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Haste makes waste: A critical review of docking‐based virtual screening in drug repurposing for SARS‐CoV‐2 main protease (M‐pro) inhibition

Guillem Macip, Pol Garcia‐Segura, Júlia Mestres‐Truyol, Bryan Saldivar‐Espinoza, María José Ojeda‐Montes, Aleix Gimeno, Adrià Cereto‐Massagué, Santiago Garcia‐Vallvé, Gerard Pujadas
2021 Medicinal research reviews (Print)  
This review makes a critical evaluation of 61 peer-reviewed manuscripts that use a docking step in a virtual screening (VS) protocol to predict SARS-CoV-2 M-pro (M-pro) inhibitors in approved or investigational  ...  In addition, a set of known 150 SARS-CoV-2 M-pro inhibitors extracted from the literature and a second set of 81 M-pro inhibitors and 113 inactive compounds obtained from the COVID Moonshot project were  ...  ACKNOWLEDGMENTS We thank OpenEye Scientific Software and Cresset for kindly providing us with a software bursary to use their programs.  ... 
doi:10.1002/med.21862 pmid:34697818 pmcid:PMC8662214 fatcat:f54dgqqmzfherlbimbx7uvfdi4

Progress in Developing Inhibitors of SARS-CoV-2 3C-Like Protease

Qingxin Li, CongBao Kang
2020 Microorganisms  
The strategies applied in developing inhibitors of the main protease of SARS-CoV-2 and currently available protein inhibitors are summarized.  ...  In this review, we describe structural studies on the main protease of SARS-CoV-2.  ...  Acknowledgments: Q.L. appreciates the support from Institute of Bioengineering, Guangdong Academy of Sciences, Guangdong, China. C.K. thanks the support from BMRC, A*STAR, Singapore.  ... 
doi:10.3390/microorganisms8081250 pmid:32824639 fatcat:vf2ykskl4jb7ritoob7dw2yxni

An Integrated Computational and Experimental Approach to Identifying Inhibitors for SARS-CoV-2 3CL Protease

Tianhua Zhai, Fangyuan Zhang, Shozeb Haider, Daniel Kraut, Zuyi Huang
2021 Frontiers in Molecular Biosciences  
The newly evolved SARS-CoV-2 has caused the COVID-19 pandemic, and the SARS-CoV-2 main protease 3CLpro is essential for the rapid replication of the virus.  ...  3CLpro SARS-CoV-2 with IC50's of 19 ± 3 μM and 38 ± 3 μM, respectively.  ...  -2 . 288 potential inhibitors of the main protease (3CLpro) of SARS-CoV-2 were identified through virtual screening of half a million compounds from existing databases.  ... 
doi:10.3389/fmolb.2021.661424 pmid:34079818 pmcid:PMC8166273 fatcat:sysupavucrei7bp2uez2jf55am

Discovery of TMPRSS2 Inhibitors from Virtual Screening as a Potential Treatment of COVID-19

Xin Hu, Jonathan H. Shrimp, Hui Guo, Miao Xu, Catherine Z. Chen, Wei Zhu, Alexey V. Zakharov, Sankalp Jain, Paul Shinn, Anton Simeonov, Matthew D. Hall, Min Shen
2021 ACS Pharmacology & Translational Science  
The hits were evaluated in the TMPRSS2 biochemical assay and the SARS-CoV-2 pseudotyped particle entry assay.  ...  The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has prompted researchers to pivot their efforts to finding antiviral compounds and vaccines.  ...  ■ ACKNOWLEDGMENTS This work was supported by the Intramural Research Programs of the National Center for Advancing Translational Sciences, National Institutes of Health.  ... 
doi:10.1021/acsptsci.0c00221 pmid:34136758 pmcid:PMC8043206 fatcat:hb2qxqv2vbcmjbnc5zfto75zdq

In Silico Drug Repositioning to Target the SARS-CoV-2 Main Protease as Covalent Inhibitors Employing a Combined Structure-Based Virtual Screening Strategy of Pharmacophore Models and Covalent Docking

Luis Heriberto Vázquez-Mendoza, Humberto L. Mendoza-Figueroa, Juan Benjamín García-Vázquez, José Correa-Basurto, Jazmín García-Machorro
2022 International Journal of Molecular Sciences  
The virtual screening on the structure-based pharmacophoric map of the SARS-CoV-2 Mpro in complex with an inhibitor N3 (reference compound) provided high efficiency by identifying 53 drugs (FDA and DrugBank  ...  The main protease of SARS-CoV-2 (Mpro) is a highly conserved cysteine proteinase, fundamental for the replication of the coronavirus and with a specific cleavage mechanism that positions it as an attractive  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms23073987 pmid:35409348 pmcid:PMC8999907 fatcat:ffv6sb6jzbfypdwbhi427yvbfe

Commercial SARS-CoV-2 Targeted, Protease Inhibitor Focused and Protein–Protein Interaction Inhibitor Focused Molecular Libraries for Virtual Screening and Drug Design

Sebastjan Kralj, Marko Jukič, Urban Bren
2021 International Journal of Molecular Sciences  
We evaluated the SARS-CoV-2-targeted, protease-inhibitor-focused and protein–protein-interaction-inhibitor-focused libraries to gain a better understanding of how these libraries were designed.  ...  Several proteins have emerged as potential therapeutic targets for drug development, and we sought out to review the commercially available and marketed SARS-CoV-2-targeted libraries ready for high-throughput  ...  Acknowledgments: We gratefully acknowledge the support of NVIDIA Corporation with the donation of GPU hardware that was used in this research. We especially thank OpenEye for their support.  ... 
doi:10.3390/ijms23010393 pmid:35008818 pmcid:PMC8745317 fatcat:3pnm3ezq55ddxnk22w34qwrhga

SARS-CoV-2 Papain-Like Protease Potential Inhibitors—In Silico Quantitative Assessment

Adam Stasiulewicz, Alicja W. Maksymiuk, Mai Lan Nguyen, Barbara Bełza, Joanna I. Sulkowska
2021 International Journal of Molecular Sciences  
SARS-CoV-2 PLpro inhibitors.  ...  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes the papain-like protease (PLpro).  ...  Acknowledgments: Authors thank Paweł Rubach for construction of the database, Agata Perlinska for preliminary structures and sequence analysis, as well as constructive discussion, and Maciej Sikora for  ... 
doi:10.3390/ijms22083957 pmid:33921228 fatcat:vxray26gqveerom4fsgpqbfeh4

Repurposing of Some Natural Product Isolates as SARS-COV-2 Main Protease Inhibitors via In Vitro Cell Free and Cell-Based Antiviral Assessments and Molecular Modeling Approaches

Hossam M. Abdallah, Ali M. El-Halawany, Alaa Sirwi, Amr M. El-Araby, Gamal A. Mohamed, Sabrin R. M. Ibrahim, Abdulrahman E. Koshak, Hani Z. Asfour, Zuhier A. Awan, Mahmoud A. Elfaky
2021 Pharmaceuticals  
natural product inhibitors of SARS-CoV-2 main protease (MPRO).  ...  The top eighteen hits from the screening were selected for in vitro evaluation on the viral protease (SARS-CoV-2 MPRO).  ...  Data Availability Statement: Data is contained within the article and Supplementary Materials. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ph14030213 pmid:33806331 fatcat:xkii5el4vbd33jl2xpot2q6miq

Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations

Anastasiia I. Petushkova, Andrey A. Zamyatnin
2020 Pharmaceuticals  
Several inhibitors have been developed to withstand SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV).  ...  Papain-like proteases (PLpro) of coronaviruses (CoVs) support viral reproduction and suppress the immune response of the host, which makes CoV PLpro perspective pharmaceutical targets.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ph13100277 pmid:32998368 fatcat:4oi5ax2xkrelhh4khlggqgz76m

An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19

Arun Bahadur Gurung, Mohammad Ajmal Ali, Joongku Lee, Mohammad Abul Farah, Khalid Mashay Al-Anazi, Bilal Alatas
2021 BioMed Research International  
of promising drug candidate molecules against various drug targets implicated in the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).  ...  The lack of approved drugs or vaccines continues to be a challenge and further necessitates the discovery of new therapeutic molecules.  ...  Acknowledgments The authors would like to extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for its funding of the research through the research group project  ... 
doi:10.1155/2021/8853056 fatcat:tmk62ju57rdbnlxpvdk62cxgvm

Fight against novel coronavirus: A perspective of medicinal chemists

Sk. Abdul Amin, Tarun Jha
2020 European Journal of Medicinal Chemistry  
This study is an initiative to recapitulate the medicinal chemistry of severe acute respiratory syndrome (SARS)-CoV-2 (SARS-CoV-2).  ...  The aim is to present an exquisite delineation of the current research from the perspective of a medicinal chemist to allow the rapid development of anti-SARS-CoV-2 agents.  ...  Further, a combination of SARS-CoV-2 Mpro structurebased VS and high-throughput screening of more than 10,000 compounds (containing approved drugs, clinical trials compounds, and other active compounds  ... 
doi:10.1016/j.ejmech.2020.112559 pmid:32563814 pmcid:PMC7289749 fatcat:kuk3gzlqxrc3fhtvpbzouqtka4

Structure-based virtual screening to discover potential lead molecules for the SARS-CoV-2 main protease

Anuj Gahlawat, Navneet Kumar, Rajender kumar, Hardeep Sandhu, Inder Pal Singh, Saranjit Singh, Anders Sjöstedt, Prabha Garg
2020 Journal of Chemical Information and Modeling  
The second objective was to screen the inhibitory effects of three different datasets (natural products, coronaviruses main protease inhibitors, and FDA-approved drugs) using structure-based virtual screening  ...  ., Ser46, and Phe134, were found to cause a significant change at the active sites of SARS-CoV-2.  ...  ■ ACKNOWLEDGMENTS The authors acknowledge the Director and Prof Srinivasa K G of NITTTR, Chandigarh for providing computational infrastructure.  ... 
doi:10.1021/acs.jcim.0c00546 pmid:32687345 pmcid:PMC7409927 fatcat:xtja5gv4ofc6hmztdfzh44misi

Structure of Mpro from COVID-19 virus and discovery of its inhibitors

Zhenming Jin, Xiaoyu Du, Yechun Xu, Yongqiang Deng, Meiqin Liu, Yao Zhao, Bing Zhang, Xiaofeng Li, Leike Zhang, Chao Peng, Yinkai Duan, Jing Yu (+19 others)
2020 Nature  
In order to rapidly discover lead compounds for clinical use, we initiated a program of combined structure-assisted drug design, virtual drug screening and high-throughput screening to identify new drug  ...  Next, through a combination of structure-based virtual and high-throughput screening, we assayed over 10,000 compounds including approved drugs, drug candidates in clinical trials, and other pharmacologically  ...  Kong from High Throughput Platform and staff from Analytical Chemistry Platform at the Shanghai Institute for Advanced Immunochemical Studies for their technical support; the National Centre for Protein  ... 
doi:10.1038/s41586-020-2223-y pmid:32272481 fatcat:whmi5zq4j5actactsnf3ow2ygm

Potential Inhibitors Targeting Papain-Like Protease of SARS-CoV-2: Two Birds With One Stone

Haihai Jiang, Peiyao Yang, Jin Zhang
2022 Frontiers in Chemistry  
In this review, we describe structural and functional features on PLpro of SARS-CoV-2 and the latest development in searching for PLpro inhibitors.  ...  Papain-like protease (PLpro) of SARS-CoV-2 supports viral reproduction and suppresses the innate immune response of the host, which makes PLpro an attractive pharmaceutical target.  ...  Virtual High Throughput Screening: Potential Inhibitors for SARS-CoV-2 PLPRO and 3CLPRO Proteases. Eur. J.  ... 
doi:10.3389/fchem.2022.822785 pmid:35281561 pmcid:PMC8905519 fatcat:lg7wzdrqczgblpqhyeipxxov2y

A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors [article]

Kuang-Yu Chen, Tim Krischuns, Laura Ortega Varga, Emna Harigua-Souiai, Sylvain Paisant, Agnes Zettor, Jeanne Chiaravalli, David Courtney, Amornrat O'Brien, Susan Baker, Catherine Isel, Fabrice Agou (+3 others)
2021 biorxiv/medrxiv  
Here we report the development of a gain-of-signal, highly sensitive cell-based luciferase assay to monitor SARS-CoV-2 nsp5 activity and show that it is suitable for high-throughput screening of compounds  ...  The here described assay will allow the screening of large-scale compound libraries for SARS-CoV-2 nsp5 inhibitors.  ...  Acknowledgments We thank Nicholas Heaton (Duke University), Rolf Hilgenfeld (University of Luebeck), Olivier Schwartz , Sylvie van der Werf and Olivier Sperandio (all from Institut Pasteur) for providing  ... 
doi:10.1101/2021.12.18.473303 pmid:34981051 pmcid:PMC8722588 fatcat:mvu24idk4reufd37xcuqnvmfda
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