Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan.
Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States.
J Chem Inf Model. 2023 Nov 13;63(21):6681-6695. doi: 10.1021/acs.jcim.3c00780. Epub 2023 Oct 17.
Antibiotic resistance by bacterial pathogens against widely used β-lactam drugs is a major concern to public health worldwide, resulting in high healthcare cost. The present study aimed to extend previous research by investigating the potential activity of reported compounds against the β-lactamase protein. 74 compounds from computational screening reported in our previous study against β-lactamase CMY-10 were subjected to docking studies against blaCTX-M15. Site-Identification by Ligand Competitive Saturation (SILCS)-Monte Carlo (SILCS-MC) was applied to the top two ligands selected from molecular docking studies to predict and refine their conformations for binding conformations against blaCTX-M15. The SILCS-MC method predicted affinities of -8.6 and -10.7 kcal/mol for Top1 and Top2, respectively, indicating low micromolar binding to the blaCTX-M15 active site. MD simulations initiated from SILCS-MC docked orientations were carried out to better characterize the dynamics and stability of the complexes. Important interactions anchoring the ligand within the active site include pi-pi stacked, amide-pi, and pi-alkyl interactions. Simulations of the Top2-blaCTX-M15 complex exhibited stability associated with a wide range of hydrogen-bond and aromatic interactions between the protein and the ligand. Experimental β-lactamase (BL) activity assays showed that Top1 has 0.1 u/mg BL activity, and Top2 has a BL activity of 0.038 u/mg with a minimum inhibitory concentration of 1 mg/mL. The inhibitors proposed in this study are non-β-lactam-based β-lactamase inhibitors that exhibit the potential to be used in combination with β-lactam antibiotics against multidrug-resistant clinical isolates. Thus, Top1 and Top2 represent lead compounds that increase the efficacy of β-lactam antibiotics with a low dose concentration.
细菌病原体对广泛使用的β-内酰胺类药物的耐药性是全球公共卫生的主要关注点，导致医疗保健成本高昂。本研究旨在通过研究报道的化合物对β-内酰胺酶蛋白的潜在活性来扩展先前的研究。在我们之前的研究中，对 74 种来自计算筛选的化合物进行了对接研究，以对抗 blaCTX-M15。应用配体竞争饱和（SILCS）-蒙特卡罗（SILCS-MC）对分子对接研究中选择的前两个配体进行了位点鉴定，以预测和细化它们与 blaCTX-M15 的结合构象。SILCS-MC 方法预测 Top1 和 Top2 的亲和力分别为-8.6 和-10.7 kcal/mol，表明对 blaCTX-M15 活性位点的低微摩尔结合。从 SILCS-MC 对接取向开始进行 MD 模拟，以更好地描述复合物的动力学和稳定性。将配体锚定在活性位点内的重要相互作用包括 pi-pi 堆积、酰胺-pi 和 pi-烷基相互作用。Top2-blaCTX-M15 复合物的模拟显示出与广泛的氢键和芳香族相互作用相关的稳定性，这些相互作用存在于蛋白质和配体之间。实验性β-内酰胺酶（BL）活性测定表明，Top1 的 BL 活性为 0.1 u/mg，Top2 的 BL 活性为 0.038 u/mg，最小抑菌浓度为 1 mg/mL。本研究提出的抑制剂是非β-内酰胺类β-内酰胺酶抑制剂，具有与β-内酰胺类抗生素联合用于对抗多药耐药临床分离株的潜力。因此，Top1 和 Top2 代表了增加β-内酰胺类抗生素疗效的先导化合物，其剂量浓度较低。
