Literature DB >> 32072438

Covalent Versus Non-covalent Enzyme Inhibition: Which Route Should We Take? A Justification of the Good and Bad from Molecular Modelling Perspective.

Aimen Aljoundi1, Imane Bjij1,2, Ahmed El Rashedy1, Mahmoud E S Soliman3.   

Abstract

The pace and efficiency of drug target strategies have been emanating debates among researchers in the field of drug development. Covalent inhibitors possess significant advantages over non-covalent inhibitors, such that covalent warheads can target rare residues of a particular target protein, thus leading to the development of highly selective inhibitors. However, toxicity can be a real challenge related to this class of therapeutics. From the challenges of irreversible drug toxicity to the declining reactivity of reversible drugs, herein we provide justifications from the computational point of view. It was evident that both classes had its merits; however, with the increase in drug resistance, covalent inhibition seemed more suitable. There also seems to be enhanced selectivity of the covalent systems, proving its use as a therapeutic regimen worldwide. We believe that this study will assist researchers in making informed decisions on which drug class to choose as lead compounds in the drug discovery pipeline.

Entities:  

Keywords:  Covalent inhibition; Merits; Non-covalent inhibition; Pitfalls

Year:  2020        PMID: 32072438     DOI: 10.1007/s10930-020-09884-2

Source DB:  PubMed          Journal:  Protein J        ISSN: 1572-3887            Impact factor:   2.371


  38 in total

1.  A systematic review of the associations between dose regimens and medication compliance.

Authors:  A J Claxton; J Cramer; C Pierce
Journal:  Clin Ther       Date:  2001-08       Impact factor: 3.393

2.  Identifying and characterizing binding sites and assessing druggability.

Authors:  Thomas A Halgren
Journal:  J Chem Inf Model       Date:  2009-02       Impact factor: 4.956

Review 3.  Covalent inhibitors in drug discovery: from accidental discoveries to avoided liabilities and designed therapies.

Authors:  Renato A Bauer
Journal:  Drug Discov Today       Date:  2015-05-19       Impact factor: 7.851

4.  Covalent simulations of covalent/irreversible enzyme inhibition in drug discovery: a reliable technical protocol.

Authors:  Shama Khan; Imane Bjij; Fisayo A Olotu; Clement Agoni; Emmanuel Adeniji; Mahmoud E S Soliman
Journal:  Future Med Chem       Date:  2018-10       Impact factor: 3.808

Review 5.  Latest developments in molecular docking: 2010-2011 in review.

Authors:  Elizabeth Yuriev; Paul A Ramsland
Journal:  J Mol Recognit       Date:  2013-05       Impact factor: 2.137

6.  Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments.

Authors:  G Madhavi Sastry; Matvey Adzhigirey; Tyler Day; Ramakrishna Annabhimoju; Woody Sherman
Journal:  J Comput Aided Mol Des       Date:  2013-04-12       Impact factor: 3.686

7.  Electrophilic fragment-based design of reversible covalent kinase inhibitors.

Authors:  Rand M Miller; Ville O Paavilainen; Shyam Krishnan; Iana M Serafimova; Jack Taunton
Journal:  J Am Chem Soc       Date:  2013-03-29       Impact factor: 15.419

8.  Hydrogen-bond relays in concerted proton-electron transfers.

Authors:  Julien Bonin; Cyrille Costentin; Marc Robert; Jean-Michel Savéant; Cédric Tard
Journal:  Acc Chem Res       Date:  2011-10-26       Impact factor: 22.384

9.  The irony of chirality - unveiling the distinct mechanistic binding and activities of 1-(3-(4-amino-5-(7-methoxy-5-methylbenzo[b]thiophen-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)pyrrolidin-1-yl)prop-2-en-1-one enantiomers as irreversible covalent FGFR4 inhibitors.

Authors:  Farideh Badichi Akher; Abdolkarim Farrokhzadeh; Fisayo A Olotu; Clement Agoni; Mahmoud E S Soliman
Journal:  Org Biomol Chem       Date:  2019-01-31       Impact factor: 3.876

Review 10.  Lysine-Targeting Covalent Inhibitors.

Authors:  Jonathan Pettinger; Keith Jones; Matthew D Cheeseman
Journal:  Angew Chem Int Ed Engl       Date:  2017-10-27       Impact factor: 15.336

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  10 in total

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Journal:  Mol Biol Rep       Date:  2021-01-20       Impact factor: 2.316

Review 2.  Reactivity-based chemical-genetic study of protein kinases.

Authors:  Renata Rezende Miranda; Chao Zhang
Journal:  RSC Med Chem       Date:  2022-03-30

3.  Design, Synthesis and Evaluation of Fused Bicyclo[2.2.2]octene as a Potential Core Scaffold for the Non-Covalent Inhibitors of SARS-CoV-2 3CLpro Main Protease.

Authors:  Barbara Herlah; Andrej Hoivik; Luka Jamšek; Katja Valjavec; Norio Yamamoto; Tyuji Hoshino; Krištof Kranjc; Andrej Perdih
Journal:  Pharmaceuticals (Basel)       Date:  2022-04-27

4.  Atomistic-Level Description of the Covalent Inhibition of SARS-CoV-2 Papain-like Protease.

Authors:  Cécilia Hognon; Marco Marazzi; Cristina García-Iriepa
Journal:  Int J Mol Sci       Date:  2022-05-23       Impact factor: 6.208

5.  Current and Emerging Tools of Computational Biology To Improve the Detoxification of Mycotoxins.

Authors:  Natalie Sandlin; Darius Russell Kish; John Kim; Marco Zaccaria; Babak Momeni
Journal:  Appl Environ Microbiol       Date:  2021-12-08       Impact factor: 5.005

6.  The Mpro structure-based modifications of ebselen derivatives for improved antiviral activity against SARS-CoV-2 virus.

Authors:  Zhen Qiao; Ningning Wei; Lin Jin; Hongyi Zhang; Jiajie Luo; Yanru Zhang; KeWei Wang
Journal:  Bioorg Chem       Date:  2021-10-30       Impact factor: 5.275

Review 7.  Potential Inhibitors Targeting Papain-Like Protease of SARS-CoV-2: Two Birds With One Stone.

Authors:  Haihai Jiang; Peiyao Yang; Jin Zhang
Journal:  Front Chem       Date:  2022-02-23       Impact factor: 5.221

8.  1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors: In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates.

Authors:  Kuppuswamy Kavitha; Subramaniam Sivakumar; Balasubramanian Ramesh
Journal:  Biophys Chem       Date:  2020-09-22       Impact factor: 2.352

9.  Isolation and Characterization of an Endophytic Fungus Colletotrichum coccodes Producing Tyrosol From Houttuynia cordata Thunb. Using ITS2 RNA Secondary Structure and Molecular Docking Study.

Authors:  Rajreepa Talukdar; Srichandan Padhi; Amit K Rai; Marco Masi; Antonio Evidente; Dhruva Kumar Jha; Alessio Cimmino; Kumananda Tayung
Journal:  Front Bioeng Biotechnol       Date:  2021-06-17

10.  Repurposing of FDA-approved drugs against active site and potential allosteric drug-binding sites of COVID-19 main protease.

Authors:  Merve Yuce; Erdem Cicek; Tugce Inan; Aslihan Basak Dag; Ozge Kurkcuoglu; Fethiye Aylin Sungur
Journal:  Proteins       Date:  2021-07-05
  10 in total

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