Structure-based computational design of novel covalent binders for the treatment of sickle cell disease
The quest in finding an everlasting panacea to the pernicious impact of sickle cell disease (SCD) in the society hit a turn of success since the recent discovery of a small molecule reversible covalent inhibitor, Voxelotor. A drug that primarily promotes the stability of oxygenated hemoglobin and in...
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| Published in: | Journal of molecular graphics & modelling Vol. 124; p. 108549 |
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| Main Authors: | , , , , , , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
United States
Elsevier Inc
01-11-2023
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| Subjects: | |
| Online Access: | Get full text |
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| Summary: | The quest in finding an everlasting panacea to the pernicious impact of sickle cell disease (SCD) in the society hit a turn of success since the recent discovery of a small molecule reversible covalent inhibitor, Voxelotor. A drug that primarily promotes the stability of oxygenated hemoglobin and inhibit the polymerization of HbS by enhancing hemoglobin's affinity for oxygen has opened a new frontier in drug discovery and development. Despite eminent efforts made to reproduce small molecules with better therapeutic targets, none has been successful. To this end, we employed the use of structure-based computational techniques with emphasis on the electrophilic warhead group of Voxelotor to harness novel covalent binders that could elicit better therapeutic response against HbS. The PubChem database and DataWarrior software were used to design random molecules using Voxelotor's electrophilic functionality. Following the compilation of these chemical entities, a high-throughput covalent docking-based virtual screening campaign was conducted which revealed three (Compound_166, Compound_2301, and Compound_2335) putative druglike candidates with higher baseline energy value compared to the standard drug. Subsequently, in silico ADMET profiling was carried out to evaluate their pharmacokinetics and pharmacodynamics properties, and their stability was evaluated for 1 μs (1 μs) using molecular dynamics simulation. Finally, to prioritize these compounds for further development in drug discovery, MM/PBSA calculations was employed to evaluate their molecular interactions and solvation energy within the HbS protein. Despite the admirable druglike and stability properties of these compounds, further experimental validations are required to establish their preclinical relevance for drug development.
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•Covalent docking-based virtual screening campaign was used to identify potential inhibitors with higher binding affinity than the standard drug, Voxelotor against SCD.•Evaluation of pharmacokinetics and pharmacodynamics properties showed promising results for prospective drug-like compounds (Compound_166, Compound_2301, and Compound_2335).•While MD simulation revealed Compound_166 as a novel HbS inhibitor with structural stability, MM/PBSA calculations confirm Compound_166 and Compound_2301 as top candidates for future drug development.•Potential for Compound_166 to advance translational research and clinical trials for sickle cell disease is propitious as it emerges as the most promising candidate in all screening criteria. |
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| Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1093-3263 1873-4243 |
| DOI: | 10.1016/j.jmgm.2023.108549 |