Brefeldin A variant via combinatorial screening acts as an effective antagonist inducing structural modification in EPAC2

布雷菲尔德A 化学 对接(动物) 敌手 基因亚型 立体化学 计算生物学 组合化学 生物化学 受体 生物 高尔基体 细胞 医学 护理部 基因
作者
Akshay Uttarkar,Vidya Niranjan
出处
期刊:Molecular Simulation [Informa]
卷期号:48 (17): 1592-1603 被引量:3
标识
DOI:10.1080/08927022.2022.2110271
摘要

Drug discovery can be impactful with re-purposing and combinatorial strategies leading to potential pharmaceutical outputs. EPAC isoform inhibition is crucial in vascular functions to prevent chronic inflammation leading to hypertension and myocardial infarction. Current drugs fail to induce a conformational change in EPAC isoforms. An attempt utilising brefeldin A, a natural inhibitor was subjected to a substitution of 3 side-chain groups with 43 fragments via combinatorial strategy. This resulted in generating a library of 79,507 brefeldin A variants. High throughput virtual screening yielded 68,043 variants followed by precision docking providing 117 lead-like brefeldin A variants. The best-docked variant labelled as BrefA1 has increased binding efficiency of −10.841 kcal/mol compared to cAMP2 (positive control) with −10.692 kcal/mol. Simulation studies up to 200 ns of complex lead to re-orientation of target tertiary structure resulted in RMSD change of 30.221 Å, suggesting the EPAC2 structure modification leading to unavailability of RAS-GEF domain and its interaction with Rap1b. To identify the new conformation of EPAC2 single domain antibody was designed to bind specifically to re-structured EPAC2 for potential identification over the native target structure. The resulting Brefeldin variant can be potentially labelled as the most effective antagonist against EPAC2 which induces theoretically irreversible structural re-conformation.
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