of MPro. Each subunit has unique inactive conformations stabilized by π stacking interactions involving residues Phe140, Tyr118, His163, and His172, a hydrogen bonding network centered around His163 and His172, and a modified network of interactions in the dimer interface. The importance of these residues in maintaining an active structure explains the sensitivity of enzymatic activity to site-directed mutagenesis.
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Affiliation(s)
- Hong Ha Nguyen
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Jim Tufts
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - David D. L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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117
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Chen J, Zhou Y, Wei X, Xu X, Qin Z, Ong CP, Ye ZW, Jin DY, Boitrel B, Yuan S, Chan JFW, Li H, Sun H. Development of Pan-Anti-SARS-CoV-2 Agents through Allosteric Inhibition of nsp14/nsp10 Complex. ACS Infect Dis 2024; 10:858-869. [PMID: 37897418 DOI: 10.1021/acsinfecdis.3c00356] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
SARS-CoV-2 nsp14 functions both as an exoribonuclease (ExoN) together with its critical cofactor nsp10 and as an S-adenosyl methionine-dependent (guanine-N7) methyltransferase (MTase), which makes it an attractive target for the development of pan-anti-SARS-CoV-2 drugs. Herein, we screened a panel of compounds (and drugs) and found that certain compounds, especially Bi(III)-based compounds, could allosterically inhibit both MTase and ExoN activities of nsp14 potently. We further demonstrated that Bi(III) binds to both nsp14 and nsp10, resulting in the release of Zn(II) ions from the enzymes as well as alternation of protein quaternary structures. The in vitro activities of the compounds were also validated in SARS-CoV-2-infected mammalian cells. Importantly, we showed that nsp14 serves as an authentic target of Bi(III)-based antivirals in SARS-CoV-2-infected mammalian cells by quantification of both the protein and inhibitor. This study highlights the importance of nsp14/nsp10 as a potential target for the development of pan-antivirals against SARS-CoV-2 infection.
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Affiliation(s)
- Jingxin Chen
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Ying Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Xueying Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Xiaohan Xu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Zhenzhi Qin
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Chon Phin Ong
- School of Biomedical Sciences, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Zi-Wei Ye
- School of Biomedical Sciences, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Bernard Boitrel
- University of Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Rennes 35000, France
| | - Shuofeng Yuan
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Jasper F-W Chan
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
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118
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Ibrahim M, Sun X, de Oliveira VM, Liu R, Clayton J, El Kilani H, Shen J, Hilgenfeld R. Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study of the free enzyme and its complex with inhibitor 13b-K. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583178. [PMID: 38496596 PMCID: PMC10942327 DOI: 10.1101/2024.03.04.583178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
During the continuing evolution of SARS-CoV-2, the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November that year. Along with its sublineages, it has maintained a prominent role ever since. The Nsp5 main protease (Mpro) of the Omicron virus is characterized by a single dominant mutation, P132H. Here we determined the X-ray crystal structures of the P132H mutant (or O-Mpro) as free enzyme and in complex with the Mpro inhibitor, the alpha-ketoamide 13b-K, and we conducted enzymology, biophysical as well as theoretical studies to characterize the O-Mpro. We found that O-Mpro has a similar overall structure and binding with 13b-K; however, it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro (with "WT" referring to the original Wuhan-1 strain). Intriguingly, the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here. The empirical folding free energy calculations suggest that the O-Mpro dimer is destabilized relative to the WT-Mpro due to the less favorable van der Waals interactions and backbone conformation in the individual protomers. The all-atom continuous constant pH molecular dynamics (MD) simulations reveal that His132 and Glu240 display coupled titration. At pH 7, His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged. In order to examine whether the Omicron mutation eases the emergence of further Mpro mutations, we also determined crystal structures of the relatively frequent P132H+T169S double mutant but found little evidence for a correlation between the two sites.
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Affiliation(s)
- Mohamed Ibrahim
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Vinicius Martins de Oliveira
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Ruibin Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Joseph Clayton
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Haifa El Kilani
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg - Lübeck - Borstel - Riems Site, University of Lübeck, 23562 Lübeck, Germany
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119
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Ghosh AK, Yadav M, Iddum S, Ghazi S, Lendy EK, Jayashankar U, Beechboard SN, Takamatsu Y, Hattori SI, Aamano M, Higashi-Kuwata N, Mitsuya H, Mesecar AD. Exploration of P1 and P4 modifications of nirmatrelvir: Design, synthesis, biological evaluation, and X-ray structural studies of SARS-CoV-2 Mpro inhibitors. Eur J Med Chem 2024; 267:116132. [PMID: 38335815 PMCID: PMC10964431 DOI: 10.1016/j.ejmech.2024.116132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/12/2024]
Abstract
We report the synthesis, biological evaluation, and X-ray structural studies of a series of SARS-CoV-2 Mpro inhibitors based upon the X-ray crystal structure of nirmatrelvir, an FDA approved drug that targets the main protease of SARS-CoV-2. The studies involved examination of various P4 moieties, P1 five- and six-membered lactam rings to improve potency. In particular, the six-membered P1 lactam ring analogs exhibited high SARS-CoV-2 Mpro inhibitory activity. Several compounds effectively blocked SARS-CoV-2 replication in VeroE6 cells. One of these compounds maintained good antiviral activity against variants of concern including Delta and Omicron variants. A high-resolution X-ray crystal structure of an inhibitor bound to SARS-CoV-2 Mpro was determined to gain insight into the ligand-binding properties in the Mpro active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Monika Yadav
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Satyanarayana Iddum
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Somayeh Ghazi
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Emma K Lendy
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Uttara Jayashankar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Sydney N Beechboard
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yuki Takamatsu
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan
| | - Masayuki Aamano
- Department of Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, 162-8655, Japan; Department of Infectious Diseases, Kumamoto University School of Medicine, Kumamoto, 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD, 20892, USA
| | - Andrew D Mesecar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA; Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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120
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Omar R, Abd El-Salam M, Elsbaey M, Hassan M. Fourteen immunomodulatory alkaloids and two prenylated phenylpropanoids with dual therapeutic approach for COVID-19: molecular docking and dynamics studies. J Biomol Struct Dyn 2024; 42:2298-2315. [PMID: 37116054 DOI: 10.1080/07391102.2023.2204973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 04/11/2023] [Indexed: 04/30/2023]
Abstract
The pandemic outbreak of COVID-19 caused by the new severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a global health burden. To date, there is no highly effective antiviral therapy to eradicate the virus; as a result, researchers are racing to introduce new potential therapeutic agents. Alternatively, traditional immunity boosters and symptomatic treatment based on natural bioactive compounds are also an option. The 3-chymotrypsin-like protease (3CLpro) crystal structure, the main proteolytic enzyme of SARS-CoV-2, has been unraveled, allowing the development of effective protease inhibitors via in silico and biological studies. In COVID-19 infected patients, the loss of lung function, and mortality are reported to be linked to several inflammatory mediators and cytokines. In this context, the approach of introducing immunomodulatory agents may be considered a dual lifesaving strategy in combination with antiviral drugs. This study aims to provide immunomodulatory natural products exhibiting potential protease inhibitory activities. Selected groups of alkaloids of different classes and two prenylated phenylpropanoids from the Brazilian green propolis were in silico screened for their ability to inhibit COVID-19 3CLpro protease. Results showed that compounds exhibited binding energy scores with values ranging from -6.96 to -3.70 compared to the reference synthetic protease inhibitor O6K with a binding energy score of -7.57. O6K binding energy was found comparable with lead phytochemicals in our study, while their toxicity and drug-likeness criteria are better than that of O6K. The activities of these molecules are mainly ascribed to their ability to form hydrogen bonding with 3CLpro crucial amino acid residues of the catalytic site. In addition, the molecular dynamics simulations further showed that some of these compounds formed stable complexes as evidenced by the occupancy fraction measurements. The study suggested that the major immunomodulators 3β, 20α-diacetamido-5α-pregnane, (20S)-(benzamido)-3β-(N,N-dimethyamino)-pregnane, and baccharin are 3CLpro inhibitors. Biological screenings of these phytochemicals will be valuable to experimentally validate and consolidate the results of this study before a rigid conclusion is reached, which may pave the way for the development of efficient modulatory bioactive compounds with dual bioactions in COVID-19 intervention. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rowida Omar
- Department of Pharmacognosy, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa, Egypt
| | - Mohamed Abd El-Salam
- Department of Pharmacognosy, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa, Egypt
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Marwa Elsbaey
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Madiha Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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121
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Mahgoub RE, Mohamed FE, Ali BR, Ferreira J, Rabeh WM, Atatreh N, Ghattas MA. Discovery of pyrimidoindol and benzylpyrrolyl inhibitors targeting SARS-CoV-2 main protease (M pro) through pharmacophore modelling, covalent docking, and biological evaluation. J Mol Graph Model 2024; 127:108672. [PMID: 37992552 DOI: 10.1016/j.jmgm.2023.108672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
The main protease (Mpro) enzyme has an imperative function in disease progression and the life cycle of the SARS-CoV-2 virus. Although the orally active drug nirmatrelvir (co-administered with ritonavir as paxlovid) has been approved for emergency use as the frontline antiviral agent, there are a number of limitations that necessitate the discovery of new drug scaffolds, such as poor pharmacokinetics and susceptibility to proteolytic degradation due to its peptidomimetic nature. This study utilized a novel virtual screening workflow that combines pharmacophore modelling, multiple-receptor covalent docking, and biological evaluation in order to find new Mpro inhibitors. After filtering and analysing ∼66,000 ligands from three different electrophilic libraries, 29 compounds were shortlisted for experimental testing, and two of them exhibited ≥20% inhibition at 100 μM. Our top candidate, GF04, is a benzylpyrrolyl compound that exhibited the highest inhibition activity of 38.3%, with a relatively small size (<350 Da) and leadlike character. Interestingly, our approach also identified another hit, DR07, a pyrimidoindol with a non-peptide character, and a molecular weight of 438.9 Da, reporting an inhibition of 26.3%. The established approach detailed in this study, in conjunction with the discovered inhibitors, has the capacity to yield novel perspectives for devising covalent inhibitors targeting the COVID-19 Mpro enzyme and other comparable targets.
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Affiliation(s)
- Radwa E Mahgoub
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Juliana Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates.
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122
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Bhat ZA, Khan MM, Rehman A, Iqbal J, Sanjeev BS, Madhumalar A. MD simulations indicate Omicron P132H of SARS-CoV-2 M pro is a potential allosteric mutant involved in modulating the dynamics of catalytic site entry loop. Int J Biol Macromol 2024; 262:130077. [PMID: 38346625 DOI: 10.1016/j.ijbiomac.2024.130077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
The SARS-CoV-2 main protease Mpro, essential for viral replication is an important drug target. It plays a critical role in processing viral polyproteins necessary for viral replication assembly. One of the predominant SARS-CoV-2 Mpro mutations of Omicron variant is Pro132His. Structurally, this mutation site is located ∼22 Å away from the catalytic site. The solved crystal structure of this mutant in complex with inhibitors as well as its reported catalytic efficiency did not show any difference with respect to the wild type. Thus, the mutation was concluded to be non-allosteric. Based on microsecond long MD simulation of the Pro132His mutant and wild type, we show that Pro132His mutation affects the conformational equilibrium with more population of conformational substates having open catalytic site, modulated by the dynamics of the catalytic site entry loop, implying the allosteric nature of this mutation. The structural analysis indicates that rearrangement of hydrogen bonds between His132 and adjacent residues enhances the dynamics of the linker, which in turn is augmented by the inherent dynamic flexibility of the catalytic pocket entry site due to the presence of charged residues. The altered dynamics leading to loss of secondary structures corroborate well with the reported compromised thermal stability.
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Affiliation(s)
- Zahoor Ahmad Bhat
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Mohd Muzammil Khan
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Ayyub Rehman
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Jawed Iqbal
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - B S Sanjeev
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj -211012, India
| | - Arumugam Madhumalar
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India.
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123
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Claussen ER, Renfrew PD, Müller CL, Drew K. Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds. Proteins 2024; 92:343-355. [PMID: 37874196 PMCID: PMC10873094 DOI: 10.1002/prot.26619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
The design of protein interaction inhibitors is a promising approach to address aberrant protein interactions that cause disease. One strategy in designing inhibitors is to use peptidomimetic scaffolds that mimic the natural interaction interface. A central challenge in using peptidomimetics as protein interaction inhibitors, however, is determining how best the molecular scaffold aligns to the residues of the interface it is attempting to mimic. Here we present the Scaffold Matcher algorithm that aligns a given molecular scaffold onto hotspot residues from a protein interaction interface. To optimize the degrees of freedom of the molecular scaffold we implement the covariance matrix adaptation evolution strategy (CMA-ES), a state-of-the-art derivative-free optimization algorithm in Rosetta. To evaluate the performance of the CMA-ES, we used 26 peptides from the FlexPepDock Benchmark and compared with three other algorithms in Rosetta, specifically, Rosetta's default minimizer, a Monte Carlo protocol of small backbone perturbations, and a Genetic algorithm. We test the algorithms' performance on their ability to align a molecular scaffold to a series of hotspot residues (i.e., constraints) along native peptides. Of the 4 methods, CMA-ES was able to find the lowest energy conformation for all 26 benchmark peptides. Additionally, as a proof of concept, we apply the Scaffold Match algorithm with CMA-ES to align a peptidomimetic oligooxopiperazine scaffold to the hotspot residues of the substrate of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our implementation of CMA-ES into Rosetta allows for an alternative optimization method to be used on macromolecular modeling problems with rough energy landscapes. Finally, our Scaffold Matcher algorithm allows for the identification of initial conformations of interaction inhibitors that can be further designed and optimized as high-affinity reagents.
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Affiliation(s)
- Erin R. Claussen
- Department of Biological Sciences, University of Illinois
at Chicago, Chicago, Il, 60607, USA
| | - P. Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New
York, NY, 10010, USA
| | - Christian L. Müller
- Ludwig-Maximilians-Universität München
- Helmholtz Munich, München
- Center for Computational Mathematics, Flatiron Institute,
New York
| | - Kevin Drew
- Department of Biological Sciences, University of Illinois
at Chicago, Chicago, Il, 60607, USA
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124
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Borges PHO, Ferreira SB, Silva FP. Recent Advances on Targeting Proteases for Antiviral Development. Viruses 2024; 16:366. [PMID: 38543732 PMCID: PMC10976044 DOI: 10.3390/v16030366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.
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Affiliation(s)
- Pedro Henrique Oliveira Borges
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Sabrina Baptista Ferreira
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Floriano Paes Silva
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
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125
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Jin X, Zhang M, Fu B, Li M, Yang J, Zhang Z, Li C, Zhang H, Wu H, Xue W, Liu Y. Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine. J Chem Inf Model 2024; 64:1319-1330. [PMID: 38346323 DOI: 10.1021/acs.jcim.3c01327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Traditional Chinese medicine (TCM) has been extensively employed for the treatment of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is demand for discovering more SARS-CoV-2 Mpro inhibitors with diverse scaffolds to optimize anti-SARS-CoV-2 lead compounds. In this study, comprehensive in silico and in vitro assays were utilized to determine the potential inhibitors from TCM compounds against SARS-CoV-2 Mpro, which is an important therapeutic target for SARS-CoV-2. The ensemble docking analysis of 18263 TCM compounds against 15 SARS-CoV-2 Mpro conformations identified 19 TCM compounds as promising candidates. Further in vitro testing validated three compounds as inhibitors of SARS-CoV-2 Mpro and showed IC50 values of 4.64 ± 0.11, 7.56 ± 0.78, and 11.16 ± 0.26 μM, with EC50 values of 12.25 ± 1.68, 15.58 ± 0.77, and 29.32 ± 1.25 μM, respectively. Molecular dynamics (MD) simulations indicated that the three complexes remained stable over the last 100 ns of production run. An analysis of the binding mode revealed that the active compounds occupy different subsites (S1, S2, S3, and S4) of the active site of SARS-CoV-2 Mpro via specific poses through noncovalent interactions with key amino acids (e.g., HIS 41, ASN 142, GLY 143, MET 165, GLU 166, or GLN 189). Overall, this study provides evidence indicating that the three natural products obtained from TCM could be further used for anti-COVID-19 research, justifying the investigation of Chinese herbal medicinal ingredients as bioactive constituents for therapeutic targets.
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Affiliation(s)
- Xiaojie Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou 730000, China
- Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Min Zhang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Mi Li
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Jingyi Yang
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Zhiming Zhang
- Gansu Provincial Hospital of TCM, Lanzhou 730000, China
| | - Chenghao Li
- Medical College, Yangzhou University, Yangzhou 225000, China
| | - Huijuan Zhang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, China
| | - Yongqi Liu
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou 730000, China
- Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou 730000, China
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126
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Saquib Q, Bakheit AH, Ahmed S, Ansari SM, Al-Salem AM, Al-Khedhairy AA. Identification of Phytochemicals from Arabian Peninsula Medicinal Plants as Strong Binders to SARS-CoV-2 Proteases (3CL Pro and PL Pro) by Molecular Docking and Dynamic Simulation Studies. Molecules 2024; 29:998. [PMID: 38474509 DOI: 10.3390/molecules29050998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/04/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
We provide promising computational (in silico) data on phytochemicals (compounds 1-10) from Arabian Peninsula medicinal plants as strong binders, targeting 3-chymotrypsin-like protease (3CLPro) and papain-like proteases (PLPro) of SARS-CoV-2. Compounds 1-10 followed the Lipinski rules of five (RO5) and ADMET analysis, exhibiting drug-like characters. Non-covalent (reversible) docking of compounds 1-10 demonstrated their binding with the catalytic dyad (CYS145 and HIS41) of 3CLPro and catalytic triad (CYS111, HIS272, and ASP286) of PLPro. Moreover, the implementation of the covalent (irreversible) docking protocol revealed that only compounds 7, 8, and 9 possess covalent warheads, which allowed the formation of the covalent bond with the catalytic dyad (CYS145) in 3CLPro and the catalytic triad (CYS111) in PLPro. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and radius of gyration (Rg) analysis from molecular dynamic (MD) simulations revealed that complexation between ligands (compounds 7, 8, and 9) and 3CLPro and PLPro was stable, and there was less deviation of ligands. Overall, the in silico data on the inherent properties of the above phytochemicals unravel the fact that they can act as reversible inhibitors for 3CLPro and PLPro. Moreover, compounds 7, 8, and 9 also showed their novel properties to inhibit dual targets by irreversible inhibition, indicating their effectiveness for possibly developing future drugs against SARS-CoV-2. Nonetheless, to confirm the theoretical findings here, the effectiveness of the above compounds as inhibitors of 3CLPro and PLPro warrants future investigations using suitable in vitro and in vivo tests.
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Affiliation(s)
- Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sarfaraz Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sabiha M Ansari
- Botany & Microbiology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah M Al-Salem
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulaziz A Al-Khedhairy
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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127
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da Rocha JAP, da Costa RA, da Costa ADSS, da Rocha ECM, Gomes AJB, Machado AK, Fagan SB, Brasil DDSB, Lima e Lima AH. Harnessing Brazilian biodiversity database: identification of flavonoids as potential inhibitors of SARS-CoV-2 main protease using computational approaches and all-atom molecular dynamics simulation. Front Chem 2024; 12:1336001. [PMID: 38456183 PMCID: PMC10917896 DOI: 10.3389/fchem.2024.1336001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the etiological agent responsible for the global outbreak of COVID-19 (Coronavirus Disease 2019). The main protease of SARS-CoV-2, Mpro, is a key enzyme that plays a vital role in mediating viral replication and transcription. In this study, a comprehensive computational approach was employed to investigate the binding affinity, selectivity, and stability of natural product candidates as potential new antivirals acting on the viral polyprotein processing mediated by SARS-CoV-2 Mpro. A library of 288 flavonoids extracted from Brazilian biodiversity was screened to select potential Mpro inhibitors. An initial filter based on Lipinski's rule of five was applied, and 204 compounds that did not violate any of the Lipinski rules were selected. The compounds were then docked into the active site of Mpro using the GOLD program, and the poses were subsequently re-scored using MM-GBSA (Molecular Mechanics Generalized Born Surface Area) binding free energy calculations performed by AmberTools23. The top five flavonoids with the best MM-GBSA binding free energy values were selected for analysis of their interactions with the active site residues of the protein. Next, we conducted a toxicity and drug-likeness analysis, and non-toxic compounds were subjected to molecular dynamics simulation and free energy calculation using the MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) method. It was observed that the five selected flavonoids had lower MM-GBSA binding free energy with Mpro than the co-crystal ligand. Furthermore, these compounds also formed hydrogen bonds with two important residues, Cys145 and Glu166, in the active site of Mpro. Two compounds that passed the drug-likeness filter showed stable conformations during the molecular dynamics simulations. Among these, NuBBE_867 exhibited the best MM-PBSA binding free energy value compared to the crystallographic inhibitor. Therefore, this study suggests that NuBBE_867 could be a potential inhibitor against the main protease of SARS-CoV-2 and may be further examined to confirm our results.
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Affiliation(s)
- João Augusto Pereira da Rocha
- Laboratory of Modeling and Computational Chemistry, Federal Institute of Education, Science and Technology of Paraná (IFPA) Campus Bragança, Bragança, Brazil
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
| | - Renato Araújo da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education Science and Technology of Paraná (IFPA) Campus Abaetetuba, Abaetetuba, Brazil
| | - Andreia do Socorro Silva da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
| | - Elaine Cristina Medeiros da Rocha
- Laboratory of Modeling and Computational Chemistry, Federal Institute of Education, Science and Technology of Paraná (IFPA) Campus Bragança, Bragança, Brazil
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
| | - Anderson José Bahia Gomes
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education Science and Technology of Paraná (IFPA) Campus Abaetetuba, Abaetetuba, Brazil
| | | | | | - Davi do Socorro Barros Brasil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
| | - Anderson Henrique Lima e Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
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128
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Ferreira P, Soares R, López-Fernández H, Vazquez N, Reboiro-Jato M, Vieira CP, Vieira J. Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites. Int J Mol Sci 2024; 25:2428. [PMID: 38397104 PMCID: PMC10889775 DOI: 10.3390/ijms25042428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
SARS-CoV-2 amino acid variants that contribute to an increased transmissibility or to host immune system escape are likely to increase in frequency due to positive selection and may be identified using different methods, such as codeML, FEL, FUBAR, and MEME. Nevertheless, when using different methods, the results do not always agree. The sampling scheme used in different studies may partially explain the differences that are found, but there is also the possibility that some of the identified positively selected amino acid sites are false positives. This is especially important in the context of very large-scale projects where hundreds of analyses have been performed for the same protein-coding gene. To account for these issues, in this work, we have identified positively selected amino acid sites in SARS-CoV-2 and 15 other coronavirus species, using both codeML and FUBAR, and compared the location of such sites in the different species. Moreover, we also compared our results to those that are available in the COV2Var database and the frequency of the 10 most frequent variants and predicted protein location to identify those sites that are supported by multiple lines of evidence. Amino acid changes observed at these sites should always be of concern. The information reported for SARS-CoV-2 can also be used to identify variants of concern in other coronaviruses.
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Affiliation(s)
- Pedro Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.F.); (R.S.); (C.P.V.)
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), Porto University, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Ricardo Soares
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.F.); (R.S.); (C.P.V.)
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), Porto University, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
- Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Hugo López-Fernández
- CINBIO, Department of Computer Science, ESEI—Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain; (H.L.-F.); (M.R.-J.)
- CINBIO, SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Noé Vazquez
- CINBIO, Department of Computer Science, ESEI—Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain; (H.L.-F.); (M.R.-J.)
- CINBIO, SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Miguel Reboiro-Jato
- CINBIO, Department of Computer Science, ESEI—Escuela Superior de Ingeniería Informática, Universidade de Vigo, 32004 Ourense, Spain; (H.L.-F.); (M.R.-J.)
- CINBIO, SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Cristina P. Vieira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.F.); (R.S.); (C.P.V.)
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Jorge Vieira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.F.); (R.S.); (C.P.V.)
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen 208, 4200-135 Porto, Portugal
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129
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Altincekic N, Jores N, Löhr F, Richter C, Ehrhardt C, Blommers MJJ, Berg H, Öztürk S, Gande SL, Linhard V, Orts J, Abi Saad MJ, Bütikofer M, Kaderli J, Karlsson BG, Brath U, Hedenström M, Gröbner G, Sauer UH, Perrakis A, Langer J, Banci L, Cantini F, Fragai M, Grifagni D, Barthel T, Wollenhaupt J, Weiss MS, Robertson A, Bax A, Sreeramulu S, Schwalbe H. Targeting the Main Protease (M pro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies. ACS Chem Biol 2024; 19:563-574. [PMID: 38232960 PMCID: PMC10877576 DOI: 10.1021/acschembio.3c00720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 01/19/2024]
Abstract
The main protease Mpro, nsp5, of SARS-CoV-2 (SCoV2) is one of its most attractive drug targets. Here, we report primary screening data using nuclear magnetic resonance spectroscopy (NMR) of four different libraries and detailed follow-up synthesis on the promising uracil-containing fragment Z604 derived from these libraries. Z604 shows time-dependent binding. Its inhibitory effect is sensitive to reducing conditions. Starting with Z604, we synthesized and characterized 13 compounds designed by fragment growth strategies. Each compound was characterized by NMR and/or activity assays to investigate their interaction with Mpro. These investigations resulted in the four-armed compound 35b that binds directly to Mpro. 35b could be cocrystallized with Mpro revealing its noncovalent binding mode, which fills all four active site subpockets. Herein, we describe the NMR-derived fragment-to-hit pipeline and its application for the development of promising starting points for inhibitors of the main protease of SCoV2.
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Affiliation(s)
- Nadide Altincekic
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Nathalie Jores
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Frank Löhr
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Institute
of Biophysical Chemistry, Goethe University
Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Christian Richter
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Claus Ehrhardt
- Department
of Biochemistry, University of Zurich, 8093 Zurich, Switzerland
| | | | - Hannes Berg
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Sare Öztürk
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Santosh L. Gande
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Verena Linhard
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Julien Orts
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Marie Jose Abi Saad
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Matthias Bütikofer
- Swiss
Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - Janina Kaderli
- Swiss
Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - B. Göran Karlsson
- Swedish
NMR Centre, Department of Chemistry and Molecular Biology, University of Gothenburg, SE40530 Göteborg, Sweden
- SciLifeLab, University of Gothenburg, SE40530 Göteborg, Sweden
| | - Ulrika Brath
- Swedish
NMR Centre, Department of Chemistry and Molecular Biology, University of Gothenburg, SE40530 Göteborg, Sweden
| | - Mattias Hedenström
- Swedish
NMR Centre, Department of Chemistry, University
of Umeå, SE-90187 Umeå, Sweden
| | - Gerhard Gröbner
- Swedish
NMR Centre, Department of Chemistry, University
of Umeå, SE-90187 Umeå, Sweden
| | - Uwe H. Sauer
- Protein
Production Sweden, Department of Chemistry, University of Umeå, SE-90187 Umeå, Sweden
| | - Anastassis Perrakis
- Oncode
Institute and Division of Biochemistry, The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Julian Langer
- Max Planck Institute of
Biophysics, D-60438 Frankfurt am Main, Germany
| | - Lucia Banci
- Magnetic
Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Francesca Cantini
- Magnetic
Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic
Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Deborah Grifagni
- Magnetic
Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Tatjana Barthel
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Jan Wollenhaupt
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Manfred S. Weiss
- Macromolecular
Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | | | - Adriaan Bax
- NIH, LCP NIDDK, Bethesda, Maryland 20892, United States
| | - Sridhar Sreeramulu
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
| | - Harald Schwalbe
- Institute
for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
- Center
of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, D-60438 Frankfurt, Germany
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130
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Giri-Rachman EA, Effendy VV, Azmi MHS, Yamahoki N, Stephanie R, Agustiyanti DF, Wisnuwardhani PH, Angelina M, Rubiyana Y, Aditama R, Ningrum RA, Wardiana A, Fibriani A. The SARS-CoV-2 M pro Dimer-Based Screening System: A Synthetic Biology Tool for Identifying Compounds with Dimerization Inhibitory Potential. ACS Synth Biol 2024; 13:509-520. [PMID: 38316139 PMCID: PMC10877612 DOI: 10.1021/acssynbio.3c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 12/11/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024]
Abstract
The COVID-19 endemic remains a global concern. The search for effective antiviral candidates is still needed to reduce disease risk. However, the availability of high biosafety level laboratory facilities for drug screening is limited in number. To address this issue, a screening system that could be utilized at lower biosafety levels remains essential. This study aimed to develop a novel SARS-CoV-2 main protease (Mpro) dimer-based screening system (DBSS) utilizing synthetic biology in Escherichia coli BL21(DE3). We linked the SARS-CoV-2 Mpro with the DNA-binding domain of AraC regulatory protein, which regulates the reporter gene expression. Protein modeling and molecular docking showed that saquinavir could bind to AraC-Mpro both in its monomer and dimer forms. The constructed DBSS assay indicated the screening system could detect saquinavir inhibitory activity at a concentration range of 4-10 μg/mL compared to the untreated control (P ≤ 0.05). The Vero E6 cell assay validated the DBSS result that saquinavir at 4-10 μg/mL exhibited antiviral activity against SARS-CoV-2. Our DBSS could be used for preliminary screening of numerous drug candidates that possess a dimerization inhibitor activity of SARS-CoV-2 Mpro and also minimize the use of a high biosafety level laboratory.
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Affiliation(s)
| | - Vergio V. Effendy
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Muhammad H. S. Azmi
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Nicholas Yamahoki
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Rebecca Stephanie
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
| | - Dian F. Agustiyanti
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Popi H. Wisnuwardhani
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Marissa Angelina
- Research
Center for Pharmaceutical Ingredients and Traditional Medicine, Indonesian National Research and Innovation Agency
(BRIN), Serpong 15314, Indonesia
| | - Yana Rubiyana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Reza Aditama
- Biochemistry
Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Ratih A. Ningrum
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Andri Wardiana
- Research
Center for Genetic Engineering, Indonesian
National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Azzania Fibriani
- School
of Life Sciences and Technology, Institut
Teknologi Bandung, Bandung 40132, Indonesia
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131
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Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
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Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
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132
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Juárez-Mercado KE, Gómez-Hernández MA, Salinas-Trujano J, Córdova-Bahena L, Espitia C, Pérez-Tapia SM, Medina-Franco JL, Velasco-Velázquez MA. Identification of SARS-CoV-2 Main Protease Inhibitors Using Chemical Similarity Analysis Combined with Machine Learning. Pharmaceuticals (Basel) 2024; 17:240. [PMID: 38399455 PMCID: PMC10892746 DOI: 10.3390/ph17020240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
SARS-CoV-2 Main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome, which is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development. Herein, we performed a large-scale virtual screening by comparing multiple structural descriptors of reference molecules with reported anti-coronavirus activity against a library with >17 million compounds. Further filtering, performed by applying two machine learning algorithms, identified eighteen computational hits as anti-SARS-CoV-2 compounds with high structural diversity and drug-like properties. The activities of twelve compounds on Mpro's enzymatic activity were evaluated by fluorescence resonance energy transfer (FRET) assays. Compound 13 (ZINC13878776) significantly inhibited SARS-CoV-2 Mpro activity and was employed as a reference for an experimentally hit expansion. The structural analogues 13a (ZINC4248385), 13b (ZNC13523222), and 13c (ZINC4248365) were tested as Mpro inhibitors, reducing the enzymatic activity of recombinant Mpro with potency as follows: 13c > 13 > 13b > 13a. Then, their anti-SARS-CoV-2 activities were evaluated in plaque reduction assays using Vero CCL81 cells. Subtoxic concentrations of compounds 13a, 13c, and 13b displayed in vitro antiviral activity with IC50 in the mid micromolar range. Compounds 13a-c could become lead compounds for the development of new Mpro inhibitors with improved activity against anti-SARS-CoV-2.
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Affiliation(s)
| | - Milton Abraham Gómez-Hernández
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Graduate Program in Biomedical Sciences, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Juana Salinas-Trujano
- Research and Development in Biotherapeutics Unit (UDIBI), National School of Biological Sciences, Instituto Politécnico Nacional, Mexico City 11350, Mexico
- National Laboratory for Specialized Services of Investigation, Development and Innovation (I+D+i) for Pharma Chemicals and Biotechnological Products, LANSEIDI-FarBiotech-CONACHyT, Mexico City 11350, Mexico
| | - Luis Córdova-Bahena
- School of Medicine, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- National Council of Humanities, Science and Technology (CONAHCYT), Mexico City 03940, Mexico
| | - Clara Espitia
- Immunology Department, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Sonia Mayra Pérez-Tapia
- Research and Development in Biotherapeutics Unit (UDIBI), National School of Biological Sciences, Instituto Politécnico Nacional, Mexico City 11350, Mexico
- National Laboratory for Specialized Services of Investigation, Development and Innovation (I+D+i) for Pharma Chemicals and Biotechnological Products, LANSEIDI-FarBiotech-CONACHyT, Mexico City 11350, Mexico
- Immunology Department, National School of Biological Sciences, Instituto Politécnico Nacional, Mexico City 11350, Mexico
| | - José L. Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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133
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Khamto N, Utama K, Boontawee P, Janthong A, Tatieng S, Arthan S, Choommongkol V, Sangthong P, Yenjai C, Suree N, Meepowpan P. Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CL pro: Insights from the Computational and Experimental Investigations. J Chem Inf Model 2024; 64:874-891. [PMID: 38277124 DOI: 10.1021/acs.jcim.3c01477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The emergence of the COVID-19 situation has become a global issue due to the lack of effective antiviral drugs for treatment. Flavonoids are a class of plant secondary metabolites that have antiviral activity against SARS-CoV-2 through inhibition of the main protease (3CLpro). In this study, 22 flavonoids obtained from natural sources and semisynthetic approaches were investigated for their inhibitory activity against SARS-CoV-2 3CLpro, along with cytotoxicity on Vero cells. The protein-ligand interactions were examined using molecular dynamics simulation. Moreover, QSAR analysis was conducted to clarify the structural effects on bioactivity. Accordingly, the in vitro investigation demonstrated that four flavonoids, namely, tectochrysin (7), 6″,6″-dimethylchromeno-[2″,3″:7,8]-flavone (9), panduratin A (19), and genistein (20), showed higher protease inhibitory activity compared to the standard flavonoid baicalein. Finally, our finding suggests that genistein (20), an isoflavone discovered in Millettia brandisiana, has potential for further development as a SARS-CoV-2 3CLpro inhibitor.
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Affiliation(s)
- Nopawit Khamto
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Multidisciplinary and Interdisciplinary School, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Kraikrit Utama
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Office of Research Administration, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Panida Boontawee
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Multidisciplinary and Interdisciplinary School, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Atchara Janthong
- Program in Biotechnology, Multidisciplinary and Interdisciplinary School, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Suriya Tatieng
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Supakorn Arthan
- Program of Chemistry, Faculty of Science and Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon47000, Thailand
| | - Vachira Choommongkol
- Department of Chemistry, Faculty of Science, Maejo University, 63 Nong Han, Chiang Mai 50290, Thailand
| | - Padchanee Sangthong
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Center of Excellence in Materials Science and Technology, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Chavi Yenjai
- Natural Products Research Unit, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, 123, Khon Kaen 40002, Thailand
| | - Nuttee Suree
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Center of Excellence in Materials Science and Technology, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
| | - Puttinan Meepowpan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Center of Excellence in Materials Science and Technology, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Chiang Mai 50200, Thailand
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134
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Ashraf-Uz-Zaman M, Chua TK, Li X, Yao Y, Moku BK, Mishra CB, Avadhanula V, Piedra PA, Song Y. Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease. ACS Infect Dis 2024; 10:715-731. [PMID: 38192109 PMCID: PMC10922772 DOI: 10.1021/acsinfecdis.3c00565] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Highly contagious SARS-CoV-2 coronavirus has infected billions of people worldwide with flu-like symptoms since its emergence in 2019. It has caused deaths of several million people. The viral main protease (Mpro) is essential for SARS-CoV-2 replication and therefore a drug target. Several series of covalent inhibitors of Mpro were designed and synthesized. Structure-activity relationship studies show that (1) several chloroacetamide- and epoxide-based compounds targeting Cys145 are potent inhibitors with IC50 values as low as 0.49 μM and (2) Cys44 of Mpro is not nucleophilic for covalent inhibitor design. High-resolution X-ray studies revealed the protein-inhibitor interactions and mechanisms of inhibition. It is of interest that Cys145 preferably attacks the more hindered Cα atom of several epoxide inhibitors. Chloroacetamide inhibitor 13 and epoxide inhibitor 30 were found to inhibit cellular SARS-CoV-2 replication with an EC68 (half-log reduction of virus titer) of 3 and 5 μM. These compounds represent new pharmacological leads for anti-SARS-CoV-2 drug development.
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Affiliation(s)
- Md Ashraf-Uz-Zaman
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Teck Khiang Chua
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Yuan Yao
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Bala Krishna Moku
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Chandra Bhushan Mishra
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Pedro A. Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
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135
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Grifagni D, Lenci E, De Santis A, Orsetti A, Barracchia CG, Tedesco F, Bellini Puglielli R, Lucarelli F, Lauriola A, Assfalg M, Cantini F, Calderone V, Guardavaccaro D, Trabocchi A, D’Onofrio M, Ciofi-Baffoni S. Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2. ACS Med Chem Lett 2024; 15:250-257. [PMID: 38352832 PMCID: PMC10860180 DOI: 10.1021/acsmedchemlett.3c00498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 02/16/2024] Open
Abstract
We have applied a proteolysis targeting chimera (PROTAC) technology to obtain a peptidomimetic molecule able to trigger the degradation of SARS-CoV-2 3-chymotrypsin-like protease (3CLPro). The PROTAC molecule was designed by conjugating a GC-376 based dipeptidyl 3CLPro ligand to a pomalidomide moiety through a piperazine-piperidine linker. NMR and crystallographic data complemented with enzymatic and cellular studies showed that (i) the dipeptidyl moiety of PROTAC binds to the active site of the dimeric state of SARS-CoV-2 3CLPro forming a reversible covalent bond with the sulfur atom of catalytic Cys145, (ii) the linker and the pomalidomide cereblon-ligand of PROTAC protrude from the protein, displaying a high degree of flexibility and no interactions with other regions of the protein, and (iii) PROTAC reduces the protein levels of SARS-CoV-2 3CLPro in cultured cells. This study paves the way for the future applicability of peptidomimetic PROTACs to tackle 3CLPro-dependent viral infections.
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Affiliation(s)
- Deborah Grifagni
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Elena Lenci
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Alessia De Santis
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Andrea Orsetti
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | | | - Filomena Tedesco
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Raffaele Bellini Puglielli
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Francesca Lucarelli
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Angela Lauriola
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Michael Assfalg
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Francesca Cantini
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Vito Calderone
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Daniele Guardavaccaro
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Andrea Trabocchi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Mariapina D’Onofrio
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Simone Ciofi-Baffoni
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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136
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Sheng YJ, Kuo STA, Yang T, Russell DH, Yan X, Xu S, Liu WR, Fierke CA. BRD4354 Is a Potent Covalent Inhibitor against the SARS-CoV-2 Main Protease. Biochemistry 2024:10.1021/acs.biochem.3c00685. [PMID: 38329238 PMCID: PMC11306412 DOI: 10.1021/acs.biochem.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Numerous organic molecules are known to inhibit the main protease (MPro) of SARS-CoV-2, the pathogen of Coronavirus Disease 2019 (COVID-19). Guided by previous research on zinc-ligand inhibitors of MPro and zinc-dependent histone deacetylases (HDACs), we identified BRD4354 as a potent inhibitor of MPro. The in vitro protease activity assays show that BRD4354 displays time-dependent inhibition against MPro with an IC50 (concentration that inhibits activity by 50%) of 0.72 ± 0.04 μM after 60 min of incubation. Inactivation follows a two-step process with an initial rapid binding step with a KI of 1.9 ± 0.5 μM followed by a second slow inactivation step, kinact,max of 0.040 ± 0.002 min-1. Native mass spectrometry studies indicate that a covalent intermediate is formed where the ortho-quinone methide fragment of BRD4354 forms a covalent bond with the catalytic cysteine C145 of MPro. Based on these data, a Michael-addition reaction mechanism between MPro C145 and BRD4354 was proposed. These results suggest that both preclinical testing of BRD4354 and structure-activity relationship studies based on BRD4354 are warranted to develop more effective anti-COVID therapeutics.
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Affiliation(s)
- Yan J. Sheng
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Syuan-Ting Alex Kuo
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Tingyuan Yang
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Xin Yan
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
- Department of Cell Biology and Genetics, College of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Carol A. Fierke
- Department of Biochemistry, Brandeis University, Waltham, MA 02453, USA
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137
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Chan HTH, Brewitz L, Lukacik P, Strain-Damerell C, Walsh MA, Schofield CJ, Duarte F. Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2' proline of the viral polyprotein. RSC Chem Biol 2024; 5:117-130. [PMID: 38333195 PMCID: PMC10849127 DOI: 10.1039/d3cb00128h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 02/10/2024] Open
Abstract
The SARS-CoV-2 papain-like protease (PLpro) is an antiviral drug target that catalyzes the hydrolysis of the viral polyproteins pp1a/1ab, so releasing the non-structural proteins (nsps) 1-3 that are essential for the coronavirus lifecycle. The LXGG↓X motif in pp1a/1ab is crucial for recognition and cleavage by PLpro. We describe molecular dynamics, docking, and quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how oligopeptide substrates derived from the viral polyprotein bind to PLpro. The results reveal how the substrate sequence affects the efficiency of PLpro-catalyzed hydrolysis. In particular, a proline at the P2' position promotes catalysis, as validated by residue substitutions and mass spectrometry-based analyses. Analysis of PLpro catalyzed hydrolysis of LXGG motif-containing oligopeptides derived from human proteins suggests that factors beyond the LXGG motif and the presence of a proline residue at P2' contribute to catalytic efficiency, possibly reflecting the promiscuity of PLpro. The results will help in identifying PLpro substrates and guiding inhibitor design.
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Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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138
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Allayeh AK, El-boghdady AH, Said MA, Saleh MGA, Abdel-Aal MT, Abouelenein MG. Discovery of Pyrano[2,3- c]pyrazole Derivatives as Novel Potential Human Coronavirus Inhibitors: Design, Synthesis, In Silico, In Vitro, and ADME Studies. Pharmaceuticals (Basel) 2024; 17:198. [PMID: 38399412 PMCID: PMC10892497 DOI: 10.3390/ph17020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
The SARS-CoV-2 pandemic at the end of 2019 had major worldwide health and economic consequences. Until effective vaccination approaches were created, the healthcare sectors endured a shortage of operative treatments that might prevent the infection's spread. As a result, academia and the pharmaceutical industry prioritized the development of SARS-CoV2 antiviral medication. Pyranopyrazoles have been shown to play a prominent function in pharmaceutical chemistry and drug sighting because of their significant bioactive properties. We provide herein a novel sequence of pyranopyrazoles and their annulated systems whose antiviral efficacy and cytotoxicity were explored versus human coronavirus 229E (HCoV-229E) Vero-E6 cell lines as a model for the Coronaviridae family. Fifteen synthetic congeners pointed out miscellaneous antiviral efficacies against HCoV-229E with variable inhibition degrees. Compound 18 showed a high selectivity index (SI = 12.6) that established spectacular inhibitory capacity against human coronavirus 229E. Compounds 6, 7, and 14 exposed moderate efficacies. Compounds 6, 7, 14, and 18 exhibited substantial antiviral action through the replication phase with reduction percentages extending from 53.6%, 60.7%, and 55% to 82.2%, correspondingly. Likewise, when assessed to the positive control tipranavir (88.6%), the inhibitory efficiency of compounds 6, 7, 14, and 18 versus the SARS-CoV2 Mpro provided high percentages of 80.4%, 73.1%, 81.4% and up to 84.5%, respectively. In silico studies were performed to investigate further the biological activity and the target compounds' physical and chemical features, including molecular dynamic (MD) simulations, protein-ligand docking, ADME studies, and density functional theory (DFT) calculations. These inquiries demonstrated that this series of metabolically stable pyranopyrazoles and their annulated systems are effective human coronavirus inhibitors that inhibit the viral Mpro protein and may have emerged as a novel COVID-19 curative option.
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Affiliation(s)
- Abdou K. Allayeh
- Environmental Virology Laboratory 176, Water Pollution Research Department, Environment and Climate Change Institute, National Research Centre (NRC), 33 El-Behouth St., Dokki, Giza 12622, Egypt;
| | - Aliaa H. El-boghdady
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Kom 32511, Egypt; (A.H.E.-b.); (M.T.A.-A.); (M.G.A.)
| | - Mohamed A. Said
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt;
| | - Mahmoud G. A. Saleh
- Department of Chemistry, College of Science, Northern Border University, Arar 91431, Saudi Arabia
| | - Mohammed T. Abdel-Aal
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Kom 32511, Egypt; (A.H.E.-b.); (M.T.A.-A.); (M.G.A.)
| | - Mohamed G. Abouelenein
- Chemistry Department, Faculty of Science, Menofia University, Shebin El-Kom 32511, Egypt; (A.H.E.-b.); (M.T.A.-A.); (M.G.A.)
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139
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Huang Q, Quan B, Chen Y, Zhao X, Zhou Y, Huang C, Qiao J, Wang Y, Li Y, Yang S, Lei J, Li L. Discovery of α-Ketoamide inhibitors of SARS-CoV-2 main protease derived from quaternized P1 groups. Bioorg Chem 2024; 143:107001. [PMID: 38101266 DOI: 10.1016/j.bioorg.2023.107001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023]
Abstract
Although the SARS-CoV-2 pandemic has ended, multiple sporadic cases still exist, posing a request for more antivirals. The main protease (Mpro) of SARS-CoV-2, a key enzyme for viral replication, is an attractive target for drug development. Here, we report the discovery of a new potent α-ketoamide-containing Mpro inhibitor, N-((R)-1-cyclohexyl-2-(((R)-3-methoxy-1-oxo-1-((1-(2-oxo-2-((thiazol-2-ylmethyl)amino)acetyl)cyclobutyl)amino)propan-2-yl)amino)-2-oxoethyl)-4,4-difluorocyclohexane-1-carboxamide (20j). This compound presented promising enzymatic inhibitory activity against SARS-CoV-2 Mpro with an IC50 value of 19.0 nM, and an excellent antiviral activity in cell-based assay with an EC50 value of 138.1 nM. This novel covalent inhibitor may be used as a lead compound for subsequent drug discovery against SARS-CoV-2.
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Affiliation(s)
- Qiao Huang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Baoxue Quan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yan Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiu Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanmei Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chong Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jingxin Qiao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yifei Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yueyue Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shengyong Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan 610212, China
| | - Jian Lei
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China.
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140
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Abbasi M, Mansourian M, Oskouie AA, Taheri S, Mahnam K. In-silico study MM/GBSA binding free energy and molecular dynamics simulation of some designed remdesivir derivatives as the inhibitory potential of SARS-CoV-2 main protease. Res Pharm Sci 2024; 19:29-41. [PMID: 39006973 PMCID: PMC11244705 DOI: 10.4103/1735-5362.394818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/16/2023] [Accepted: 01/17/2024] [Indexed: 07/16/2024] Open
Abstract
Background and purpose Coronavirus disease (COVID-19) is one of the greatest challenges of the twentieth century. Recently, in silico tools help to predict new inhibitors of SARS-CoV-2. In this study, the new compounds based on the remdesivir structure (12 compounds) were designed. Experimental approach The main interactions of remdesivir and designed compounds were investigated in the 3CLpro active site. The binding free energy of compounds by the MM-GBSA method was calculated and the best compound (compound 12 with the value of -88.173 kcal/mol) was introduced to the molecular dynamics simulation study. Findings/Results The simulation results were compared with the results of protein simulation without the presence of an inhibitor and in the presence of remdesivir. Additionally, the RMSD results for the protein backbone showed that compound 12 in the second 50 nanoseconds has less fluctuation than the protein alone and in the presence of remdesivir, which indicates the stability of the compound in the active site of the Mpro protein. Furthermore, protein compactness was investigated in the absence of compounds and the presence of compound 12 and remdesivir. The Rg diagram shows a fluctuation of approximately 0.05 A, which indicates the compressibility of the protein in the presence and absence of compounds. The results of the RMSF plot also show the stability of essential amino acids during protein binding. Conclusion and implications Supported by the theoretical results, compound 12 could have the potential to inhibit the 3CLpro enzyme, which requires further in vitro studies and enzyme inhibition must also be confirmed at protein levels.
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Affiliation(s)
- Maryam Abbasi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahboubeh Mansourian
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, I.R. Iran
- Department of Pharmacology, Faculty of Medicine, Yasuj University of Medical Sciences, Yasuj, I.R. Iran
| | - Afsaneh Arefi Oskouie
- Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Salman Taheri
- Chemistry & Chemical Engineering Research Center of Iran, P.O. Box 14335-186, Tehran, I.R. Iran
| | - Karim Mahnam
- Faculty of Science, Department of Biology, Shahrekord University, Shahrekord, I.R. Iran
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141
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Huang CY, Metz A, Lange R, Artico N, Potot C, Hazemann J, Müller M, Dos Santos M, Chambovey A, Ritz D, Eris D, Meyer S, Bourquin G, Sharpe M, Mac Sweeney A. Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket. Acta Crystallogr D Struct Biol 2024; 80:123-136. [PMID: 38289714 PMCID: PMC10836397 DOI: 10.1107/s2059798324000329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. The structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography.
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Affiliation(s)
- Chia Ying Huang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Alexander Metz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Roland Lange
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Nadia Artico
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Céline Potot
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - Manon Müller
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | | | - Daniel Ritz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Deniz Eris
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Solange Meyer
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - May Sharpe
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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142
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Gutti G, He Y, Coldren WH, Lalisse RF, Border SE, Hadad CM, McElroy CA, Ekici ÖD. In-silico guided design, screening, and molecular dynamic simulation studies for the identification of potential SARS-CoV-2 main protease inhibitors for the targeted treatment of COVID-19. J Biomol Struct Dyn 2024; 42:1733-1750. [PMID: 37114441 DOI: 10.1080/07391102.2023.2202247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023]
Abstract
COVID-19, the disease responsible for the recent pandemic, is caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (Mpro) of SARS-CoV-2 is an essential proteolytic enzyme that plays a number of important roles in the replication of the virus in human host cells. Blocking the function of SARS-CoV-2 Mpro offers a promising and targeted, therapeutic option for the treatment of the COVID-19 infection. Such an inhibitory strategy is currently successful in treating COVID-19 under FDA's emergency use authorization, although with limited benefit to the immunocompromised along with an unfortunate number of side effects and drug-drug interactions. Current COVID vaccines protect against severe disease and death but are mostly ineffective toward long COVID which has been seen in 5-36% of patients. SARS-CoV-2 is a rapidly mutating virus and is here to stay endemically. Hence, alternate therapeutics to treat SARS-CoV-2 infections are still needed. Moreover, because of the high degree of conservation of Mpro among different coronaviruses, any newly developed antiviral agents should better prepare us for potential future epidemics or pandemics. In this paper, we first describe the design and computational docking of a library of novel 188 first-generation peptidomimetic protease inhibitors using various electrophilic warheads with aza-peptide epoxides, α-ketoesters, and β-diketones identified as the most effective. Second-generation designs, 192 compounds in total, focused on aza-peptide epoxides with drug-like properties, incorporating dipeptidyl backbones and heterocyclic ring motifs such as proline, indole, and pyrrole groups, yielding 8 hit candidates. These novel and specific inhibitors for SARS-CoV-2 Mpro can ultimately serve as valuable alternate and broad-spectrum antivirals against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gopichand Gutti
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Yiran He
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - William H Coldren
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Remy F Lalisse
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah E Border
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Christopher M Hadad
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Craig A McElroy
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Özlem Doğan Ekici
- Department of Chemistry and Biochemistry, The Ohio State University, Newark, Ohio, USA
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143
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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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144
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Wang R, Chen X, Li H, Chen X, Sun D, Yu D, Lu J, Xie Y, Zhang Q, Xu J, Zhang W, Chen H, Liu S, Chen L. Danshensu inhibits SARS-CoV-2 by targeting its main protease as a specific covalent inhibitor and discovery of bifunctional compounds eliciting antiviral and anti-inflammatory activity. Int J Biol Macromol 2024; 257:128623. [PMID: 38070810 DOI: 10.1016/j.ijbiomac.2023.128623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023]
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to human. Since there are still no effective treatment options against the new emerging variants of SARS-CoV-2, it is necessary to devote a continuous endeavor for more targeted drugs and the preparation for the next pandemic. Salvia miltiorrhiza and its active ingredients possess wide antiviral activities, including against SARS-CoV-2. Danshensu, as one of the most important active ingredients in Salvia miltiorrhiza, has been reported to inhibit the entry of SARS-CoV-2 into ACE2 (angiotensin-converting enzyme 2)-overexpressed HEK-293T cells and Vero-E6 cells. However, there is a paucity of information regarding its detailed target and mechanism against SARS-CoV-2. Here, we present Danshensu as a covalent inhibitor of 3-chymotrypsin-like protease (3CLpro) against SARS-CoV-2 by the time-dependent inhibition assay (TDI) and mass spectrometry analysis. Further molecular docking, site-directed mutagenesis, circular dichroism (CD) and fluorescence spectra revealed that Danshensu covalently binds to C145 of SARS-CoV-2 3CLpro, meanwhile forming the hydrogen bonds with S144, H163 and E166 in the S1 site. Structure-based optimization of Danshensu led to the discovery of the promising compounds with good inhibitory activity and microsomal stability in vitro. Due to Danshensu inhibiting lung inflammation in the mouse model, we found that Danshensu derivatives also showed better anti-inflammatory activity than Danshensu in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells. Thus, our study provides not only the clue of the efficacy of Salvia miltiorrhiza against SARS-CoV-2, but also a detailed mechanistic insight into the covalent mode of action of Danshensu for design of covalent inhibitors against SARS-CoV-2 3CLpro, highlighting its potential as a bifunctional molecule with antivirus and anti-inflammation.
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Affiliation(s)
- Ruyu Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xuwen Chen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Donghui Sun
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuanyuan Xie
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Qian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jianrong Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Weidong Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shunying Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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145
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Yarovaya OI, Filimonov AS, Baev DS, Borisevich SS, Zaykovskaya AV, Chirkova VY, Marenina MK, Meshkova YV, Belenkaya SV, Shcherbakov DN, Gureev MA, Luzina OA, Pyankov OV, Salakhutdinov NF, Khvostov MV. The Potential of Usnic-Acid-Based Thiazolo-Thiophenes as Inhibitors of the Main Protease of SARS-CoV-2 Viruses. Viruses 2024; 16:215. [PMID: 38399993 PMCID: PMC10893357 DOI: 10.3390/v16020215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on (+)- and (-)-usnic acid and studied their ability to inhibit the main protease of SARS-CoV-2. Substances containing unsubstituted thiophene groups or methyl- or bromo-substituted thiophene moieties showed moderate activity. Derivatives containing nitro substituents in the thiophene heterocycle-just as pure (+)- and (-)-usnic acids-showed no anti-3CLpro activity. Kinetic parameters of the most active compound, (+)-3e, were investigated, and molecular modeling of the possible interaction of the new thiazolo-thiophenes with the active site of the main protease was carried out. We evaluated the binding energies of the ligand and protein in a ligand-protein complex. Active compound (+)-3e was found to bind with minimum free energy; the binding of inactive compound (+)-3g is characterized by higher values of minimum free energy; the positioning of pure (+)-usnic acid proved to be unstable and is accompanied by the formation of intermolecular contacts with many amino acids of the catalytic binding site. Thus, the molecular dynamics results were consistent with the experimental data. In an in vitro antiviral assay against six strains (Wuhan, Delta, and four Omicron sublineages) of SARS-CoV-2, (+)-3e demonstrated pronounced antiviral activity against all the strains.
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Affiliation(s)
- Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Aleksandr S. Filimonov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Dmitriy S. Baev
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
| | - Sophia S. Borisevich
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
- Laboratory of Chemical Physics, Ufa Institute of Chemistry, Ufa Federal Research Centre, 450078 Ufa, Russia
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Varvara Yu. Chirkova
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Mariya K. Marenina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Yulia V. Meshkova
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Svetlana V. Belenkaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Dmitriy N. Shcherbakov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Maxim A. Gureev
- Laboratory of Bio- and Cheminformatics, St. Petersburg School of Physics, Mathematics and Computer Science, HSE University, 194100 St. Peterburg, Russia;
| | - Olga A. Luzina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Mikhail V. Khvostov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
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146
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Wang Q, Lu X, Jia R, Yan X, Wang J, Zhao L, Zhong R, Sun G. Recent advances in chemometric modelling of inhibitors against SARS-CoV-2. Heliyon 2024; 10:e24209. [PMID: 38293468 PMCID: PMC10826659 DOI: 10.1016/j.heliyon.2024.e24209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused great harm to all countries worldwide. This disease can be prevented by vaccination and managed using various treatment methods, including injections, oral medications, or aerosol therapies. However, the selection of suitable compounds for the research and development of anti-SARS-CoV-2 drugs is a daunting task because of the vast databases of available compounds. The traditional process of drug research and development is time-consuming, labour-intensive, and costly. The application of chemometrics can significantly expedite drug R&D. This is particularly necessary and important for drug development against pandemic public emergency diseases, such as COVID-19. Through various chemometric techniques, such as quantitative structure-activity relationship (QSAR) modelling, molecular docking, and molecular dynamics (MD) simulations, compounds with inhibitory activity against SARS-CoV-2 can be quickly screened, allowing researchers to focus on the few prioritised candidates. In addition, the ADMET properties of the screened candidate compounds should be further explored to promote the successful discovery of anti-SARS-CoV-2 drugs. In this case, considerable time and economic costs can be saved while minimising the need for extensive animal experiments, in line with the 3R principles. This paper focuses on recent advances in chemometric modelling studies of COVID-19-related inhibitors, highlights current limitations, and outlines potential future directions for development.
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Affiliation(s)
- Qianqian Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Xinyi Lu
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Runqing Jia
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Xinlong Yan
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Jianhua Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing 100124, PR China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Guohui Sun
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
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147
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Tiwari G, Chauhan MS, Sharma D. In silico study of inhibition activity of boceprevir drug against 2019-nCoV main protease. Z NATURFORSCH C 2024; 79:1-12. [PMID: 38156366 DOI: 10.1515/znc-2023-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Boceprevir drug is a ketoamide serine protease inhibitor with a linear peptidomimetic structure that exhibits inhibition activity against 2019-nCoV main protease. This paper reports electronic properties of boceprevir and its molecular docking as well as molecular dynamics simulation analysis with protein receptor. For this, the equilibrium structure of boceprevir has been obtained by DFT at B3LYP and ωB97XD levels with 6-311+G(d,p) basis set in gas and water mediums. HOMO-LUMO and absorption spectrum analysis have been used to evaluate the boceprevir's toxicity and photosensitivity, respectively. Molecular docking simulation has been performed to test the binding affinity of boceprevir with 2019-nCoV MPRO; which rendered a variety of desirable binding locations between the ligand and target protein's residue positions. The optimum binding location has been considered for molecular dynamics simulation. The findings have been addressed to clarify the boceprevir drug efficacy against the 2019-nCoV MPRO.
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Affiliation(s)
- Gargi Tiwari
- Department of Physics, Patna University, Patna-800005, India
| | | | - Dipendra Sharma
- Department of Physics, DDU Gorakhpur University, Gorakhpur-273009, India
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148
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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149
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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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150
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Bhattacharya P, Mandal A. Identification of amentoflavone as a potent SARS-CoV-2 M pro inhibitor: a combination of computational studies and in vitro biological evaluation. J Biomol Struct Dyn 2024:1-19. [PMID: 38263736 DOI: 10.1080/07391102.2024.2304676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024]
Abstract
Small-molecule inhibitors of SARS-CoV-2 Mpro that block the active site pocket of the viral main protease have been considered potential therapeutics for the development of drugs against SARS-CoV-2. Here, we report the identification of amentoflavone (a biflavonoid) through docking-based virtual screening of a library comprised of 231 compounds consisting of flavonoids and isoflavonoids. The docking results were further substantiated through extensive analysis of the data obtained from all-atom 150 ns MD simulation. End-state effective free energy calculations using MM-PBSA calculations further suggested that (Ra)-amentoflavone (C3'-C8''-atropisomer) may show a greater binding affinity towards the Mpro than (Sa)-amentoflavone. In vitro cytotoxicity assay established that amentoflavone showed a high CC50 value indicating much lower toxicity. Further, potent inhibition of the Mpro by amentoflavone was established by studying the effect on HEK293T cells treated with SARS-CoV-2 Mpro expressing plasmid.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Anirban Mandal
- Department of Microbiology, Mrinalini Datta Mahavidyapith, Kolkata, India
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