Structure-based drug design, synthesis and screening of MmaA1 inhibitors as novel anti-TB agents
作者:Hymavathi Veeravarapu、Vasavi Malkhed、Kiran Kumar Mustyala、Rajender Vadija、Ramesh Malikanti、Uma Vuruputuri、Murali Krishna Kumar Muthyala
DOI:10.1007/s11030-020-10107-0
日期:2021.2
Tuberculosis is one of the leading causes of death across the world. The treatment regimens for tuberculosis are well established, but still the control of the disease faces many challenges such as lengthy treatment protocols, drug resistance and toxicity. In the present work, mycolic acid methyl transferase (MmaA1), a protein involved in the maturation of mycolic acids in the biochemical pathway of the Mycobacterium, was studied for novel drug discovery. The homology model of the MmaA1 protein was built and validated by using computational techniques. The MmaA1 protein has 286 amino acid residues consisting of 10 α-helices and 7 β-sheets. The active site of the MmaA1 protein was identified using CASTp, SiteMap and PatchDock. Virtual screening studies were performed with two small molecule ligand databases: Asinex synergy and Diverse_Elite_Gold_Platinum databases having a total of 43,446 molecules and generated 1,30,814 conformers against the predicted and validated active site of the MmaA1 protein. Binding analysis showed that the residues ASP 19, PHE 22, TRP 30, TYR 32, TRP 74 and ALA 77 of MmaA1 protein have consistent interactions with the ligands. The hit ligands were further filtered by in silico ADME properties to eliminate potentially toxic molecules. Of the top 10 molecules, 3-(2-morpholinoacetamido)-N-(1,4-dihydro-4-oxoquinazolin-6-yl) benzamide was synthesised and screened for in vitro anti-TB activity against Mtb H37Rv using MABA assay. The compound and its intermediates exhibited good in vitro anti-TB activity which can be taken up for future lead optimisation studies. Structure based virtual screening study was performed using a validated homology model against small molecules from two virtual compound libraries. Synthesised the lead compound 3-(2-morpholinoacetamido)-N-(1,4-dihydro-4-oxoquinazolin-6-yl)benzamide obtained from virtual screening. In vitro activity against Mtb H37Rv has given a promising result.
结核病是导致全球死亡的主要原因之一。结核病的治疗方案已经非常成熟,但该疾病的控制仍然面临着许多挑战,如治疗方案冗长、耐药性和毒性。霉菌酸甲基转移酶(MmaA1)是分枝杆菌生化途径中参与霉菌酸成熟的一种蛋白质,本研究对其进行了研究,以发现新的药物。利用计算技术建立并验证了 MmaA1 蛋白的同源模型。MmaA1 蛋白有 286 个氨基酸残基,由 10 个 α-螺旋和 7 个 β-片层组成。利用 CASTp、SiteMap 和 PatchDock 确定了 MmaA1 蛋白的活性位点。利用两个小分子配体数据库进行了虚拟筛选研究:虚拟筛选研究使用了两个小分子配体数据库:Asinex synergy 和 Diverse_Elite_Gold_Platinum 数据库,这两个数据库共有 43,446 个分子,根据预测和验证的 MmaA1 蛋白活性位点生成了 1,30,814 个构象。结合分析表明,MmaA1 蛋白的残基 ASP 19、PHE 22、TRP 30、TYR 32、TRP 74 和 ALA 77 与配体具有一致的相互作用。根据硅学 ADME 特性对命中配体进行了进一步筛选,以剔除潜在的毒性分子。在前 10 个分子中,合成了 3-(2-吗啉乙酰氨基)-N-(1,4-二氢-4-氧代喹唑啉-6-基)苯甲酰胺,并使用 MABA 试验筛选了其对 Mtb H37Rv 的体外抗结核活性。该化合物及其中间体表现出良好的体外抗结核活性,可用于未来的先导优化研究。利用经过验证的同源模型,对两个虚拟化合物库中的小分子化合物进行了基于结构的虚拟筛选研究。合成了从虚拟筛选中获得的先导化合物 3-(2-吗啉乙酰氨基)-N-(1,4-二氢-4-氧代喹唑啉-6-基)苯甲酰胺。对 Mtb H37Rv 的体外活性结果令人鼓舞。