1
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Mangione W, Falls Z, Samudrala R. Optimal COVID-19 therapeutic candidate discovery using the CANDO platform. Front Pharmacol 2022; 13:970494. [PMID: 36091793 PMCID: PMC9452636 DOI: 10.3389/fphar.2022.970494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/07/2022] [Indexed: 01/22/2023] Open
Abstract
The worldwide outbreak of SARS-CoV-2 in early 2020 caused numerous deaths and unprecedented measures to control its spread. We employed our Computational Analysis of Novel Drug Opportunities (CANDO) multiscale therapeutic discovery, repurposing, and design platform to identify small molecule inhibitors of the virus to treat its resulting indication, COVID-19. Initially, few experimental studies existed on SARS-CoV-2, so we optimized our drug candidate prediction pipelines using results from two independent high-throughput screens against prevalent human coronaviruses. Ranked lists of candidate drugs were generated using our open source cando.py software based on viral protein inhibition and proteomic interaction similarity. For the former viral protein inhibition pipeline, we computed interaction scores between all compounds in the corresponding candidate library and eighteen SARS-CoV proteins using an interaction scoring protocol with extensive parameter optimization which was then applied to the SARS-CoV-2 proteome for prediction. For the latter similarity based pipeline, we computed interaction scores between all compounds and human protein structures in our libraries then used a consensus scoring approach to identify candidates with highly similar proteomic interaction signatures to multiple known anti-coronavirus actives. We published our ranked candidate lists at the very beginning of the COVID-19 pandemic. Since then, 51 of our 276 predictions have demonstrated anti-SARS-CoV-2 activity in published clinical and experimental studies. These results illustrate the ability of our platform to rapidly respond to emergent pathogens and provide greater evidence that treating compounds in a multitarget context more accurately describes their behavior in biological systems.
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Affiliation(s)
| | | | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
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2
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Schuler J, Falls Z, Mangione W, Hudson ML, Bruggemann L, Samudrala R. Evaluating the performance of drug-repurposing technologies. Drug Discov Today 2022; 27:49-64. [PMID: 34400352 PMCID: PMC10014214 DOI: 10.1016/j.drudis.2021.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 06/20/2021] [Accepted: 08/08/2021] [Indexed: 01/22/2023]
Abstract
Drug-repurposing technologies are growing in number and maturing. However, comparisons to each other and to reality are hindered because of a lack of consensus with respect to performance evaluation. Such comparability is necessary to determine scientific merit and to ensure that only meaningful predictions from repurposing technologies carry through to further validation and eventual patient use. Here, we review and compare performance evaluation measures for these technologies using version 2 of our shotgun repurposing Computational Analysis of Novel Drug Opportunities (CANDO) platform to illustrate their benefits, drawbacks, and limitations. Understanding and using different performance evaluation metrics ensures robust cross-platform comparability, enabling us to continue to strive toward optimal repurposing by decreasing the time and cost of drug discovery and development.
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Affiliation(s)
- James Schuler
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Zackary Falls
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - William Mangione
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Matthew L Hudson
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Liana Bruggemann
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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3
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Sulimov VB, Kutov DC, Taschilova AS, Ilin IS, Tyrtyshnikov EE, Sulimov AV. Docking Paradigm in Drug Design. Curr Top Med Chem 2021; 21:507-546. [PMID: 33292135 DOI: 10.2174/1568026620666201207095626] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/28/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described. They include docking of non-covalent small ligands, protein-protein docking, supercomputer docking, quantum docking, the new generation of docking programs and the application of docking for covalent inhibitors discovery. Taking into account the threat of COVID-19, we present here a short review of docking applications to the discovery of inhibitors of SARS-CoV and SARS-CoV-2 target proteins, including our own result of the search for inhibitors of SARS-CoV-2 main protease using docking and quantum chemical post-processing. The conclusion is made that docking is extremely important in the fight against COVID-19 during the process of development of antivirus drugs having a direct action on SARS-CoV-2 target proteins.
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Affiliation(s)
- Vladimir B Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Danil C Kutov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Anna S Taschilova
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Ivan S Ilin
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Eugene E Tyrtyshnikov
- Institute of Numerical Mathematics of Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey V Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
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4
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Sabbah DA, Hajjo R, Bardaweel SK, Zhong HA. An Updated Review on SARS-CoV-2 Main Proteinase (M Pro): Protein Structure and Small-Molecule Inhibitors. Curr Top Med Chem 2021; 21:442-460. [PMID: 33292134 DOI: 10.2174/1568026620666201207095117] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022]
Abstract
[Coronaviruses (CoVs) are enveloped positive-stranded RNA viruses with spike (S) protein projections that allow the virus to enter and infect host cells. The S protein is a key virulence factor determining viral pathogenesis, host tropism, and disease pathogenesis. There are currently diverse corona viruses that are known to cause disease in humans. The occurrence of Middle East respiratory syndrome coronavirus (MERS-CoV) and Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), as fatal human CoV diseases, has induced significant interest in the medical field. The novel coronavirus disease (COVID-19) is an infectious disease caused by a novel strain of coronavirus (SAR-CoV-2). The SARS-CoV2 outbreak has been evolved in Wuhan, China, in December 2019, and identified as a pandemic in March 2020, resulting in 53.24 M cases and 1.20M deaths worldwide. SARS-CoV-2 main proteinase (MPro), a key protease of CoV-2, mediates viral replication and transcription. SARS-CoV-2 MPro has been emerged as an attractive target for SARS-CoV-2 drug design and development. Diverse scaffolds have been released targeting SARS-CoV-2 MPro. In this review, we culminate the latest published information about SARS-CoV-2 main proteinase (MPro) and reported inhibitors.
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Affiliation(s)
- Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Sanaa K Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman 11942, Jordan
| | - Haizhen A Zhong
- Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, Nebraska 68182, United States
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5
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Zhuo LS, Wang MS, Yang JF, Xu HC, Huang W, Shang LQ, Yang GF. Insights into SARS-CoV-2: Medicinal Chemistry Approaches to Combat Its Structural and Functional Biology. Top Curr Chem (Cham) 2021; 379:23. [PMID: 33886017 PMCID: PMC8061463 DOI: 10.1007/s41061-021-00335-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 04/03/2021] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still a pandemic around the world. Currently, specific antiviral drugs to control the epidemic remain deficient. Understanding the details of SARS-CoV-2 structural biology is extremely important for development of antiviral agents that will enable regulation of its life cycle. This review focuses on the structural biology and medicinal chemistry of various key proteins (Spike, ACE2, TMPRSS2, RdRp and Mpro) in the life cycle of SARS-CoV-2, as well as their inhibitors/drug candidates. Representative broad-spectrum antiviral drugs, especially those against the homologous virus SARS-CoV, are summarized with the expectation they will drive the development of effective, broad-spectrum inhibitors against coronaviruses. We are hopeful that this review will be a useful aid for discovery of novel, potent anti-SARS-CoV-2 drugs with excellent therapeutic results in the near future.
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Affiliation(s)
- Lin-Sheng Zhuo
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Ming-Shu Wang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Hong-Chuang Xu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Wei Huang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Lu-Qing Shang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300350, People's Republic of China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China.
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6
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Chen CC, Yu X, Kuo CJ, Min J, Chen S, Ma L, Liu K, Guo RT. Overview of antiviral drug candidates targeting coronaviral 3C-like main proteases. FEBS J 2021; 288:5089-5121. [PMID: 33400393 DOI: 10.1111/febs.15696] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/15/2020] [Accepted: 01/04/2021] [Indexed: 01/18/2023]
Abstract
Coronaviruses (CoVs) are positive single-stranded RNA viruses that cause severe respiratory syndromes in humans, including severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). Coronavirus disease 2019 (COVID-19) caused by a novel severe acute respiratory syndrome CoV (SARS-CoV-2) at the end of 2019 became a global pandemic. The 3C-like cysteine protease (3CLpro) processes viral polyproteins to yield mature non-structural proteins, thus playing an important role in the CoV life cycle, and therefore is considered as a prominent target for antiviral drugs. To date, many 3CLpro inhibitors have been reported, and their molecular mechanisms have been illustrated. Here, we briefly introduce the structural features of 3CLpro of the human-related SARS-CoV, MERS-CoV and SARS-CoV-2, and explore the potency and mechanism of their cognate inhibitors. This information will shed light on the development and optimization of CoV 3CLpro inhibitors, which may benefit the further designation of therapeutic strategies for treating CoV diseases.
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Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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7
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Gahlawat A, Kumar N, Kumar R, Sandhu H, Singh IP, Singh S, Sjöstedt A, Garg P. Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease. J Chem Inf Model 2020; 60:5781-5793. [PMID: 32687345 PMCID: PMC7409927 DOI: 10.1021/acs.jcim.0c00546] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Indexed: 01/08/2023]
Abstract
The COVID-19 disease is caused by a new strain of the coronavirus family (SARS-CoV-2), and it has affected at present millions of people all over the world. The indispensable role of the main protease (Mpro) in viral replication and gene expression makes this enzyme an attractive drug target. Therefore, inhibition of SARS-CoV-2 Mpro as a proposition to halt virus ingression is being pursued by scientists globally. Here we carried out a study with two objectives: the first being to perform comparative protein sequence and 3D structural analysis to understand the effect of 12 point mutations on the active site. Among these, two mutations, viz., Ser46 and Phe134, were found to cause a significant change at the active sites of SARS-CoV-2. The Ser46 mutation present at the entrance of the S5 subpocket of SARS-CoV-2 increases the contribution of other two hydrophilic residues, while the Phe134 mutation, present in the catalytic cysteine loop, can cause an increase in catalytic efficiency of Mpro by facilitating fast proton transfer from the Cys145 to His41 residue. It was observed that active site remained conserved among Mpro of both SARS-CoVs, except at the entrance of the S5 subpocket, suggesting sustenance of substrate specificity. The second objective was to screen the inhibitory effects of three different data sets (natural products, coronaviruses main protease inhibitors, and FDA-approved drugs) using a structure-based virtual screening approach. A total of 73 hits had a combo score >2.0. Eight different structural scaffold classes were identified, such as one/two tetrahydropyran ring(s), dipeptide/tripeptide/oligopeptide, large (approximately 20 atoms) cyclic peptide, and miscellaneous. The screened hits showed key interactions with subpockets of the active site. Further, molecular dynamics studies of selected screened compounds confirmed their perfect fitting into the subpockets of the active site. This study suggests promising structures that can fit into the SARS-CoV-2 Mpro active site and also offers direction for further lead optimization and rational drug design.
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Affiliation(s)
- Anuj Gahlawat
- Department of Pharmacoinformatics,
National Institute of Pharmaceutical Education and
Research (NIPER), S.A.S. Nagar 160062, Punjab,
India
| | - Navneet Kumar
- Department of Pharmacoinformatics,
National Institute of Pharmaceutical Education and
Research (NIPER), S.A.S. Nagar 160062, Punjab,
India
| | - Rajender Kumar
- Department of Clinical Microbiology
and Laboratory for Molecular Infection Medicine Sweden (MIMS),
Umeå University, SE-90185
Umeå, Sweden
| | - Hardeep Sandhu
- Department of Pharmacoinformatics,
National Institute of Pharmaceutical Education and
Research (NIPER), S.A.S. Nagar 160062, Punjab,
India
| | - Inder Pal Singh
- Department of Natural Products,
National Institute of Pharmaceutical Education and
Research (NIPER), S.A.S. Nagar 160062, Punjab,
India
| | - Saranjit Singh
- Department of Pharmaceutical Analysis,
National Institute of Pharmaceutical Education and
Research (NIPER), S.A.S. Nagar 160062, Punjab,
India
| | - Anders Sjöstedt
- Department of Clinical Microbiology
and Laboratory for Molecular Infection Medicine Sweden (MIMS),
Umeå University, SE-90185
Umeå, Sweden
| | - Prabha Garg
- Department of Pharmacoinformatics,
National Institute of Pharmaceutical Education and
Research (NIPER), S.A.S. Nagar 160062, Punjab,
India
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8
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Mandour YM, Zlotos DP, Alaraby Salem M. A multi-stage virtual screening of FDA-approved drugs reveals potential inhibitors of SARS-CoV-2 main protease. J Biomol Struct Dyn 2020; 40:2327-2338. [PMID: 33094680 PMCID: PMC7597227 DOI: 10.1080/07391102.2020.1837680] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. Repurposing of approved pharmaceutical drugs for COVID-19 treatment represents an attractive approach to quickly identify promising drug candidates. SARS-CoV-2 main protease (Mpro) is responsible for the maturation of viral functional proteins making it a key antiviral target. Based on the recently revealed crystal structures of SARS-CoV-2 Mpro, we herein describe a multi-stage virtual screening protocol including pharmacophore screening, molecular docking and protein-ligand interaction fingerprints (PLIF) post-docking filtration for efficient enrichment of potent SARS-CoV-2 Mpro inhibitors. Potential hits, along with a cocrystallized control were further studied via molecular dynamics. A 150-ns production trajectory was followed by RMSD, free energy calculation, and H-bond analysis for each compound. The applied virtual screening protocol led to identification of five FDA-approved drugs with promising binding modes to key subsites of the substrate-binding pocket of SARS-CoV-2 Mpro. The identified compounds belong to different pharmaceutical classes, including several protease inhibitors, antineoplastic agents and a natural flavonoid. The drug candidates discovered in this study present a potential extension of the recently reported SARS-CoV-2 Mpro inhibitors that have been identified using other virtual screening protocols and may be repurposed for COVID-19 treatment.
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Affiliation(s)
- Yasmine M Mandour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Biotechnology, The German University in Cairo, Cairo, Egypt.,School of Life and Medical Sciences, University of Hertfordshire hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt
| | - Darius P Zlotos
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Biotechnology, The German University in Cairo, Cairo, Egypt
| | - M Alaraby Salem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, October University of Modern Sciences and Arts (MSA), Giza, Egypt
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9
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Lisi L, Lacal PM, Barbaccia ML, Graziani G. Approaching coronavirus disease 2019: Mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2. Biochem Pharmacol 2020; 180:114169. [PMID: 32710969 PMCID: PMC7375972 DOI: 10.1016/j.bcp.2020.114169] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
On March 11, 2020, the World Health Organization (WHO) declared the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) a global pandemic. As of July 2020, SARS-CoV-2 has infected more than 14 million people and provoked more than 590,000 deaths, worldwide. From the beginning, a variety of pharmacological treatments has been empirically used to cope with the life-threatening complications associated with Corona Virus Disease 2019 (COVID-19). Thus far, only a couple of them and not consistently across reports have been shown to further decrease mortality, respect to what can be achieved with supportive care. In most cases, and due to the urgency imposed by the number and severity of the patients' clinical conditions, the choice of treatment has been limited to repurposed drugs, approved for other indications, or investigational agents used for other viral infections often rendered available on a compassionate-use basis. The rationale for drug selection was mainly, though not exclusively, based either i) on the activity against other coronaviruses or RNA viruses in order to potentially hamper viral entry and replication in the epithelial cells of the airways, and/or ii) on the ability to modulate the excessive inflammatory reaction deriving from dysregulated host immune responses against the SARS-CoV-2. In several months, an exceptionally large number of clinical trials have been designed to evaluate the safety and efficacy of anti-COVID-19 therapies in different clinical settings (treatment or pre- and post-exposure prophylaxis) and levels of disease severity, but only few of them have been completed so far. This review focuses on the molecular mechanisms of action that have provided the scientific rationale for the empirical use and evaluation in clinical trials of structurally different and often functionally unrelated drugs during the SARS-CoV-2 pandemic.
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Affiliation(s)
- Lucia Lisi
- Dipartimento di Bioetica e Sicurezza, Sezione di Farmacologia, Catholic University Medical School, 00168 Rome, Italy
| | | | | | - Grazia Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy.
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10
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Hosseini-Zare MS, Thilagavathi R, Selvam C. Targeting severe acute respiratory syndrome-coronavirus (SARS-CoV-1) with structurally diverse inhibitors: a comprehensive review. RSC Adv 2020; 10:28287-28299. [PMID: 35519094 PMCID: PMC9055768 DOI: 10.1039/d0ra04395h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses, which were discovered in 1968, can lead to some human viral disorders, like severe acute respiratory syndrome (SARS), Middle East respiratory syndrome-related (MERS), and, recently, coronavirus disease 2019 (COVID-19). The coronavirus that leads to COVID-19 is rapidly spreading all over the world and is the reason for the deaths of thousands of people. Recent research has revealed that there is about 80% sequence homology between the coronaviruses that cause SARS and COVID-19. Considering this fact, we decided to collect the maximum available information on targets, structures, and inhibitors reported so far for SARS-CoV-1 that could be useful for researchers who work on closely related COVID-19. There are vital proteases, like papain-like protease 2 (PL2pro) and 3C-like protease (3CLpro), or main protease (Mpro), that are involved in and are essential for the replication of SARS coronavirus and so are valuable targets for the treatment of patients affected by this type of virus. SARS-CoV-1 NTPase/helicase plays an important role in the release of several non-structural proteins (nsps), so it is another essential target relating to the viral life cycle. In this paper, we provide extensive information about diverse molecules with anti-SARS activity. In addition to traditional medicinal chemistry outcomes, HTS, virtual screening efforts, and structural insights for better understanding inhibitors and SARS-CoV-1 target complexes are also discussed. This study covers a wide range of anti-SARS agents, particularly SARS-CoV-1 inhibitors, and provides new insights into drug design for the deadly SARS-CoV-2 virus.
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Affiliation(s)
- Maryam S Hosseini-Zare
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University Houston TX-77004 USA +1-713-313-7552
| | - Ramasamy Thilagavathi
- Department of Biotechnology, Faculty of Engineering, Karpagam Academy of Higher Education Coimbatore India
| | - Chelliah Selvam
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University Houston TX-77004 USA +1-713-313-7552
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11
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Tou WI, Tam KW, Ng H. The Evolution of Computational Chemistry Along with Coronaviruses. Curr Top Med Chem 2020; 20:1339-1341. [DOI: 10.2174/1568026620999200518222552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Weng Ieong Tou
- Macau Academy of Medicine, Centro Hospitalar Conde de Sao Januario, Macau Health Bureau, Macau SAR, China
| | - Kuok Wa Tam
- Department of Internal Medicine, Centro Hospitalar Conde de Sao Januario, Macau Health Bureau, Macau SAR, China
| | - Hou Ng
- Department of Internal Medicine, Centro Hospitalar Conde de Sao Januario, Macau Health Bureau, Macau SAR, China
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12
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Ortega JT, Serrano ML, Pujol FH, Rangel HR. Unrevealing sequence and structural features of novel coronavirus using in silico approaches: The main protease as molecular target. EXCLI JOURNAL 2020; 19:400-409. [PMID: 32210741 PMCID: PMC7081067 DOI: 10.17179/excli2020-1189] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022]
Abstract
Direct-acting antivirals are effective tools to control viral infections. SARS-CoV-2 is a coronavirus associated with the epidemiological outbreak in late 2019. Previous reports showed that HIV-1 protease inhibitors could block SARS-CoV main protease. Based on that and using an in silico approach, we evaluated SARS-CoV-2 main protease as a target for HIV-1 protease inhibitors to reveal the structural features related to their antiviral effect. Our results showed that several HIV inhibitors such as lopinavir, ritonavir, and saquinavir produce strong interaction with the active site of SARS-CoV-2 main protease. Furthermore, broad library protease inhibitors obtained from PubChem and ZINC (www.zinc.docking.org) were evaluated. Our analysis revealed 20 compounds that could be clustered into three groups based on their chemical features. Then, these structures could serve as leading compounds to develop a series of derivatives optimizing their activity against SARS-CoV-2 and other coronaviruses. Altogether, the results presented in this work contribute to gain a deep understanding of the molecular pharmacology of SARS-CoV-2 treatment and validate the use of protease inhibitors against SARS-CoV-2.
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Affiliation(s)
- Joseph Thomas Ortega
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Maria Luisa Serrano
- Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas, Venezuela
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Hector Rafael Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
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13
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Characterization of an Immunodominant Epitope in the Endodomain of the Coronavirus Membrane Protein. Viruses 2016; 8:v8120327. [PMID: 27973413 PMCID: PMC5192388 DOI: 10.3390/v8120327] [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: 10/24/2016] [Revised: 11/26/2016] [Accepted: 12/06/2016] [Indexed: 11/17/2022] Open
Abstract
The coronavirus membrane (M) protein acts as a dominant immunogen and is a major player in virus assembly. In this study, we prepared two monoclonal antibodies (mAbs; 1C3 and 4C7) directed against the transmissible gastroenteritis virus (TGEV) M protein. The 1C3 and 4C7 mAbs both reacted with the native TGEV M protein in western blotting and immunofluorescence (IFA) assays. Two linear epitopes, 243YSTEART249 (1C3) and 243YSTEARTDNLSEQEKLLHMV262 (4C7), were identified in the endodomain of the TGEV M protein. The 1C3 mAb can be used for the detection of the TGEV M protein in different assays. An IFA method for the detection of TGEV M protein was optimized using mAb 1C3. Furthermore, the ability of the epitope identified in this study to stimulate antibody production was also evaluated. An immunodominant epitope in the TGEV membrane protein endodomain was identified. The results of this study have implications for further research on TGEV replication.
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Characterization of Two Monoclonal Antibodies That Recognize Linker Region and Carboxyl Terminal Domain of Coronavirus Nucleocapsid Protein. PLoS One 2016; 11:e0163920. [PMID: 27689694 PMCID: PMC5045181 DOI: 10.1371/journal.pone.0163920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/17/2016] [Indexed: 12/27/2022] Open
Abstract
The transmissible gastroenteritis virus (TGEV) nucleocapsid (N) protein plays important roles in the replication and translation of viral RNA. The present study provides the first description of two monoclonal antibodies (mAbs) (5E8 and 3D7) directed against the TGEV N protein linker region (LKR) and carboxyl terminal domain (CTD). The mAbs 5E8 and 3D7 reacted with native N protein in western blotting and immunofluorescence assay (IFA). Two linear epitopes, 189SVEQAVLAALKKLG202 and 246VTRFYGARSSSA257, located in the LKR and CTD of TGEV N protein, respectively, were identified after truncating the protein and applying a peptide scanning technique. Using mAb 5E8, we observed that the N protein was expressed in the cytoplasm during TGEV replication and that the protein could be immunoprecipitated from TGEV-infected PK-15 cells. The mAb 5E8 can be applied for different approaches to diagnosis of TGEV infection. In addition, the antibodies represent useful tools for investigating the antigenic properties of the N protein.
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Pillaiyar T, Manickam M, Namasivayam V, Hayashi Y, Jung SH. An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy. J Med Chem 2016; 59:6595-628. [PMID: 26878082 PMCID: PMC7075650 DOI: 10.1021/acs.jmedchem.5b01461] [Citation(s) in RCA: 509] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Indexed: 01/17/2023]
Abstract
Severe acute respiratory syndrome (SARS) is caused by a newly emerged coronavirus that infected more than 8000 individuals and resulted in more than 800 (10-15%) fatalities in 2003. The causative agent of SARS has been identified as a novel human coronavirus (SARS-CoV), and its viral protease, SARS-CoV 3CL(pro), has been shown to be essential for replication and has hence been recognized as a potent drug target for SARS infection. Currently, there is no effective treatment for this epidemic despite the intensive research that has been undertaken since 2003 (over 3500 publications). This perspective focuses on the status of various efficacious anti-SARS-CoV 3CL(pro) chemotherapies discovered during the last 12 years (2003-2015) from all sources, including laboratory synthetic methods, natural products, and virtual screening. We describe here mainly peptidomimetic and small molecule inhibitors of SARS-CoV 3CL(pro). Attempts have been made to provide a complete description of the structural features and binding modes of these inhibitors under many conditions.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Pharmaceutical
Institute, Pharmaceutical Chemistry I, University
of Bonn, An der Immenburg
4, D-53121 Bonn, Germany
| | - Manoj Manickam
- College
of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Vigneshwaran Namasivayam
- Pharmaceutical
Institute, Pharmaceutical Chemistry I, University
of Bonn, An der Immenburg
4, D-53121 Bonn, Germany
| | - Yoshio Hayashi
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Sang-Hun Jung
- College
of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
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Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K, Samudrala R. CANDO and the infinite drug discovery frontier. Drug Discov Today 2014; 19:1353-63. [PMID: 24980786 DOI: 10.1016/j.drudis.2014.06.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 12/21/2022]
Abstract
The Computational Analysis of Novel Drug Opportunities (CANDO) platform (http://protinfo.org/cando) uses similarity of compound-proteome interaction signatures to infer homology of compound/drug behavior. We constructed interaction signatures for 3733 human ingestible compounds covering 48,278 protein structures mapping to 2030 indications based on basic science methodologies to predict and analyze protein structure, function, and interactions developed by us and others. Our signature comparison and ranking approach yielded benchmarking accuracies of 12-25% for 1439 indications with at least two approved compounds. We prospectively validated 49/82 'high value' predictions from nine studies covering seven indications, with comparable or better activity to existing drugs, which serve as novel repurposed therapeutics. Our approach may be generalized to compounds beyond those approved by the FDA, and can also consider mutations in protein structures to enable personalization. Our platform provides a holistic multiscale modeling framework of complex atomic, molecular, and physiological systems with broader applications in medicine and engineering.
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Affiliation(s)
- Mark Minie
- University of Washington, Department of Bioengineering, Seattle, WA 98109, United States
| | - Gaurav Chopra
- University of Washington, Department of Microbiology, Seattle, WA 98109, United States; University of California, San Francisco, Diabetes Center, San Francisco, CA 94143, United States
| | - Geetika Sethi
- University of Washington, Department of Microbiology, Seattle, WA 98109, United States
| | - Jeremy Horst
- University of California, School of Medicine, San Francisco, CA 94143, United States
| | - George White
- University of Washington, Department of Microbiology, Seattle, WA 98109, United States
| | - Ambrish Roy
- Georgia Institute of Technology, Center for the Study of Systems Biology, Atlanta, GA 30318, United States
| | - Kaushik Hatti
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, 560012, India
| | - Ram Samudrala
- University of Washington, Department of Microbiology, Seattle, WA 98109, United States.
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Lin D, Qian W, Hilgenfeld R, Jiang H, Chen K, Liu H. Improved synthesis of rupintrivir. Sci China Chem 2012; 55:1101-1107. [PMID: 32215000 PMCID: PMC7088791 DOI: 10.1007/s11426-011-4478-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 10/12/2011] [Indexed: 02/02/2023]
Abstract
An improved synthesis of rupintrivir (AG7088) was accomplished using three amino acids (l-glutamic acid, d-4-fluorophenylalanine, and l-valine) as the building blocks. The key fragment ketomethylene dipeptide isostere was constructed with the valine derivative and phenylpropionic acid derivative, followed by coupling with a lactam derivative and an isoxazole acid chloride to provide AG7088 totally in eight steps.
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Affiliation(s)
- DaiZong Lin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201203 China
| | - WangKe Qian
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016 China
| | - Rolf Hilgenfeld
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201203 China
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Luebeck, 23538 Luebeck, Germany
| | - HuaLiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201203 China
| | - KaiXian Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201203 China
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Nukoolkarn V, Lee VS, Malaisree M, Aruksakulwong O, Hannongbua S. Molecular dynamic simulations analysis of ritonavir and lopinavir as SARS-CoV 3CL(pro) inhibitors. J Theor Biol 2008; 254:861-7. [PMID: 18706430 PMCID: PMC7094092 DOI: 10.1016/j.jtbi.2008.07.030] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 07/16/2008] [Accepted: 07/16/2008] [Indexed: 02/04/2023]
Abstract
Since the emergence of the severe acute respiratory syndrome (SARS) to date, neither an effective antiviral drug nor a vaccine against SARS is available. However, it was found that a mixture of two HIV-1 proteinase inhibitors, lopinavir and ritonavir, exhibited some signs of effectiveness against the SARS virus. To understand the fine details of the molecular interactions between these proteinase inhibitors and the SARS virus via complexation, molecular dynamics simulations were carried out for the SARS-CoV 3CL(pro) free enzyme (free SARS) and its complexes with lopinavir (SARS-LPV) and ritonavir (SARS-RTV). The results show that flap closing was clearly observed when the inhibitors bind to the active site of SARS-CoV 3CL(pro). The binding affinities of LPV and RTV to SARS-CoV 3CL(pro) do not show any significant difference. In addition, six hydrogen bonds were detected in the SARS-LPV system, while seven hydrogen bonds were found in SARS-RTV complex.
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Affiliation(s)
- Veena Nukoolkarn
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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Majumder HK. Searching the Tritryp genomes for drug targets. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 625:133-40. [PMID: 18365664 PMCID: PMC7123030 DOI: 10.1007/978-0-387-77570-8_11] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent publication of the complete genome sequences of Leishmania major, Trypanosoma brucei and Trypanosoma cruzi revealed that each genome contains 8300-12,000 protein-coding genes, of which approximately 6500 are common to all three genomes, and ushers in a new, post-genomic, era for trypanosomatid drug discovery. This vast amount of new information makes possible more comprehensive and accurate target identification using several new computational approaches, including identification of metabolic "choke-points", searching the parasite proteomes for orthologues of known drug targets, and identification of parasite proteins likely to interact with known drugs and drug-like small molecules. In this chapter, we describe several databases (such as GENEDB, BRENDA, KEGG, METACYC, the THERAPEUTIC TARGET DATABASE, and CHEMBANK) and algorithms (including PATHOLOGIC, PATHWAY HUNTER TOOL, AND AUToDOCK) which have been developed to facilitate the bioinformatic analyses underlying these approaches. While target identification is only the first step in the drug development pipeline, these new approaches give rise to renewed optimism for the discovery of new drugs to combat the devastating diseases caused by these parasites. Traditionally, drug discovery in the trypanosomatids (and other organisms) has proceeded from two different starting points: screening large numbers of existing compounds for activity against whole parasites or more focused screening of compounds for activity against defined molecular targets. Most existing anti-trypanosomatids drugs were developed using the former approach, although the latter has gained much attention in the last twenty years under the rubric of "rational drug design". Until recently, one of the major bottlenecks in anti-trypanosomatid drug development has been our ability to identify good targets, since only a very small percentage of the total number of trypanosomatid genes were known. That has now changed forever, with the recent (July, 2005) publication of the "Tritryp" (Trypanosoma brucei, Trypanosoma cruzi and Leishmania major) genome sequences. This vast amount of information now makes possible several new approaches for target identification and ushers in a post-genomic era for trypanosomatid drug discovery.
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Affiliation(s)
- Hemanta K. Majumder
- Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata, India
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20
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Di Trani L, Savarino A, Campitelli L, Norelli S, Puzelli S, D'Ostilio D, Vignolo E, Donatelli I, Cassone A. Different pH requirements are associated with divergent inhibitory effects of chloroquine on human and avian influenza A viruses. Virol J 2007; 4:39. [PMID: 17477867 PMCID: PMC1878474 DOI: 10.1186/1743-422x-4-39] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 05/03/2007] [Indexed: 11/10/2022] Open
Abstract
Chloroquine is a 4-aminoquinoline previously used in malaria therapy and now becoming an emerging investigational antiviral drug due to its broad spectrum of antiviral activities. To explore whether the low pH-dependency of influenza A viruses might affect the antiviral effects of chloroquine at clinically achievable concentrations, we tested the antiviral effects of this drug on selected human and avian viruses belonging to different subtypes and displaying different pH requirements. Results showed a correlation between the responses to chloroquine and NH4Cl, a lysosomotropic agent known to increase the pH of intracellular vesicles. Time-of-addition experiments showed that the inhibitory effect of chloroquine was maximal when the drug had been added at the time of infection and was lost after 2 h post-infection. This timing approximately corresponds to that of virus/cell fusion. Moreover, there was a clear correlation between the EC50 of chloroquine in vitro and the electrostatic potential of the HA subunit (HA2) mediating the virus/cell fusion process. Overall, the present study highlights the critical importance of a host cell factor such as intravesicular pH in determining the anti-influenza activity of chloroquine and other lysosomotropic agents.
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MESH Headings
- Ammonium Chloride/metabolism
- Ammonium Chloride/pharmacology
- Animals
- Antiviral Agents/pharmacology
- Cell Line
- Cell Survival
- Chloroquine/pharmacology
- Cytopathogenic Effect, Viral/drug effects
- Dogs
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/physiology
- Hydrogen-Ion Concentration
- Influenza A Virus, H1N1 Subtype/drug effects
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza A Virus, H3N2 Subtype/drug effects
- Influenza A Virus, H3N2 Subtype/physiology
- Influenza A Virus, H5N1 Subtype/drug effects
- Influenza A Virus, H5N1 Subtype/physiology
- Influenza A virus/drug effects
- Influenza A virus/physiology
- Lysosomes/metabolism
- Poultry
- RNA, Viral/biosynthesis
- Time Factors
- Virus Replication/drug effects
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Affiliation(s)
- Livia Di Trani
- Dept. of Food and Animal Health, Istituto Superiore di Sanità, Rome, Italy
| | - Andrea Savarino
- Dept. of Infectious, Parasitic, and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Laura Campitelli
- Dept. of Infectious, Parasitic, and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Sandro Norelli
- Dept. of Infectious, Parasitic, and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Simona Puzelli
- Dept. of Infectious, Parasitic, and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Daniela D'Ostilio
- Dept. of Infectious, Parasitic, and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Edoardo Vignolo
- Dept. of Food and Animal Health, Istituto Superiore di Sanità, Rome, Italy
| | - Isabella Donatelli
- Dept. of Infectious, Parasitic, and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Cassone
- Dept. of Infectious, Parasitic, and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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21
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Wang HM, Liang PH. Pharmacophores and biological activities of severe acute respiratory syndrome viral protease inhibitors. Expert Opin Ther Pat 2007. [DOI: 10.1517/13543776.17.5.533] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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22
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Lu IL, Mahindroo N, Liang PH, Peng YH, Kuo CJ, Tsai KC, Hsieh HP, Chao YS, Wu SY. Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease. J Med Chem 2006; 49:5154-61. [PMID: 16913704 DOI: 10.1021/jm060207o] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) main protease (M(pro)), a protein required for the maturation of SARS-CoV, is vital for its life cycle, making it an attractive target for structure-based drug design of anti-SARS drugs. The structure-based virtual screening of a chemical database containing 58,855 compounds followed by the testing of potential compounds for SARS-CoV M(pro) inhibition leads to two hit compounds. The core structures of these two hits, defined by the docking study, are used for further analogue search. Twenty-one analogues derived from these two hits exhibited IC50 values below 50 microM, with the most potent one showing 0.3 microM. Furthermore, the complex structures of two potent inhibitors with SARS-CoV M(pro) were solved by X-ray crystallography. They bind to the protein in a distinct manner compared to all published SARS-CoV M(pro) complex structures. They inhibit SARS-CoV M(pro) activity via intensive H-bond network and hydrophobic interactions, without the formation of a covalent bond. Interestingly, the most potent inhibitor induces protein conformational changes, and the inhibition mechanisms, particularly the disruption of catalytic dyad (His41 and Cys145), are elaborated.
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Affiliation(s)
- I-Lin Lu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China
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23
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24
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Tsai KC, Chen SY, Liang PH, Lu IL, Mahindroo N, Hsieh HP, Chao YS, Liu L, Liu D, Lien W, Lin TH, Wu SY. Discovery of a Novel Family of SARS-CoV Protease Inhibitors by Virtual Screening and 3D-QSAR Studies. J Med Chem 2006; 49:3485-95. [PMID: 16759091 DOI: 10.1021/jm050852f] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The severe acute respiratory syndrome-associated coronavirus (SARS-CoV) 3C-like protease (3CL(pro) or M(pro)) is an attractive target for the development of anti-SARS drugs because of its crucial role in the viral life cycle. In this study, a compound database was screened by the structure-based virtual screening approach to identify initial hits as inhibitors of SARS-CoV 3CL(pro). Out of the 59,363 compounds docked, 93 were selected for the inhibition assay, and 21 showed inhibition against SARS-CoV 3CL(pro) (IC(50) <or= 30 microM), with three of them having common substructures. Furthermore, a search for analogues with common substructure in the Maybridge, ChemBridge, and SPECS_SC databases led to the identification of another 25 compounds that exhibited inhibition against SARS-CoV 3CL(pro) (IC(50) = 3-1,000 microM). These compounds, 28 in total, were subjected to 3D-QSAR studies to elucidate the pharmacophore of SARS-CoV 3CL(pro).
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Affiliation(s)
- Keng-Chang Tsai
- Department of Life Science, Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 300, Taiwan, Republic of China
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25
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Dooley AJ, Shindo N, Taggart B, Park JG, Pang YP. From genome to drug lead: identification of a small-molecule inhibitor of the SARS virus. Bioorg Med Chem Lett 2006; 16:830-3. [PMID: 16325400 PMCID: PMC7119130 DOI: 10.1016/j.bmcl.2005.11.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Revised: 11/04/2005] [Accepted: 11/04/2005] [Indexed: 11/02/2022]
Abstract
Virtual screening, a fast, computational approach to identify drug leads [Perola, E.; Xu, K.; Kollmeyer, T. M.; Kaufmann, S. H.; Prendergast, F. G. J. Med. Chem.2000, 43, 401; Miller, M. A. Nat. Rev. Drug Disc.2002, 1 220], is limited by a known challenge in crystallographically determining flexible regions of proteins. This approach has not been able to identify active inhibitors of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) using solely the crystal structures of a SARS-CoV cysteine proteinase with a flexible loop in the active site [Yang, H. T.; Yang, M. J.; Ding, Y.; Liu, Y. W.; Lou, Z. Y. Proc. Natl. Acad. Sci. U.S.A.2003, 100, 13190; Jenwitheesuk, E.; Samudrala, R. Bioorg. Med. Chem. Lett.2003, 13, 3989; Rajnarayanan, R. V.; Dakshanamurthy, S.; Pattabiraman, N. Biochem. Biophys. Res. Commun.2004, 321, 370; Du, Q.; Wang, S.; Wei, D.; Sirois, S.; Chou, K. Anal. Biochem.2005, 337, 262; Du, Q.; Wang, S.; Zhu, Y.; Wei, D.; Guo, H. Peptides2004, 25, 1857; Lee, V.; Wittayanarakul, K.; Remsungenen, T.; Parasuk, V.; Sompornpisut, P. Science (Asia)2003, 29, 181; Toney, J.; Navas-Martin, S.; Weiss, S.; Koeller, A. J. Med. Chem.2004, 47, 1079; Zhang, X. W.; Yap, Y. L. Bioorg. Med. Chem.2004, 12, 2517]. This article demonstrates a genome-to-drug-lead approach that uses terascale computing to model flexible regions of proteins, thus permitting the utilization of genetic information to identify drug leads expeditiously. A small-molecule inhibitor of SARS-CoV, exhibiting an effective concentration (EC50) of 23 microM in cell-based assays, was identified through virtual screening against a computer-predicted model of the cysteine proteinase. Screening against two crystal structures of the same proteinase failed to identify the 23-microM inhibitor. This study suggests that terascale computing can complement crystallography, broaden the scope of virtual screening, and accelerate the development of therapeutics to treat emerging infectious diseases such as SARS and Bird Flu.
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Affiliation(s)
- Andrea J Dooley
- Computer-Aided Molecular Design Laboratory, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
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26
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Savarino A. Expanding the frontiers of existing antiviral drugs: possible effects of HIV-1 protease inhibitors against SARS and avian influenza. J Clin Virol 2006; 34:170-8. [PMID: 15893956 PMCID: PMC7108403 DOI: 10.1016/j.jcv.2005.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 02/27/2005] [Accepted: 03/03/2005] [Indexed: 01/08/2023]
Abstract
When unexpected diseases such as the severe acute respiratory syndrome (SARS) and avian influenza become a serious threat to public health, an immediate response is imperative. This should take into consideration existing licensed antiviral drugs against other viral diseases already known to be safe for use in humans. In this report, evidence is presented that HIV-1 protease inhibitors (PIs) currently used in anti-HIV-1 therapies might exert some effects on SARS and perhaps, on avian influenza. Evidence for the potential benefits of PIs against the SARS coronavirus (SARS-CoV) is provided by empirical clinical studies, in vivo viral inhibition assays and computational simulations of the docking of these compounds to the active site of the main SARS-CoV protease. As suggested by in silico docking of these molecules to a theoretical model of a subunit of type A influenza virus RNA-dependent RNA polymerase, there also exists a remote possibility that these PIs may have an effect on avian influenza viruses. Although this evidence is still far from being definitive, the results so far obtained suggest that PIs should be seriously taken into consideration for further testing as potential therapeutic agents for SARS and avian influenza.
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Affiliation(s)
- Andrea Savarino
- Laboratory of Viral Immunology, Department of Infectious Diseases, Università Cattolica del Sacro Cuore, Largo Agostino Gemelli 8, I-00168 Rome, Italy.
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27
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Kaeppler U, Stiefl N, Schiller M, Vicik R, Breuning A, Schmitz W, Rupprecht D, Schmuck C, Baumann K, Ziebuhr J, Schirmeister T. A new lead for nonpeptidic active-site-directed inhibitors of the severe acute respiratory syndrome coronavirus main protease discovered by a combination of screening and docking methods. J Med Chem 2005; 48:6832-42. [PMID: 16250642 DOI: 10.1021/jm0501782] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The coronavirus main protease, M(pro), is considered to be a major target for drugs suitable for combating coronavirus infections including severe acute respiratory syndrome (SARS). An HPLC-based screening of electrophilic compounds that was performed to identify potential M(pro) inhibitors revealed etacrynic acid tert-butylamide (6a) as an effective nonpeptidic inhibitor. Docking studies suggested a binding mode in which the phenyl ring acts as a spacer bridging the inhibitor's activated double bond and its hydrophobic tert-butyl moiety. The latter is supposed to fit into the S4 pocket of the target protease. Furthermore, these studies revealed etacrynic acid amide (6b) as a promising lead for nonpeptidic active-site-directed M(pro) inhibitors. In a fluorimetric enzyme assay using a novel fluorescence resonance energy transfer (FRET) pair labeled substrate, compound 6b showed a K(i) value of 35.3 muM. Since the novel lead compound does not target the S1', S1, and S2 subsites of the enzyme's substrate-binding pockets, there is room for improvement that underlines the lead character of compound 6b.
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Affiliation(s)
- Ulrich Kaeppler
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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28
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Martina E, Stiefl N, Degel B, Schulz F, Breuning A, Schiller M, Vicik R, Baumann K, Ziebuhr J, Schirmeister T. Screening of electrophilic compounds yields an aziridinyl peptide as new active-site directed SARS-CoV main protease inhibitor. Bioorg Med Chem Lett 2005; 15:5365-9. [PMID: 16216498 PMCID: PMC7127417 DOI: 10.1016/j.bmcl.2005.09.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 08/30/2005] [Accepted: 09/06/2005] [Indexed: 11/26/2022]
Abstract
The coronavirus main protease, M(pro), is considered a major target for drugs suitable to combat coronavirus infections including the severe acute respiratory syndrome (SARS). In this study, comprehensive HPLC- and FRET-substrate-based screenings of various electrophilic compounds were performed to identify potential M(pro) inhibitors. The data revealed that the coronaviral main protease is inhibited by aziridine- and oxirane-2-carboxylates. Among the trans-configured aziridine-2,3-dicarboxylates the Gly-Gly-containing peptide 2c was found to be the most potent inhibitor.
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Affiliation(s)
- Erika Martina
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Nikolaus Stiefl
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Björn Degel
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Franziska Schulz
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Alexander Breuning
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Markus Schiller
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Radim Vicik
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - Knut Baumann
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
| | - John Ziebuhr
- Institute of Virology and Immunology, Versbacher Street 7, D-97078 Würzburg, University of Würzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmacy and Food Chemistry, Am Hubland, D-97074 Würzburg, University of Würzburg, Germany
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29
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Wei P, Fan K, Chen H, Ma L, Huang C, Tan L, Xi D, Li C, Liu Y, Cao A, Lai L. The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase. Biochem Biophys Res Commun 2005; 339:865-72. [PMID: 16329994 PMCID: PMC7092940 DOI: 10.1016/j.bbrc.2005.11.102] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 11/16/2005] [Indexed: 11/21/2022]
Abstract
The 3C-like proteinase of severe acute respiratory syndrome (SARS) coronavirus has been proposed to be a key target for structural-based drug design against SARS. Accurate determination of the dimer dissociation constant and the role of the N-finger (residues 1–7) will provide more insights into the enzyme catalytic mechanism of SARS 3CL proteinase. The dimer dissociation constant of the wild-type protein was determined to be 14.0 μM by analytical ultracentrifugation method. The N-finger fragment of the enzyme plays an important role in enzyme dimerization as shown in the crystal structure. Key residues in the N-finger have been studied by site-directed mutagenesis, enzyme assay, and analytical ultracentrifugation. A single mutation of M6A was found to be critical to maintain the dimer structure of the enzyme. The N-terminal octapeptide N8 and its mutants were also synthesized and tested for their potency as dimerization inhibitors. Peptide cleavage assay confirms that peptide N8 is a dimerization inhibitor with a Ki of 2.20 mM. The comparison of the inhibitory activities of N8 and its mutants indicates that the hydrophobic interaction of Met-6 and the electrostatic interaction of Arg-4 contribute most for inhibitor binding. This study describes the first example of inhibitors targeting the dimeric interface of SARS 3CL proteinase, providing a novel strategy for drug design against SARS and other coronaviruses.
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Affiliation(s)
- Ping Wei
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
| | - Keqiang Fan
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
| | - Hao Chen
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
- Center for Theoretical Biology, Peking University, Beijing 100871, China
| | - Liang Ma
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
| | - Changkang Huang
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
| | - Lei Tan
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
| | - Dong Xi
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
| | - Chunmei Li
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
| | - Ying Liu
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
| | - Aoneng Cao
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
| | - Luhua Lai
- State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
- Center for Theoretical Biology, Peking University, Beijing 100871, China
- Corresponding author. Fax: +86 10 62751725.
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30
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Steindl T, Laggner C, Langer T. Human rhinovirus 3C protease: generation of pharmacophore models for peptidic and nonpeptidic inhibitors and their application in virtual screening. J Chem Inf Model 2005; 45:716-24. [PMID: 15921461 DOI: 10.1021/ci049638a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three-dimensional pharmacophore models for peptidic and small organic nonpeptidic inhibitors of the human rhinovirus 3C protease were generated in a structure-based as well as in a ligand-based approach, using the software package Catalyst. The inhibitors possess an electrophilic moiety, often a Michael acceptor function, which covalently binds to a cysteine in the active site of the enzyme. Since this process presents the key step for virus inactivation, the creation of a new function in Catalyst was required in order to include this decisive functionality into the pharmacophore models. In the present study we focus on this feature definition process because it presents an innovative strategy to expand the pharmacophore description ability of the Catalyst software to also include covalent bonds between ligand and binding site. The resulting hypotheses were then used for virtual screening of 3D databases in order to verify their quality and to search for structurally diverse, possible new lead substances.
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Affiliation(s)
- Theodora Steindl
- Institute of Pharmacy, Computer Aided Molecular Design Group, University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
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31
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Chen LR, Wang YC, Lin YW, Chou SY, Chen SF, Liu LT, Wu YT, Kuo CJ, Chen TSS, Juang SH. Synthesis and evaluation of isatin derivatives as effective SARS coronavirus 3CL protease inhibitors. Bioorg Med Chem Lett 2005; 15:3058-62. [PMID: 15896959 PMCID: PMC7119080 DOI: 10.1016/j.bmcl.2005.04.027] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 04/08/2005] [Accepted: 04/14/2005] [Indexed: 01/13/2023]
Abstract
N-Substituted isatin derivatives were prepared from the reaction of isatin and various bromides via two steps. Bioactivity assay results (in vitro tests) demonstrated that some of these compounds are potent and selective inhibitors against SARS coronavirus 3CL protease with IC50 values ranging from 0.95 to 17.50 microM. Additionally, isatin 4o exhibited more potent inhibition for SARS coronavirus protease than for other proteases including papain, chymotrypsin, and trypsin.
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Affiliation(s)
- Li-Rung Chen
- Development Center for Biotechnology, 102, Lane 169, Kang Ning St., Xi Zhi 221, Taipei, Taiwan, ROC
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32
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Chen L, Gui C, Luo X, Yang Q, Günther S, Scandella E, Drosten C, Bai D, He X, Ludewig B, Chen J, Luo H, Yang Y, Yang Y, Zou J, Thiel V, Chen K, Shen J, Shen X, Jiang H. Cinanserin is an inhibitor of the 3C-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro. J Virol 2005; 79:7095-103. [PMID: 15890949 PMCID: PMC1112131 DOI: 10.1128/jvi.79.11.7095-7103.2005] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 3C-like proteinase (3CLpro) of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is one of the most promising targets for anti-SARS-CoV drugs due to its crucial role in the viral life cycle. In this study, a database containing structural information of more than 8,000 existing drugs was virtually screened by a docking approach to identify potential binding molecules of SARS-CoV 3CLpro. As a target for screening, both a homology model and the crystallographic structure of the binding pocket of the enzyme were used. Cinanserin (SQ 10,643), a well-characterized serotonin antagonist that has undergone preliminary clinical testing in humans in the 1960s, showed a high score in the screening and was chosen for further experimental evaluation. Binding of both cinanserin and its hydrochloride to bacterially expressed 3CLpro of SARS-CoV and the related human coronavirus 229E (HCoV-229E) was demonstrated by surface plasmon resonance technology. The catalytic activity of both enzymes was inhibited with 50% inhibitory concentration (IC50) values of 5 microM, as tested with a fluorogenic substrate. The antiviral activity of cinanserin was further evaluated in tissue culture assays, namely, a replicon system based on HCoV-229E and quantitative test assays with infectious SARS-CoV and HCoV-229E. All assays revealed a strong inhibition of coronavirus replication at nontoxic drug concentrations. The level of virus RNA and infectious particles was reduced by up to 4 log units, with IC50 values ranging from 19 to 34 microM. These findings demonstrate that the old drug cinanserin is an inhibitor of SARS-CoV replication, acting most likely via inhibition of the 3CL proteinase.
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Affiliation(s)
- Lili Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
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33
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Abstract
Severe acute respiratory syndrome (SARS) is a disease that has newly emerged in the 21st century, and is both severe and highly contagious. SARS first surfaced in late 2002 and spread within a few months from its origin in Guandong province, China, to more than 30 countries (World Health Organization, 2003). In this review, several antiviral substances shown to be active in vitro will be introduced and summarized in the order of the virus' replication steps; that is, binding to cellular receptor, fusion and entry to the cells, viral RNA replication and transcription, protein processing and so on. The possible clinical use of several synthetic peptides, including those that mimic the S-binding domain, the HR2 fusion protein and SARS proteinase substrates, will be discussed. Monoclonal antibodies (Mabs) and established drugs, such as interferons and HIV proteinase inhibitors, are also discussed in relation to anti-SARS clinical use.
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Affiliation(s)
- Shiro Shigeta
- Department of Microbiology, Fukushima Medical University, School of Medicine, Fukushima, Japan.
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34
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Liu B, Zhou J. SARS-CoV protease inhibitors design using virtual screening method from natural products libraries. J Comput Chem 2005; 26:484-90. [PMID: 15693056 PMCID: PMC7166849 DOI: 10.1002/jcc.20186] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 11/08/2004] [Indexed: 11/05/2022]
Abstract
Two natural products databases, the marine natural products database (MNPD) and the traditional Chinese medicines database (TCMD), were used to find novel structures of potent SARS-CoV protease inhibitors through virtual screening. Before the procedure, the databases were filtered by Lipinski's ROF and Xu's extension rules. The results were analyzed by statistic methods to eliminate the bias in target-based database screening toward higher molecular weight compounds for enhancing the hit rate. Eighteen lead compounds were recommended by the screening procedure. They were useful for experimental scientists in prioritizing drug candidates and studying the interaction mechanism. The binding mechanism was also analyzed between the best screening compound and the SARS protein.
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Affiliation(s)
- Bing Liu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100080, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Jiaju Zhou
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100080, People's Republic of China
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35
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Jenwitheesuk E, Samudrala R. Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics. AIDS 2005; 19:529-31. [PMID: 15764860 DOI: 10.1097/01.aids.0000162343.96674.4c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The clearance of cytomegalovirus viraemia in HIV-1-infected patients may partly result from the inhibition of cytomegalovirus protease by HIV-1 protease inhibitors contained in highly active antiretroviral therapy. We used a computational method to calculate the binding affinity of six HIV-1 protease inhibitors to cytomegalovirus protease based on its X-ray crystallography structure. The calculations showed that amprenavir and indinavir occupy the substrate-binding site of the cytomegalovirus protease with high affinity, and may be implicated in alleviating cytomegalovirus infection.
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Affiliation(s)
- Ekachai Jenwitheesuk
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
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36
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Blanchard JE, Elowe NH, Huitema C, Fortin PD, Cechetto JD, Eltis LD, Brown ED. High-throughput screening identifies inhibitors of the SARS coronavirus main proteinase. ACTA ACUST UNITED AC 2005; 11:1445-53. [PMID: 15489171 PMCID: PMC7134594 DOI: 10.1016/j.chembiol.2004.08.011] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2004] [Revised: 07/20/2004] [Accepted: 08/10/2004] [Indexed: 11/24/2022]
Abstract
The causative agent of severe acute respiratory syndrome (SARS) has been identified as a novel coronavirus, SARS-CoV. The main proteinase of SARS-CoV, 3CLpro, is an attractive target for therapeutics against SARS owing to its fundamental role in viral replication. We sought to identify novel inhibitors of 3CLpro to advance the development of appropriate therapies in the treatment of SARS. 3CLpro was cloned, expressed, and purified from the Tor2 isolate. A quenched fluorescence resonance energy transfer assay was developed for 3CLpro to screen the proteinase against 50,000 drug-like small molecules on a fully automated system. The primary screen identified 572 hits; through a series of virtual and experimental filters, this number was reduced to five novel small molecules that show potent inhibitory activity (IC50 = 0.5-7 microM) toward SARS-CoV 3CLpro.
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Affiliation(s)
- Jan E Blanchard
- McMaster High Throughput Screening Laboratory, Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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37
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Liu Z, Huang C, Fan K, Wei P, Chen H, Liu S, Pei J, Shi L, Li B, Yang K, Liu Y, Lai L. Virtual screening of novel noncovalent inhibitors for SARS-CoV 3C-like proteinase. J Chem Inf Model 2005; 45:10-17. [PMID: 15667124 DOI: 10.1021/ci049809b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The SARS coronavirus 3C-like proteinase is considered as a potential drug design target for the treatment of severe acute respiratory syndrome (SARS). Owing to the lack of available drugs for the treatment of SARS, the discovery of inhibitors for SARS coronavirus 3C-like proteinase that can potentially be optimized as drugs appears to be highly desirable. We have built a "flexible" three-dimensional model for SARS 3C-like proteinase by homology modeling and multicanonical molecular dynamics method and used the model for virtual screening of chemical databases. After Dock procedures, strategies including pharmocophore model, consensus scoring, and "drug-like" filters were applied in order to accelerate the process and improve the success rate of virtual docking screening hit lists. Forty compounds were purchased and tested by HPLC and colorimetric assay against SARS 3C-like proteinase. Three of them including calmidazolium, a well-known antagonist of calmodulin, were found to inhibit the enzyme with an apparent K(i) from 61 to 178 microM. These active compounds and their binding modes provide useful information for understanding the binding sites and for further selective drug design against SARS and other coronavirus.
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Affiliation(s)
- Zhenming Liu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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38
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Groneberg DA, Hilgenfeld R, Zabel P. Molecular mechanisms of severe acute respiratory syndrome (SARS). Respir Res 2005; 6:8. [PMID: 15661082 PMCID: PMC548145 DOI: 10.1186/1465-9921-6-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Accepted: 01/20/2005] [Indexed: 02/08/2023] Open
Abstract
Severe acute respiratory syndrome (SARS) is a new infectious disease caused by a novel coronavirus that leads to deleterious pulmonary pathological features. Due to its high morbidity and mortality and widespread occurrence, SARS has evolved as an important respiratory disease which may be encountered everywhere in the world. The virus was identified as the causative agent of SARS due to the efforts of a WHO-led laboratory network. The potential mutability of the SARS-CoV genome may lead to new SARS outbreaks and several regions of the viral genomes open reading frames have been identified which may contribute to the severe virulence of the virus. With regard to the pathogenesis of SARS, several mechanisms involving both direct effects on target cells and indirect effects via the immune system may exist. Vaccination would offer the most attractive approach to prevent new epidemics of SARS, but the development of vaccines is difficult due to missing data on the role of immune system-virus interactions and the potential mutability of the virus. Even in a situation of no new infections, SARS remains a major health hazard, as new epidemics may arise. Therefore, further experimental and clinical research is required to control the disease.
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Affiliation(s)
- David A Groneberg
- Pneumology and Immunology, Otto-Heubner-Centre, Charité School of Medicine, Free University and Humboldt-University, D-13353 Berlin, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, University of Lübeck, D-23538 Lübeck, Germany
| | - Peter Zabel
- Division of Clinical Infectiology and Immunology, Department of Medicine, Research Center Borstel, D-23845 Borstel, Germany
- Division of Thoracic Medicine, Department of Medicine, University of Lübeck, D-23538 Lübeck, Germany
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39
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Kao RY, To APC, Ng LWY, Tsui WHW, Lee TSW, Tsoi HW, Yuen KY. Characterization of SARS-CoV main protease and identification of biologically active small molecule inhibitors using a continuous fluorescence-based assay. FEBS Lett 2004; 576:325-30. [PMID: 15498556 PMCID: PMC7134596 DOI: 10.1016/j.febslet.2004.09.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Revised: 09/09/2004] [Accepted: 09/13/2004] [Indexed: 11/25/2022]
Abstract
Severe acute respiratory syndrome associated coronavirus main protease (SARS‐CoV Mpro) has been proposed as a prime target for anti‐SARS drug development. We have cloned and overexpressed the SARS‐CoV Mpro in Escherichia coli, and purified the recombinant Mpro to homogeneity. The kinetic parameters of the recombinant SARS‐CoV Mpro were characterized by high performance liquid chromatography‐based assay and continuous fluorescence‐based assay. Two novel small molecule inhibitors of the SARS‐CoV Mpro were identified by high‐throughput screening using an internally quenched fluorogenic substrate. The identified inhibitors have Ki values at low μM range with comparable anti‐SARS‐CoV activity in cell‐based assays.
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Affiliation(s)
- Richard Y Kao
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong, China.
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40
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Zhang XW, Yap YL. Old drugs as lead compounds for a new disease? Binding analysis of SARS coronavirus main proteinase with HIV, psychotic and parasite drugs. Bioorg Med Chem 2004; 12:2517-21. [PMID: 15110833 PMCID: PMC7126105 DOI: 10.1016/j.bmc.2004.03.035] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Revised: 03/16/2004] [Accepted: 03/16/2004] [Indexed: 11/15/2022]
Abstract
The SARS-associated coronavirus (SARS-CoV) main proteinase is a key enzyme in viral polyprotein processing. To allow structure-based design of drugs directed at SARS-CoV main proteinase, we predicted its binding pockets and affinities with existing HIV, psychotic and parasite drugs (lopinavir, ritonavir, niclosamide and promazine), which show signs of inhibiting the replication of SARS-CoV. Our results suggest that these drugs and another two HIV inhibitors (PNU and UC2) could be used as templates for designing SARS-CoV proteinase inhibitors.
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Affiliation(s)
- Xue Wu Zhang
- HKU-Pasteur Research Center, 8 Sassoon Road, Pokfulam, Hong Kong.
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41
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Rajnarayanan RV, Dakshanamurthy S, Pattabiraman N. "Teaching old drugs to kill new bugs": structure-based discovery of anti-SARS drugs. Biochem Biophys Res Commun 2004; 321:370-8. [PMID: 15358186 PMCID: PMC7092804 DOI: 10.1016/j.bbrc.2004.06.155] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2004] [Indexed: 11/22/2022]
Abstract
Severe acute respiratory syndrome (SARS) main protease or 3C-like protease (3CLpro) is essential for the propagation of the coronaviral life cycle and is regarded as one of the main targets for structure-based anti-SARS drug design. It is an attractive approach to find new uses for old drugs as they have already been through extensive clinical testing and could easily be accelerated for clinical approval. Briefly, we performed virtual screening of a database of small molecules against SARS 3CLpro, analyzed inhibitor–protease complexes, and identified several covalent and non-covalent inhibitors. Several old drugs that bind to SARS 3CLpro active site were selected and in silico derivatized to generate covalent irreversible inhibitors with enhanced affinity. Furthermore, we show that pharmacophores derived from clusters of compounds resulting out of virtual screening could be useful probes for future structure–activity relationship studies (SARs) and fine-tune the lead molecules identified.
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Affiliation(s)
- Rajendram V Rajnarayanan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
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42
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Hsu JTA, Kuo CJ, Hsieh HP, Wang YC, Huang KK, Lin CPC, Huang PF, Chen X, Liang PH. Evaluation of metal-conjugated compounds as inhibitors of 3CL protease of SARS-CoV. FEBS Lett 2004; 574:116-20. [PMID: 15358550 PMCID: PMC7134601 DOI: 10.1016/j.febslet.2004.08.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2004] [Revised: 08/06/2004] [Accepted: 08/10/2004] [Indexed: 11/21/2022]
Abstract
3C-like (3CL) protease is essential for the life cycle of severe acute respiratory syndrome-coronavirus (SARS-CoV) and therefore represents a key anti-viral target. A compound library consisting of 960 commercially available drugs and biologically active substances was screened for inhibition of SARS-CoV 3CL protease. Potent inhibition was achieved using the mercury-containing compounds thimerosal and phenylmercuric acetate, as well as hexachlorophene. As well, 1-10 microM of each compound inhibited viral replication in Vero E6 cell culture. Detailed mechanism studies using a fluorescence-based protease assay demonstrated that the three compounds acted as competitive inhibitors (Ki=0.7, 2.4, and 13.7 microM for phenylmercuric acetate, thimerosal, and hexachlorophene, respectively). A panel of metal ions including Zn2+ and its conjugates were then evaluated for their anti-3CL protease activities. Inhibition was more pronounced using a zinc-conjugated compound (1-hydroxypyridine-2-thione zinc; Ki=0.17 microM) than using the ion alone (Ki=1.1 microM).
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Affiliation(s)
- John T.-A. Hsu
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, National Defense Medical Center, Taipei 115, Taiwan, ROC
| | - Chih-Jung Kuo
- Institute of Biological Chemistry, Academia Sinica, National Defense Medical Center, Taipei 115, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, National Defense Medical Center, Taipei 115, Taiwan, ROC
| | - Yeau-Ching Wang
- Institute of Preventive Medicine, National Defense Medical Center, Taipei 115, Taiwan, ROC
| | - Kuo-Kuei Huang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, National Defense Medical Center, Taipei 115, Taiwan, ROC
| | - Coney P.-C. Lin
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, National Defense Medical Center, Taipei 115, Taiwan, ROC
| | - Ping-Fang Huang
- Institute of Biological Chemistry, Academia Sinica, National Defense Medical Center, Taipei 115, Taiwan, ROC
| | - Xin Chen
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, National Defense Medical Center, Taipei 115, Taiwan, ROC
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, National Defense Medical Center, Taipei 115, Taiwan, ROC
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43
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Zhang XW, Yap YL. The 3D structure analysis of SARS-CoV S1 protein reveals a link to influenza virus neuraminidase and implications for drug and antibody discovery. THEOCHEM 2004; 681:137-141. [PMID: 32287547 PMCID: PMC7126208 DOI: 10.1016/j.theochem.2004.04.065] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Accepted: 04/19/2004] [Indexed: 10/28/2022]
Abstract
The spike protein of SARS-associated coronavirus (SARS-CoV) is an important target for anti-SARS drug discovery. Its S1 domain is responsible for receptor binding and SARS-CoV entry into cells. In this study, we constructed a rational 3D model for S1 domain of SARS-CoV spike protein by fold recognition and molecular modeling techniques. We found that there is a structure similarity between S1 protein and influenza virus neuraminidase. Our analyses suggest that the existing anti-influenza virus inhibitors and anti-neuraminidase antibody could be used as a starting point for designing anti-SARS drugs, vaccines and antibodies. Interestingly, our prediction for antibody is consistent with a recently experimental discovery of anti-SARS antibody.
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Affiliation(s)
- Xue Wu Zhang
- Hong Kong University-Pasteur Research Centre, Dexter H.C. Man Building, 8 Sassoon Road, Pokfulam, HongKong, China
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