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Yang Y, Zhu Z, Wang X, Zhang X, Mu K, Shi Y, Peng C, Xu Z, Zhu W. Ligand-based approach for predicting drug targets and for virtual screening against COVID-19. Brief Bioinform 2021; 22:1053-1064. [PMID: 33461215 PMCID: PMC7929377 DOI: 10.1093/bib/bbaa422] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/18/2020] [Accepted: 12/19/2020] [Indexed: 01/18/2023] Open
Abstract
Discovering efficient drugs and identifying target proteins are still an unmet but urgent need for curing coronavirus disease 2019 (COVID-19). Protein structure-based docking is a widely applied approach for discovering active compounds against drug targets and for predicting potential targets of active compounds. However, this approach has its inherent deficiency caused by e.g. various different conformations with largely varied binding pockets adopted by proteins, or the lack of true target proteins in the database. This deficiency may result in false negative results. As a complementary approach to the protein structure-based platform for COVID-19, termed as D3Docking in our previous work, we developed in this study a ligand-based method, named D3Similarity, which is based on the molecular similarity evaluation between the submitted molecule(s) and those in an active compound database. The database is constituted by all the reported bioactive molecules against the coronaviruses, viz., severe acute respiratory syndrome coronavirus (SARS), Middle East respiratory syndrome coronavirus (MERS), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human betacoronavirus 2c EMC/2012 (HCoV-EMC), human CoV 229E (HCoV-229E) and feline infectious peritonitis virus (FIPV), some of which have target or mechanism information but some do not. Based on the two-dimensional (2D) and three-dimensional (3D) similarity evaluation of molecular structures, virtual screening and target prediction could be performed according to similarity ranking results. With two examples, we demonstrated the reliability and efficiency of D3Similarity by using 2D × 3D value as score for drug discovery and target prediction against COVID-19. The database, which will be updated regularly, is available free of charge at https://www.d3pharma.com/D3Targets-2019-nCoV/D3Similarity/index.php.
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Affiliation(s)
- Yanqing Yang
- Shanghai Institute of Materia Medica.,CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Zhengdan Zhu
- Shanghai Institute of Materia Medica in 2020. His research interest is halogen bond interaction. His affiliation is with CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Xiaoyu Wang
- Shanghai University of Electric Power. Her research interest is database construction. Her affiliation is with College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai, 200090, China
| | - Xinben Zhang
- East China University of Science and Technology. His research interest is software development. His affiliation is with CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Kaijie Mu
- Nano Science and Technology Institute, University of Science and Technology of China. Her research interest is QM/MM calculations and molecular modeling. Her affiliation is with Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, Jiangsu, 215123, China
| | - Yulong Shi
- Shanghai Institute of Materia Medica. His research interest is molecular docking method development. His affiliation is with CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Cheng Peng
- Shanghai Institute of Materia Medica. His research interest is molecular dynamics. His affiliation is with CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Zhijian Xu
- Shanghai Institute of Materia Medica in 2012
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The role of chemical biology in the fight against SARS-CoV-2. Biochem J 2021; 478:157-177. [PMID: 33439990 DOI: 10.1042/bcj20200514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 01/18/2023]
Abstract
Since late 2019, biomedical labs all over the world have been struggling to cope with the 'new normal' and to find ways in which they can contribute to the fight against COVID-19. In this unique situation where a biomedical issue dominates people's lives and the news cycle, chemical biology has a great deal to contribute. This review will describe the importance of science at the chemistry/biology interface to both understand and combat the SARS-CoV-2 pandemic.
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Tubbs JD, Hwang LD, Luong J, Evans DM, Sham PC. Modeling Parent-Specific Genetic Nurture in Families with Missing Parental Genotypes: Application to Birthweight and BMI. Behav Genet 2021; 51:289-300. [PMID: 33454873 DOI: 10.1007/s10519-020-10040-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/15/2020] [Accepted: 12/15/2020] [Indexed: 12/25/2022]
Abstract
Disaggregation and estimation of genetic effects from offspring and parents has long been of interest to statistical geneticists. Recently, technical and methodological advances have made the genome-wide and loci-specific estimation of direct offspring and parental genetic nurture effects more possible. However, unbiased estimation using these methods requires datasets where both parents and at least one child have been genotyped, which are relatively scarce. Our group has recently developed a method and accompanying software (IMPISH; Hwang et al. in PLoS Genet 16:e1009154, 2020) which is able to impute missing parental genotypes from observed data on sibships and estimate their effects on an offspring phenotype conditional on the effects of genetic transmission. However, this method is unable to disentangle maternal and paternal effects, which may differ in magnitude and direction. Here, we introduce an extension to the original IMPISH routine which takes advantage of all available nuclear families to impute parent-specific missing genotypes and obtain asymptotically unbiased estimates of genetic effects on offspring phenotypes. We apply this this method to data from related individuals in the UK Biobank, showing concordance with previous estimates of maternal genetic effects on offspring birthweight. We also conduct the first GWAS jointly estimating offspring-, maternal-, and paternal-specific genetic effects on body-mass index.
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Affiliation(s)
- Justin D Tubbs
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Liang-Dar Hwang
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Justin Luong
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - David M Evans
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Pak C Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China. .,Centre for PanorOmic Sciences, University of Hong Kong, Hong Kong, China. .,State Key Laboratory for Cognitive and Brain Sciences, University of Hong Kong, Hong Kong, China. .,The University of Hong Kong, 1/F, Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam, Hong Kong, China.
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Shafer RW. A SARS-CoV-2 antiviral therapy score card. Glob Health Med 2020; 2:346-349. [PMID: 33409413 PMCID: PMC7780285 DOI: 10.35772/ghm.2020.01082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/07/2020] [Accepted: 09/13/2020] [Indexed: 06/12/2023]
Abstract
The COVID-19 pandemic has unleashed an unprecedented effort to identify efficacious treatments for persons infected with SARS-CoV-2. As of September 2020, more than 750 completed, ongoing, or planned clinical trials of drugs intended to inhibit SARS-CoV-2 replication have been registered on the ClinicalTrials.gov or WHO International Clinical Trials Platform websites. Most of the treatments studied in these trials are repurposed licensed or investigational drugs targeting viral proteins or cellular pathways required for virus replication. The use of repurposed compounds is understandable because with the exception of monoclonal antibodies, it will be several months before novel SARS-CoV-2-specific drugs will be available for human testing. This editorial describes those compounds that I believe should be prioritized for clinical testing: i) viral RNA polymerase inhibitors including GS-441524, its prodrug remdesivir, and EIDD-2801; ii) entry inhibitors including monoclonal antibodies, ACE2 molecular decoys, and peptide fusion inhibitors; iii) parenteral and inhalational preparations of interferon β and λ; and iv) inhibitors of host transmembrane protease serine 2 (TMPRSS2), endosomal trafficking, and pyrimidine synthesis. As SARS-CoV-2 is pandemic and as its most severe consequences result from a dysregulated immunological response to infection, the ideal therapies should be inexpensive and should be able to be administered to non-hospitalized persons at the time of their initial diagnosis.
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Affiliation(s)
- Robert W. Shafer
- Address correspondence to:Robert W. Shafer, Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, 1000 Welch Rd Ste 202, Palo Alto, CA 94304, USA. E-mail:
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Tzou PL, Tao K, Nouhin J, Rhee SY, Hu BD, Pai S, Parkin N, Shafer RW. Coronavirus Antiviral Research Database (CoV-RDB): An Online Database Designed to Facilitate Comparisons between Candidate Anti-Coronavirus Compounds. Viruses 2020; 12:E1006. [PMID: 32916958 PMCID: PMC7551675 DOI: 10.3390/v12091006] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND To prioritize the development of antiviral compounds, it is necessary to compare their relative preclinical activity and clinical efficacy. METHODS We reviewed in vitro, animal model, and clinical studies of candidate anti-coronavirus compounds and placed extracted data in an online relational database. RESULTS As of August 2020, the Coronavirus Antiviral Research Database (CoV-RDB; covdb.stanford.edu) contained over 2800 cell culture, entry assay, and biochemical experiments, 259 animal model studies, and 73 clinical studies from over 400 published papers. SARS-CoV-2, SARS-CoV, and MERS-CoV account for 85% of the data. Approximately 75% of experiments involved compounds with known or likely mechanisms of action, including monoclonal antibodies and receptor binding inhibitors (21%), viral protease inhibitors (17%), miscellaneous host-acting inhibitors (10%), polymerase inhibitors (9%), interferons (7%), fusion inhibitors (5%), and host protease inhibitors (5%). Of 975 compounds with known or likely mechanism, 135 (14%) are licensed in the U.S. for other indications, 197 (20%) are licensed outside the U.S. or are in human trials, and 595 (61%) are pre-clinical investigational compounds. CONCLUSION CoV-RDB facilitates comparisons between different candidate antiviral compounds, thereby helping scientists, clinical investigators, public health officials, and funding agencies prioritize the most promising compounds and repurposed drugs for further development.
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Affiliation(s)
- Philip L. Tzou
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA 94305, USA; (K.T.); (J.N.); (S.-Y.R.)
| | - Kaiming Tao
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA 94305, USA; (K.T.); (J.N.); (S.-Y.R.)
| | - Janin Nouhin
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA 94305, USA; (K.T.); (J.N.); (S.-Y.R.)
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA 94305, USA; (K.T.); (J.N.); (S.-Y.R.)
| | - Benjamin D. Hu
- Undergraduate School of Humanities and Sciences, Stanford University, Stanford, CA 94305, USA;
| | - Shruti Pai
- Undergraduate Studies, University of California, Berkeley, CA 94720, USA;
| | - Neil Parkin
- Data First Consulting Inc., Sebastopol, CA 95472, USA;
| | - Robert W. Shafer
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA 94305, USA; (K.T.); (J.N.); (S.-Y.R.)
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