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Koshlan T, Kulikov K. Analysis to determine the effect of mutations on binding to small chemical molecules. J Bioinform Comput Biol 2022; 20:2240003. [DOI: 10.1142/s0219720022400030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, the authors present and describe, in detail, an original software-implemented numerical methodology used to determine the effect of mutations on binding to small chemical molecules, on the example of gefitinib, AMPPNP, CO-1686, ASP8273, erlotinib binding with EGFR protein, and imatinib binding with PPARgamma. Furthermore, the developed numerical approach makes it possible to determine the stability of a molecular complex, which consists of a protein and a small chemical molecule. The description of the software package that implements the presented algorithm is given in the website: https://binomlabs.com/ .
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Affiliation(s)
- T. V. Koshlan
- Department of Molecular Biophysics, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - K. G. Kulikov
- Department of Medical Physics, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
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Shanmugam A, Muralidharan N, Velmurugan D, Gromiha MM. Therapeutic Targets and Computational Approaches on Drug Development for COVID-19. Curr Top Med Chem 2020; 20:2210-2220. [DOI: 10.2174/1568026620666200710105507] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/20/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022]
Abstract
World Health Organization declared coronavirus disease (COVID-19) caused by SARS
coronavirus-2 (SARS-CoV-2) as pandemic. Its outbreak started in China in Dec 2019 and rapidly spread
all over the world. SARS-CoV-2 has infected more than 800,000 people and caused about 35,000 deaths
so far, moreover, no approved drugs are available to treat COVID-19. Several investigations have been
carried out to identify potent drugs for COVID-19 based on drug repurposing, potential novel compounds
from ligand libraries, natural products, short peptides, and RNAseq analysis. This review is focused
on three different aspects; (i) targets for drug design (ii) computational methods to identify lead
compounds and (iii) drugs for COVID-19. It also covers the latest literature on various hit molecules
proposed by computational methods and experimental techniques.
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Affiliation(s)
- Anusuya Shanmugam
- Department of Pharmaceutical Engineering, Vinayaka Mission’s KirupanandaVariyar Engineering College, Vinayaka Mission’s Research Foundation (Deemed to be University), Salem – 636308, Tamil Nadu, India
| | - Nisha Muralidharan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai – 600036, Tamil Nadu, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai - 600025, India
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai – 600036, Tamil Nadu, India
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Kanakaveti V, Shanmugam A, Ramakrishnan C, Anoosha P, Sakthivel R, Rayala SK, Gromiha MM. Computational approaches for identifying potential inhibitors on targeting protein interactions in drug discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 121:25-47. [PMID: 32312424 DOI: 10.1016/bs.apcsb.2019.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the era of big data, the interplay of artificial and human intelligence is the demanding job to address the concerns involving exchange of decisions between both sides. Drug discovery is one of the key sources of the big data, which involves synergy among various computational methods to achieve a clinical success. Rightful acquisition, mining and analysis of the data related to ligand and targets are crucial to accomplish reliable outcomes in the entire process. Novel designing and screening tactics are necessary to substantiate a potent and efficient lead compounds. Such methods are emphasized and portrayed in the current review targeting protein-ligand and protein-protein interactions involved in various diseases with potential applications.
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Affiliation(s)
- Vishnupriya Kanakaveti
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Anusuya Shanmugam
- Department of Pharmaceutical Engineering, Vinayaka Mission's Kirupananda Variyar Engineering College, Vinayaka Mission's Research Foundation (Deemed to be University), Salem, Tamil Nadu, India
| | - C Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - P Anoosha
- Department of Internal Medicine, Division of Medical Oncology and Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - R Sakthivel
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - S K Rayala
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India; Advanced Computational Drug Discovery Unit (ACDD), Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
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Karuppasamy R, Veerappapillai S, Maiti S, Shin WH, Kihara D. Current progress and future perspectives of polypharmacology : From the view of non-small cell lung cancer. Semin Cancer Biol 2019; 68:84-91. [PMID: 31698087 DOI: 10.1016/j.semcancer.2019.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 12/17/2022]
Abstract
A pre-eminent subtype of lung carcinoma, Non-small cell lung cancer accounts for paramount causes of cancer-associated mortality worldwide. Undeterred by the endeavour in the treatment strategies, the overall cure and survival rates for NSCLC remain substandard, particularly in metastatic diseases. Moreover, the emergence of resistance to classic anticancer drugs further deteriorates the situation. These demanding circumstances culminate the need of extended and revamped research for the establishment of upcoming generation cancer therapeutics. Drug repositioning introduces an affordable and efficient strategy to discover novel drug action, especially when integrated with recent systems biology driven stratagem. This review illustrates the trendsetting approaches in repurposing along with their numerous success stories with an emphasize on the NSCLC therapeutics. Indeed, these novel hits, in combination with conventional anticancer agents, will ideally make their way the clinics and strengthen the therapeutic arsenal to combat drug resistance in the near future.
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Affiliation(s)
- Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sayoni Maiti
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Woong-Hee Shin
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, United States; Department of Chemistry Education, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Daisuke Kihara
- Department of Biological Science, Purdue University, West Lafayette, IN, 47907, United States; Department of Computer Science, Purdue University, West Lafayette, IN, 47907, United States; Purdue University, Center for Cancer Research, West Lafayette, IN, 47907, United States; Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45229, United States
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Kanakaveti V, Anoosha P, Sakthivel R, Rayala S, Gromiha M. Influence of Amino Acid Mutations and Small Molecules on Targeted Inhibition of Proteins Involved in Cancer. Curr Top Med Chem 2019; 19:457-466. [DOI: 10.2174/1568026619666190304143354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/19/2018] [Accepted: 12/28/2018] [Indexed: 12/23/2022]
Abstract
Background:Protein-protein interactions (PPIs) are of crucial importance in regulating the biological processes of cells both in normal and diseased conditions. Significant progress has been made in targeting PPIs using small molecules and achieved promising results. However, PPI drug discovery should be further accelerated with better understanding of chemical space along with various functional aspects.Objective:In this review, we focus on the advancements in computational research for targeted inhibition of protein-protein interactions involved in cancer.Methods:Here, we mainly focused on two aspects: (i) understanding the key roles of amino acid mutations in epidermal growth factor receptor (EGFR) as well as mutation-specific inhibitors and (ii) design of small molecule inhibitors for Bcl-2 to disrupt PPIs.Results:The paradigm of PPI inhibition to date reflect the certainty that inclination towards novel and versatile strategies enormously dictate the success of PPI inhibition. As the chemical space highly differs from the normal drug like compounds the lead optimization process has to be given the utmost priority to ensure the clinical success. Here, we provided a broader perspective on effect of mutations in oncogene EGFR connected to Bcl-2 PPIs and focused on the potential challenges.Conclusion:Understanding and bridging mutations and altered PPIs will provide insights into the alarming signals leading to massive malfunctioning of a biological system in various diseases. Finding rational elucidations from a pharmaceutical stand point will presumably broaden the horizons in future.
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Affiliation(s)
- V. Kanakaveti
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - P. Anoosha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - R. Sakthivel
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - S.K. Rayala
- Molecular Oncology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai - 600036, Tamil Nadu, India
| | - M.M. Gromiha
- Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
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