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Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices

The continuous approval of covalent drugs in recent years for the treatment of diseases has led to an increased search for covalent agents by medicinal chemists and computational scientists worldwide. In the computational parlance, molecular docking which is a popular tool to investigate the interac...

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Autores principales: Oyedele, Abdul-Quddus Kehinde, Ogunlana, Abdeen Tunde, Boyenle, Ibrahim Damilare, Adeyemi, Ayodeji Oluwadamilare, Rita, Temionu Oluwakemi, Adelusi, Temitope Isaac, Abdul-Hammed, Misbaudeen, Elegbeleye, Oluwabamise Emmanuel, Odunitan, Tope Tunji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9441019/
https://www.ncbi.nlm.nih.gov/pubmed/36057867
http://dx.doi.org/10.1007/s11030-022-10523-4
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author Oyedele, Abdul-Quddus Kehinde
Ogunlana, Abdeen Tunde
Boyenle, Ibrahim Damilare
Adeyemi, Ayodeji Oluwadamilare
Rita, Temionu Oluwakemi
Adelusi, Temitope Isaac
Abdul-Hammed, Misbaudeen
Elegbeleye, Oluwabamise Emmanuel
Odunitan, Tope Tunji
author_facet Oyedele, Abdul-Quddus Kehinde
Ogunlana, Abdeen Tunde
Boyenle, Ibrahim Damilare
Adeyemi, Ayodeji Oluwadamilare
Rita, Temionu Oluwakemi
Adelusi, Temitope Isaac
Abdul-Hammed, Misbaudeen
Elegbeleye, Oluwabamise Emmanuel
Odunitan, Tope Tunji
author_sort Oyedele, Abdul-Quddus Kehinde
collection PubMed
description The continuous approval of covalent drugs in recent years for the treatment of diseases has led to an increased search for covalent agents by medicinal chemists and computational scientists worldwide. In the computational parlance, molecular docking which is a popular tool to investigate the interaction of a ligand and a protein target, does not account for the formation of covalent bond, and the increasing application of these conventional programs to covalent targets in early drug discovery practice is a matter of utmost concern. Thus, in this comprehensive review, we sought to educate the docking community about the realization of covalent docking and the existence of suitable programs to make their future virtual-screening events on covalent targets worthwhile and scientifically rational. More interestingly, we went beyond the classical description of the functionality of covalent-docking programs down to selecting the ‘best’ program to consult with during a virtual-screening campaign based on receptor class and covalent warhead chemistry. In addition, we made a highlight on how covalent docking could be achieved using random conventional docking software. And lastly, we raised an alert on the growing erroneous molecular docking practices with covalent targets. Our aim is to guide scientists in the rational docking pursuit when dealing with covalent targets, as this will reduce false-positive results and also increase the reliability of their work for translational research. GRAPHICAL ABSTRACT: [Image: see text]
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spelling pubmed-94410192022-09-06 Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices Oyedele, Abdul-Quddus Kehinde Ogunlana, Abdeen Tunde Boyenle, Ibrahim Damilare Adeyemi, Ayodeji Oluwadamilare Rita, Temionu Oluwakemi Adelusi, Temitope Isaac Abdul-Hammed, Misbaudeen Elegbeleye, Oluwabamise Emmanuel Odunitan, Tope Tunji Mol Divers Comprehensive Review The continuous approval of covalent drugs in recent years for the treatment of diseases has led to an increased search for covalent agents by medicinal chemists and computational scientists worldwide. In the computational parlance, molecular docking which is a popular tool to investigate the interaction of a ligand and a protein target, does not account for the formation of covalent bond, and the increasing application of these conventional programs to covalent targets in early drug discovery practice is a matter of utmost concern. Thus, in this comprehensive review, we sought to educate the docking community about the realization of covalent docking and the existence of suitable programs to make their future virtual-screening events on covalent targets worthwhile and scientifically rational. More interestingly, we went beyond the classical description of the functionality of covalent-docking programs down to selecting the ‘best’ program to consult with during a virtual-screening campaign based on receptor class and covalent warhead chemistry. In addition, we made a highlight on how covalent docking could be achieved using random conventional docking software. And lastly, we raised an alert on the growing erroneous molecular docking practices with covalent targets. Our aim is to guide scientists in the rational docking pursuit when dealing with covalent targets, as this will reduce false-positive results and also increase the reliability of their work for translational research. GRAPHICAL ABSTRACT: [Image: see text] Springer International Publishing 2022-09-04 /pmc/articles/PMC9441019/ /pubmed/36057867 http://dx.doi.org/10.1007/s11030-022-10523-4 Text en © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2022, Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Comprehensive Review
Oyedele, Abdul-Quddus Kehinde
Ogunlana, Abdeen Tunde
Boyenle, Ibrahim Damilare
Adeyemi, Ayodeji Oluwadamilare
Rita, Temionu Oluwakemi
Adelusi, Temitope Isaac
Abdul-Hammed, Misbaudeen
Elegbeleye, Oluwabamise Emmanuel
Odunitan, Tope Tunji
Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices
title Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices
title_full Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices
title_fullStr Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices
title_full_unstemmed Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices
title_short Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices
title_sort docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices
topic Comprehensive Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9441019/
https://www.ncbi.nlm.nih.gov/pubmed/36057867
http://dx.doi.org/10.1007/s11030-022-10523-4
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