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Borkar MR, Coutinho E. Amalgamation of comparative protein modeling with quantitative structure-retention relationship for prediction of the chromatographic behavior of peptides. J Chromatogr A 2022; 1669:462967. [DOI: 10.1016/j.chroma.2022.462967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 10/18/2022]
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Olotu FA, Agoni C, Soremekun O, Soliman MES. The recent application of 3D-QSAR and docking studies to novel HIV-protease inhibitor drug discovery. Expert Opin Drug Discov 2020; 15:1095-1110. [PMID: 32692273 DOI: 10.1080/17460441.2020.1773428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Despite the availability of FDA approved inhibitors of HIV protease, numerous efforts are still ongoing to achieve 'near-perfect' drugs devoid of characteristic adverse side effects, toxicities, and mutational resistance. While experimental methods have been plagued with huge consumption of time and resources, there has been an incessant shift towards the use of computational simulations in HIV protease inhibitor drug discovery. AREAS COVERED Herein, the authors review the numerous applications of 3D-QSAR modeling methods over recent years relative to the design of new HIV protease inhibitors from a series of experimentally derived compounds. Also, the augmentative contributions of molecular docking are discussed. EXPERT OPINION Efforts to optimize 3D QSAR and molecular docking for HIV-1 drug discovery are ongoing, which could further incorporate inhibitor motions at the active site using molecular dynamics parameters. Also, highly predictive machine learning algorithms such as random forest, K-means, decision trees, linear regression, hierarchical clustering, and Bayesian classifiers could be employed.
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Affiliation(s)
- Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Opeyemi Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
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Khan MT, Ali S, Zeb MT, Kaushik AC, Malik SI, Wei DQ. Gibbs Free Energy Calculation of Mutation in PncA and RpsA Associated With Pyrazinamide Resistance. Front Mol Biosci 2020; 7:52. [PMID: 32328498 PMCID: PMC7160322 DOI: 10.3389/fmolb.2020.00052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/16/2020] [Indexed: 12/16/2022] Open
Abstract
A central approach for better understanding the forces involved in maintaining protein structures is to investigate the protein folding and thermodynamic properties. The effect of the folding process is often disturbed in mutated states. To explore the dynamic properties behind mutations, molecular dynamic (MD) simulations have been widely performed, especially in unveiling the mechanism of drug failure behind mutation. When comparing wild type (WT) and mutants (MTs), the structural changes along with solvation free energy (SFE), and Gibbs free energy (GFE) are calculated after the MD simulation, to measure the effect of mutations on protein structure. Pyrazinamide (PZA) is one of the first-line drugs, effective against latent Mycobacterium tuberculosis isolates, affecting the global TB control program 2030. Resistance to this drug emerges due to mutations in pncA and rpsA genes, encoding pyrazinamidase (PZase) and ribosomal protein S1 (RpsA) respectively. The question of how the GFE may be a measure of PZase and RpsA stabilities, has been addressed in the current review. The GFE and SFE of MTs have been compared with WT, which were already found to be PZA-resistant. WT structures attained a more stable state in comparison with MTs. The physiological effect of a mutation in PZase and RpsA may be due to the difference in energies. This difference between WT and MTs, depicted through GFE plots, might be useful in predicting the stability and PZA-resistance behind mutation. This study provides useful information for better management of drug resistance, to control the global TB problem.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | | | - Aman Chandra Kaushik
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
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Learning epistatic interactions from sequence-activity data to predict enantioselectivity. J Comput Aided Mol Des 2017; 31:1085-1096. [DOI: 10.1007/s10822-017-0090-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
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Khedkar VM, Coutinho EC. CoRILISA: A Local Similarity Based Receptor Dependent QSAR Method. J Chem Inf Model 2015; 55:194-205. [DOI: 10.1021/ci5006367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vijay M. Khedkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
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Borkar MR, Pissurlenkar RRS, Coutinho EC. Mapping activity elements of protegrin antimicrobial peptides by HomoSAR. RSC Adv 2015. [DOI: 10.1039/c5ra14402g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
HomoSAR has been able to shed light on the relationship between sequences of protegrin peptides and their activity on six specific micro-organisms.
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Affiliation(s)
| | | | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry
- Bombay College of Pharmacy
- Mumbai 400098
- India
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Other Related Techniques. UNDERSTANDING THE BASICS OF QSAR FOR APPLICATIONS IN PHARMACEUTICAL SCIENCES AND RISK ASSESSMENT 2015. [PMCID: PMC7149793 DOI: 10.1016/b978-0-12-801505-6.00010-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
With the advances in computational resources, there is an increasing urge among the computational researchers to make the in silico approaches fast, convenient, reproducible, acceptable, and sensible ones. Along with the typical two-dimensional (2D) and three-dimensional (3D) quantitative structure–activity relationship (QSAR) methods, approaches like pharmacophore, structure-based docking studies, and combinations of ligand- and structure-based approaches like comparative residue interaction analysis (CoRIA) and comparative binding energy analysis (COMBINE) have gained a significant popularity in the computational drug design process. A pharmacophore can be developed either in a ligand-based method, by superposing a set of active molecules and extracting common chemical features which are vital for their bioactivity; or in a structure-based manner, by probing probable interaction points between the macromolecular target and ligands. The interaction of protein and ligand molecules with each other is one of the interesting studies in modern molecular biology and molecular recognition. This interaction can well be explained with the conceptof a docking study to show how a molecule can bind to another molecule to exert the bioactivity. Docking and pharmacophore are non-QSAR approaches in in silico drug design that can support the QSAR findings. Approaches like CoRIA and COMBINE can use information generated from the ligand–receptor complexes to extract the critical clue concerning the types of significant interaction at the level of both the receptor and the ligand. Employing the abovementioned ligand- and structure-based methodologies and chemical libraries, virtual screening (VS) emerged as an important tool in the quest to develop novel drug compounds. VS serves as an efficient computational tool that integrates structural data with lead optimization as a cost-effective approach to drug discovery.
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Martis EA, Chandarana RC, Shaikh MS, Ambre PK, D’Souza JS, Iyer KR, Coutinho EC, Nandan SR, Pissurlenkar RR. Quantifying ligand–receptor interactions for gorge-spanning acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease. J Biomol Struct Dyn 2014; 33:1107-25. [DOI: 10.1080/07391102.2014.931824] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Quantitative structure–activity relationship (QSAR) studies as strategic approach in drug discovery. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1072-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Khedkar VM, Joseph J, Pissurlenkar R, Saran A, Coutinho EC. How good are ensembles in improving QSAR models? The case with eCoRIA. J Biomol Struct Dyn 2014; 33:749-69. [DOI: 10.1080/07391102.2014.909744] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Vijay M. Khedkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Jose Joseph
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Raghuvir Pissurlenkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Anil Saran
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
| | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400098, India
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Ambre PK, Pissurlenkar RRS, Coutinho EC, Iyer RP. Identification of new checkpoint kinase-1 (Chk1) inhibitors by docking, 3D-QSAR, and pharmacophore-modeling methods. CAN J CHEM 2012. [DOI: 10.1139/v2012-047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Inhibition of checkpoint kinase-1 (Chk1) by small molecules is of great therapeutic interest in the field of oncology and for understanding cell-cycle regulations. This paper presents a model with elements from docking, pharmacophore mapping, the 3D-QSAR approaches CoMFA, CoMSIA and CoRIA, and virtual screening to identify novel hits against Chk1. Docking, 3D-QSAR (CoRIA, CoMFA and CoMSIA), and pharmacophore studies delineate crucial site points on the Chk1 inhibitors, which can be modified to improve activity. The docking analysis showed residues in the proximity of the ligands that are involved in ligand–receptor interactions, whereas CoRIA models were able to derive the magnitude of these interactions that impact the activity. The ligand-based 3D-QSAR methods (CoMFA and CoMSIA) highlight key areas on the molecules that are beneficial and (or) detrimental for activity. The docking studies and 3D-QSAR models are in excellent agreement in terms of binding-site interactions. The pharmacophore hypotheses validated using sensitivity, selectivity, and specificity parameters is a four-point model, characterized by a hydrogen-bond acceptor (A), hydrogen-bond donor (D), and two hydrophobes (H). This map was used to screen a database of 2.7 million druglike compounds, which were pruned to a small set of potential inhibitors by CoRIA, CoMFA, and CoMSIA models with predicted activity in the range of 8.5–10.5 log units.
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Affiliation(s)
- Premlata K. Ambre
- Molecular Simulations Group, Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (East), Mumbai 400 098 India
| | - Raghuvir R. S. Pissurlenkar
- Molecular Simulations Group, Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (East), Mumbai 400 098 India
| | - Evans C. Coutinho
- Molecular Simulations Group, Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (East), Mumbai 400 098 India
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Sivakumar PM, Vignesh N, Senthilkumaran M, Doble M. Quantitative structure–cytotoxicity relationships (QSCR) for semi-synthetic Taxoteres against cancer cell lines. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.583647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Chintakrindi AS, Shaikh MS, Coutinho EC. De novo design of 7-aminocoumarin derivatives as novel falcipain-3 inhibitors. J Mol Model 2011; 18:1481-93. [DOI: 10.1007/s00894-011-1177-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 07/01/2011] [Indexed: 11/24/2022]
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Verma J, Malde A, Khedkar S, Iyer R, Coutinho E. Local Indices for Similarity Analysis (LISA)—A 3D-QSAR Formalism Based on Local Molecular Similarity. J Chem Inf Model 2009; 49:2695-707. [DOI: 10.1021/ci900224u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jitender Verma
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
| | - Alpeshkumar Malde
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
| | - Santosh Khedkar
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
| | - Radhakrishnan Iyer
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
| | - Evans Coutinho
- Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India, and Spring Bank Pharmaceuticals, Inc., 113 Cedar Street, Milford, Massachusetts 01757
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Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA). J Mol Model 2008; 15:233-45. [DOI: 10.1007/s00894-008-0399-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 09/06/2008] [Indexed: 11/26/2022]
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