1
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Badawy AM, Donia MSM, Hamdy NG, El-Ayouty MM, Mohamed OG, Darwish KM, Tripathi A, Ahmed SA. Dual SARS-CoV-2 and MERS-CoV inhibitors from Artemisia monosperma: isolation, structure elucidation, molecular modelling studies, and in vitro activities. Org Biomol Chem 2024; 22:7006-7016. [PMID: 39135436 DOI: 10.1039/d4ob00929k] [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: 08/29/2024]
Abstract
The COVID-19 pandemic has spread throughout the whole globe, so it is imperative that all available resources be used to treat this scourge. In reality, the development of new pharmaceuticals has mostly benefited from natural products. The widespread medicinal usage of species in the Asteraceae family is extensively researched. In this study, compounds isolated from methanolic extract of Artemisia monosperma Delile, a wild plant whose grows in Egypt's Sinai Peninsula. Three compounds, stigmasterol 3-O-β-D-glucopyranoside 1, rhamnetin 3, and padmatin 6, were first isolated from this species. In addition, five previously reported compounds, arcapillin 2, jaceosidin 4, hispidulin 5, 7-O-methyleriodictyol 7, and eupatilin 8, were isolated. Applying molecular modelling simulations revealed two compounds, arcapillin 2 and rhamnetin 3 with the best docking interactions and energies within SARS-CoV-2 Mpro-binding site (-6.16, and -6.70 kcal mol-1, respectively). The top-docked compounds (2-3) were further evaluated for inhibitory concentrations (IC50), and half-maximal cytotoxicity (CC50) of both SARS-CoV-2 and MERS-CoV. Interestingly, arcapillin showed high antiviral activity towards SARS-CoV-2 and MERS-CoV, with IC50 values of 190.8 μg mL-1 and 16.58 μg mL-1, respectively. These findings may hold promise for further preclinical and clinical research, particularly on arcapillin itself or in collaboration with other drugs for COVID-19 treatment.
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Affiliation(s)
- Ahmed M Badawy
- Department of Pharmacognosy, Faculty of Pharmacy, Sinai University, El-Arish 45511, Egypt.
| | - Marwa Samir M Donia
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt.
| | - Nehal G Hamdy
- Department of Pharmacognosy, Faculty of Pharmacy, Sinai University, El-Arish 45511, Egypt.
| | - Mayada M El-Ayouty
- Department of Pharmacognosy, Faculty of Pharmacy, Sinai University, El-Arish 45511, Egypt.
| | - Osama G Mohamed
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr el Aini St., Cairo 11562, Egypt.
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Khaled M Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt.
| | - Ashootosh Tripathi
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Safwat A Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt.
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2
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Delgado R, Vishwakarma J, Moghadasi SA, Otsuka Y, Shumate J, Cuell A, Tansiongco M, Cooley CB, Chen Y, Dabrowska A, Basu R, Anindita PD, Luo D, Dosa PI, Harki DA, Bannister T, Scampavia L, Spicer TP, Harris RS. SARS-CoV-2 M pro inhibitor identification using a cellular gain-of-signal assay for high-throughput screening. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024:100181. [PMID: 39173830 DOI: 10.1016/j.slasd.2024.100181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2, SARS2) is responsible for the COVID-19 pandemic and infections that continue to affect the lives of millions of people worldwide, especially those who are older and/or immunocompromised. The SARS2 main protease enzyme, Mpro (also called 3C-like protease, 3CLpro), is a bona fide drug target as evidenced by potent inhibition with nirmatrelvir and ensitrelvir, the active components of the drugs Paxlovid and Xocova, respectively. However, the existence of nirmatrelvir and ensitrelvir-resistant isolates underscores the need to develop next-generation drugs with different resistance profiles and/or distinct mechanisms of action. Here, we report the results of a high-throughput screen of 649,568 compounds using a cellular gain-of-signal assay. In this assay, Mpro inhibits expression of a luciferase reporter, and 8,777 small molecules were considered hits by causing a gain in luciferase activity 3x SD above the sample field activity (6.8% gain-of-signal relative to 100 µM GC376). Single concentration and dose-response gain-of-signal experiments confirmed 3,522/8,762 compounds as candidate inhibitors. In parallel, all initial high-throughput screening hits were tested in a peptide cleavage assay with purified Mpro and only 39/8,762 showed inhibition. Importantly, 19/39 compounds (49%) re-tested positive in both SARS2 assays, including two previously reported Mpro inhibitors, demonstrating the efficacy of the overall screening strategy. This approach led to the rediscovery of known Mpro inhibitors such as calpain inhibitor II, as well as to the discovery of novel compounds that provide chemical information for future drug development efforts.
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Affiliation(s)
- Renee Delgado
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Jyoti Vishwakarma
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Yuka Otsuka
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Justin Shumate
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Ashley Cuell
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Megan Tansiongco
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Department of Chemistry, Trinity University, San Antonio, TX 78212, USA
| | | | - Yanjun Chen
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Agnieszka Dabrowska
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Rahul Basu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paulina Duhita Anindita
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore; Institute of Structural Biology, Nanyang Technological University, Singapore, 639798, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore; Institute of Structural Biology, Nanyang Technological University, Singapore, 639798, Singapore
| | - Peter I Dosa
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Thomas Bannister
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Louis Scampavia
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Timothy P Spicer
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL 33458, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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3
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Yang Y, Luo YD, Zhang CB, Xiang Y, Bai XY, Zhang D, Fu ZY, Hao RB, Liu XL. Progress in Research on Inhibitors Targeting SARS-CoV-2 Main Protease (M pro). ACS OMEGA 2024; 9:34196-34219. [PMID: 39157135 PMCID: PMC11325518 DOI: 10.1021/acsomega.4c03023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024]
Abstract
Since 2019, the novel coronavirus (SARS-CoV-2) has caused significant morbidity and millions of deaths worldwide. The Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 and its variants, has further highlighted the urgent need for the development of effective therapeutic agents. Currently, the highly conserved and broad-spectrum nature of main proteases (Mpro) renders them of great importance in the field of inhibitor study. In this study, we categorize inhibitors targeting Mpro into three major groups: mimetic, nonmimetic, and natural inhibitors. We then present the research progress of these inhibitors in detail, including their mechanism of action, antiviral activity, pharmacokinetic properties, animal experiments, and clinical studies. This review aims to provide valuable insights and potential avenues for the development of more effective antiviral drugs against SARS-CoV-2.
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Affiliation(s)
- Yue Yang
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Yi-Dan Luo
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Chen-Bo Zhang
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Yang Xiang
- School
of Medicine, Yan’an University, Yan’an 716000, China
- College
of Physical Education, Yan’an University, Yan’an 716000, China
| | - Xin-Yue Bai
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Die Zhang
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Zhao-Ying Fu
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Ruo-Bing Hao
- School
of Medicine, Yan’an University, Yan’an 716000, China
| | - Xiao-Long Liu
- School
of Medicine, Yan’an University, Yan’an 716000, China
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4
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Zhang Y, Tian Y, Yan A. A SAR and QSAR study on 3CLpro inhibitors of SARS-CoV-2 using machine learning methods. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:531-563. [PMID: 39077983 DOI: 10.1080/1062936x.2024.2375513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 06/27/2024] [Indexed: 07/31/2024]
Abstract
The 3C-like Proteinase (3CLpro) of novel coronaviruses is intricately linked to viral replication, making it a crucial target for antiviral agents. In this study, we employed two fingerprint descriptors (ECFP_4 and MACCS) to comprehensively characterize 889 compounds in our dataset. We constructed 24 classification models using machine learning algorithms, including Support Vector Machine (SVM), Random Forest (RF), extreme Gradient Boosting (XGBoost), and Deep Neural Networks (DNN). Among these models, the DNN- and ECFP_4-based Model 1D_2 achieved the most promising results, with a remarkable Matthews correlation coefficient (MCC) value of 0.796 in the 5-fold cross-validation and 0.722 on the test set. The application domains of the models were analysed using dSTD-PRO calculations. The collected 889 compounds were clustered by K-means algorithm, and the relationships between structural fragments and inhibitory activities of the highly active compounds were analysed for the 10 obtained subsets. In addition, based on 464 3CLpro inhibitors, 27 QSAR models were constructed using three machine learning algorithms with a minimum root mean square error (RMSE) of 0.509 on the test set. The applicability domains of the models and the structure-activity relationships responded from the descriptors were also analysed.
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Affiliation(s)
- Y Zhang
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Y Tian
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - A Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
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5
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Le UNP, Chang YJ, Lu CH, Chen Y, Su WC, Chao ST, Baltina LA, Petrova SF, Li SR, Hung MC, Lai MMC, Baltina LA, Lin CW. Glycyrrhizic acid conjugates with amino acid methyl esters target the main protease, exhibiting antiviral activity against wild-type and nirmatrelvir-resistant SARS-CoV-2 variants. Antiviral Res 2024; 227:105920. [PMID: 38821317 DOI: 10.1016/j.antiviral.2024.105920] [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: 04/02/2024] [Revised: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
COVID-19 pandemic is predominantly caused by SARS-CoV-2, with its main protease, Mpro, playing a pivotal role in viral replication and serving as a potential target for inhibiting different variants. In this study, potent Mpro inhibitors were identified from glycyrrhizic acid (GL) derivatives with amino acid methyl/ethyl esters. Out of the 17 derivatives semisynthesized, Compounds 2, 6, 9, and 15, with methionine methyl esters, D-tyrosine methyl esters, glutamic acid methyl esters, and methionines in the carbohydrate moiety, respectively, significantly inhibited wild-type SARS-CoV-2 Mpro-mediated proteolysis, with IC50 values ranging from 0.06 μM to 0.84 μM. They also demonstrated efficacy in inhibiting trans-cleavage by mutant Mpro variants (Mpro_P132H, Mpro_E166V, Mpro_P168A, Mpro_Q189I), with IC50 values ranging from 0.05 to 0.92 μM, surpassing nirmatrelvir (IC50: 1.17-152.9 μM). Molecular modeling revealed stronger interactions with Valine166 in the structural complex of Mpro_E166V with the compounds compared to nirmatrelvir. Moreover, these compounds efficiently inhibited the post-entry viral processes of wild-type SARS-CoV-2 single-round infectious particles (SRIPs), mitigating viral cytopathic effects and reducing replicon-driven GFP reporter signals, as well as in vitro infectivity of wild-type, Mpro_E166V, and Mpro_Q189I SRIPs, with EC50 values ranging from 0.02 to 0.53 μM. However, nirmatrelvir showed a significant decrease in inhibiting the replication of mutant SARS-CoV-2 SRIPs carrying Mpro_E166V (EC50: >20 μM) and Mpro_Q189I (EC50: 13.2 μM) compared to wild-type SRIPs (EC50: 0.06 μM). Overall, this study identifies four GL derivatives as promising lead compounds for developing treatments against various SARS-CoV-2 strains, including Omicron, and nirmatrelvir-resistant variants.
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Affiliation(s)
- Uyen Nguyen Phuong Le
- Graduate Institute of Biological Science and Technology, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Yu-Jen Chang
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan
| | - Chih-Hao Lu
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan; Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yeh Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Shao-Ting Chao
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Lia A Baltina
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, Russia
| | - Svetlana F Petrova
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, Russia
| | - Sin-Rong Li
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Mien-Chie Hung
- Research Center for Cancer Biology, China Medical University, Taichung, 404327, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Michael M C Lai
- Institute of Molecular Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Lidia A Baltina
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, Russia.
| | - Cheng-Wen Lin
- Graduate Institute of Biological Science and Technology, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan.
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6
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Ruiz-Moreno AJ, Cedillo-González R, Cordova-Bahena L, An Z, Medina-Franco JL, Velasco-Velázquez MA. Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 M pro Inhibitors from Large Chemical Libraries. J Chem Inf Model 2024; 64:1984-1995. [PMID: 38472094 PMCID: PMC10966741 DOI: 10.1021/acs.jcim.3c01439] [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: 09/10/2023] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome and is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development, and multiple Mpro crystals complexed with competitive inhibitors have been reported. In this study, we aimed to develop an Mpro consensus pharmacophore as a tool to expand the search for inhibitors. We generated a consensus model by aligning and summarizing pharmacophoric points from 152 bioactive conformers of SARS-CoV-2 Mpro inhibitors. Validation against a library of conformers from a subset of ligands showed that our model retrieved poses that reproduced the crystal-binding mode in 77% of the cases. Using models derived from a consensus pharmacophore, we screened >340 million compounds. Pharmacophore-matching and chemoinformatics analyses identified new potential Mpro inhibitors. The candidate compounds were chemically dissimilar to the reference set, and among them, demonstrating the relevance of our model. We evaluated the effect of 16 candidates on Mpro enzymatic activity finding that seven have inhibitory activity. Three compounds (1, 4, and 5) had IC50 values in the midmicromolar range. The Mpro consensus pharmacophore reported herein can be used to identify compounds with improved activity and novel chemical scaffolds against Mpro. The method developed for its generation is provided as an open-access code (https://github.com/AngelRuizMoreno/ConcensusPharmacophore) and can be applied to other pharmacological targets.
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Affiliation(s)
- Angel J. Ruiz-Moreno
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
| | - Raziel Cedillo-González
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Graduate
Program in Biochemical Sciences, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
- DIFACQUIM
Research Group, School of Chemistry, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Luis Cordova-Bahena
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Consejo
Nacional de Humanidades, Ciencias y Tecnología, Mexico City 03940, Mexico
| | - Zhiqiang An
- Texas
Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - José L. Medina-Franco
- DIFACQUIM
Research Group, School of Chemistry, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Marco A. Velasco-Velázquez
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Texas
Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
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7
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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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8
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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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9
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Rieder GS, Nogara PA, Omage FB, Duarte T, Dalla Corte CL, da Rocha JBT. Computational analysis of the interactions between Ebselen and derivatives with the active site of the main protease from SARS-CoV-2. Comput Biol Chem 2023; 107:107956. [PMID: 37748316 DOI: 10.1016/j.compbiolchem.2023.107956] [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: 05/18/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023]
Abstract
The main protease (Mpro) of the novel coronavirus SARS-CoV-2 is a key target for developing antiviral drugs. Ebselen (EbSe) is a selenium-containing compound that has been shown to inhibit Mpro in vitro by forming a covalent bond with the cysteine (Cys) residue in the active site of the enzyme. However, EbSe can also bind to other proteins, like albumin, and low molecular weight compounds that have free thiol groups, such as Cys and glutathione (GSH), which may affect its availability and activity. In this study, we analyzed the Mpro interaction with EbSe, its analogues, and its metabolites with Cys, GSH, and albumin by molecular docking. We also simulated the electronic structure of the generated molecules by density functional theory (DFT) and explored the stability of EbSe and one of its best derivatives, EbSe-2,5-MeClPh, in the catalytic pocket of Mpro through covalent docking and molecular dynamics. Our results show that EbSe and its analogues bound to GSH/albumin have larger distance between the selenium atom of the ligands and the sulfur atom of Cys145 of Mpro than the other compounds. This suggests that EbSe and its GSH/albumin-analogues may have less affinity for the active site of Mpro. EbSe-2,5-MeClPh was found one of the best molecules, and in molecular dynamics simulations, it showed to undergo more conformational changes in the active site of Mpro, in relation to EbSe, which remained stable in the catalytic pocket. Moreover, this study also reveals that all compounds have the potential to interact closely with the active site of Mpro, providing us with a concept of which derivatives may be promising for in vitro analysis in the future. We propose that these compounds are potential covalent inhibitors of Mpro and that organoselenium compounds are molecules that should be studied for their antiviral properties.
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Affiliation(s)
- Guilherme Schmitt Rieder
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Pablo Andrei Nogara
- Federal Institute of Education, Science and Technology Sul-rio-grandense (IFSul), Bagé 96418-400, RS, Brazil
| | - Folorunsho Bright Omage
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Computational Biology Research Group, Embrapa Agricultural Informatics, Campinas, São Paulo, Brazil
| | - Tâmie Duarte
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Cristiane Lenz Dalla Corte
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - João Batista Teixeira da Rocha
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil; Department of Biochemistry, Institute of Basic Health Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil, 90035-003.
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10
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, 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.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, 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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11
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Tao Y, Qu H, Wang S, Yan F, Wang C, Zhang M. Computational assessment of herbal medicine-derived compounds as potential inhibitors of SARS-CoV-2 main protease. J Biomol Struct Dyn 2023; 41:9602-9613. [PMID: 36373329 DOI: 10.1080/07391102.2022.2144949] [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: 07/21/2022] [Accepted: 10/30/2022] [Indexed: 11/16/2022]
Abstract
Since the main protease (Mpro) is crucial for the COVID-19 virus replication and transcription, searching for Mpro inhibitors is one possible treatment option. In our study, 258 small molecules were collected from lung-related herbal medicines, and their structures were optimized with the B3LYP-D3/6-31G* method. After the molecular docking with Mpro, we selected the top 20 compounds for the further geometry optimization with the larger basis sets. After the further molecular docking, the top eight compounds were screened out. Then we performed molecular dynamics simulations and binding free energy calculations to determine stability of the complexes. Our results show that mulberrofuran G, Xambioona, and kuwanon D can bind Mpro well. In quantum chemistry studies, such as ESP and CDFT analyses, the compounds properties are predicted. Additionally, the drug-likeness analyses and ADME studies on these three candidate compounds verified that all of them conform to Libinski's rule and may be drug-like compounds.
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Affiliation(s)
- Yulian Tao
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Hanyang Qu
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Shengpeng Wang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Fei Yan
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Cuihong Wang
- School of Science, Tianjin Chengjian University, Tianjin, China
| | - Meiling Zhang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
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12
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Puhl AC, Godoy AS, Noske GD, Nakamura AM, Gawriljuk VO, Fernandes RS, Oliva G, Ekins S. Discovery of PL pro and M pro Inhibitors for SARS-CoV-2. ACS OMEGA 2023; 8:22603-22612. [PMID: 37387790 PMCID: PMC10275482 DOI: 10.1021/acsomega.3c01110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
There are very few small-molecule antivirals for SARS-CoV-2 that are either currently approved (or emergency authorized) in the US or globally, including remdesivir, molnupiravir, and paxlovid. The increasing number of SARS-CoV-2 variants that have appeared since the outbreak began over three years ago raises the need for continual development of updated vaccines and orally available antivirals in order to fully protect or treat the population. The viral main protease (Mpro) and the papain-like protease (PLpro) are key for viral replication; therefore, they represent valuable targets for antiviral therapy. We herein describe an in vitro screen performed using the 2560 compounds from the Microsource Spectrum library against Mpro and PLpro in an attempt to identify additional small-molecule hits that could be repurposed for SARS-CoV-2. We subsequently identified 2 hits for Mpro and 8 hits for PLpro. One of these hits was the quaternary ammonium compound cetylpyridinium chloride with dual activity (IC50 = 2.72 ± 0.09 μM for PLpro and IC50 = 7.25 ± 0.15 μM for Mpro). A second inhibitor of PLpro was the selective estrogen receptor modulator raloxifene (IC50 = 3.28 ± 0.29 μM for PLpro and IC50 = 42.8 ± 6.7 μM for Mpro). We additionally tested several kinase inhibitors and identified olmutinib (IC50 = 0.54 ± 0.04 μM), bosutinib (IC50 = 4.23 ± 0.28 μM), crizotinib (IC50 = 3.81 ± 0.04 μM), and dacominitinib (IC50 = IC50 3.33 ± 0.06 μM) as PLpro inhibitors for the first time. In some cases, these molecules have also been tested by others for antiviral activity for this virus, or we have used Calu-3 cells infected with SARS-CoV-2. The results suggest that approved drugs can be identified with promising activity against these proteases, and in several cases we or others have validated their antiviral activity. The additional identification of known kinase inhibitors as molecules targeting PLpro may provide new repurposing opportunities or starting points for chemical optimization.
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Affiliation(s)
- Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Andre S. Godoy
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Gabriela D. Noske
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Aline M. Nakamura
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Victor O. Gawriljuk
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Rafaela S. Fernandes
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Glaucius Oliva
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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13
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Pang X, Xu W, Liu Y, Li H, Chen L. The research progress of SARS-CoV-2 main protease inhibitors from 2020 to 2022. Eur J Med Chem 2023; 257:115491. [PMID: 37244162 DOI: 10.1016/j.ejmech.2023.115491] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/06/2023] [Accepted: 05/14/2023] [Indexed: 05/29/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. The main protease (Mpro) of SARS-CoV-2 plays a central role in viral replication and transcription and represents an attractive drug target for fighting COVID-19. Many SARS-CoV-2 Mpro inhibitors have been reported, including covalent and noncovalent inhibitors. The SARS-CoV-2 Mpro inhibitor PF-07321332 (Nirmatrelvir) designed by Pfizer has been put on the market. This paper briefly introduces the structural characteristics of SARS-CoV-2 Mpro and summarizes the research progress of SARS-CoV-2 Mpro inhibitors from the aspects of drug repurposing and drug design. These information will provide a basis for the drug development of treating the infection of SARS-CoV-2 and even other coronaviruses in the future.
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Affiliation(s)
- Xiaojing Pang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Wei Xu
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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14
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Zhang W, Lin SX. Search of Novel Small Molecule Inhibitors for the Main Protease of SARS-CoV-2. Viruses 2023; 15:v15020580. [PMID: 36851795 PMCID: PMC9967108 DOI: 10.3390/v15020580] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The current outbreak of coronavirus disease 2019 (COVID-19) has prompted the necessity of efficient treatment strategies. The COVID-19 pandemic was caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Main protease (Mpro), also called 3-chymotrypsin-like protease (3CL protease), plays an essential role in cleaving virus polyproteins for the functional replication complex. Therefore, Mpro is a promising drug target for COVID-19 therapy. Through molecular modelling, docking and a protease activity assay, we found four novel inhibitors targeting Mpro with the half maximal inhibitory concentration (IC50) and their binding affinities shown by the dissociation constants (KDs). Our new inhibitors CB-21, CB-25, CP-1 and LC24-20 have IC50s at 14.88 µM (95% Confidence Interval (95% CI): 10.35 µM to 20.48 µM), 22.74 µM (95% CI: 13.01 µM to 38.16 µM), 18.54µM (95% CI: 6.54 µM to 36.30 µM) and 32.87µM (95% CI: 18.37 µM to 54.80 µM)), respectively. The evaluation of interactions suggested that each inhibitor has a hydrogen bond or hydrophobic interactions with important residues, including the most essential catalytic residues: His41 and Cys145. All the four inhibitors have a much higher 50% lethal dose (LD50) compared with the well-known Mpro inhibitor GC376, demonstrating its low toxicity. These four inhibitors can be potential drug candidates for further in vitro and in vivo studies against COVID-19.
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15
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Ye X, Li Y, Guo L, Yao Y, Zhu R, Wei S, Diao H, Shao Z. Synthesis and enzymatic inhibition effects of thiazolidinedione 3C-like protease inhibitors. JOURNAL OF CHEMICAL RESEARCH 2023. [DOI: 10.1177/17475198231152556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The 3C-like protease (also known as Mpro) plays a key role in SARS-CoV-2 replication and has similar substrates across mutant coronaviruses, making it an ideal drug target. We synthesized 19 thiazolidinedione derivatives via the Knoevenagel condensations and Mitsunobu reactions as potential 3C-like protease inhibitors. The activity of these inhibitors is screened in vitro by employing the enzymatic screening model of 3C-like protease using fluorescence resonance energy transfer. Dithiothreitol is included in the enzymatic reaction system to avoid non-specific enzymatic inhibition. Active inhibitors with diverse activity are found in this series of compounds, and two representative inhibitors with potent inhibitory activity are highlighted.
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Affiliation(s)
- Xin Ye
- College of Chemistry and Chemical Engineering, Donghua University, Shanghai, China
| | - Yuhua Li
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lina Guo
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yiling Yao
- College of Chemistry and Chemical Engineering, Donghua University, Shanghai, China
| | - Rouyu Zhu
- College of Chemistry and Chemical Engineering, Donghua University, Shanghai, China
| | - Shuang Wei
- College of Chemistry and Chemical Engineering, Donghua University, Shanghai, China
| | - Hua Diao
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhiyu Shao
- College of Chemistry and Chemical Engineering, Donghua University, Shanghai, China
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16
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Iype E, Pillai U J, Kumar I, Gaastra-Nedea SV, Subramanian R, Saha RN, Dutta M. In silico and in vitro assays reveal potential inhibitors against 3CL pro main protease of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:12800-12811. [PMID: 34550861 DOI: 10.1080/07391102.2021.1977181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is not showing any sign of slowing down even after the ongoing efforts of vaccination. The threats of new strains are concerning, as some of them are more infectious than the original one. A therapeutic against the disease is, therefore, of urgent need. Here, we use the DrugBank database to screen for potential inhibitors against the 3CLpro main protease of SARS-CoV-2. Instead of using the traditional approach of computational screening by docking, we developed a kernel ridge regressor (using a part of the docking data) to predict the binding energy of ligands. We used this model to screen the DrugBank database and shortlist two lead candidates (bromocriptine and avoralstat) for in vitro enzymatic study. Our results show that the 3CLpro enzyme activity in presence of 100 μM concentration of bromocriptine and avoralstat is 9.9% and 15.9%, respectively. Remarkably, bromocriptine exhibited submicromolar IC50 of 130 nM (0.13 μM). Avoralstat showed an IC50 of 2.16 μM. Further, the interactions of both drugs with 3CLpro were analyzed using molecular dynamics simulations of 100 ns. Results indicate that both ligands are stable in the binding pocket of the 3CLpro receptor. In addition, the MM-PBSA analysis revealed that bromocriptine (-29.37 kcal/mol) has a lower binding free energy compared to avoralstat (-6.91 kcal/mol). Further, hydrogen bond analysis also showed that bromocriptine interacts with the two catalytic residues, His41 and Cys145, more frequently than avoralstat.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Eldhose Iype
- Department of Chemical Engineering, BITS Pilani, Dubai Campus, Dubai, United Arab Emirates
| | - Jisha Pillai U
- Department of Biotechnology, BITS Pilani, Dubai Campus, Dubai, United Arab Emirates
| | - Indresh Kumar
- Department of Chemistry, BITS Pilani, Pilani Campus, Pilani, India
| | - Silvia V Gaastra-Nedea
- Department of Mechanical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | | | | | - Mainak Dutta
- Department of Biotechnology, BITS Pilani, Dubai Campus, Dubai, United Arab Emirates
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17
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Santos LH, Kronenberger T, Almeida RG, Silva EB, Rocha REO, Oliveira JC, Barreto LV, Skinner D, Fajtová P, Giardini MA, Woodworth B, Bardine C, Lourenço AL, Craik CS, Poso A, Podust LM, McKerrow JH, Siqueira-Neto JL, O’Donoghue AJ, da Silva
Júnior EN, Ferreira RS. Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease M pro and Papain-like Protease PL pro of SARS-CoV-2. J Chem Inf Model 2022; 62:6553-6573. [PMID: 35960688 PMCID: PMC9397563 DOI: 10.1021/acs.jcim.2c00693] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Indexed: 01/07/2023]
Abstract
The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In this study, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 μM and 9.0 μM. In addition, three compounds inhibited PLpro with IC50 ranging from 1.9 μM to 3.3 μM. To verify the specificity of Mpro and PLpro inhibitors, our experiments included an assessment of common causes of false positives such as aggregation, high compound fluorescence, and inhibition by enzyme oxidation. Altogether, we confirmed novel classes of specific Mpro and PLpro inhibitors. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.
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Affiliation(s)
- Lucianna H. Santos
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Thales Kronenberger
- Department of Oncology and Pneumonology, Internal
Medicine VIII, University Hospital Tübingen,
Otfried-Müller-Straße 10, DE72076 Tübingen,
Germany
- School of Pharmacy, Faculty of Health Sciences,
University of Eastern Finland, 70211 Kuopio,
Finland
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2),
Eberhard Karls University Tübingen, Auf der
Morgenstelle 8, 72076 Tübingen, Germany
| | - Renata G. Almeida
- Institute of Exact Sciences, Department of Chemistry,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Elany B. Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Rafael E. O. Rocha
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Joyce C. Oliveira
- Institute of Exact Sciences, Department of Chemistry,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Luiza V. Barreto
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Danielle Skinner
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
- Institute of Organic Chemistry and Biochemistry,
Academy of Sciences of the Czech Republic, 16610 Prague,
Czech Republic
| | - Miriam A. Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Brendon Woodworth
- Department of Medicine, Division of Infectious
Diseases, University of California San Diego, La Jolla,
California 92093, United States
| | - Conner Bardine
- Department of Pharmaceutical Chemistry,
University of California San Francisco, San Francisco,
California 94143, United States
| | - André L. Lourenço
- Department of Pharmaceutical Chemistry,
University of California San Francisco, San Francisco,
California 94143, United States
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry,
University of California San Francisco, San Francisco,
California 94143, United States
| | - Antti Poso
- Department of Oncology and Pneumonology, Internal
Medicine VIII, University Hospital Tübingen,
Otfried-Müller-Straße 10, DE72076 Tübingen,
Germany
- School of Pharmacy, Faculty of Health Sciences,
University of Eastern Finland, 70211 Kuopio,
Finland
| | - Larissa M. Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Jair L. Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Eufrânio N. da Silva
Júnior
- Institute of Exact Sciences, Department of Chemistry,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Rafaela S. Ferreira
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
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18
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The Potential of Stilbene Compounds to Inhibit M pro Protease as a Natural Treatment Strategy for Coronavirus Disease-2019. Curr Issues Mol Biol 2022; 45:12-32. [PMID: 36661488 PMCID: PMC9857500 DOI: 10.3390/cimb45010002] [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: 10/11/2022] [Revised: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
COVID-19 disease has had a global impact on human health with increased levels of morbidity and mortality. There is an unmet need to design and produce effective antivirals to treat COVID-19. This study aimed to explore the potential ability of natural stilbenes to inhibit the Mpro protease, an acute respiratory syndrome coronavirus-2 (SARS-CoV-2) enzyme involved in viral replication. The binding affinities of stilbene compounds against Mpro were scrutinized using molecular docking, prime molecular mechanics-generalized Born surface area (MM-GBSA) energy calculations, and molecular dynamic simulations. Seven stilbene molecules were docked with Mpro and compared with GC376 and N3, antivirals with demonstrated efficacy against Mpro. Ligand binding efficiencies and polar and non-polar interactions between stilbene compounds and Mpro were analyzed. The binding affinities of astringin, isorhapontin, and piceatannol were -9.319, -8.166, and -6.291 kcal/mol, respectively, and higher than either GC376 or N3 at -6.976 and -6.345 kcal/mol, respectively. Prime MM-GBSA revealed that these stilbene compounds exhibited useful ligand efficacy and binding affinity to Mpro. Molecular dynamic simulation studies of astringin, isorhapontin, and piceatannol showed their stability at 300 K throughout the simulation time. Collectively, these results suggest that stilbenes such as astringin, isorhapontin, and piceatannol could provide useful natural inhibitors of Mpro and thereby act as novel treatments to limit SARS-CoV-2 replication.
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19
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Geethakumari AM, Ahmed WS, Rasool S, Fatima A, Nasir Uddin SM, Aouida M, Biswas KH. A genetically encoded BRET-based SARS-CoV-2 M pro protease activity sensor. Commun Chem 2022; 5:117. [PMID: 36187754 PMCID: PMC9516532 DOI: 10.1038/s42004-022-00731-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
The main protease, Mpro, is critical for SARS-CoV-2 replication and an appealing target for designing anti-SARS-CoV-2 agents. Therefore, there is a demand for the development of improved sensors to monitor its activity. Here, we report a pair of genetically encoded, bioluminescence resonance energy transfer (BRET)-based sensors for detecting Mpro proteolytic activity in live cells as well as in vitro. The sensors were generated by sandwiching peptides containing the Mpro N-terminal autocleavage sites, either AVLQSGFR (short) or KTSAVLQSGFRKME (long), in between the mNeonGreen and NanoLuc proteins. Co-expression of the sensors with Mpro in live cells resulted in their cleavage while mutation of the critical C145 residue (C145A) in Mpro completely abrogated their cleavage. Additionally, the sensors recapitulated the inhibition of Mpro by the well-characterized pharmacological agent GC376. Further, in vitro assays with the BRET-based Mpro sensors revealed a molecular crowding-mediated increase in the rate of Mpro activity and a decrease in the inhibitory potential of GC376. The sensors developed here will find direct utility in studies related to drug discovery targeting the SARS-CoV-2 Mpro and functional genomics application to determine the effect of sequence variation in Mpro.
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Affiliation(s)
- Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Wesam S. Ahmed
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Saad Rasool
- Division of Genomics and Precision Medicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Asma Fatima
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - S. M. Nasir Uddin
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
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20
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Hu Q, Xiong Y, Zhu G, Zhang Y, Zhang Y, Huang P, Ge G. The SARS-CoV-2 main protease (M pro): Structure, function, and emerging therapies for COVID-19. MedComm (Beijing) 2022; 3:e151. [PMID: 35845352 PMCID: PMC9283855 DOI: 10.1002/mco2.151] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The main proteases (Mpro), also termed 3-chymotrypsin-like proteases (3CLpro), are a class of highly conserved cysteine hydrolases in β-coronaviruses. Increasing evidence has demonstrated that 3CLpros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus-caused infectious diseases, including COVID-19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease Mpro (also known as 3CLpro), as well as recent advances in discovering and developing SARS-CoV-2 3CLpro inhibitors. To better understand the characteristics of SARS-CoV-2 3CLpro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CLpro inhibitors (including marketed drugs, peptidomimetic, and non-peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CLpro inhibitors as novel anti-coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS-CoV-2 3CLpro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CLpro inhibitors as novel anti-coronavirus agents.
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Affiliation(s)
- Qing Hu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guang‐Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Ya‐Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yi‐Wen Zhang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Ping Huang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Guang‐Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
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21
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Ou J, Lewandowski EM, Hu Y, Lipinski AA, Morgan RT, Jacobs LM, Zhang X, Bikowitz MJ, Langlais P, Tan H, Wang J, Chen Y, Choy JS. A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations. RESEARCH SQUARE 2022:rs.3.rs-1942964. [PMID: 36052369 PMCID: PMC9435405 DOI: 10.21203/rs.3.rs-1942964/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is a major therapeutic target. The Mpro inhibitor, nirmatrelvir, is the antiviral component of Paxlovid, an orally available treatment for COVID-19. As Mpro inhibitor use increases, drug resistant mutations will likely emerge. We have established a non-pathogenic system, in which yeast growth serves as a proxy for Mpro activity, enabling rapid identification of mutants with altered enzymatic activity and drug sensitivity. The E166 residue is known to be a potential hot spot for drug resistance and yeast assays showed that an E166R substitution conferred strong nirmatrelvir resistance while an E166N mutation compromised activity. On the other hand, N142A and P132H mutations caused little to no change in drug response and activity. Standard enzymatic assays confirmed the yeast results. In turn, we solved the structures of Mpro E166R, and Mpro E166N, providing insights into how arginine may drive drug resistance while asparagine leads to reduced activity. The work presented here will help characterize novel resistant variants of Mpro that may arise as Mpro antivirals become more widely used.
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Affiliation(s)
- Jin Ou
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, United States
| | - Eric M. Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Austin A. Lipinski
- Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ 85724, United States
| | - Ryan T. Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Lian M.C. Jacobs
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
- Drug Discovery Department, Moffit Cancer Center, Tampa, FL 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Melissa J. Bikowitz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Paul Langlais
- Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ 85724, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - John S. Choy
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, United States
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22
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Germano C, Messina A, Tavella E, Vitale R, Avellis V, Barboni M, Attini R, Revelli A, Zola P, Manzoni P, Masturzo B. Fetal Brain Damage during Maternal COVID-19: Emerging Hypothesis, Mechanism, and Possible Mitigation through Maternal-Targeted Nutritional Supplementation. Nutrients 2022; 14:3303. [PMID: 36014809 PMCID: PMC9414753 DOI: 10.3390/nu14163303] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/24/2022] Open
Abstract
The recent outbreak of the novel Coronavirus (SARS-CoV-2 or CoV-2) pandemic in 2019 and the risk of CoV-2 infection during pregnancy led the scientific community to investigate the potential negative effects of Coronavirus infection on pregnancy outcomes and fetal development. In particular, as CoV-2 neurotropism has been demonstrated in adults, recent studies suggested a possible risk of fetal brain damage and fetal brain development impairment, with consequent psychiatric manifestations in offspring of mothers affected by COronaVIrus Disease (COVID) during pregnancy. Through the understanding of CoV-2's pathogenesis and the pathways responsible for cell damage, along with the available data about neurotropic virus attitudes, different strategies have been suggested to lower the risk of neurologic disease in newborns. In this regard, the role of nutrition in mitigating fetal damages related to oxidative stress and the inflammatory environment during viral infection has been investigated, and arginine, n3PUFA, vitamins B1 and B9, choline, and flavonoids were found to be promising in and out of pregnancy. The aim of this review is to provide an overview of the current knowledge on the mechanism of fetal brain damage and the impact of nutrition in reducing inflammation related to worse neurological outcomes in the context of CoV-2 infections during pregnancy.
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Affiliation(s)
- Chiara Germano
- Department of Maternal, Neonatal and Infant Medicine, University Hospital “Degli Infermi”, 13875 Ponderano, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy
| | - Alessandro Messina
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy
| | - Elena Tavella
- Sant’Anna Hospital, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Raffaele Vitale
- Sant’Anna Hospital, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Vincenzo Avellis
- Sant’Anna Hospital, Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Martina Barboni
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy
| | - Rossella Attini
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy
| | - Alberto Revelli
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy
| | - Paolo Zola
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy
| | - Paolo Manzoni
- Department of Maternal, Neonatal and Infant Medicine, University Hospital “Degli Infermi”, 13875 Ponderano, Italy
| | - Bianca Masturzo
- Department of Maternal, Neonatal and Infant Medicine, University Hospital “Degli Infermi”, 13875 Ponderano, Italy
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23
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Ou J, Lewandowski EM, Hu Y, Lipinski AA, Morgan RT, Jacobs LM, Zhang X, Bikowitz MJ, Langlais P, Tan H, Wang J, Chen Y, Choy JS. A yeast-based system to study SARS-CoV-2 M pro structure and to identify nirmatrelvir resistant mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.06.503039. [PMID: 35982672 PMCID: PMC9387140 DOI: 10.1101/2022.08.06.503039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The SARS-CoV-2 main protease (M pro ) is a major therapeutic target. The M pro inhibitor, nirmatrelvir, is the antiviral component of Paxlovid, an orally available treatment for COVID-19. As M pro inhibitor use increases, drug resistant mutations will likely emerge. We have established a non-pathogenic system, in which yeast growth serves as a proxy for M pro activity, enabling rapid identification of mutants with altered enzymatic activity and drug sensitivity. The E166 residue is known to be a potential hot spot for drug resistance and yeast assays showed that an E166R substitution conferred strong nirmatrelvir resistance while an E166N mutation compromised activity. On the other hand, N142A and P132H mutations caused little to no change in drug response and activity. Standard enzymatic assays confirmed the yeast results. In turn, we solved the structures of M pro E166R, and M pro E166N, providing insights into how arginine may drive drug resistance while asparagine leads to reduced activity. The work presented here will help characterize novel resistant variants of M pro that may arise as M pro antivirals become more widely used.
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Affiliation(s)
- Jin Ou
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, United States
| | - Eric M. Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Yanmei Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Austin A. Lipinski
- Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ 85724, United States
| | - Ryan T. Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Lian M.C. Jacobs
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
- Drug Discovery Department, Moffit Cancer Center, Tampa, FL 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Melissa J. Bikowitz
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - Paul Langlais
- Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ 85724, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, United States
| | - John S. Choy
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, United States
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24
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Discovery of Triple Inhibitors of Both SARS-CoV-2 Proteases and Human Cathepsin L. Pharmaceuticals (Basel) 2022; 15:ph15060744. [PMID: 35745663 PMCID: PMC9230533 DOI: 10.3390/ph15060744] [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: 05/17/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/15/2022] Open
Abstract
One inhibitor of the main SARS-CoV-2 protease has been approved recently by the FDA, yet it targets only SARS-CoV-2 main protease (Mpro). Here, we discovered inhibitors containing thiuram disulfide or dithiobis-(thioformate) tested against three key proteases involved in SARS-CoV-2 replication, including Mpro, SARS-CoV-2 papain-like protease (PLpro), and human cathepsin L. The use of thiuram disulfide and dithiobis-(thioformate) covalent inhibitor warheads was inspired by an idea to find a better alternative than disulfiram, an approved treatment for chronic alcoholism that is currently in phase 2 clinical trials against SARS-CoV-2. Our goal was to find more potent inhibitors that target both viral proteases and one essential human protease to reduce the dosage, improve the efficacy, and minimize the adverse effects associated with these agents. We found that compounds coded as RI175, RI173, and RI172 were the most potent inhibitors in an enzymatic assay against SARS-CoV-2 Mpro, SARS-CoV-2 PLpro, and human cathepsin L, with IC50s of 300, 200, and 200 nM, which is about 5-, 19-, and 11-fold more potent than disulfiram, respectively. In addition, RI173 was tested against SARS-CoV-2 in a cell-based and toxicity assay and was shown to have a greater antiviral effect than disulfiram. The identified compounds demonstrated the promising potential of thiuram disulfide or dithiobis-(thioformate) as a reactive functional group in small molecules that could be further developed for treatment of the COVID-19 virus or related variants.
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25
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Brewitz L, Kamps JJAG, Lukacik P, Strain‐Damerell C, Zhao Y, Tumber A, Malla TR, Orville AM, Walsh MA, Schofield CJ. Mass Spectrometric Assays Reveal Discrepancies in Inhibition Profiles for the SARS-CoV-2 Papain-Like Protease. ChemMedChem 2022; 17:e202200016. [PMID: 35085423 PMCID: PMC9015526 DOI: 10.1002/cmdc.202200016] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/26/2022] [Indexed: 11/20/2022]
Abstract
The two SARS-CoV-2 proteases, i. e. the main protease (Mpro ) and the papain-like protease (PLpro ), which hydrolyze the viral polypeptide chain giving functional non-structural proteins, are essential for viral replication and are medicinal chemistry targets. We report a high-throughput mass spectrometry (MS)-based assay which directly monitors PLpro catalysis in vitro. The assay was applied to investigate the effect of reported small-molecule PLpro inhibitors and selected Mpro inhibitors on PLpro catalysis. The results reveal that some, but not all, PLpro inhibitor potencies differ substantially from those obtained using fluorescence-based assays. Some substrate-competing Mpro inhibitors, notably PF-07321332 (nirmatrelvir) which is in clinical development, do not inhibit PLpro . Less selective Mpro inhibitors, e. g. auranofin, inhibit PLpro , highlighting the potential for dual PLpro /Mpro inhibition. MS-based PLpro assays, which are orthogonal to widely employed fluorescence-based assays, are of utility in validating inhibitor potencies, especially for inhibitors operating by non-covalent mechanisms.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Jos J. A. G. Kamps
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Petra Lukacik
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Claire Strain‐Damerell
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Yilin Zhao
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Tika R. Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Allen M. Orville
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Martin A. Walsh
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
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26
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A VSV-based assay quantifies coronavirus Mpro/3CLpro/Nsp5 main protease activity and chemical inhibition. Commun Biol 2022; 5:391. [PMID: 35478219 PMCID: PMC9046202 DOI: 10.1038/s42003-022-03277-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/15/2022] [Indexed: 11/08/2022] Open
Abstract
Protease inhibitors are among the most powerful antiviral drugs. However, for SARS-CoV-2 only a small number of protease inhibitors have been identified thus far and there is still a great need for assays that efficiently report protease activity and inhibition in living cells. Here, we engineer a safe VSV-based system to report both gain- and loss-of-function of coronavirus main protease (Mpro/3CLpro/Nsp5) activity in living cells. We use SARS-CoV-2 3CLpro in this system to confirm susceptibility to known inhibitors (boceprevir, GC376, PF-00835231, and PF-07321332/nirmatrelvir) and reevaluate other reported inhibitors (baicalein, ebselen, carmofur, ethacridine, ivermectin, masitinib, darunavir, and atazanavir). Moreover, we show that the system can be adapted to report both the function and the chemical inhibition of proteases from different coronavirus species as well as from distantly related viruses. Together with the fact that live cell assays also reflect compound permeability and toxicity, we anticipate that this system will be useful for both identification and optimization of additional coronavirus protease inhibitors.
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27
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Airas J, Bayas CA, N'Ait Ousidi A, Ait Itto MY, Auhmani A, Loubidi M, Esseffar M, Pollock JA, Parish CA. Investigating novel thiazolyl-indazole derivatives as scaffolds for SARS-CoV-2 M Pro inhibitors. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY REPORTS 2022; 4:100034. [PMID: 37519829 PMCID: PMC8828376 DOI: 10.1016/j.ejmcr.2022.100034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/20/2021] [Accepted: 02/07/2022] [Indexed: 11/29/2022]
Abstract
COVID-19 is a global pandemic caused by infection with the SARS-CoV-2 virus. Remdesivir, a SARS-CoV-2 RNA polymerase inhibitor, is the only drug to have received widespread approval for treatment of COVID-19. The SARS-CoV-2 main protease enzyme (MPro), essential for viral replication and transcription, remains an active target in the search for new treatments. In this study, the ability of novel thiazolyl-indazole derivatives to inhibit MPro is evaluated. These compounds were synthesized via the heterocyclization of phenacyl bromide with (R)-carvone, (R)-pulegone and (R)-menthone thiosemicarbazones. The binding affinity and binding interactions of each compound were evaluated through Schrödinger Glide docking, AMBER molecular dynamics simulations, and MM-GBSA free energy estimation, and these results were compared with similar calculations of MPro binding various 5-mer substrates (VKLQA, VKLQS, VKLQG) and a previously identified MPro tight-binder X77. From these simulations, we can see that binding is driven by residue specific interactions such as π-stacking with His41, and S/π interactions with Met49 and Met165. The compounds were also experimentally evaluated in a MPro biochemical assay and the most potent compound containing a phenylthiazole moiety inhibited protease activity with an IC50 of 92.9 μM. This suggests that the phenylthiazole scaffold is a promising candidate for the development of future MPro inhibitors.
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Affiliation(s)
- Justin Airas
- Department of Chemistry, University of Richmond, Gottwald Center for the Sciences, Richmond, VA, 23173, USA
| | - Catherine A Bayas
- Department of Chemistry, University of Richmond, Gottwald Center for the Sciences, Richmond, VA, 23173, USA
| | - Abdellah N'Ait Ousidi
- Département de Chimie, Faculté des Sciences Semlalia, Cadi Ayyad University, BP, 2390, Marrakech, Morocco
| | - Moulay Youssef Ait Itto
- Département de Chimie, Faculté des Sciences Semlalia, Cadi Ayyad University, BP, 2390, Marrakech, Morocco
| | - Aziz Auhmani
- Département de Chimie, Faculté des Sciences Semlalia, Cadi Ayyad University, BP, 2390, Marrakech, Morocco
| | - Mohamed Loubidi
- Département de Chimie, Faculté des Sciences Semlalia, Cadi Ayyad University, BP, 2390, Marrakech, Morocco
| | - M'hamed Esseffar
- Département de Chimie, Faculté des Sciences Semlalia, Cadi Ayyad University, BP, 2390, Marrakech, Morocco
| | - Julie A Pollock
- Department of Chemistry, University of Richmond, Gottwald Center for the Sciences, Richmond, VA, 23173, USA
| | - Carol A Parish
- Department of Chemistry, University of Richmond, Gottwald Center for the Sciences, Richmond, VA, 23173, USA
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28
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Chen K, Krischuns T, Varga L, Harigua-Souiai E, Paisant S, Zettor A, Chiaravalli J, Delpal A, Courtney D, O'Brien A, Baker S, Decroly E, Isel C, Agou F, Jacob Y, Blondel A, Naffakh N. A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. Antiviral Res 2022; 201:105272. [PMID: 35278581 PMCID: PMC8906008 DOI: 10.1016/j.antiviral.2022.105272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for the screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified two molecules which show anti-nsp5 activity, both in our cell-based assay and in vitro on purified nsp5 protein, and inhibit SARS-CoV-2 replication in A549-ACE2 cells with EC50 values in the 4–8 μM range. The here described high-throughput-compatible assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.
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29
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Jin Z, Mantri Y, Retout M, Cheng Y, Zhou J, Jorns A, Fajtova P, Yim W, Moore C, Xu M, Creyer MN, Borum RM, Zhou J, Wu Z, He T, Penny WF, O’Donoghue A, Jokerst JV. A Charge-Switchable Zwitterionic Peptide for Rapid Detection of SARS-CoV-2 Main Protease. Angew Chem Int Ed Engl 2022; 61:e202112995. [PMID: 34936725 PMCID: PMC8854333 DOI: 10.1002/anie.202112995] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Indexed: 11/06/2022]
Abstract
The transmission of SARS-CoV-2 coronavirus has led to the COVID-19 pandemic. Nucleic acid testing while specific has limitations for mass surveillance. One alternative is the main protease (Mpro ) due to its functional importance in mediating the viral life cycle. Here, we describe a combination of modular substrate and gold colloids to detect Mpro via visual readout. The strategy involves zwitterionic peptide that carries opposite charges at the C-/N-terminus to exploit the specific recognition by Mpro . Autolytic cleavage releases a positively charged moiety that assembles the nanoparticles with rapid color changes (t<10 min). We determine a limit of detection for Mpro in breath condensate matrices <10 nM. We further assayed ten COVID-negative subjects and found no false-positive result. In the light of simplicity, our test for viral protease is not limited to an equipped laboratory, but also is amenable to integrating as portable point-of-care devices including those on face-coverings.
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Affiliation(s)
- Zhicheng Jin
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yash Mantri
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Maurice Retout
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yong Cheng
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jiajing Zhou
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Alec Jorns
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Pavla Fajtova
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Colman Moore
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ming Xu
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Matthew N. Creyer
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Raina M. Borum
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jingcheng Zhou
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Zhuohong Wu
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Tengyu He
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - William F. Penny
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Anthony O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Jesse V. Jokerst
- Department of NanoEngineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Department of Radiology, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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30
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Jin Z, Yeung J, Zhou J, Cheng Y, Li Y, Mantri Y, He T, Yim W, Xu M, Wu Z, Fajtova P, Creyer MN, Moore C, Fu L, Penny WF, O'Donoghue AJ, Jokerst JV. Peptidic Sulfhydryl for Interfacing Nanocrystals and Subsequent Sensing of SARS-CoV-2 Protease. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2022; 34:1259-1268. [PMID: 37406055 PMCID: PMC8791034 DOI: 10.1021/acs.chemmater.1c03871] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
There is a need for surveillance of COVID-19 to identify individuals infected with SARS-CoV-2 coronavirus. Although specific, nucleic acid testing has limitations in terms of point-of-care testing. One potential alternative is the nonstructural protease (nsp5, also known as Mpro/3CLpro) implicated in SARS-CoV-2 viral replication but not incorporated into virions. Here, we report a divalent substrate with a novel design, (Cys)2-(AA)x-(Asp)3, to interface gold colloids in the specific presence of Mpro leading to a rapid and colorimetric readout. Citrate- and tris(2-carboxyethyl)phosphine (TCEP)-AuNPs were identified as the best reporter out of the 17 ligated nanoparticles. Furthermore, we empirically determined the effects of varying cysteine valence and biological media on the sensor specificity and sensitivity. The divalent peptide was specific to Mpro, that is, there was no response when tested with other proteins or enzymes. Furthermore, the Mpro detection limits in Tris buffer and exhaled breath matrices are 12.2 and 18.9 nM, respectively, which are comparable to other reported methods (i.e., at low nanomolar concentrations) yet with a rapid and visual readout. These results from our work would provide informative rationales to design a practical and noninvasive alternative for COVID-19 diagnostic testing-the presence of viral proteases in biofluids is validated.
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Affiliation(s)
- Zhicheng Jin
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Justin Yeung
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Jiajing Zhou
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Yong Cheng
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Yi Li
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Yash Mantri
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
| | - Tengyu He
- Materials Science and Engineering Program, University of California San Diego, La Jolla, California 92093, United States
| | - Wonjun Yim
- Materials Science and Engineering Program, University of California San Diego, La Jolla, California 92093, United States
| | - Ming Xu
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Zhuohong Wu
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Pavla Fajtova
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Matthew N Creyer
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Colman Moore
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - Lei Fu
- Department of NanoEngineering, University of California San Diego, La Jolla, California 92093, United States
| | - William F Penny
- Division of Cardiology, University of California San Diego, San Diego, California 92161, United States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Jesse V Jokerst
- Department of NanoEngineering, Materials Science and Engineering Program, and Department of Radiology, University of California San Diego, La Jolla, California 92093, United States
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31
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Jin Z, Mantri Y, Retout M, Cheng Y, Zhou J, Jorns A, Fajtova P, Yim W, Moore C, Xu M, Creyer MN, Borum RM, Zhou J, Wu Z, He T, Penny WF, O'Donoghue AJ, Jokerst JV. A Charge‐Switchable Zwitterionic Peptide for Rapid Detection of SARS‐CoV‐2 Main Protease. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhicheng Jin
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Yash Mantri
- Department of Bioengineering University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Maurice Retout
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Yong Cheng
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Jiajing Zhou
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Alec Jorns
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Pavla Fajtova
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Wonjun Yim
- Materials Science and Engineering Program University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Colman Moore
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Ming Xu
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Matthew N. Creyer
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Raina M. Borum
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Jingcheng Zhou
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Zhuohong Wu
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Tengyu He
- Materials Science and Engineering Program University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - William F. Penny
- Department of Medicine University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
| | - Jesse V. Jokerst
- Department of NanoEngineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
- Materials Science and Engineering Program University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
- Department of Radiology University of California San Diego 9500 Gilman Drive La Jolla California 92093 USA
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32
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Santos LH, Kronenberger T, Almeida RG, Silva EB, Rocha REO, Oliveira JC, Barreto LV, Skinner D, Fajtová P, Giardini MA, Woodworth B, Bardine C, Lourenço AL, Craik CS, Poso A, Podust LM, McKerrow JH, Siqueira-Neto JL, O'Donoghue AJ, da Silva Júnior EN, Ferreira RS. Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.05.475095. [PMID: 35018373 PMCID: PMC8750648 DOI: 10.1101/2022.01.05.475095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In the present work, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC 50 ) values between 0.41 µM and 66 µM. In addition, eight compounds inhibited PLpro with IC 50 ranging from 1.7 µM to 46 µM. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.
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33
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Clinically available/under trial drugs and vaccines for treatment of SARS-COV-2. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300481 DOI: 10.1016/b978-0-323-91172-6.00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Prior 2019 to work date entire world is seriously influenced by an appalling illness called COVID sickness [Coronavirus disease-2019 (COVID-19)] which is brought about by another strain of coronavirus known as severe acute respiratory syndrome-Coronavirus-2. This pandemic was first seen in the Hubei area in Wuhan city of China. To date above 170 million individuals have been influenced by this infection and more than 3 million individuals died. The race of finding specific therapeutic drugs and efficacious vaccine candidates is still going on to tackle the pandemic-associated morbidities. This chapter discussed different clinically accessible medications (remdesivir, hydroxychloroquine, azithromycin, etc.) and immunizations (mRNA-1273, Sputanik, Pfizer, etc.) which are either in use or under trial for the treatment of COVID-19.
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34
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Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Pujadas G, Garcia-Vallvé S. A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet? Int J Mol Sci 2021; 23:259. [PMID: 35008685 PMCID: PMC8745775 DOI: 10.3390/ijms23010259] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 01/01/2023] Open
Abstract
In this review, we collected 1765 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) M-pro inhibitors from the bibliography and other sources, such as the COVID Moonshot project and the ChEMBL database. This set of inhibitors includes only those compounds whose inhibitory capacity, mainly expressed as the half-maximal inhibitory concentration (IC50) value, against M-pro from SARS-CoV-2 has been determined. Several covalent warheads are used to treat covalent and non-covalent inhibitors separately. Chemical space, the variation of the IC50 inhibitory activity when measured by different methods or laboratories, and the influence of 1,4-dithiothreitol (DTT) are discussed. When available, we have collected the values of inhibition of viral replication measured with a cellular antiviral assay and expressed as half maximal effective concentration (EC50) values, and their possible relationship to inhibitory potency against M-pro is analyzed. Finally, the most potent covalent and non-covalent inhibitors that simultaneously inhibit the SARS-CoV-2 M-pro and the virus replication in vitro are discussed.
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Affiliation(s)
| | | | | | | | - Gerard Pujadas
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
| | - Santiago Garcia-Vallvé
- Research Group in Cheminformatics & Nutrition, Departament de Bioquímica i Biotecnologia, Campus Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Catalonia, Spain; (G.M.); (P.G.-S.); (J.M.-T.); (B.S.-E.)
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35
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Zakharova MY, Kuznetsova AA, Uvarova VI, Fomina AD, Kozlovskaya LI, Kaliberda EN, Kurbatskaia IN, Smirnov IV, Bulygin AA, Knorre VD, Fedorova OS, Varnek A, Osolodkin DI, Ishmukhametov AA, Egorov AM, Gabibov AG, Kuznetsov NA. Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Front Pharmacol 2021; 12:773198. [PMID: 34938188 PMCID: PMC8686763 DOI: 10.3389/fphar.2021.773198] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/29/2021] [Indexed: 02/05/2023] Open
Abstract
The design of effective target-specific drugs for COVID-19 treatment has become an intriguing challenge for modern science. The SARS-CoV-2 main protease, Mpro, responsible for the processing of SARS-CoV-2 polyproteins and production of individual components of viral replication machinery, is an attractive candidate target for drug discovery. Specific Mpro inhibitors have turned out to be promising anticoronaviral agents. Thus, an effective platform for quantitative screening of Mpro-targeting molecules is urgently needed. Here, we propose a pre-steady-state kinetic analysis of the interaction of Mpro with inhibitors as a basis for such a platform. We examined the kinetic mechanism of peptide substrate binding and cleavage by wild-type Mpro and by its catalytically inactive mutant C145A. The enzyme induces conformational changes of the peptide during the reaction. The inhibition of Mpro by boceprevir, telaprevir, GC-376, PF-00835231, or thimerosal was investigated. Detailed pre-steady-state kinetics of the interaction of the wild-type enzyme with the most potent inhibitor, PF-00835231, revealed a two-step binding mechanism, followed by covalent complex formation. The C145A Mpro mutant interacts with PF-00835231 approximately 100-fold less effectively. Nevertheless, the binding constant of PF-00835231 toward C145A Mpro is still good enough to inhibit the enzyme. Therefore, our results suggest that even noncovalent inhibitor binding due to a fine conformational fit into the active site is sufficient for efficient inhibition. A structure-based virtual screening and a subsequent detailed assessment of inhibition efficacy allowed us to select two compounds as promising noncovalent inhibitor leads of SARS-CoV-2 Mpro.
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Affiliation(s)
- Maria Yu Zakharova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia
| | - Victoria I Uvarova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
| | - Anastasiia D Fomina
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Liubov I Kozlovskaya
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Elena N Kaliberda
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Inna N Kurbatskaia
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Ivan V Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Anatoly A Bulygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia
| | - Vera D Knorre
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia
| | - Alexandre Varnek
- Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, Strasbourg, France
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey M Egorov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Alexander G Gabibov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia.,Department of Biology and Biotechnology, Higher School of Economics, Moscow, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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36
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Chen KY, Krischuns T, Ortega Varga L, Harigua-Souiai E, Paisant S, Zettor A, Chiaravalli J, Courtney D, O’Brien A, Baker SC, Isel C, Agou F, Jacob Y, Blondel A, Naffakh N. A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.18.473303. [PMID: 34981051 PMCID: PMC8722588 DOI: 10.1101/2021.12.18.473303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Effective drugs against SARS-CoV-2 are urgently needed to treat severe cases of infection and for prophylactic use. The main viral protease (nsp5 or 3CLpro) represents an attractive and possibly broad-spectrum target for drug development as it is essential to the virus life cycle and highly conserved among betacoronaviruses. Sensitive and efficient high-throughput screening methods are key for drug discovery. Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for high-throughput screening of compounds in a 384-well format. A benefit of miniaturisation and automation is that screening can be performed in parallel on a wild-type and a catalytically inactive nsp5, which improves the selectivity of the assay. We performed molecular docking-based screening on a set of 14,468 compounds from an in-house chemical database, selected 359 candidate nsp5 inhibitors and tested them experimentally. We identified four molecules, including the broad-spectrum antiviral merimepodib/VX-497, which show anti-nsp5 activity and inhibit SARS-CoV-2 replication in A549-ACE2 cells with IC 50 values in the 4-21 µM range. The here described assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors. Moreover, we provide evidence that this assay can be adapted to other coronaviruses and viruses which rely on a viral protease.
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Affiliation(s)
- KY Chen
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - T Krischuns
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - L Ortega Varga
- Structural Bioinformatics Unit, Institut Pasteur, Université de Paris, Paris, France
| | - E Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology – LR16IPT04, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - S Paisant
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A Zettor
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - J Chiaravalli
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - D Courtney
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A O’Brien
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - SC Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, IL, USA
| | - C Isel
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - F Agou
- Chemogenomic and Biological Screening Platform, Institut Pasteur, Université de Paris, Paris, France
| | - Y Jacob
- Molecular Genetics of RNA Viruses, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
| | - A Blondel
- Structural Bioinformatics Unit, Institut Pasteur, Université de Paris, Paris, France
| | - N Naffakh
- RNA Biology and Influenza Virus Unit, Institut Pasteur, CNRS UMR3569, Université de Paris, Paris, France
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37
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Abstract
The ongoing COVID-19 pandemic urges searches for antiviral agents that can block infection or ameliorate its symptoms. Using dissimilar search strategies for new antivirals will improve our overall chances of finding effective treatments. Here, we have established an experimental platform for screening of small molecule inhibitors of the SARS-CoV-2 main protease in Saccharomyces cerevisiae cells, genetically engineered to enhance cellular uptake of small molecules in the environment. The system consists of a fusion of the Escherichia coli toxin MazF and its antitoxin MazE, with insertion of a protease cleavage site in the linker peptide connecting the MazE and MazF moieties. Expression of the viral protease confers cleavage of the MazEF fusion, releasing the MazF toxin from its antitoxin, resulting in growth inhibition. In the presence of a small molecule inhibiting the protease, cleavage is blocked and the MazF toxin remains inhibited, promoting growth. The system thus allows positive selection for inhibitors. The engineered yeast strain is tagged with a fluorescent marker protein, allowing precise monitoring of its growth in the presence or absence of inhibitor. We detect an established main protease inhibitor by a robust growth increase, discernible down to 1 μM. The system is suitable for robotized large-scale screens. It allows in vivo evaluation of drug candidates and is rapidly adaptable for new variants of the protease with deviant site specificities. IMPORTANCE The COVID-19 pandemic may continue for several years before vaccination campaigns can put an end to it globally. Thus, the need for discovery of new antiviral drug candidates will remain. We have engineered a system in yeast cells for the detection of small molecule inhibitors of one attractive drug target of SARS-CoV-2, its main protease, which is required for viral replication. The ability to detect inhibitors in live cells brings the advantage that only compounds capable of entering the cell and remain stable there will score in the system. Moreover, because of its design in yeast cells, the system is rapidly adaptable for tuning the detection level and eventual modification of the protease cleavage site in the case of future mutant variants of the SARS-CoV-2 main protease or even for other proteases.
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38
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Lima NM, Fernandes BL, Alves GF, de Souza JC, Siqueira MM, Patrícia do Nascimento M, Moreira OB, Sussulini A, de Oliveira MA. Mass spectrometry applied to diagnosis, prognosis, and therapeutic targets identification for the novel coronavirus SARS-CoV-2: A review. Anal Chim Acta 2021; 1195:339385. [PMID: 35090661 PMCID: PMC8687343 DOI: 10.1016/j.aca.2021.339385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/27/2022]
Abstract
Mass spectrometry (MS) has found numerous applications in medicine and has been widely used in the detection and characterization of biomolecules associated with viral infections such as COVID-19. COVID-19 is a multisystem disease and, therefore, the need arises to carry out a careful and conclusive assessment of the pathophysiological parameters involved in the infection, to develop an effective therapeutic approach, assess the prognosis of the disease, and especially the early diagnosis of the infected population. Thus, the urgent need for highly accurate methods of diagnosis and prognosis of this infection presents new challenges for the development of laboratory medicine, whose methods require sensitivity, speed, and accuracy of the techniques for analyzing the biological markers involved in the infection. In this context, MS stands out as a robust analytical tool, with high sensitivity and selectivity, accuracy, low turnaround time, and versatility for the analysis of biological samples. However, it has not yet been adopted as a frontline clinical laboratory technique. Therefore, this review explores the potential and trends of current MS methods and their contribution to the development of new strategies to COVID-19 diagnosis and prognosis and how this tool can assist in the discovery of new therapeutic targets, in addition, to comment what could be the future of MS in medicine.
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39
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Adhikari N, Banerjee S, Baidya SK, Ghosh B, Jha T. Ligand-based quantitative structural assessments of SARS-CoV-2 3CL pro inhibitors: An analysis in light of structure-based multi-molecular modeling evidences. J Mol Struct 2021; 1251:132041. [PMID: 34866654 PMCID: PMC8627846 DOI: 10.1016/j.molstruc.2021.132041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/10/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022]
Abstract
Due to COVID-19, the whole world is undergoing a devastating situation, but treatment with no such drug candidates still has been established exclusively. In that context, 69 diverse chemicals with potential SARS-CoV-2 3CLpro inhibitory property were taken into consideration for building different internally and externally validated linear (SW-MLR and GA-MLR), non-linear (ANN and SVM) QSAR, and HQSAR models to identify important structural and physicochemical characters required for SARS-CoV-2 3CLpro inhibition. Importantly, 2-oxopyrrolidinyl methyl and benzylester functions, and methylene (hydroxy) sulphonic acid warhead group, were crucial for retaining higher SARS-CoV-2 3CLpro inhibition. These GA-MLR and HQSAR models were also applied to predict some already repurposed drugs. As per the GA-MLR model, curcumin, ribavirin, saquinavir, sepimostat, and remdesivir were found to be the potent ones, whereas according to the HQSAR model, lurasidone, saquinavir, lopinavir, elbasvir, and paritaprevir were the highly effective SARS-CoV-2 3CLpro inhibitors. The binding modes of those repurposed drugs were also justified by the molecular docking, molecular dynamics (MD) simulation, and binding energy calculations conducted by several groups of researchers. This current work, therefore, may be able to find out important structural parameters to accelerate the COVID-19 drug discovery processes in the future.
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Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, India, 500078
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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Costanzi E, Kuzikov M, Esposito F, Albani S, Demitri N, Giabbai B, Camasta M, Tramontano E, Rossetti G, Zaliani A, Storici P. Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L. Int J Mol Sci 2021; 22:11779. [PMID: 34769210 PMCID: PMC8583849 DOI: 10.3390/ijms222111779] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
After almost two years from its first evidence, the COVID-19 pandemic continues to afflict people worldwide, highlighting the need for multiple antiviral strategies. SARS-CoV-2 main protease (Mpro/3CLpro) is a recognized promising target for the development of effective drugs. Because single target inhibition might not be sufficient to block SARS-CoV-2 infection and replication, multi enzymatic-based therapies may provide a better strategy. Here we present a structural and biochemical characterization of the binding mode of MG-132 to both the main protease of SARS-CoV-2, and to the human Cathepsin-L, suggesting thus an interesting scaffold for the development of double-inhibitors. X-ray diffraction data show that MG-132 well fits into the Mpro active site, forming a covalent bond with Cys145 independently from reducing agents and crystallization conditions. Docking of MG-132 into Cathepsin-L well-matches with a covalent binding to the catalytic cysteine. Accordingly, MG-132 inhibits Cathepsin-L with nanomolar potency and reversibly inhibits Mpro with micromolar potency, but with a prolonged residency time. We compared the apo and MG-132-inhibited structures of Mpro solved in different space groups and we identified a new apo structure that features several similarities with the inhibited ones, offering interesting perspectives for future drug design and in silico efforts.
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Affiliation(s)
- Elisa Costanzi
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany; (M.K.); (A.Z.)
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, 28759 Bremen, Germany
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (F.E.); (M.C.); (E.T.)
| | - Simone Albani
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational Biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (S.A.); (G.R.)
- Department of Biology, Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Nicola Demitri
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
| | - Barbara Giabbai
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
| | - Marianna Camasta
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (F.E.); (M.C.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (F.E.); (M.C.); (E.T.)
| | - Giulia Rossetti
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational Biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (S.A.); (G.R.)
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Neurology, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany; (M.K.); (A.Z.)
| | - Paola Storici
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
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Macip G, Garcia-Segura P, Mestres-Truyol J, Saldivar-Espinoza B, Ojeda-Montes MJ, Gimeno A, Cereto-Massagué A, Garcia-Vallvé S, Pujadas G. Haste makes waste: A critical review of docking-based virtual screening in drug repurposing for SARS-CoV-2 main protease (M-pro) inhibition. Med Res Rev 2021; 42:744-769. [PMID: 34697818 PMCID: PMC8662214 DOI: 10.1002/med.21862] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/30/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022]
Abstract
This review makes a critical evaluation of 61 peer‐reviewed manuscripts that use a docking step in a virtual screening (VS) protocol to predict SARS‐CoV‐2 M‐pro (M‐pro) inhibitors in approved or investigational drugs. Various manuscripts predict different compounds, even when they use a similar initial dataset and methodology, and most of them do not validate their methodology or results. In addition, a set of known 150 SARS‐CoV‐2 M‐pro inhibitors extracted from the literature and a second set of 81 M‐pro inhibitors and 113 inactive compounds obtained from the COVID Moonshot project were used to evaluate the reliability of using docking scores as feasible predictors of the potency of a SARS‐CoV‐2 M‐pro inhibitor. Using two SARS‐CoV‐2 M‐pro structures and five protein‐ligand docking programs, we proved that the correlation between the pIC50 and docking scores is not good. Neither was any correlation found between the pIC50 and the ∆G calculated with an MM‐GBSA method. When a group of experimentally known inactive compounds was added, neither the docking scores or the ∆G were able to distinguish between compounds with or without M‐pro experimental inhibitory activity. Performances improved when covalent and noncovalent inhibitors were treated separately, but were not good enough to fully support using a docking score as a cutoff value for selecting new putative M‐pro inhibitors or predicting the relative bioactivity of a compound by comparison with a reference compound. The two sets of known SARS‐CoV‐2 M‐pro inhibitors presented here could be used for validating future VS protocols which aim to predict M‐pro inhibitors.
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Affiliation(s)
- Guillem Macip
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, Tarragona, Tarragona, Spain
| | - Pol Garcia-Segura
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, Tarragona, Tarragona, Spain
| | - Júlia Mestres-Truyol
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, Tarragona, Tarragona, Spain
| | - Bryan Saldivar-Espinoza
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, Tarragona, Tarragona, Spain
| | | | - Aleix Gimeno
- Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Adrià Cereto-Massagué
- EURECAT Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Reus, Spain
| | - Santiago Garcia-Vallvé
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, Tarragona, Tarragona, Spain.,EURECAT, TECNIO, CEICS, Avinguda Universitat 1, Reus, Spain
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, Tarragona, Tarragona, Spain.,EURECAT, TECNIO, CEICS, Avinguda Universitat 1, Reus, Spain
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Vuong W, Fischer C, Khan MB, van Belkum MJ, Lamer T, Willoughby KD, Lu J, Arutyunova E, Joyce MA, Saffran HA, Shields JA, Young HS, Nieman JA, Tyrrell DL, Lemieux MJ, Vederas JC. Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies. Eur J Med Chem 2021; 222:113584. [PMID: 34118724 PMCID: PMC8164773 DOI: 10.1016/j.ejmech.2021.113584] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/03/2021] [Accepted: 05/22/2021] [Indexed: 12/31/2022]
Abstract
Replication of SARS-CoV-2, the coronavirus causing COVID-19, requires a main protease (Mpro) to cleave viral proteins. Consequently, Mpro is a target for antiviral agents. We and others previously demonstrated that GC376, a bisulfite prodrug with efficacy as an anti-coronaviral agent in animals, is an effective inhibitor of Mpro in SARS-CoV-2. Here, we report structure-activity studies of improved GC376 derivatives with nanomolar affinities and therapeutic indices >200. Crystallographic structures of inhibitor-Mpro complexes reveal that an alternative binding pocket in Mpro, S4, accommodates the P3 position. Alternative binding is induced by polar P3 groups or a nearby methyl. NMR and solubility studies with GC376 show that it exists as a mixture of stereoisomers and forms colloids in aqueous media at higher concentrations, a property not previously reported. Replacement of its Na+ counter ion with choline greatly increases solubility. The physical, biochemical, crystallographic, and cellular data reveal new avenues for Mpro inhibitor design.
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Affiliation(s)
- Wayne Vuong
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Conrad Fischer
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada
| | - Marco J van Belkum
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Tess Lamer
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Kurtis D Willoughby
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada
| | - Jimmy Lu
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Elena Arutyunova
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Holly A Saffran
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Justin A Shields
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - Howard S Young
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada
| | - James A Nieman
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - D Lorne Tyrrell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton AB, T6G 2R3, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton AB, T6G 2E1, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada.
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Ihssen J, Faccio G, Yao C, Sirec T, Spitz U. Fluorogenic in vitro activity assay for the main protease M pro from SARS-CoV-2 and its adaptation to the identification of inhibitors. STAR Protoc 2021; 2:100793. [PMID: 34423318 PMCID: PMC8367757 DOI: 10.1016/j.xpro.2021.100793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This protocol describes an in vitro fluorogenic assay to measure the proteolytic activity and identify inhibitors of Mpro, the main protease produced by SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2). Studies to identify potential inhibitors of Mpro mainly rely on in silico molecular dynamics simulations or on FRET (Fluorescence Resonance Energy Transfer) substrates. The protocol is based on an aminomethyl coumarin substrate. High sensitivity, specificity, and an easily detectable fluorescent read-out are the advantages offered by this rapid assay, which allows high throughput screening of new Mpro inhibitors. Mpro is the main protease produced by SARS-CoV-2 An in vitro fluorogenic assay for the measurement of the proteolytic activity of Mpro An in vitro fluorogenic assay for the inhibitor screening of Mpro High sensitivity, specificity, and an easily detectable fluorescent read-out
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Affiliation(s)
- Julien Ihssen
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
| | - Greta Faccio
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
| | - Chunyan Yao
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
| | - Teja Sirec
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
| | - Urs Spitz
- Biosynth Carbosynth, Rietlistrasse 4, 9422 Staad, Switzerland
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Parise A, Romeo I, Russo N, Marino T. The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study. Int J Mol Sci 2021; 22:9792. [PMID: 34575955 PMCID: PMC8467846 DOI: 10.3390/ijms22189792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022] Open
Abstract
The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.
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Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Isabella Romeo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
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45
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Asfour HZ, Alhakamy NA, Eljaaly K, Alaofi AL, Tantawy MA, Hussein KS, Aldarmahi AA, Elfaky MA. Molecular docking studies of HIV TAT and sitagliptin nano-formula as potential therapeutic targeting SARS-CoV2 protease. J INDIAN CHEM SOC 2021. [PMCID: PMC8349443 DOI: 10.1016/j.jics.2021.100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The outbreak of COVID-19 pandemic regarded as a major health/economic hazard. The importance of coming up with mechanisms for preventing or treating SARS-CoV-2infection has been felt across the world. This work aimed at examining the efficiency of Sitagliptin (SIT) and human immunodeficiency virus type 1 (HIV-1) trans-activator transcription peptide (TAT) against SARS-CoV-2 virus. 3CL-protease inhibition activity and docking studies were examined. According to the results, the prepared complex's formula was as follows 1: 1 SIT: TAT molar ratio, whereas zeta potential and particle size values were at 34.17 mV and 97.19 nm, respectively. This combination did exhibit its antiviral potentiality against SARS-CoV-2 via IC50 values of 9.083 5.415, and 16.14 μM for TAT, SIT-TAT, and SIT, respectively. In addition, the complex SIT-TAT showed a significant (P < 0.001) viral-3CL-protease inhibitory effect. This was further confirmed via in silico study. Molecular docking investigation has shown promising binding affinity of the formula components towards SARS-CoV-2 main protease (3-CL).
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Hamdy R, Fayed B, Mostafa A, Shama NMA, Mahmoud SH, Mehta CH, Nayak Y, M. Soliman SS. Iterated Virtual Screening-Assisted Antiviral and Enzyme Inhibition Assays Reveal the Discovery of Novel Promising Anti-SARS-CoV-2 with Dual Activity. Int J Mol Sci 2021; 22:9057. [PMID: 34445763 PMCID: PMC8396542 DOI: 10.3390/ijms22169057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 02/06/2023] Open
Abstract
Unfortunately, COVID-19 is still a threat to humankind and has a dramatic impact on human health, social life, the world economy, and food security. With the limited number of suggested therapies under clinical trials, the discovery of novel therapeutic agents is essential. Here, a previously identified anti-SARS-CoV-2 compound named Compound 13 (1,2,5-Oxadiazole-3-carboximidic acid, 4,4'-(methylenediimino) bis,bis[[(2-hydroxyphenyl)methylene]hydrazide) was subjected to an iterated virtual screening against SARS-CoV-2 Mpro using a combination of Ligand Designer and PathFinder. PathFinder, a computational reaction enumeration tool, was used for the rapid generation of enumerated structures via default reaction library. Ligand designer was employed for the computerized lead optimization and selection of the best structural modification that resulted in a favorable ligand-protein complex. The obtained compounds that showed the best binding to Mpro were re-screened against TMPRSS2, leading to the identification of 20 shared compounds. The compounds were further visually inspected, which resulted in the identification of five shared compounds M1-5 with dual binding affinity. In vitro evaluation and enzyme inhibition assay indicated that M3, an analogue of Compound 13 afforded by replacing the phenolic moiety with pyridinyl, possesses an improved antiviral activity and safety. M3 displayed in vitro antiviral activity with IC50 0.016 µM and Mpro inhibition activity with IC50 0.013 µM, 7-fold more potent than the parent Compound 13 and potent than the antivirals drugs that are currently under clinical trials. Moreover, M3 showed potent activity against human TMPRSS2 and furin enzymes with IC50 0.05, and 0.08 µM, respectively. Molecular docking, WaterMap analysis, molecular dynamics simulation, and R-group analysis confirmed the superiority of the binding fit to M3 with the target enzymes. WaterMap analysis calculated the thermodynamic properties of the hydration site in the binding pocket that significantly affects the biological activity. Loading M3 on zinc oxide nanoparticles (ZnO NPs) increased the antiviral activity of the compound 1.5-fold, while maintaining a higher safety profile. In conclusion, lead optimized discovery following an iterated virtual screening in association with molecular docking and biological evaluation revealed a novel compound named M3 with promising dual activity against SARS-CoV-2. The compound deserves further investigation for potential clinical-based studies.
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Affiliation(s)
- Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.H.); (B.F.)
- Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Bahgat Fayed
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.H.); (B.F.)
- Chemistry of Natural and Microbial Product Department, National Research Centre, Cairo 12622, Egypt
| | - Ahmed Mostafa
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.M.); (N.M.A.S.); (S.H.M.)
| | - Noura M. Abo Shama
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.M.); (N.M.A.S.); (S.H.M.)
| | - Sara Hussein Mahmoud
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.M.); (N.M.A.S.); (S.H.M.)
| | - Chetan Hasmukh Mehta
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, India; (C.H.M.); (Y.N.)
| | - Yogendra Nayak
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, India; (C.H.M.); (Y.N.)
| | - Sameh S. M. Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.H.); (B.F.)
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
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Bhavaniramya S, Ramar V, Vishnupriya S, Palaniappan R, Sibiya A, Baskaralingam V. Comprehensive analysis of SARS-COV-2 drug targets and pharmacological aspects in treating the COVID-19. Curr Mol Pharmacol 2021; 15:393-417. [PMID: 34382513 DOI: 10.2174/1874467214666210811120635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/27/2021] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
Corona viruses are enveloped, single-stranded RNA (Ribonucleic acid) viruses and they cause pandemic diseases having a devastating effect on both human healthcare and the global economy. To date, six corona viruses have been identified as pathogenic organisms which are significantly responsible for the infection and also cause severe respiratory diseases. Among them, the novel SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) caused a major outbreak of corona virus diseases 2019 (COVID-19). Coronaviridae family members can affects both humans and animals. In human, corona viruses cause severe acute respiratory syndrome with mild to severe outcomes. Several structural and genomics have been investigated, and the genome encodes about 28 proteins most of them with unknown function though it shares remarkable sequence identity with other proteins. There is no potent and licensed vaccine against SARS-CoV-2 and several trials are underway to investigate the possible therapeutic agents against viral infection. However, some of the antiviral drugs that have been investigated against SARS-CoV-2 are under clinical trials. In the current review we comparatively emphasize the emergence and pathogenicity of the SARS-CoV-2 and their infection and discuss the various putative drug targets of both viral and host receptors for developing effective vaccines and therapeutic combinations to overcome the viral outbreak.
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Affiliation(s)
- Sundaresan Bhavaniramya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vanajothi Ramar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024. India
| | - Selvaraju Vishnupriya
- College of Food and Dairy Technology, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600052. India
| | - Ramasamy Palaniappan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education (BIHER), Chennai-600044, Tamilnadu. India
| | - Ashokkumar Sibiya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vaseeharan Baskaralingam
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
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Pohl MO, Busnadiego I, Marrafino F, Wiedmer L, Hunziker A, Fernbach S, Glas I, Moroz-Omori EV, Hale BG, Caflisch A, Stertz S. Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir. J Gen Virol 2021; 102:001625. [PMID: 34319869 PMCID: PMC8491895 DOI: 10.1099/jgv.0.001625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/09/2021] [Indexed: 01/10/2023] Open
Abstract
Rapid repurposing of existing drugs as new therapeutics for COVID-19 has been an important strategy in the management of disease severity during the ongoing SARS-CoV-2 pandemic. Here, we used high-throughput docking to screen 6000 compounds within the DrugBank library for their potential to bind and inhibit the SARS-CoV-2 3 CL main protease, a chymotrypsin-like enzyme that is essential for viral replication. For 19 candidate hits, parallel in vitro fluorescence-based protease-inhibition assays and Vero-CCL81 cell-based SARS-CoV-2 replication-inhibition assays were performed. One hit, diclazuril (an investigational anti-protozoal compound), was validated as a SARS-CoV-2 3 CL main protease inhibitor in vitro (IC50 value of 29 µM) and modestly inhibited SARS-CoV-2 replication in Vero-CCL81 cells. Another hit, lenvatinib (approved for use in humans as an anti-cancer treatment), could not be validated as a SARS-CoV-2 3 CL main protease inhibitor in vitro, but serendipitously exhibited a striking functional synergy with the approved nucleoside analogue remdesivir to inhibit SARS-CoV-2 replication, albeit this was specific to Vero-CCL81 cells. Lenvatinib is a broadly-acting host receptor tyrosine kinase (RTK) inhibitor, but the synergistic effect with remdesivir was not observed with other approved RTK inhibitors (such as pazopanib or sunitinib), suggesting that the mechanism-of-action is independent of host RTKs. Furthermore, time-of-addition studies revealed that lenvatinib/remdesivir synergy probably targets SARS-CoV-2 replication subsequent to host-cell entry. Our work shows that combining computational and cellular screening is a means to identify existing drugs with repurposing potential as antiviral compounds. Future studies could be aimed at understanding and optimizing the lenvatinib/remdesivir synergistic mechanism as a therapeutic option.
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Affiliation(s)
- Marie O. Pohl
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Idoia Busnadiego
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Francesco Marrafino
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Pharmacy, University of Salerno, Fisciano SA, 84084, Italy
| | - Lars Wiedmer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Annika Hunziker
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Sonja Fernbach
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Irina Glas
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Elena V. Moroz-Omori
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Benjamin G. Hale
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Inhibitors of Coronavirus 3CL Proteases Protect Cells from Protease-Mediated Cytotoxicity. J Virol 2021; 95:e0237420. [PMID: 33910954 DOI: 10.1128/jvi.02374-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We describe a mammalian cell-based assay to identify coronavirus 3CL protease (3CLpro) inhibitors. This assay is based on rescuing protease-mediated cytotoxicity and does not require live virus. By enabling the facile testing of compounds across a range of 15 distantly related coronavirus 3CLpro enzymes, we identified compounds with broad 3CLpro-inhibitory activity. We also adapted the assay for use in compound screening and in doing so uncovered additional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 3CLpro inhibitors. We observed strong concordance between data emerging from this assay and those obtained from live-virus testing. The reported approach democratizes the testing of 3CLpro inhibitors by developing a simplified method for identifying coronavirus 3CLpro inhibitors that can be used by the majority of laboratories, rather than the few with extensive biosafety infrastructure. We identified two lead compounds, GC376 and compound 4, with broad activity against all 3CL proteases tested, including 3CLpro enzymes from understudied zoonotic coronaviruses. IMPORTANCE Multiple coronavirus pandemics have occurred over the last 2 decades. This has highlighted a need to be proactive in the development of therapeutics that can be readily deployed in the case of future coronavirus pandemics. We developed and validated a simplified cell-based assay for the identification of chemical inhibitors of 3CL proteases encoded by a wide range of coronaviruses. This assay is reporter free, does not require specialized biocontainment, and is optimized for performance in high-throughput screening. By testing reported 3CL protease inhibitors against a large collection of 3CL proteases with variable sequence similarity, we identified compounds with broad activity against 3CL proteases and uncovered structural insights into features that contribute to their broad activity. Furthermore, we demonstrated that this assay is suitable for identifying chemical inhibitors of proteases from families other than 3CL proteases.
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Dražić T, Kühl N, Leuthold MM, Behnam MA, Klein CD. Efficiency Improvements and Discovery of New Substrates for a SARS-CoV-2 Main Protease FRET Assay. SLAS DISCOVERY 2021; 26:1189-1199. [PMID: 34151620 PMCID: PMC8458682 DOI: 10.1177/24725552211020681] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has a huge impact on the world. Although several vaccines have recently reached the market, the development of specific antiviral drugs against SARS-CoV-2 is an important additional strategy in fighting the pandemic. One of the most promising pharmacological targets is the viral main protease (Mpro). Here, we present an optimized biochemical assay procedure for SARS-CoV-2 Mpro. We have comprehensively investigated the influence of different buffer components and conditions on the assay performance and characterized Förster resonance energy transfer (FRET) substrates with a preference for 2-Abz/Tyr(3-NO2) FRET pairs. The substrates 2-AbzSAVLQSGTyr(3-NO2)R-OH, a truncated version of the established DABCYL/EDANS FRET substrate, and 2-AbzVVTLQSGTyr(3-NO2)R-OH are promising candidates for screening and inhibitor characterization. In the latter substrate, the incorporation of Val at position P5 improved the catalytic efficiency. Based on the obtained results, we present here a reproducible, reliable assay protocol using highly affordable buffer components.
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Affiliation(s)
- Tonko Dražić
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Nikos Kühl
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Mila M. Leuthold
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Mira A.M. Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
| | - Christian D. Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Heidelberg, Germany
- Corresponding Author: Christian D. Klein, Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany.
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