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ElSawy KM. Competitive Interaction of the SGFRKMAF Peptide with 3CLpro Dimerization Intermediates: A Brownian Dynamics Investigation. J Phys Chem B 2024; 128:7313-7321. [PMID: 39028939 DOI: 10.1021/acs.jpcb.4c01938] [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: 07/21/2024]
Abstract
The SGFRKMAF peptide is known to inhibit the dimerization of 3CLpro monomers, which is essential for SARS-CoV-2 replication. The mechanism behind this, however, is largely unknown. In this work, we used Brownian dynamics simulations to compare and contrast 3CLpro monomer-monomer interactions and 3CLpro monomer-SGFRKMAF peptide interactions. We found that formation of the 3CLpro wild-type dimer could potentially involve formation of three intermediates that are primarily stabilized by G11-G124, S1-S301, and T118-G278 interactions. Analysis of 3CLpro monomer interaction with the SGFRKMAF peptide, however, revealed the presence of eight basins of interactions where the peptide assumes the highest local densities at the 3CLPro monomer surface. The second highest-density basin was found to coincide with the interface region of the wild-type 3CLpro dimer, thereby directly blocking the 3CLpro dimer-dimer interactions. The other basins, however, were found to lie far from the interface region. Notably, we found that only 6% of the BD trajectories end up directly into the basin at the interface region and ∼39% of the trajectories end up into those basins lying away from the interface region, indicating a greater role for peptide binding at sites away from the dimer interface region. Importantly, the locations of the basins lying away from the interface were found to coincide with the 3CLpro residues involved in stabilization of the 3CLpro monomer-monomer intermediates. Given that the rate constant of the peptide reaching the monomer surface was found to be almost an order of magnitude higher than the rate constant of monomer-monomer association, the SGFRKMAF peptide has the potential to inhibit dimerization of 3CLpro monomers not only through blocking the interface region but also through blocking the formation of the intermediates involved in the dimerization process. This could potentially open new avenues for 3CLpro dimerization inhibitors that transcend traditional X-ray-based discovery approaches.
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Affiliation(s)
- Karim M ElSawy
- Department of Chemistry, College of Science, Qassim University, Buraydah 52571, Saudi Arabia
- York Cross-disciplinary Centre for Systems Analysis (YCCSA), University of York, York YO10 5GE, United Kingdom
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2
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Ho WY, Shen ZH, Chen Y, Chen TH, Lu X, Fu YS. Therapeutic implications of quercetin and its derived-products in COVID-19 protection and prophylactic. Heliyon 2024; 10:e30080. [PMID: 38765079 PMCID: PMC11098804 DOI: 10.1016/j.heliyon.2024.e30080] [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: 12/01/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/21/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel human coronavirus, which has triggered a global pandemic of the coronavirus infectious disease 2019 (COVID-19). Outbreaks of emerging infectious diseases continue to challenge human health worldwide. The virus conquers human cells through the angiotensin-converting enzyme 2 receptor-driven pathway by mostly targeting the human respiratory tract. Quercetin is a natural flavonoid widely represented in the plant kingdom. Cumulative evidence has demonstrated that quercetin and its derivatives have various pharmacological properties including anti-cancer, anti-hypertension, anti-hyperlipidemia, anti-hyperglycemia, anti-microbial, antiviral, neuroprotective, and cardio-protective effects, because it is a potential treatment for severe inflammation and acute respiratory distress syndrome. Furthermore, it is the main life-threatening condition in patients with COVID-19. This article provides a comprehensive review of the primary literature on the predictable effectiveness of quercetin and its derivatives docked to multi-target of SARS-CoV-2 and host cells via in silico and some of validation through in vitro, in vivo, and clinically to fight SARS-CoV-2 infections, contribute to the reduction of inflammation, which suggests the preventive and therapeutic latency of quercetin and its derived-products against COVID-19 pandemic, multisystem inflammatory syndromes (MIS), and long-COVID.
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Affiliation(s)
- Wan-Yi Ho
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Zi-Han Shen
- Department of Clinical Medicine, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Yijing Chen
- Department of Dentisty, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Ting-Hsu Chen
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - XiaoLin Lu
- Anatomy Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Yaw-Syan Fu
- Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
- Anatomy Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
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3
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Ridgway H, Moore GJ, Gadanec LK, Zulli A, Apostolopoulos V, Hoffmann W, Węgrzyn K, Vassilaki N, Mpekoulis G, Zouridakis M, Giastas P, Vidali VP, Kelaidonis K, Matsoukas MT, Dimitriou M, Mavromoustakos T, Tsiodras S, Gorgoulis VG, Karakasiliotis I, Chasapis CT, Matsoukas JM. Novel benzimidazole angiotensin receptor blockers with anti-SARS-CoV-2 activity equipotent to that of nirmatrelvir: computational and enzymatic studies. Expert Opin Ther Targets 2024; 28:437-459. [PMID: 38828744 DOI: 10.1080/14728222.2024.2362675] [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: 02/13/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Hypertension worsens outcomes in SARS-CoV-2 patients. Sartans, a type of antihypertensive angiotensin receptor blocker-(ARB), reduce COVID-19 morbidity and mortality by targeting angiotensin-converting enzyme-2 (ACE2). This study aimed to evaluate the antiviral and antihypertensive effects of nirmatrelvir, commercial sartans (candesartan, losartan, and losartan carboxylic (Exp3174)), and newly synthesized sartans (benzimidazole-N-biphenyl carboxyl (ACC519C) and benzimidazole-N-biphenyl tetrazole (ACC519T)), compared to nirmatrelvir, the antiviral component of Paxlovid. RESEARCH DESIGN AND METHODS Surface plasmon resonance (SPR) and enzymatic studies assessed drug effects on ACE2. Antiviral abilities were tested with SARS-CoV-2-infected Vero E6 cells, and antihypertensive effects were evaluated using angiotensin II-contracted rabbit iliac arteries. RESULTS Benzimidazole-based candesartan and ACC519C showed antiviral activity comparable to nirmatrelvir (95% inhibition). Imidazole-based losartan, Exp3174, and ACC519T were less potent (75%-80% and 50%, respectively), with Exp3174 being the least effective. SPR analysis indicated high sartans-ACE2 binding affinity. Candesartan and nirmatrelvir combined had greater inhibitory and cytopathic effects (3.96%) than individually (6.10% and 5.08%). ACE2 enzymatic assays showed varying effects of novel sartans on ACE2. ACC519T significantly reduced angiotensin II-mediated contraction, unlike nirmatrelvir and ACC519T(2). CONCLUSION This study reports the discovery of a new class of benzimidazole-based sartans that significantly inhibit SARS-CoV-2, likely due to their interaction with ACE2.
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Affiliation(s)
- Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, Australia
- AquaMem Consultants, Rodeo, NM, USA
| | - Graham J Moore
- Pepmetics Inc, 772 Murphy Place, Victoria, BC, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Laura Kate Gadanec
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, Australia
| | - Anthony Zulli
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, Australia
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, Australia
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, Australia
| | - Weronika Hoffmann
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Katarzyna Węgrzyn
- Laboratory of Molecular Biology, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Niki Vassilaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens, Greece
| | - George Mpekoulis
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, Athens, Greece
| | - Marios Zouridakis
- Structural Neurobiology Research Group, Laboratory of Molecular Neurobiology and Immunology, Hellenic Pasteur Institute, Athens, Greece
| | - Petros Giastas
- Structural Neurobiology Research Group, Laboratory of Molecular Neurobiology and Immunology, Hellenic Pasteur Institute, Athens, Greece
- Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Veroniki P Vidali
- Natural Products and Bioorganic Chemistry Laboratory, Institute of Nanoscience & Nanotechnology, NCSR "Demokritos", Athens, Greece
| | | | | | - Marios Dimitriou
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Xanthi, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, Athens, Greece
| | - Sotirios Tsiodras
- Faculty of Medicine, 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Vassilis G Gorgoulis
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, Athens, Greece
- Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Xanthi, Greece
| | - Christos T Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - John M Matsoukas
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, Australia
- NewDrug PC, Patras Science Park, Patras, Greece
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Department of Chemistry, University of Patras, Patras, Greece
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Yang S, Huang X, Li S, Wang C, Jansen CA, Savelkoul HFJ, Liu G. Linoleic acid: a natural feed compound against porcine epidemic diarrhea disease. J Virol 2023; 97:e0170023. [PMID: 38009930 PMCID: PMC10734519 DOI: 10.1128/jvi.01700-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Porcine epidemic diarrhea virus (PEDV) is a pig coronavirus that causes severe diarrhea and high mortality in piglets, but as no effective drugs are available, this virus threatens the pig industry. Here, we found that the intestinal contents of specific pathogen-free pigs effectively blocked PEDV invasion. Through proteomic and metabolic analyses of the intestinal contents, we screened 10 metabolites to investigate their function and found that linoleic acid (LA) significantly inhibited PEDV replication. Further investigations revealed that LA inhibited viral replication and release mainly by binding with PEDV NSP5 to regulate the PI3K pathway and, in particular, inhibiting AKT phosphorylation. In vivo experiments illustrated that orally administered LA protected pigs from PEDV challenge and severe diarrhea. These findings provide strong support for exploring antiviral drugs for coronavirus treatment.
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Affiliation(s)
- Shanshan Yang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, the Netherlands
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xin Huang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Shuxian Li
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Caiying Wang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Christine A. Jansen
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Huub F. J. Savelkoul
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Guangliang Liu
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
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5
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Yazdani B, Sirous H, Brogi S, Calderone V. Structure-Based High-Throughput Virtual Screening and Molecular Dynamics Simulation for the Discovery of Novel SARS-CoV-2 NSP3 Mac1 Domain Inhibitors. Viruses 2023; 15:2291. [PMID: 38140532 PMCID: PMC10747130 DOI: 10.3390/v15122291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Since the emergence of SARS-CoV-2, many genetic variations within its genome have been identified, but only a few mutations have been found in nonstructural proteins (NSPs). Among this class of viral proteins, NSP3 is a multidomain protein with 16 different domains, and its largest domain is known as the macrodomain or Mac1 domain. In this study, we present a virtual screening campaign in which we computationally evaluated the NCI anticancer library against the NSP3 Mac1 domain, using Molegro Virtual Docker. The top hits with the best MolDock and Re-Rank scores were selected. The physicochemical analysis and drug-like potential of the top hits were analyzed using the SwissADME data server. The binding stability and affinity of the top NSC compounds against the NSP3 Mac1 domain were analyzed using molecular dynamics (MD) simulation, using Desmond software, and their interaction energies were analyzed using the MM/GBSA method. In particular, by applying subsequent computational filters, we identified 10 compounds as possible NSP3 Mac1 domain inhibitors. Among them, after the assessment of binding energies (ΔGbind) on the whole MD trajectories, we identified the four most interesting compounds that acted as strong binders of the NSP3 Mac1 domain (NSC-358078, NSC-287067, NSC-123472, and NSC-142843), and, remarkably, it could be further characterized for developing innovative antivirals against SARS-CoV-2.
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Affiliation(s)
- Behnaz Yazdani
- Bioscience Department, Faculty of Science and Technology (FCT), Universitat de Vic—Universitat Central de Catalunya (Uvic-UCC), 08500 Vic, Spain;
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Simone Brogi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy;
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy;
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6
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Zhang YN, Zhu GH, Liu W, Chen XX, Xie YY, Xu JR, Jiang MF, Zhuang XY, Zhang WD, Chen HZ, Ge GB. Discovery of the covalent SARS-CoV-2 M pro inhibitors from antiviral herbs via integrating target-based high-throughput screening and chemoproteomic approaches. J Med Virol 2023; 95:e29208. [PMID: 37947293 DOI: 10.1002/jmv.29208] [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: 07/10/2023] [Revised: 09/20/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023]
Abstract
The main proteases (Mpro ) are highly conserved cysteine-rich proteins that can be covalently modified by numerous natural and synthetic compounds. Herein, we constructed an integrative approach to efficiently discover covalent inhibitors of Mpro from complex herbal matrices. This work begins with biological screening of 60 clinically used antiviral herbal medicines, among which Lonicera japonica Flos (LJF) demonstrated the strongest anti-Mpro effect (IC50 = 37.82 μg/mL). Mass spectrometry (MS)-based chemical analysis and chemoproteomic profiling revealed that LJF extract contains at least 50 constituents, of which 22 exhibited the capability to covalently modify Mpro . We subsequently verified the anti-Mpro effects of these covalent binders. Gallic acid and quercetin were found to potently inhibit severe acute respiratory syndrome coronavirus 2 Mpro in dose- and time- dependent manners, with the IC50 values below 10 µM. The inactivation kinetics, binding affinity and binding mode of gallic acid and quercetin were further characterized by fluorescence resonance energy transfer, surface plasmon resonance, and covalent docking simulations. Overall, this study established a practical approach for efficiently discovering the covalent inhibitors of Mpro from herbal medicines by integrating target-based high-throughput screening and MS-based assays, which would greatly facilitate the discovery of key antiviral constituents from medicinal plants.
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Affiliation(s)
- Ya-Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guang-Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Liu
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xi-Xiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuan-Yuan Xie
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jian-Rong Xu
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mei-Fang Jiang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiao-Yu Zhuang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei-Dong Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Zhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guang-Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Justo Arevalo S, Castillo-Chávez A, Uribe Calampa CS, Zapata Sifuentes D, Huallpa CJ, Landa Bianchi G, Garavito-Salini Casas R, Quiñones Aguilar M, Pineda Chavarría R. What do we know about the function of SARS-CoV-2 proteins? Front Immunol 2023; 14:1249607. [PMID: 37790934 PMCID: PMC10544941 DOI: 10.3389/fimmu.2023.1249607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
The COVID-19 pandemic has highlighted the importance in the understanding of the biology of SARS-CoV-2. After more than two years since the first report of COVID-19, it remains crucial to continue studying how SARS-CoV-2 proteins interact with the host metabolism to cause COVID-19. In this review, we summarize the findings regarding the functions of the 16 non-structural, 6 accessory and 4 structural SARS-CoV-2 proteins. We place less emphasis on the spike protein, which has been the subject of several recent reviews. Furthermore, comprehensive reviews about COVID-19 therapeutic have been also published. Therefore, we do not delve into details on these topics; instead we direct the readers to those other reviews. To avoid confusions with what we know about proteins from other coronaviruses, we exclusively report findings that have been experimentally confirmed in SARS-CoV-2. We have identified host mechanisms that appear to be the primary targets of SARS-CoV-2 proteins, including gene expression and immune response pathways such as ribosome translation, JAK/STAT, RIG-1/MDA5 and NF-kβ pathways. Additionally, we emphasize the multiple functions exhibited by SARS-CoV-2 proteins, along with the limited information available for some of these proteins. Our aim with this review is to assist researchers and contribute to the ongoing comprehension of SARS-CoV-2's pathogenesis.
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Affiliation(s)
- Santiago Justo Arevalo
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Daniela Zapata Sifuentes
- Facultad de Ciencias Biológicas, Universidad Ricardo Palma, Lima, Peru
- Departmento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, São Paulo, Brazil
| | - César J. Huallpa
- Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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Jeong JH, Choi JH, Kim BK, Min SC, Chokkakula S, Oh S, Park JH, Shim SM, Kim EG, Choi YK, Lee JY, Baek YH, Song MS. Evaluating Z-FA-FMK, a host cathepsin L protease inhibitor, as a potent and broad-spectrum antiviral therapy against SARS-CoV-2 and related coronaviruses. Antiviral Res 2023; 216:105669. [PMID: 37437781 DOI: 10.1016/j.antiviral.2023.105669] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/22/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
Even though the World Health Organization announced the end of the COVID-19 pandemic as a global public health emergency on May 5, 2023, SARS-CoV-2 continues to pose a significant health threat worldwide, resulting in substantial numbers of infections and fatalities. This study investigated the antiviral potential of Z-FA-FMK (FMK), a novel host cathepsin L protease inhibitor, against SARS-CoV-2 infection using both in vitro and in vivo models. In vitro assessments of FMK against a diverse set of SARS-CoV-2 strains, including the Wuhan-like strain and nine variants, demonstrated potent inhibition with EC50 values ranging from 0.55 to 2.41 μM, showcasing similar or superior efficacy compared to FDA-approved antivirals nirmatrelvir (NTV) and molnupiravir (MPV). In vivo experiments using orally administered FMK (25 mg/kg) in SARS-CoV-2-infected K18 hACE2 transgenic mice revealed improved survival rates of 60% and accelerated recovery compared to NTV and MPV treatments. Additionally, FMK displayed a longer half-life (17.26 ± 8.89 h) than NTV and MPV in the mouse model. Due to its host-targeting mechanism, FMK offers potential advantages such as reduced drug resistance and broad-spectrum antiviral activity against multiple coronaviruses. These findings indicate that FMK may serve as a promising candidate for further clinical evaluation in the fight against SARS-CoV-2.
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Affiliation(s)
- Ju Hwan Jeong
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Jang-Hoon Choi
- Division of Acute Viral Disease, Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of Health, Cheongju, 28159, Republic of Korea
| | - Beom Kyu Kim
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Seong Cheol Min
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Santosh Chokkakula
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Sol Oh
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Ji-Hyun Park
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Sang-Mu Shim
- Division of Acute Viral Disease, Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of Health, Cheongju, 28159, Republic of Korea
| | - Eung-Gook Kim
- Department of Biochemistry, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Young Ki Choi
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea; Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Joo-Yeon Lee
- Center for Emerging Virus Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si, Republic of Korea.
| | - Yun Hee Baek
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea.
| | - Min-Suk Song
- Department of Microbiology, Chungbuk National University College of Medicine and Medical Research Institute, Cheongju, Chungbuk, 28644, Republic of Korea.
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9
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Xue Y, Mei H, Chen Y, Griffin JD, Liu Q, Weisberg E, Yang J. Repurposing clinically available drugs and therapies for pathogenic targets to combat SARS-CoV-2. MedComm (Beijing) 2023; 4:e254. [PMID: 37193304 PMCID: PMC10183156 DOI: 10.1002/mco2.254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/11/2023] [Accepted: 03/07/2023] [Indexed: 05/18/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected a large portion of the global population, both physically and mentally. Current evidence suggests that the rapidly evolving coronavirus subvariants risk rendering vaccines and antibodies ineffective due to their potential to evade existing immunity, with enhanced transmission activity and higher reinfection rates that could lead to new outbreaks across the globe. The goal of viral management is to disrupt the viral life cycle as well as to relieve severe symptoms such as lung damage, cytokine storm, and organ failure. In the fight against viruses, the combination of viral genome sequencing, elucidation of the structure of viral proteins, and identifying proteins that are highly conserved across multiple coronaviruses has revealed many potential molecular targets. In addition, the time- and cost-effective repurposing of preexisting antiviral drugs or approved/clinical drugs for these targets offers considerable clinical advantages for COVID-19 patients. This review provides a comprehensive overview of various identified pathogenic targets and pathways as well as corresponding repurposed approved/clinical drugs and their potential against COVID-19. These findings provide new insight into the discovery of novel therapeutic strategies that could be applied to the control of disease symptoms emanating from evolving SARS-CoV-2 variants.
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Affiliation(s)
- Yiying Xue
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Husheng Mei
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
| | - Yisa Chen
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - James D. Griffin
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
- University of Science and Technology of ChinaHefeiAnhuiChina
- Hefei Cancer HospitalChinese Academy of SciencesHefeiChina
| | - Ellen Weisberg
- Department of Medical Oncology, Dana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medicine, Harvard Medical SchoolBostonMassachusettsUSA
| | - Jing Yang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical ScienceChinese Academy of SciencesHefeiChina
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10
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Andrianov AM, Shuldau MA, Furs KV, Yushkevich AM, Tuzikov AV. AI-Driven De Novo Design and Molecular Modeling for Discovery of Small-Molecule Compounds as Potential Drug Candidates Targeting SARS-CoV-2 Main Protease. Int J Mol Sci 2023; 24:ijms24098083. [PMID: 37175788 PMCID: PMC10178971 DOI: 10.3390/ijms24098083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Over the past three years, significant progress has been made in the development of novel promising drug candidates against COVID-19. However, SARS-CoV-2 mutations resulting in the emergence of new viral strains that can be resistant to the drugs used currently in the clinic necessitate the development of novel potent and broad therapeutic agents targeting different vulnerable spots of the viral proteins. In this study, two deep learning generative models were developed and used in combination with molecular modeling tools for de novo design of small molecule compounds that can inhibit the catalytic activity of SARS-CoV-2 main protease (Mpro), an enzyme critically important for mediating viral replication and transcription. As a result, the seven best scoring compounds that exhibited low values of binding free energy comparable with those calculated for two potent inhibitors of Mpro, via the same computational protocol, were selected as the most probable inhibitors of the enzyme catalytic site. In light of the data obtained, the identified compounds are assumed to present promising scaffolds for the development of new potent and broad-spectrum drugs inhibiting SARS-CoV-2 Mpro, an attractive therapeutic target for anti-COVID-19 agents.
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Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Mikita A Shuldau
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
| | - Konstantin V Furs
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
| | - Artsemi M Yushkevich
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
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11
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Jiang H, Chen J, Li X, Zhong YT, Kang LP, Wang G, Yu M, Fu LF, Wang P, Xu HY. Systematic identification of chemical components in Fufang Shuanghua oral liquid and screening of potential active components against SARS-CoV-2 protease. J Pharm Biomed Anal 2023; 223:115118. [PMID: 36332330 PMCID: PMC9584763 DOI: 10.1016/j.jpba.2022.115118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/24/2022]
Abstract
Coronavirus disease (COVID-19) caused by SARS-COV-2 infection has been widely prevalent in many countries and has become a common challenge facing mankind. Traditional Chinese medicine (TCM) has played a prominent role in this pandemic, and especially TCM with the function of “heat-clearing and detoxifying” has shown an excellent role in anti-virus. Fufang Shuanghua oral liquid (FFSH) has been used to treat the corresponding symptoms of influenza such as fever, nasal congestion, runny nose, sore throat, and upper respiratory tract infections in clinic, which are typical symptoms of COVID-19. The content of chlorogenic acid, andrographolide and dehydrated andrographolide as the quality control components of FFSH is not less than 1.0 mg/mL, 60 μg/mL and 60 μg/mL respectively. In this study, UPLC-Q-TOF-MS/MS was employed to describe the chemical profile of FFSH. Virtual screening and fluorescence resonance energy transfer (FRET) were used to screen the effective components of FFSH acting on SARS-CoV-2 main protease (Mpro). As a result, 214 compounds in FFSH were identified or preliminarily characterized by UPLC-Q-TOF-MS/MS, and 61 active ingredients with potential inhibitory effects on Mpro were selected through receptor-based and ligand-based virtual screening. In particular, quercetin, forsythoside A, and linoleic acid showed a good inhibitory effect on Mpro in FRET evaluation with IC50 values of 26.15 μM, 22.26 μM and 47.09 μM respectively, and had a strong binding affinity with the receptor Mpro (6LU7) in molecular docking. CYS145 and HIS41 were the main amino acid residues affected by small molecules in the protein binding domain. In brief, we characterized, for the first time, 214 chemical components in FFSH, and three of them, including quercetin, forsythoside A and linoleic acid, were screened out to exert beneficial anti-COVID-19 effects through CYS145 and HIS41 sites, which may provide a new research strategy for TCM to develop new therapeutic drugs against COVID-19.
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Affiliation(s)
- Hong Jiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China,School of Pharmacy, Anhui University of Traditional Chinese Medicine, Hefei 230031, China
| | - Jie Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China,School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yu-te Zhong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Li-ping Kang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guohua Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Meng Yu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Li-feng Fu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,Corresponding authors
| | - Ping Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China,Corresponding authors
| | - Hai-yu Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China,Key Laboratory for Research and Evaluation of Traditional Chinese Medicine, National Medical Products Administration, China Academy of Chinese Medical Sciences, Beijing 100700, China,Corresponding author at: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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12
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Dong J, Varbanov M, Philippot S, Vreken F, Zeng WB, Blay V. Ligand-based discovery of coronavirus main protease inhibitors using MACAW molecular embeddings. J Enzyme Inhib Med Chem 2023; 38:24-35. [PMID: 36305272 PMCID: PMC9621234 DOI: 10.1080/14756366.2022.2132486] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ligand-based drug design methods are thought to require large experimental datasets to become useful for virtual screening. In this work, we propose a computational strategy to design novel inhibitors of coronavirus main protease, Mpro. The pipeline integrates publicly available screening and binding affinity data in a two-stage machine-learning model using the recent MACAW embeddings. Once trained, the model can be deployed to rapidly screen large libraries of molecules in silico. Several hundred thousand compounds were virtually screened and 10 of them were selected for experimental testing. From these 10 compounds, 8 showed a clear inhibitory effect on recombinant Mpro, with half-maximal inhibitory concentration values (IC50) in the range 0.18–18.82 μM. Cellular assays were also conducted to evaluate cytotoxic, haemolytic, and antiviral properties. A promising lead compound against coronavirus Mpro was identified with dose-dependent inhibition of virus infectivity and minimal toxicity on human MRC-5 cells.
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Affiliation(s)
- Jie Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, P. R. China
| | - Mihayl Varbanov
- Université de Lorraine, CNRS, Nancy, France
- Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
| | | | | | - Wen-bin Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, P. R. China
| | - Vincent Blay
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, USA
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13
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Progress on COVID-19 Chemotherapeutics Discovery and Novel Technology. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238257. [PMID: 36500347 PMCID: PMC9736643 DOI: 10.3390/molecules27238257] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 11/29/2022]
Abstract
COVID-19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel highly contagious and pathogenic coronavirus that emerged in late 2019. SARS-CoV-2 spreads primarily through virus-containing droplets and small particles of air pollution, which greatly increases the risk of inhaling these virus particles when people are in close proximity. COVID-19 is spreading across the world, and the COVID-19 pandemic poses a threat to human health and public safety. To date, there are no specific vaccines or effective drugs against SARS-CoV-2. In this review, we focus on the enzyme targets of the virus and host that may be critical for the discovery of chemical compounds and natural products as antiviral drugs, and describe the development of potential antiviral drugs in the preclinical and clinical stages. At the same time, we summarize novel emerging technologies applied to the research on new drug development and the pathological mechanisms of COVID-19.
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14
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Attiq N, Arshad U, Brogi S, Shafiq N, Imtiaz F, Parveen S, Rashid M, Noor N. Exploring the anti-SARS-CoV-2 main protease potential of FDA approved marine drugs using integrated machine learning templates as predictive tools. Int J Biol Macromol 2022; 220:1415-1428. [PMID: 36122771 PMCID: PMC9479384 DOI: 10.1016/j.ijbiomac.2022.09.086] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/22/2022]
Abstract
Since the inception of COVID-19 pandemic in December 2019, socio-economic crisis begins to rise globally and SARS-CoV-2 was responsible for this outbreak. With this outbreak, currently, world is in need of effective and safe eradication of COVID-19. Hence, in this study anti-SAR-Co-2 potential of FDA approved marine drugs (Biological macromolecules) data set is explored computationally using machine learning algorithm of Flare by Cresset Group, Field template, 3D-QSAR and activity Atlas model was generated against FDA approved M-pro SARS-CoV-2 repurposed drugs including Nafamostat, Hydroxyprogesterone caporate, and Camostat mesylate. Data sets were categorized into active and inactive molecules on the basis of their structural and biological resemblance with repurposed COVID-19 drugs. Then these active compounds were docked against the five different M-pro proteins co-crystal structures. Highest LF VS score of Holichondrin B against all main protease co-crystal structures ranked it as lead drug. Finally, this new technique of drug repurposing remained efficient to explore the anti-SARS-CoV-2 potential of FDA approved marine drugs.
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Affiliation(s)
- Naila Attiq
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Uzma Arshad
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.
| | - Nusrat Shafiq
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan.
| | - Fazeelat Imtiaz
- Green Chemistry Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Nadia Noor
- Micro-biology Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
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15
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Makati AC, Ananda AN, Putri JA, Amellia SF, Setiawan B. Molecular docking of ethanol extracts of katuk leaf ( Sauropus androgynus) on functional proteins of severe acute respiratory syndrome coronavirus 2. SOUTH AFRICAN JOURNAL OF BOTANY : OFFICIAL JOURNAL OF THE SOUTH AFRICAN ASSOCIATION OF BOTANISTS = SUID-AFRIKAANSE TYDSKRIF VIR PLANTKUNDE : AMPTELIKE TYDSKRIF VAN DIE SUID-AFRIKAANSE GENOOTSKAP VAN PLANTKUNDIGES 2022; 149:1-5. [PMID: 35668920 PMCID: PMC9158454 DOI: 10.1016/j.sajb.2022.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 06/15/2023]
Abstract
The COVID-19 pandemic has become a major health crisis globally. Alternative treatment approaches include using food sources rich in flavonoid compounds, such as the leaves of katuk plant (Sauropus androgynus). The purpose of this study was to analyze the characteristics of the flavonoid group present in active compounds of katuk leaves (Sauropus androgynus) and to study the mechanism underlying interactions (molecular docking) of these compounds with 3CLpro, Nsp1, Nsp3, RdRp, Nsp7_Nsp8 complex, and PLpro in SARS-CoV-2, and ACE2 in humans. In silico analysis was performed using Hex 8.0. software, which is primary tool of docking analysis. Interaction between the ligand and its receptors were analyzed using the software Discovery studio 4.1. The results of this study indicated that ABCD chains of 3CLpro had the highest bond energy with afzelin (-42.77 Kcal/mol), RdRp Nsp7_Nsp8 complex had the highest bond energy with trifolin (-310.87 Kcal/mol), PLpro had the highest bond energy with afzelin (-190.23 Kcal/mol), Nsp1 had the highest bond energy with afzelin (-286.89 Kcal/mol), Nsp3 had the highest bond energy with trifolin (-334.97 Kcal/mol), and ACE2 had the highest bond energy with trifolin (-307.96 Kcal/mol). Thus, on comparison with conventionally used drugs, the active flavonoid compounds in katuk leaves (Sauropus androgynus) showed specific affinity for 3CLpro, Nsp1, Nsp3, RdRp Nsp7_Nsp8 complex, and PLpro in SARS-CoV-2 and ACE2 in humans. Thus, katuk leaves a potential herbal candidates to derive new drugs or complementary medicines for COVID-19.
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Affiliation(s)
- Annisa Camellia Makati
- Faculty of Medicine, Universitas Lambung Mangkurat, Banjarmasin, South Kalimantan, Indonesia
| | - Aghnia Nabila Ananda
- Faculty of Medicine, Universitas Lambung Mangkurat, Banjarmasin, South Kalimantan, Indonesia
| | - Jasmine Aisyah Putri
- Faculty of Medicine, Universitas Lambung Mangkurat, Banjarmasin, South Kalimantan, Indonesia
| | - Siti Feritasia Amellia
- Faculty of Medicine, Universitas Lambung Mangkurat, Banjarmasin, South Kalimantan, Indonesia
| | - Bambang Setiawan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Lambung Mangkurat, Banjarmasin, South Kalimantan, Indonesia
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16
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Curcumin partly prevents ISG15 activation via ubiquitin-activating enzyme E1-like protein and decreases ISGylation. Biochem Biophys Res Commun 2022; 625:94-101. [PMID: 35952613 PMCID: PMC9352433 DOI: 10.1016/j.bbrc.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022]
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17
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Abdizadeh R, Hadizadeh F, Abdizadeh T. Evaluation of apigenin-based biflavonoid derivatives as potential therapeutic agents against viral protease (3CLpro) of SARS-CoV-2 via molecular docking, molecular dynamics and quantum mechanics studies. J Biomol Struct Dyn 2022:1-31. [PMID: 35848354 DOI: 10.1080/07391102.2022.2098821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic COVID-19 disease that affects human respiratory function. Despite the scientific progression made in the development of the vaccine, there is an urgent need for the discovery of antiviral drugs for better performance at different stages of SARS-CoV-2 reproduction. The main protease (Mpro or 3CLpro) plays a pivotal role in the life cycle of the virus, making it an attractive target for the development of antiviral agents effective against the new strains of coronaviruses (CoVs). In this study, a series of apigenin-based natural biflavonoid derivatives as potential inhibitors of coronaviruses 3CLpro was investigated by in silico approaches. For this purpose, the molecular docking was performed to analyze the interaction of the natural biflavonoids with SARS-Cov-2 main protease and for further investigation, docking to the 3CLpro of SARS-CoV and MERS-CoV. Based on docking scores and comparison with the reference inhibitors (ritonavir and lopinavir), more than half of the biflavonoids had strong interactions with the residues of the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward the main protease than ritonavir and lopinavir. The top biflavonoids were further explored through molecular dynamics simulation, binding free energy calculation and residual energy contributions estimated by the MM-PBSA. Also, drug likeness property investigation by Swiss ADME tools and density functional theory (DFT) calculations were performed. The results confirmed that the 3CLpro-amentoflavone, 3CLpro-bilobetin, 3CLpro-ginkgetin, and 3CLpro-sotetsuflavone complexes possess a large amount of dynamic properties such as high stability, significant binding energy and fewer conformation fluctuations. Also, the pharmacokinetics and drug-likeness studies and HOMO-LUMO and DFT descriptor values indicated a promising result of the selected natural biflavonoids. Overall findings indicate that the apigenin-based biflavonoids may inhibit COVID-19 by significant interactions in the binding pocket and those results can pave the way in drug discovery although the effectiveness of these bioactive compounds should be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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18
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Ferreira GM, Pillaiyar T, Hirata MH, Poso A, Kronenberger T. Inhibitor induced conformational changes in SARS-COV-2 papain-like protease. Sci Rep 2022; 12:11585. [PMID: 35803957 PMCID: PMC9270405 DOI: 10.1038/s41598-022-15181-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/20/2022] [Indexed: 01/24/2023] Open
Abstract
SARS-CoV-2's papain-like protease (PLpro) interaction with ligands has recently been explored with a myriad of crystal structures. We used molecular dynamics (MD) simulations to study different PLpro-ligand complexes, their ligand-induced conformational changes, and interactions. We focused on inhibitors reported with known IC50 against PLpro, namely GRL-0617, XR8-89, PLP_Snyder530, and Sander's recently published compound 7 (CPD7), and compared these trajectories against the apostructure (Apo), with a total of around 60 µs worth simulation data. We aimed to study the conformational changes using molecular dynamics simulations for the inhibitors in the PLpro. PCA analyses and the MSM models revealed distinct conformations of PLpro in the absence/presence of ligands and proposed that BL2-loop contributes to the accessibility of these inhibitors. Further, bulkier substituents closer to Tyr268 and Gln269 could improve inhibition of SARS-CoV-2 PLpro by occupying the region between BL2-groove and BL2-loop, but we also expand on the relevance of exploring multiple PLpro sub-pockets to improve inhibition.
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Affiliation(s)
- Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Antti Poso
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076, Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076, Tübingen, Germany.
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland.
- Tübingen Center for Academic Drug Discovery and Development (TüCAD2), 72076, Tübingen, Germany.
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19
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Jin Y, Ouyang M, Yu T, Zhuang J, Wang W, Liu X, Duan F, Guo D, Peng X, Pan JA. Genome-Wide Analysis of the Indispensable Role of Non-structural Proteins in the Replication of SARS-CoV-2. Front Microbiol 2022; 13:907422. [PMID: 35722274 PMCID: PMC9198553 DOI: 10.3389/fmicb.2022.907422] [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: 03/29/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022] Open
Abstract
Understanding the process of replication and transcription of SARS-CoV-2 is essential for antiviral strategy development. The replicase polyprotein is indispensable for viral replication. However, whether all nsps derived from the replicase polyprotein of SARS-CoV-2 are indispensable is not fully understood. In this study, we utilized the SARS-CoV-2 replicon as the system to investigate the role of each nsp in viral replication. We found that except for nsp16, all the nsp deletions drastically impair the replication of the replicon, and nsp14 could recover the replication deficiency caused by its deletion in the viral replicon. Due to the unsuccessful expressions of nsp1, nsp3, and nsp16, we could not draw a conclusion about their in trans-rescue functions. Our study provided a new angle to understand the role of each nsp in viral replication and transcription, helping the evaluation of nsps as the target for antiviral drug development.
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Affiliation(s)
- Yunyun Jin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Muzi Ouyang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Ting Yu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Jiaxin Zhuang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Wenhao Wang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xue Liu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Fangfang Duan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Deyin Guo
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xiaoxue Peng
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
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20
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Reina J, Iglesias C. [Nirmatrelvir plus ritonavir (Paxlovid) a potent SARS-CoV-2 3CLpro protease inhibitor combination]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2022; 35:236-240. [PMID: 35183067 PMCID: PMC9134883 DOI: 10.37201/req/002.2022] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 12/17/2022]
Abstract
All coronavirus, including SARS-CoV-2, encode two proteases needed for the processing of PP1A and PP1AB polyproteins. The main protease 3CL (chemotripsine-like) gives rise to the formation of NSP11/16 proteins. The 3CL protease has been constituted as one of the possible therapeutic targets for the development of antiviral drugs against SARS-COV-2 due to its highly conserved sequence and structure among all coronaviruses. During the SARS-COV-1 pandemic, a hydroxymethyl ketone derivative (PF-00835231) was identified with an intense inhibitory activity against the 3CL protease. Subsequent chemical modifications gave rise to derivative PF-07321332 (nirmatrelvir) which has shown a high antiviral efficacy against SARS-COV-2. The company's data indicate that it is capable of reducing 89% the risk of hospitalization and death of patients infected with hardly adverse effects. Its effectiveness improves if it is administered orally in the first 24-48 hours and the duration of treatment has been established between 3-5 days. The commercial form has been associated with the antiviral ritonavir that has shown the metabolism of nirmatrelvir, lengthening its average life. This antiviral would be effective against current and future viral variants, since 3CL is not modified in them. The FDA approved this antiviral in November 2021 and EMA is in the final evaluation phase.
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Affiliation(s)
- J Reina
- Jordi Reina, Unidad de Virología, Servicio de Microbiología, Hospital Universitario Son Espases, Facultad de Medicina (UIB). Carretera Valldemossa 79, 07120 Palma de Mallorca. Spain.
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21
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Martín V, Sanz-Novo M, León I, Redondo P, Largo A, Barrientos C. Computational study on the affinity of potential drugs to SARS-CoV-2 main protease. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:294005. [PMID: 35504274 DOI: 10.1088/1361-648x/ac6c6c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
Herein, we report a computational investigation of the binding affinity of dexamethasone, betamethasone, chloroquine and hydroxychloroquine to SARS-CoV-2 main protease using molecular and quantum mechanics as well as molecular docking methodologies. We aim to provide information on the anti-COVID-19 mechanism of the abovementioned potential drugs against SARS-CoV-2 coronavirus. Hence, the 6w63 structure of the SARS-CoV-2 main protease was selected as potential target site for the docking analysis. The study includes an initial conformational analysis of dexamethasone, betamethasone, chloroquine and hydroxychloroquine. For the most stable conformers, a spectroscopic analysis has been carried out. In addition, global and local reactivity indexes have been calculated to predict the chemical reactivity of these molecules. The molecular docking results indicate that dexamethasone and betamethasone have a higher affinity than chloroquine and hydroxychloroquine for their theoretical 6w63 target. Additionally, dexamethasone and betamethasone show a hydrogen bond with the His41 residue of the 6w63 protein, while the interaction between chloroquine and hydroxychloroquine with this amino acid is weak. Thus, we confirm the importance of His41 amino acid as a target to inhibit the SARS-CoV-2 Mpro activity.
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Affiliation(s)
- Verónica Martín
- Departamento de Química Física y Química Inorgánica, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Miguel Sanz-Novo
- Departamento de Química Física y Química Inorgánica, Universidad de Valladolid, 47011 Valladolid, Spain
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopía y Bioespectroscopía, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Iker León
- Departamento de Química Física y Química Inorgánica, Universidad de Valladolid, 47011 Valladolid, Spain
- Grupo de Espectroscopía Molecular (GEM), Edificio Quifima, Área de Química-Física, Laboratorios de Espectroscopía y Bioespectroscopía, Parque Científico UVa, Unidad Asociada CSIC, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Pilar Redondo
- Departamento de Química Física y Química Inorgánica, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Antonio Largo
- Departamento de Química Física y Química Inorgánica, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Carmen Barrientos
- Departamento de Química Física y Química Inorgánica, Universidad de Valladolid, 47011 Valladolid, Spain
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22
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Mahmoudi S, Dehkordi MM, Asgarshamsi MH. The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects. Biophys Chem 2022; 288:106824. [PMID: 35728510 PMCID: PMC9095071 DOI: 10.1016/j.bpc.2022.106824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/13/2022] [Accepted: 05/07/2022] [Indexed: 02/07/2023]
Abstract
The novel coronavirus that caused COVID-19 pandemic is SARS-CoV-2. Although various vaccines are currently being used to prevent the disease's severe consequences, there is still a need for medications for those who become infected. The SARS-CoV-2 has a variety of proteins that have been studied extensively since the virus's advent. In this review article, we looked at chemical to molecular aspects of the various structures studied that have pharmaceutical activity and attempted to find a link between drug activity and compound structure. For example, designing of the compounds which bind to the allosteric site and modify hydrogen bonds or the salt bridges can disrupt SARS-CoV2 RBD–ACE2 complex. It seems that quaternary ammonium moiety and quinolin-1-ium structure could act as a negative allosteric modulator to reduce the tendency between spike-ACE2. Pharmaceutical structures with amino heads and hydrophobic tails can block envelope protein to prevent making mature SARS-CoV-2. Also, structures based on naphthalene pharmacophores or isosteres can form a strong bond with the PLpro and form a π-π and the Mpro's active site can be occupied by octapeptide compounds or linear compounds with a similar fitting ability to octapeptide compounds. And for protein RdRp, it is critical to consider pH and pKa so that pKa regulation of compounds to comply with patients is very effective, thus, the presence of tetrazole, phenylpyrazole groups, and analogs of pyrophosphate in the designed drugs increase the likelihood of the RdRp active site inhibition. Finally, it can be deduced that designing hybrid drug molecules along with considering the aforementioned characteristics would be a suitable approach for developing medicines in order to accurate targeting and complete inhibition this virus.
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Affiliation(s)
- Samira Mahmoudi
- Department of Microbial Biotechnology, School of Biological Sciences, Islamic Azad University Tehran North Branch, Tehran, Iran.
| | - Mehrdad Mohammadpour Dehkordi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mohammad Hossein Asgarshamsi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
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23
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Zothantluanga JH, Abdalla M, Rudrapal M, Tian Q, Chetia D, Li J. Computational Investigations for Identification of Bioactive Molecules from Baccaurea ramiflora and Bergenia ciliata as Inhibitors of SARS-CoV-2 M pro. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2046613] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- James H. Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Shandong Province, PR China
| | - Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education Research, Pune, Maharashtra, India
| | - Qiang Tian
- Department of Senile Neurology, The Central Hospital of Taian, Taian, Shandong, PR China
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Jin Li
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Shandong Province, PR China
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24
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Haddad M, Gaudreault R, Sasseville G, Nguyen PT, Wiebe H, Van De Ven T, Bourgault S, Mousseau N, Ramassamy C. Molecular Interactions of Tannic Acid with Proteins Associated with SARS-CoV-2 Infectivity. Int J Mol Sci 2022; 23:2643. [PMID: 35269785 PMCID: PMC8910432 DOI: 10.3390/ijms23052643] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 02/01/2023] Open
Abstract
The overall impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on our society is unprecedented. The identification of small natural ligands that could prevent the entry and/or replication of the coronavirus remains a pertinent approach to fight the coronavirus disease (COVID-19) pandemic. Previously, we showed that the phenolic compounds corilagin and 1,3,6-tri-O-galloyl-β-D-glucose (TGG) inhibit the interaction between the SARS-CoV-2 spike protein receptor binding domain (RBD) and angiotensin-converting enzyme 2 (ACE2), the SARS-CoV-2 target receptor on the cell membrane of the host organism. Building on these promising results, we now assess the effects of these phenolic ligands on two other crucial targets involved in SARS-CoV-2 cell entry and replication, respectively: transmembrane protease serine 2 (TMPRSS2) and 3-chymotrypsin like protease (3CLpro) inhibitors. Since corilagin, TGG, and tannic acid (TA) share many physicochemical and structural properties, we investigate the binding of TA to these targets. In this work, a combination of experimental methods (biochemical inhibition assays, surface plasmon resonance, and quartz crystal microbalance with dissipation monitoring) confirms the potential role of TA in the prevention of SARS-CoV-2 infectivity through the inhibition of extracellular RBD/ACE2 interactions and TMPRSS2 and 3CLpro activity. Moreover, molecular docking prediction followed by dynamic simulation and molecular mechanics Poisson-Boltzmann surface area (MMPBSA) free energy calculation also shows that TA binds to RBD, TMPRSS2, and 3CLpro with higher affinities than TGG and corilagin. Overall, these results suggest that naturally occurring TA is a promising candidate to prevent and inhibit the infectivity of SARS-CoV-2.
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Affiliation(s)
- Mohamed Haddad
- Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
- Institute on Nutrition and Functional Foods, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Roger Gaudreault
- Succursale Centre-Ville, Départment de Physique, Université de Montréal, Case Postale 6128, Montréal, QC H3C 3J7, Canada; (R.G.); (G.S.); (N.M.)
| | - Gabriel Sasseville
- Succursale Centre-Ville, Départment de Physique, Université de Montréal, Case Postale 6128, Montréal, QC H3C 3J7, Canada; (R.G.); (G.S.); (N.M.)
| | - Phuong Trang Nguyen
- Département de Chimie, Université du Québec à Montréal, 2101 Rue Jeanne-Mance, Montréal, QC H2X 2J6, Canada; (P.T.N.); (S.B.)
| | - Hannah Wiebe
- Département de Chimie, Université McGill, 3420 Rue University, Montréal, QC H3A 2A7, Canada; (H.W.); (T.V.D.V.)
| | - Theo Van De Ven
- Département de Chimie, Université McGill, 3420 Rue University, Montréal, QC H3A 2A7, Canada; (H.W.); (T.V.D.V.)
| | - Steve Bourgault
- Département de Chimie, Université du Québec à Montréal, 2101 Rue Jeanne-Mance, Montréal, QC H2X 2J6, Canada; (P.T.N.); (S.B.)
| | - Normand Mousseau
- Succursale Centre-Ville, Départment de Physique, Université de Montréal, Case Postale 6128, Montréal, QC H3C 3J7, Canada; (R.G.); (G.S.); (N.M.)
| | - Charles Ramassamy
- Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
- Institute on Nutrition and Functional Foods, Laval University, Quebec City, QC G1V 0A6, Canada
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25
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Ramos RS, Borges RS, de Souza JSN, Araujo IF, Chaves MH, Santos CBR. Identification of Potential Antiviral Inhibitors from Hydroxychloroquine and 1,2,4,5-Tetraoxanes Analogues and Investigation of the Mechanism of Action in SARS-CoV-2. Int J Mol Sci 2022; 23:1781. [PMID: 35163703 PMCID: PMC8836247 DOI: 10.3390/ijms23031781] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 12/27/2022] Open
Abstract
This study aimed to identify potential inhibitors and investigate the mechanism of action on SARS-CoV-2 ACE2 receptors using a molecular modeling study and theoretical determination of biological activity. Hydroxychloroquine was used as a pivot structure and antimalarial analogues of 1,2,4,5 tetraoxanes were used for the construction and evaluation of pharmacophoric models. The pharmacophore-based virtual screening was performed on the Molport® database (~7.9 million compounds) and obtained 313 structures. Additionally, a pharmacokinetic study was developed, obtaining 174 structures with 99% confidence for human intestinal absorption and penetration into the blood-brain barrier (BBB); posteriorly, a study of toxicological properties was realized. Toxicological predictions showed that the selected molecules do not present a risk of hepatotoxicity, carcinogenicity, mutagenicity, and skin irritation. Only 54 structures were selected for molecular docking studies, and five structures showed binding affinity (ΔG) values satisfactory for ACE2 receptors (PDB 6M0J), in which the molecule MolPort-007-913-111 had the best ΔG value of -8.540 Kcal/mol, followed by MolPort-002-693-933 with ΔG = -8.440 Kcal/mol. Theoretical determination of biological activity was realized for 54 structures, and five molecules showed potential protease inhibitors. Additionally, we investigated the Mpro receptor (6M0K) for the five structures via molecular docking, and we confirmed the possible interaction with the target. In parallel, we selected the TopsHits 9 with antiviral potential that evaluated synthetic accessibility for future synthesis studies and in vivo and in vitro tests.
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Affiliation(s)
- Ryan S. Ramos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, AP, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
| | - Rosivaldo S. Borges
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Graduate Program on Medicinal Chemistry and Molecular Modeling, Institute of Health Science, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - João S. N. de Souza
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil; (J.S.N.d.S.); (M.H.C.)
| | - Inana F. Araujo
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Binational Campus, Federal University of Amapá, Oiapoque 68980-000, AP, Brazil
| | - Mariana H. Chaves
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil; (J.S.N.d.S.); (M.H.C.)
| | - Cleydson B. R. Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, AP, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil; (J.S.N.d.S.); (M.H.C.)
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26
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Sencanski M, Perovic V, Milicevic J, Todorovic T, Prodanovic R, Veljkovic V, Paessler S, Glisic S. Identification of SARS-CoV-2 Papain-like Protease (PLpro) Inhibitors Using Combined Computational Approach. ChemistryOpen 2022; 11:e202100248. [PMID: 35103413 PMCID: PMC8805381 DOI: 10.1002/open.202100248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/13/2022] [Indexed: 11/25/2022] Open
Abstract
In the current pandemic, finding an effective drug to prevent or treat the infection is the highest priority. A rapid and safe approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 PLpro promotes viral replication and modulates the host immune system, resulting in inhibition of the host antiviral innate immune response, and therefore is an attractive drug target. In this study, we used a combined in silico virtual screening for candidates for SARS-CoV-2 PLpro protease inhibitors. We used the Informational spectrum method applied for Small Molecules for searching the Drugbank database followed by molecular docking. After in silico screening of drug space, we identified 44 drugs as potential SARS-CoV-2 PLpro inhibitors that we propose for further experimental testing.
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Affiliation(s)
- Milan Sencanski
- National Institute of the Republic of SerbiaUniversity of BelgradeMike Petrovica Alasa 12–1411000BelgradeSerbia
| | - Vladimir Perovic
- National Institute of the Republic of SerbiaUniversity of BelgradeMike Petrovica Alasa 12–1411000BelgradeSerbia
| | - Jelena Milicevic
- National Institute of the Republic of SerbiaUniversity of BelgradeMike Petrovica Alasa 12–1411000BelgradeSerbia
| | - Tamara Todorovic
- Faculty of ChemistryUniversity of BelgradeStudentski Trg 12–1611000BelgradeSerbia
| | - Radivoje Prodanovic
- Faculty of ChemistryUniversity of BelgradeStudentski Trg 12–1611000BelgradeSerbia
| | | | - Slobodan Paessler
- Department of PathologyUniversity of Texas Medical BranchGalvestonTX 77550USA
- Institute for Human Infections and ImmunityUniversity of Texas Medical BranchGalvestonTX 77555USA
| | - Sanja Glisic
- National Institute of the Republic of SerbiaUniversity of BelgradeMike Petrovica Alasa 12–1411000BelgradeSerbia
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27
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Yi Y, Li J, Lai X, Zhang M, Kuang Y, Bao YO, Yu R, Hong W, Muturi E, Xue H, Wei H, Li T, Zhuang H, Qiao X, Xiang K, Yang H, Ye M. Natural triterpenoids from licorice potently inhibit SARS-CoV-2 infection. J Adv Res 2022; 36:201-210. [PMID: 35116174 PMCID: PMC8620242 DOI: 10.1016/j.jare.2021.11.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/16/2021] [Accepted: 11/21/2021] [Indexed: 01/14/2023] Open
Abstract
Introduction The COVID-19 global epidemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a great public health emergency. Discovering antiviral drug candidates is urgent for the prevention and treatment of COVID-19. Objectives This work aims to discover natural SARS-CoV-2 inhibitors from the traditional Chinese herbal medicine licorice. Methods We screened 125 small molecules from Glycyrrhiza uralensis Fisch. (licorice, Gan-Cao) by virtual ligand screening targeting the receptor-binding domain (RBD) of SARS-CoV-2 spike protein. Potential hit compounds were further evaluated by ELISA, SPR, luciferase assay, antiviral assay and pharmacokinetic study. Results The triterpenoids licorice-saponin A3 (A3) and glycyrrhetinic acid (GA) could potently inhibit SARS-CoV-2 infection, with EC50 of 75 nM and 3.17 µM, respectively. Moreover, we reveal that A3 mainly targets the nsp7 protein, and GA binds to the spike protein RBD of SARS-CoV-2. Conclusion In this work, we found GA and A3 from licorice potently inhibit SARS-CoV-2 infection by affecting entry and replication of the virus. Our findings indicate that these triterpenoids may contribute to the clinical efficacy of licorice for COVID-19 and could be promising candidates for antiviral drug development.
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Affiliation(s)
- Yang Yi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Junhua Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyuan Lai
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Meng Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yi Kuang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yang-Oujie Bao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Rong Yu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Wei Hong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elishiba Muturi
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Xue
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Hui Zhuang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Kuanhui Xiang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing 100191, China
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28
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Hernández González JE, Eberle RJ, Willbold D, Coronado MA. A Computer-Aided Approach for the Discovery of D-Peptides as Inhibitors of SARS-CoV-2 Main Protease. Front Mol Biosci 2022; 8:816166. [PMID: 35187076 PMCID: PMC8852625 DOI: 10.3389/fmolb.2021.816166] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/30/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 main protease, also known as 3-chymotrypsin-like protease (3CLpro), is a cysteine protease responsible for the cleavage of viral polyproteins pp1a and pp1ab, at least, at eleven conserved sites, which leads to the formation of mature nonstructural proteins essential for the replication of the virus. Due to its essential role, numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat Covid-19 and have reported a vast number of inhibitors and their co-crystal structures. Despite all the ongoing efforts, D-peptides, which possess key advantages over L-peptides as therapeutic agents, have not been explored as potential drug candidates against 3CLpro. The current work fills this gap by reporting an in silico approach for the discovery of D-peptides capable of inhibiting 3CLpro that involves structure-based virtual screening (SBVS) of an in-house library of D-tripeptides and D-tetrapeptides into the protease active site and subsequent rescoring steps, including Molecular Mechanics Generalized-Born Surface Area (MM-GBSA) free energy calculations and molecular dynamics (MD) simulations. In vitro enzymatic assays conducted for the four top-scoring D-tetrapeptides at 20 μM showed that all of them caused 55–85% inhibition of 3CLpro activity, thus highlighting the suitability of the devised approach. Overall, our results present a promising computational strategy to identify D-peptides capable of inhibiting 3CLpro, with broader application in problems involving protein inhibition.
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Affiliation(s)
- Jorge E. Hernández González
- Multiuser Center for Biomolecular Innovation, IBILCE, Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, Brazil
- Laboratory for Molecular Modeling and Dynamics, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Cidade Universitária Ilha do Fundão, Rio de Janeiro, Brazil
| | - Raphael J. Eberle
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Mônika A. Coronado
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- *Correspondence: Mônika A. Coronado,
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29
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Liu N, Zhang Y, Lei Y, Wang R, Zhan M, Liu J, An Y, Zhou Y, Zhan J, Yin F, Li Z. Design and Evaluation of a Novel Peptide-Drug Conjugate Covalently Targeting SARS-CoV-2 Papain-like Protease. J Med Chem 2022; 65:876-884. [PMID: 34981929 PMCID: PMC8753845 DOI: 10.1021/acs.jmedchem.1c02022] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Indexed: 12/31/2022]
Abstract
Coronavirus disease 2019 (COVID-19) pandemic, a global health threat, was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 papain-like cysteine protease (PLpro) was recognized as a promising drug target because of multiple functions in virus maturation and antiviral immune responses. Inhibitor GRL0617 occupied the interferon-stimulated gene 15 (ISG15) C-terminus-binding pocket and showed an effective antiviral inhibition. Here, we described a novel peptide-drug conjugate (PDC), in which GRL0617 was linked to a sulfonium-tethered peptide derived from PLpro-specific substrate LRGG. The EM-C and EC-M PDCs showed a promising in vitro IC50 of 7.40 ± 0.37 and 8.63 ± 0.55 μM, respectively. EC-M could covalently label PLpro active site C111 and display anti-ISGylation activities in cellular assays. The results represent the first attempt to design PDCs composed of stabilized peptide inhibitors and GRL0617 to inhibit PLpro. These novel PDCs provide promising opportunities for antiviral drug design.
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Affiliation(s)
- Na Liu
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan
Translational Medicine Center, Shenzhen
Bay Laboratory, Shenzhen 518118, China
| | - Yichi Zhang
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yingshou Lei
- Institute
for Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen, Guangdong 518032, China
| | - Rui Wang
- Pingshan
Translational Medicine Center, Shenzhen
Bay Laboratory, Shenzhen 518118, China
| | - Meimiao Zhan
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jianbo Liu
- Pingshan
Translational Medicine Center, Shenzhen
Bay Laboratory, Shenzhen 518118, China
| | - Yuhao An
- Pingshan
Translational Medicine Center, Shenzhen
Bay Laboratory, Shenzhen 518118, China
| | - Yaoqi Zhou
- Institute
for Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen, Guangdong 518032, China
| | - Jian Zhan
- Institute
for Systems and Physical Biology, Shenzhen
Bay Laboratory, Shenzhen, Guangdong 518032, China
| | - Feng Yin
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan
Translational Medicine Center, Shenzhen
Bay Laboratory, Shenzhen 518118, China
| | - Zigang Li
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan
Translational Medicine Center, Shenzhen
Bay Laboratory, Shenzhen 518118, China
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Razali R, Asis H, Budiman C. Structure-Function Characteristics of SARS-CoV-2 Proteases and Their Potential Inhibitors from Microbial Sources. Microorganisms 2021; 9:2481. [PMID: 34946083 PMCID: PMC8706127 DOI: 10.3390/microorganisms9122481] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is considered the greatest challenge to the global health community of the century as it continues to expand. This has prompted immediate urgency to discover promising drug targets for the treatment of COVID-19. The SARS-CoV-2 viral proteases, 3-chymotrypsin-like protease (3CLpro) and papain-like cysteine protease (PLpro), have become the promising target to study due to their essential functions in spreading the virus by RNA transcription, translation, protein synthesis, processing and modification, virus replication, and infection of the host. As such, understanding of the structure and function of these two proteases is unavoidable as platforms for the development of inhibitors targeting this protein which further arrest the infection and spread of the virus. While the abundance of reports on the screening of natural compounds such as SARS-CoV-2 proteases inhibitors are available, the microorganisms-based compounds (peptides and non-peptides) remain less studied. Indeed, microorganisms-based compounds are also one of the potent antiviral candidates against COVID-19. Microbes, especially bacteria and fungi, are other resources to produce new drugs as well as nucleosides, nucleotides, and nucleic acids. Thus, we have compiled various reported literature in detail on the structures, functions of the SARS-CoV-2 proteases, and potential inhibitors from microbial sources as assistance to other researchers working with COVID-19. The compounds are also compared to HIV protease inhibitors which suggested the microorganisms-based compounds are advantageous as SARS-CoV2 proteases inhibitors. The information should serve as a platform for further development of COVID-19 drug design strategies.
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Affiliation(s)
| | | | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia; (R.R.); (H.A.)
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