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Martin HJ, Melo-Filho CC, Korn D, Eastman RT, Rai G, Simeonov A, Zakharov AV, Muratov E, Tropsha A. Small molecule antiviral compound collection (SMACC): A comprehensive, highly curated database to support the discovery of broad-spectrum antiviral drug molecules. Antiviral Res 2023; 217:105620. [PMID: 37169224 PMCID: PMC11069349 DOI: 10.1016/j.antiviral.2023.105620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/13/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
Diseases caused by new viruses cost thousands if not millions of human lives and trillions of dollars. We have identified, collected, curated, and integrated all chemogenomics data from ChEMBL for 13 emerging viruses that hold the greatest potential threat to global human health. By identifying and solving several challenges related to data annotation accuracy, we developed a highly curated and thoroughly annotated database of compounds tested in both phenotypic and target-based assays for these viruses that we dubbed SMACC (Small Molecule Antiviral Compound Collection). The pilot version of the SMACC database contains over 32,500 entries for 13 viruses. By analyzing data in SMACC, we have identified ∼50 compounds with polyviral inhibition profile, mostly covering flavi- and coronaviruses. The SMACC database may serve as a reference for virologists and medicinal chemists working on the development of novel BSA agents in preparation for future viral outbreaks. SMACC is publicly available at https://smacc.mml.unc.edu.
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Affiliation(s)
- Holli-Joi Martin
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Cleber C Melo-Filho
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel Korn
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Richard T Eastman
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, 20850, USA
| | - Ganesha Rai
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, 20850, USA
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, 20850, USA
| | - Alexey V Zakharov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, 20850, USA.
| | - Eugene Muratov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
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Martin H, Melo-filho CC, Korn D, Eastman RT, Rai G, Simeonov A, Zakharov AV, Muratov E, Tropsha A. Small Molecule Antiviral Compound Collection (SMACC): a database to support the discovery of broad-spectrum antiviral drug molecules.. [PMID: 35860225 PMCID: PMC9298133 DOI: 10.1101/2022.07.09.499397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Diseases caused by new viruses costs thousands if not millions of human lives and trillions of dollars in damage to the global economy. Despite the rapid development of vaccines for SARS-CoV-2, the lack of small molecule antiviral drugs that work against multiple viral families (broad-spectrum antivirals; BSAs) has left the entire world’s human population vulnerable to the infection between the beginning of the outbreak and the widespread availability of vaccines. Developing BSAs is an attractive, yet challenging, approach that could prevent the next, inevitable, viral outbreak from becoming a global catastrophe. To explore whether historical medicinal chemistry efforts suggest the possibility of discovering novel BSAs, we (i) identified, collected, curated, and integrated all chemical bioactivity data available in ChEMBL for molecules tested in respective assays for 13 emerging viruses that, based on published literature, hold the greatest potential threat to global human health; (ii) identified and solved the challenges related to data annotation accuracy including assay description ambiguity, missing cell or target information, and incorrect BioAssay Ontology (BAO) annotations; (iii) developed a highly curated and thoroughly annotated database of compounds tested in both phenotypic (21,392 entries) and target-based (11,123 entries) assays for these viruses; and (iv) identified a subset of compounds showing BSA activity. For the latter task, we eliminated inconclusive and annotated duplicative entries by checking the concordance between multiple assay results and identified eight compounds active against 3–4 viruses from the phenotypic data, 16 compounds active against two viruses from the target-based data, and 35 compounds active in at least one phenotypic and one target-based assay. The pilot version of our SMACC (Small Molecule Antiviral Compound Collection) database contains over 32,500 entries for 13 viruses. Our analysis indicates that previous research yielded very small number of BSA compounds. We posit that focused and coordinated efforts strategically targeting the discovery of such agents must be established and maintained going forward. The SMACC database publicly available at https://smacc.mml.unc.edu may serve as a reference for virologists and medicinal chemists working on the development of novel BSA agents in preparation for future viral outbreaks.
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Melo-Filho CC, Bobrowski T, Martin HJ, Sessions Z, Popov KI, Moorman NJ, Baric RS, Muratov EN, Tropsha A. Conserved coronavirus proteins as targets of broad-spectrum antivirals. Antiviral Res 2022; 204:105360. [PMID: 35691424 PMCID: PMC9183392 DOI: 10.1016/j.antiviral.2022.105360] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022]
Abstract
Coronaviruses are a class of single-stranded, positive-sense RNA viruses that have caused three major outbreaks over the past two decades: Middle East respiratory syndrome–related coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All outbreaks have been associated with significant morbidity and mortality. In this study, we have identified and explored conserved binding sites in the key coronavirus proteins for the development of broad-spectrum direct acting anti-coronaviral compounds and validated the significance of this conservation for drug discovery with existing experimental data. We have identified four coronaviral proteins with highly conserved binding site sequence and 3D structure similarity: PLpro, Mpro, nsp10-nsp16 complex(methyltransferase), and nsp15 endoribonuclease. We have compiled all available experimental data for known antiviral medications inhibiting these targets and identified compounds active against multiple coronaviruses. The identified compounds representing potential broad-spectrum antivirals include: GC376, which is active against six viral Mpro (out of six tested, as described in research literature); mycophenolic acid, which is active against four viral PLpro (out of four); and emetine, which is active against four viral RdRp (out of four). The approach described in this study for coronaviruses, which combines the assessment of sequence and structure conservation across a viral family with the analysis of accessible chemical structure – antiviral activity data, can be explored for the development of broad-spectrum drugs for multiple viral families.
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Affiliation(s)
- Cleber C Melo-Filho
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Holli-Joi Martin
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Zoe Sessions
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nathaniel J Moorman
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.
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Bobrowski T, Melo-Filho CC, Korn D, Alves VM, Popov KI, Auerbach S, Schmitt C, Moorman NJ, Muratov EN, Tropsha A. Learning from history: do not flatten the curve of antiviral research! Drug Discov Today 2020; 25:1604-1613. [PMID: 32679173 PMCID: PMC7361119 DOI: 10.1016/j.drudis.2020.07.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 01/20/2023]
Abstract
Here, we explore the dynamics of the response of the scientific community to several epidemics, including Coronavirus Disease 2019 (COVID-19), as assessed by the numbers of clinical trials, publications, and level of research funding over time. All six prior epidemics studied [bird flu, severe acute respiratory syndrome (SARS), swine flu, Middle East Respiratory Syndrome (MERS), Ebola, and Zika] were characterized by an initial spike of research response that flattened shortly thereafter. Unfortunately, no antiviral medications have been discovered to date as treatments for any of these diseases. By contrast, the HIV/AIDS pandemic has garnered consistent research investment since it began and resulted in drugs being developed within 7 years of its start date, with many more to follow. We argue that, to develop effective treatments for COVID-19 and be prepared for future epidemics, long-term, consistent investment in antiviral research is needed.
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Affiliation(s)
- Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Cleber C Melo-Filho
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel Korn
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Vinicius M Alves
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC 27560, USA
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Scott Auerbach
- Toxicoinformatics Group, National Toxicology Program, NIEHS, Morrisville, NC 27560, USA
| | - Charles Schmitt
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC 27560, USA
| | - Nathaniel J Moorman
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pharmaceutical Sciences, Federal University of Paraiba, Joao Pessoa, PB, Brazil.
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA.
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Alves VM, Bobrowski T, Melo-Filho CC, Korn D, Auerbach S, Schmitt C, Muratov EN, Tropsha A. QSAR Modeling of SARS-CoV M pro Inhibitors Identifies Sufugolix, Cenicriviroc, Proglumetacin, and other Drugs as Candidates for Repurposing against SARS-CoV-2. Mol Inform 2020; 40:e2000113. [PMID: 33405340 DOI: 10.1002/minf.202000113] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/28/2020] [Indexed: 12/22/2022]
Abstract
The main protease (Mpro) of the SARS-CoV-2 has been proposed as one of the major drug targets for COVID-19. We have identified the experimental data on the inhibitory activity of compounds tested against the closely related (96 % sequence identity, 100 % active site conservation) Mpro of SARS-CoV. We developed QSAR models of these inhibitors and employed these models for virtual screening of all drugs in the DrugBank database. Similarity searching and molecular docking were explored in parallel, but docking failed to correctly discriminate between experimentally active and inactive compounds, so it was not relied upon for prospective virtual screening. Forty-two compounds were identified by our models as consensus computational hits. Subsequent to our computational studies, NCATS reported the results of experimental screening of their drug collection in SARS-CoV-2 cytopathic effect assay (https://opendata.ncats.nih.gov/covid19/). Coincidentally, NCATS tested 11 of our 42 hits, and three of them, cenicriviroc (AC50 of 8.9 μM), proglumetacin (tested twice independently, with AC50 of 8.9 μM and 12.5 μM), and sufugolix (AC50 12.6 μM), were shown to be active. These observations support the value of our modeling approaches and models for guiding the experimental investigations of putative anti-COVID-19 drug candidates. All data and models used in this study are publicly available via Supplementary Materials, GitHub (https://github.com/alvesvm/sars-cov-mpro), and Chembench web portal (https://chembench.mml.unc.edu/).
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Affiliation(s)
- Vinicius M Alves
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Beard Hall, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Cleber C Melo-Filho
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Beard Hall, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel Korn
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Beard Hall, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Scott Auerbach
- Toxinformatics Group, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Charles Schmitt
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Beard Hall, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Pharmaceutical Sciences, Federal University of Paraiba, Joao Pessoa, PB, Brazil
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Beard Hall, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
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Bobrowski T, Alves VM, Melo-Filho CC, Korn D, Auerbach S, Schmitt C, Muratov EN, Tropsha A. Computational Models Identify Several FDA Approved or Experimental Drugs as Putative Agents Against SARS-CoV-2. ChemRxiv 2020:12153594. [PMID: 32511287 PMCID: PMC7252448 DOI: 10.26434/chemrxiv.12153594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 04/22/2020] [Indexed: 01/09/2023]
Abstract
The outbreak of a novel human coronavirus (SARS-CoV-2) has evolved into global health emergency, infecting hundreds of thousands of people worldwide. We have identified experimental data on the inhibitory activity of compounds tested against closely related (96% sequence identity, 100% active site conservation) protease of SARS-CoV and employed this data to build QSAR models for this dataset. We employed these models for virtual screening of all drugs from DrugBank, including compounds in clinical trials. Molecular docking and similarity search approaches were explored in parallel with QSAR modeling, but molecular docking failed to correctly discriminate between experimentally active and inactive compounds. As a result of our studies, we recommended 41 approved, experimental, or investigational drugs as potential agents against SARS-CoV-2 acting as putative inhibitors of Mpro. Ten compounds with feasible prices were purchased and are awaiting the experimental validation. .
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Affiliation(s)
- Tesia Bobrowski
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Vinicius M. Alves
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Cleber C. Melo-Filho
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel Korn
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Scott Auerbach
- Toxinformatics Group, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Charles Schmitt
- Office of Data Science, National Toxicology Program, NIEHS, Morrisville, NC, 27560, USA
| | - Eugene N. Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
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Melo-Filho CC, Braga RC, Muratov EN, Franco CH, Moraes CB, Freitas-Junior LH, Andrade CH. Discovery of new potent hits against intracellular Trypanosoma cruzi by QSAR-based virtual screening. Eur J Med Chem 2018; 163:649-659. [PMID: 30562700 DOI: 10.1016/j.ejmech.2018.11.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 12/17/2022]
Abstract
Chagas disease is a neglected tropical disease (NTD) caused by the protozoan parasite Trypanosoma cruzi and is primarily transmitted to humans by the feces of infected Triatominae insects during their blood meal. The disease affects 6-8 million people, mostly in Latin America countries, and kills more people in the region each year than any other parasite-born disease, including malaria. Moreover, patient numbers are currently increasing in non-endemic, developed countries, such as Australia, Japan, Canada, and the United States. The treatment is limited to one drug, benznidazole, which is only effective in the acute phase of the disease and is very toxic. Thus, there is an urgent need to develop new, safer, and effective drugs against the chronic phase of Chagas disease. Using a QSAR-based virtual screening followed by in vitro experimental evaluation, we report herein the identification of novel potent and selective hits against T. cruzi intracellular stage. We developed and validated binary QSAR models for prediction of anti-trypanosomal activity and cytotoxicity against mammalian cells using the best practices for QSAR modeling. These models were then used for virtual screening of a commercial database, leading to the identification of 39 virtual hits. Further in vitro assays showed that seven compounds were potent against intracellular T. cruzi at submicromolar concentrations (EC50 < 1 μM) and were very selective (SI > 30). Furthermore, other six compounds were also inside the hit criteria for Chagas disease, which presented activity at low micromolar concentrations (EC50 < 10 μM) against intracellular T. cruzi and were also selective (SI > 15). Moreover, we performed a multi-parameter analysis for the comparison of tested compounds regarding their balance between potency, selectivity, and predicted ADMET properties. In the next studies, the most promising compounds will be submitted to additional in vitro and in vivo assays in acute model of Chagas disease, and can be further optimized for the development of new promising drug candidates against this important yet neglected disease.
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Affiliation(s)
- Cleber C Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goiás - UFG, Rua 240, Qd.87, Goiania, GO, 74605-510, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goiás - UFG, Rua 240, Qd.87, Goiania, GO, 74605-510, Brazil
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA; Department of Chemical Technology, Odessa National Polytechnic University, 1. Shevchenko Ave., Odessa, 65000, Ukraine
| | - Caio Haddad Franco
- National Laboratory of Biosciences (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, 13083-970, Brazil
| | - Carolina B Moraes
- National Laboratory of Biosciences (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, 13083-970, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Lucio H Freitas-Junior
- National Laboratory of Biosciences (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, 13083-970, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goiás - UFG, Rua 240, Qd.87, Goiania, GO, 74605-510, Brazil.
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Neves BJ, Braga RC, Melo-Filho CC, Moreira-Filho JT, Muratov EN, Andrade CH. QSAR-Based Virtual Screening: Advances and Applications in Drug Discovery. Front Pharmacol 2018; 9:1275. [PMID: 30524275 PMCID: PMC6262347 DOI: 10.3389/fphar.2018.01275] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 10/18/2018] [Indexed: 02/03/2023] Open
Abstract
Virtual screening (VS) has emerged in drug discovery as a powerful computational approach to screen large libraries of small molecules for new hits with desired properties that can then be tested experimentally. Similar to other computational approaches, VS intention is not to replace in vitro or in vivo assays, but to speed up the discovery process, to reduce the number of candidates to be tested experimentally, and to rationalize their choice. Moreover, VS has become very popular in pharmaceutical companies and academic organizations due to its time-, cost-, resources-, and labor-saving. Among the VS approaches, quantitative structure–activity relationship (QSAR) analysis is the most powerful method due to its high and fast throughput and good hit rate. As the first preliminary step of a QSAR model development, relevant chemogenomics data are collected from databases and the literature. Then, chemical descriptors are calculated on different levels of representation of molecular structure, ranging from 1D to nD, and then correlated with the biological property using machine learning techniques. Once developed and validated, QSAR models are applied to predict the biological property of novel compounds. Although the experimental testing of computational hits is not an inherent part of QSAR methodology, it is highly desired and should be performed as an ultimate validation of developed models. In this mini-review, we summarize and critically analyze the recent trends of QSAR-based VS in drug discovery and demonstrate successful applications in identifying perspective compounds with desired properties. Moreover, we provide some recommendations about the best practices for QSAR-based VS along with the future perspectives of this approach.
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Affiliation(s)
- Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil.,Laboratory of Cheminformatics, Centro Universitário de Anápolis (UniEVANGÉLICA), Anápolis, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Cleber C Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - José Teófilo Moreira-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Chemical Technology, Odessa National Polytechnic University, Odessa, Ukraine
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
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Silva LC, Neves BJ, Gomes MN, Melo-Filho CC, Soares CMA, Andrade CH, Pereira M. Computer-aided identification of novel anti-paracoccidioidomycosis compounds. Future Microbiol 2018; 13:1523-1535. [DOI: 10.2217/fmb-2018-0175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: The shape-based virtual screening was used for the identification of new compounds anti-paracoccidioidomycosis (PCM). Materials & methods: The study was performed according to the following steps: collection and curation of a dataset of quinolinyl N-oxide chalcones with anti-PCM activity, development and validation of shape-based models, application of the best model for virtual screening, and experimental validation. Results & Conclusion: Among 31 computational hits, eight compounds showed potent antifungal activity and low cytotoxicity for mammalian cells. The checkerboard assay showed that most promising hit (compound 3) displayed additive effects with the antifungal cotrimoxazole and amphotericin B. Therefore, the shape-based virtual screening allowed us to discover promising compounds in prospective hit-to-lead optimization studies for tackling PCM.
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Affiliation(s)
- Lívia C Silva
- Laboratory of Molecular Biology, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Bruno J Neves
- Laboratory for Molecular Modeling & Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Goiás, 74605-510, Brazil
- Laboratory of Cheminformatics, Centro Universitário de Anápolis, UniEVANGÉLICA, Anápolis, Goiás, 75083-515, Brazil
| | - Marcelo N Gomes
- Laboratory for Molecular Modeling & Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Goiás, 74605-510, Brazil
- InSiChem Drug Discovery, Universidade Estadual de Goiás, Goiânia, Goiás, 74643-090, Brazil
| | - Cleber C Melo-Filho
- Laboratory for Molecular Modeling & Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Goiás, 74605-510, Brazil
| | - Célia MA Soares
- Laboratory of Molecular Biology, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Carolina H Andrade
- Laboratory for Molecular Modeling & Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Goiás, 74605-510, Brazil
| | - Maristela Pereira
- Laboratory of Molecular Biology, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
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Lima MNN, Melo-Filho CC, Cassiano GC, Neves BJ, Alves VM, Braga RC, Cravo PVL, Muratov EN, Calit J, Bargieri DY, Costa FTM, Andrade CH. QSAR-Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities. Front Pharmacol 2018; 9:146. [PMID: 29559909 PMCID: PMC5845645 DOI: 10.3389/fphar.2018.00146] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/12/2018] [Indexed: 11/13/2022] Open
Abstract
Malaria is a life-threatening infectious disease caused by parasites of the genus Plasmodium, affecting more than 200 million people worldwide every year and leading to about a half million deaths. Malaria parasites of humans have evolved resistance to all current antimalarial drugs, urging for the discovery of new effective compounds. Given that the inhibition of deoxyuridine triphosphatase of Plasmodium falciparum (PfdUTPase) induces wrong insertions in plasmodial DNA and consequently leading the parasite to death, this enzyme is considered an attractive antimalarial drug target. Using a combi-QSAR (quantitative structure-activity relationship) approach followed by virtual screening and in vitro experimental evaluation, we report herein the discovery of novel chemical scaffolds with in vitro potency against asexual blood stages of both P. falciparum multidrug-resistant and sensitive strains and against sporogonic development of P. berghei. We developed 2D- and 3D-QSAR models using a series of nucleosides reported in the literature as PfdUTPase inhibitors. The best models were combined in a consensus approach and used for virtual screening of the ChemBridge database, leading to the identification of five new virtual PfdUTPase inhibitors. Further in vitro testing on P. falciparum multidrug-resistant (W2) and sensitive (3D7) parasites showed that compounds LabMol-144 and LabMol-146 demonstrated fair activity against both strains and presented good selectivity versus mammalian cells. In addition, LabMol-144 showed good in vitro inhibition of P. berghei ookinete formation, demonstrating that hit-to-lead optimization based on this compound may also lead to new antimalarials with transmission blocking activity.
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Affiliation(s)
- Marilia N N Lima
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Cleber C Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Gustavo C Cassiano
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil.,Laboratory of Cheminformatics, PPG-SOMA, University Center of Anápolis/UniEVANGELICA, Anápolis, Brazil
| | - Vinicius M Alves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Pedro V L Cravo
- Global Health and Tropical Medicine Centre, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Chemical Technology, Odessa National Polytechnic University, Odessa, Ukraine
| | - Juliana Calit
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniel Y Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Carolina H Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil.,Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, Brazil
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11
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Gomes MN, Alcântara LM, Neves BJ, Melo-Filho CC, Freitas-Junior LH, Moraes CB, Ma R, Franzblau SG, Muratov E, Andrade CH. Computer-aided discovery of two novel chalcone-like compounds active and selective against Leishmania infantum. Bioorg Med Chem Lett 2017; 27:2459-2464. [PMID: 28434763 PMCID: PMC6020026 DOI: 10.1016/j.bmcl.2017.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 01/09/2023]
Abstract
Leishmaniasis are infectious diseases caused by parasites of genus Leishmania that affect affects 12 million people in 98 countries mainly in Africa, Asia, and Latin America. Effective treatments for this disease are urgently needed. In this study, we present a computer-aided approach to investigate a set of 32 recently synthesized chalcone and chalcone-like compounds to act as antileishmanial agents. As a result, nine most promising compounds and three potentially inactive compounds were experimentally evaluated against Leishmania infantum amastigotes and mammalian cells. Four compounds exhibited EC50 in the range of 6.2-10.98μM. In addition, two compounds, LabMol-65 and LabMol-73, exhibited cytotoxicity in macrophages >50μM that resulted in better selectivity compared to standard drug amphotericin B. These two compounds also demonstrated low cytotoxicity and high selectivity towards Vero cells. The results of target fishing followed by homology modeling and docking studies suggest that these chalcone compounds could act in Leishmania because of their interaction with cysteine proteases, such as procathepsin L. Finally, we have provided structural recommendations for designing new antileishmanial chalcones.
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Affiliation(s)
- Marcelo N Gomes
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias, Rua 240, Qd.87, Setor Leste Universitário, Goiania, Goias 74605-510, Brazil
| | - Laura M Alcântara
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Sao Paulo, Brazil. d Instituto Butantan - Sao Paulo, Sao Paulo 05503-900, Brazil
| | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias, Rua 240, Qd.87, Setor Leste Universitário, Goiania, Goias 74605-510, Brazil; Postgraduate Program on Society, Technology and Enviroment, University Center of Anápolis/UniEVANGELICA, Anápolis, Goiás 75083-515, Brazil
| | - Cleber C Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias, Rua 240, Qd.87, Setor Leste Universitário, Goiania, Goias 74605-510, Brazil
| | | | - Carolina B Moraes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Sao Paulo, Brazil. d Instituto Butantan - Sao Paulo, Sao Paulo 05503-900, Brazil
| | - Rui Ma
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Scott G Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States; Department of Chemical Technology, Odessa National Polytechnic University, Odessa 65000, Ukraine; Currently Visiting Professor at Universidade Federal de Goias, Goiania, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias, Rua 240, Qd.87, Setor Leste Universitário, Goiania, Goias 74605-510, Brazil.
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12
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Neves BJ, Dantas RF, Senger MR, Melo-Filho CC, Valente WCG, de Almeida ACM, Rezende-Neto JM, Lima EFC, Paveley R, Furnham N, Muratov E, Kamentsky L, Carpenter AE, Braga RC, Silva-Junior FP, Andrade CH. Discovery of New Anti-Schistosomal Hits by Integration of QSAR-Based Virtual Screening and High Content Screening. J Med Chem 2016; 59:7075-88. [PMID: 27396732 PMCID: PMC5844225 DOI: 10.1021/acs.jmedchem.5b02038] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Schistosomiasis is a debilitating neglected tropical disease, caused by flatworms of Schistosoma genus. The treatment relies on a single drug, praziquantel (PZQ), making the discovery of new compounds extremely urgent. In this work, we integrated QSAR-based virtual screening (VS) of Schistosoma mansoni thioredoxin glutathione reductase (SmTGR) inhibitors and high content screening (HCS) aiming to discover new antischistosomal agents. Initially, binary QSAR models for inhibition of SmTGR were developed and validated using the Organization for Economic Co-operation and Development (OECD) guidance. Using these models, we prioritized 29 compounds for further testing in two HCS platforms based on image analysis of assay plates. Among them, 2-[2-(3-methyl-4-nitro-5-isoxazolyl)vinyl]pyridine and 2-(benzylsulfonyl)-1,3-benzothiazole, two compounds representing new chemical scaffolds have activity against schistosomula and adult worms at low micromolar concentrations and therefore represent promising antischistosomal hits for further hit-to-lead optimization.
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Affiliation(s)
- Bruno J. Neves
- LabMol—Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia 74605-510, Brazil
| | - Rafael F. Dantas
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Mario R. Senger
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Cleber C. Melo-Filho
- LabMol—Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia 74605-510, Brazil
| | - Walter C. G. Valente
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Ana C. M. de Almeida
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - João M. Rezende-Neto
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Elid F. C. Lima
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Ross Paveley
- Department of Infection and Immunity, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Nicholas Furnham
- Department of Infection and Immunity, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill North Carolina 27955-7568, United States
| | - Lee Kamentsky
- Imaging Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, United States
| | - Anne E. Carpenter
- Imaging Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, United States
| | - Rodolpho C. Braga
- LabMol—Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia 74605-510, Brazil
| | - Floriano P. Silva-Junior
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Carolina Horta Andrade
- LabMol—Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia 74605-510, Brazil
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13
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Melo-Filho CC, Dantas RF, Braga RC, Neves BJ, Senger MR, Valente WCG, Rezende-Neto JM, Chaves WT, Muratov EN, Paveley RA, Furnham N, Kamentsky L, Carpenter AE, Silva-Junior FP, Andrade CH. QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. J Chem Inf Model 2016; 56:1357-72. [PMID: 27253773 DOI: 10.1021/acs.jcim.6b00055] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Schistosomiasis is a neglected tropical disease that affects millions of people worldwide. Thioredoxin glutathione reductase of Schistosoma mansoni (SmTGR) is a validated drug target that plays a crucial role in the redox homeostasis of the parasite. We report the discovery of new chemical scaffolds against S. mansoni using a combi-QSAR approach followed by virtual screening of a commercial database and confirmation of top ranking compounds by in vitro experimental evaluation with automated imaging of schistosomula and adult worms. We constructed 2D and 3D quantitative structure-activity relationship (QSAR) models using a series of oxadiazoles-2-oxides reported in the literature as SmTGR inhibitors and combined the best models in a consensus QSAR model. This model was used for a virtual screening of Hit2Lead set of ChemBridge database and allowed the identification of ten new potential SmTGR inhibitors. Further experimental testing on both shistosomula and adult worms showed that 4-nitro-3,5-bis(1-nitro-1H-pyrazol-4-yl)-1H-pyrazole (LabMol-17) and 3-nitro-4-{[(4-nitro-1,2,5-oxadiazol-3-yl)oxy]methyl}-1,2,5-oxadiazole (LabMol-19), two compounds representing new chemical scaffolds, have high activity in both systems. These compounds will be the subjects for additional testing and, if necessary, modification to serve as new schistosomicidal agents.
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Affiliation(s)
- Cleber C Melo-Filho
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias , Rua 240, Qd.87, Goiania, GO 74605-510, Brazil
| | - Rafael F Dantas
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute , Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - Rodolpho C Braga
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias , Rua 240, Qd.87, Goiania, GO 74605-510, Brazil
| | - Bruno J Neves
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias , Rua 240, Qd.87, Goiania, GO 74605-510, Brazil
| | - Mario R Senger
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute , Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - Walter C G Valente
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute , Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - João M Rezende-Neto
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute , Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - Willian T Chaves
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute , Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States.,Department of Chemical Technology, Odessa National Polytechnic University , 1. Shevchenko Ave., Odessa, 65000, Ukraine
| | - Ross A Paveley
- Department of Pathogen Molecular Biology & Department of Infection and Immunity, London School of Hygiene and Tropical Medicine , London WC1E 7HT, United Kingdom
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology & Department of Infection and Immunity, London School of Hygiene and Tropical Medicine , London WC1E 7HT, United Kingdom
| | - Lee Kamentsky
- Imaging Platform, Broad Institute of Massachusetts Institute of Technology and Harvard , Cambridge, Massachusetts 02142, United States
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of Massachusetts Institute of Technology and Harvard , Cambridge, Massachusetts 02142, United States
| | - Floriano P Silva-Junior
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute , Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil
| | - Carolina H Andrade
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias , Rua 240, Qd.87, Goiania, GO 74605-510, Brazil
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