Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.
Malaria Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.
Molecules. 2021 May 7;26(9):2742. doi: 10.3390/molecules26092742.
The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.
丝氨酸蛋白酶 DegP 具有蛋白水解和分子伴侣活性，这对于真核生物的细胞蛋白质量控制和正常细胞发育是必不可少的。DegP 对于寄生虫的存活至关重要，并且需要对抗感染过程中振荡的热应激条件、细胞外腔室中的蛋白质质量检查和蛋白质动态平衡，从而使其成为抗疟疾药物开发的潜在靶标。先前的研究表明，二异丙基氟磷酸酯（DFP）和肽 SPMFKGV 抑制 DegP 蛋白酶活性。为了鉴定针对 PfDegP 别构和催化结合位点的新型潜在抑制剂，我们使用 Malaria Box、Pathogen Box、Maybridge 文库、ChEMBL 文库和 FDA 批准化合物库进行了高通量计算机筛选。筛选有助于鉴定出与 PfDegP 别构（T0873、T2823、T2801、RJC02337、CD00811）和催化结合位点（T0078L、T1524、T2328、BTB11534 和 552691）具有高亲和力的五种最佳结合物。此外，分子动力学模拟分析表明，RJC02337、BTB11534 是形成稳定复合物的最佳命中物。水图和静电互补性用于评估 RJC02337 的新型生物等排化学型，从而确定了 231 种表现出更好结合亲和力的化学型。基于更好的结合亲和力对前 5 种化学型进行进一步分析表明，将供电子体（如氮和硫）添加到丁酸侧链比丁酸侧链更有利于增加结合亲和力。简而言之，本研究使用高通量计算机筛选和生物等排取代来鉴定新型、有效和特异性抑制剂，这些抑制剂可能需要通过实验验证。
