Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls
he present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to co...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2015-01-01
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| Series: | Molecules |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1420-3049/20/2/1984 |
| _version_ | 1811314671077031936 |
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| author | Hezekiel Mathambo Kumalo Soumendranath Bhakat Mahmoud E. S. Soliman |
| author_facet | Hezekiel Mathambo Kumalo Soumendranath Bhakat Mahmoud E. S. Soliman |
| author_sort | Hezekiel Mathambo Kumalo |
| collection | DOAJ |
| description | he present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages over non-covalent inhibitors such as covalent warheads can target rare, non-conserved residue of a particular target protein and thus led to development of highly selective inhibitors, covalent inhibitors can be effective in targeting proteins with shallow binding cleavage which will led to development of novel inhibitors with increased potency than non-covalent inhibitors. Several computational approaches have been developed to simulate covalent interactions; however, this is still a challenging area to explore. Covalent molecular docking has been recently implemented in the computer-aided drug design workflows to describe covalent interactions between inhibitors and biological targets. In this review we highlight: (i) covalent interactions in biomolecular systems; (ii) the mathematical framework of covalent molecular docking; (iii) implementation of covalent docking protocol in drug design workflows; (iv) applications covalent docking: case studies and (v) shortcomings and future perspectives of covalent docking. To the best of our knowledge; this review is the first account that highlights different aspects of covalent docking with its merits and pitfalls. We believe that the method and applications highlighted in this study will help future efforts towards the design of irreversible inhibitors. |
| first_indexed | 2024-04-13T11:15:25Z |
| format | Article |
| id | doaj.art-5bc4d57ebf974477a431de2784053601 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-04-13T11:15:25Z |
| publishDate | 2015-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-5bc4d57ebf974477a431de27840536012022-12-22T02:48:58ZengMDPI AGMolecules1420-30492015-01-012021984200010.3390/molecules20021984molecules20021984Theory and Applications of Covalent Docking in Drug Discovery: Merits and PitfallsHezekiel Mathambo Kumalo0Soumendranath Bhakat1Mahmoud E. S. Soliman2Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South AfricaMolecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South AfricaMolecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africahe present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages over non-covalent inhibitors such as covalent warheads can target rare, non-conserved residue of a particular target protein and thus led to development of highly selective inhibitors, covalent inhibitors can be effective in targeting proteins with shallow binding cleavage which will led to development of novel inhibitors with increased potency than non-covalent inhibitors. Several computational approaches have been developed to simulate covalent interactions; however, this is still a challenging area to explore. Covalent molecular docking has been recently implemented in the computer-aided drug design workflows to describe covalent interactions between inhibitors and biological targets. In this review we highlight: (i) covalent interactions in biomolecular systems; (ii) the mathematical framework of covalent molecular docking; (iii) implementation of covalent docking protocol in drug design workflows; (iv) applications covalent docking: case studies and (v) shortcomings and future perspectives of covalent docking. To the best of our knowledge; this review is the first account that highlights different aspects of covalent docking with its merits and pitfalls. We believe that the method and applications highlighted in this study will help future efforts towards the design of irreversible inhibitors.http://www.mdpi.com/1420-3049/20/2/1984covalent dockingcovalent inhibitioncovalent interactionsirreversible inhibition |
| spellingShingle | Hezekiel Mathambo Kumalo Soumendranath Bhakat Mahmoud E. S. Soliman Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls Molecules covalent docking covalent inhibition covalent interactions irreversible inhibition |
| title | Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls |
| title_full | Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls |
| title_fullStr | Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls |
| title_full_unstemmed | Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls |
| title_short | Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls |
| title_sort | theory and applications of covalent docking in drug discovery merits and pitfalls |
| topic | covalent docking covalent inhibition covalent interactions irreversible inhibition |
| url | http://www.mdpi.com/1420-3049/20/2/1984 |
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