Shakil Shazi, Rizvi Syed M Danish, Greig Nigel H
King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
Antibiotics (Basel). 2021 Apr 21;10(5):474. doi: 10.3390/antibiotics10050474.
Multidrug resistant bacteria are a major therapeutic challenge. CTX-M-type enzymes are an important group of class A extended-spectrum β-lactamases (ESBLs). ESBLs are the enzymes that arm bacterial pathogens with drug resistance to an array of antibiotics, notably the advanced-generation cephalosporins. The current need for an effective CTX-M-inhibitor is high.
The aim of the current study was to identify a promising anti-CTX-M-15 ligand whose chemical skeleton could be used as a 'seed-molecule' for future drug design against resistant bacteria.
Virtual screening of 5,000,000 test molecules was performed by 'MCULE Drug Discovery Platform'. 'ADME analyses' was performed by 'SWISS ADME'. TOXICITY CHECKER of MCULE was employed to predict the safety profile of the test molecules. The complex of the 'Top inhibitor' with the 'bacterial CTX-M-15 enzyme' was subjected to 102.25 ns molecular dynamics simulation. This simulation was run for 3 days on a HP ZR30w workstation. Trajectory analyses were performed by employing the macro 'md_analyze.mcr' of YASARA STRUCTURE version 20.12.24.W.64 using AMBER14 force field. YANACONDA macro language was used for complex tasks. Figures, including RMSD and RMSF plots, were generated. Snapshots were acquired after every 250 ps. Finally, two short videos of '41 s' and '1 min and 22 s' duration were recorded.
5-Amino-1-(2H-[1,2,4]triazino[5,6-b]indol-3-yl)-1H-pyrazole-4-carbonitrile, denoted by the MCULE-1352214421-0-56, displayed the most efficient binding with bacterial CTX-M-15 enzyme. This screened molecule significantly interacted with CTX-M-15 via 13 amino acid residues. Notably, nine amino acid residues were found common to avibactam binding (the reference ligand). Trajectory analysis yielded 410 snapshots. The RMSD plot revealed that around 26 ns, equilibrium was achieved and, thereafter, the complex remained reasonably stable. After a duration of 26 ns and onwards until 102.25 ns, the backbone RMSD fluctuations were found to be confined within a range of 0.8-1.4 Å.
5-Amino-1-(2H-[1,2,4]triazino[5,6-b]indol-3-yl)-1H-pyrazole-4-carbonitrile could emerge as a promising seed molecule for CTX-M-15-inhibitor design. It satisfied ADMET features and displayed encouraging 'simulation results'. Advanced plots obtained by trajectory analyses predicted the stability of the proposed protein-ligand complex. 'Hands on' wet laboratory validation is warranted.
多重耐药菌是主要的治疗挑战。CTX-M型酶是A类超广谱β-内酰胺酶（ESBLs）中的重要一组。ESBLs是使细菌病原体对一系列抗生素产生耐药性的酶，尤其是对新一代头孢菌素。目前对有效的CTX-M抑制剂的需求很高。
本研究的目的是鉴定一种有前景的抗CTX-M-15配体，其化学骨架可作为未来抗耐药菌药物设计的“种子分子”。
通过“MCULE药物发现平台”对500万个测试分子进行虚拟筛选。通过“SWISS ADME”进行“ADME分析”。使用MCULE的毒性检查器预测测试分子的安全性。将“顶级抑制剂”与“细菌CTX-M-15酶”的复合物进行102.25纳秒的分子动力学模拟。该模拟在HP ZR30w工作站上运行3天。使用YASARA STRUCTURE 20.12.24.W.64版本的宏“md_analyze.mcr”并采用AMBER14力场进行轨迹分析。使用YANACONDA宏语言处理复杂任务。生成了包括均方根偏差（RMSD）和均方根波动（RMSF）图在内的图表。每250皮秒获取一次快照。最后，记录了时长分别为“41秒”和“1分22秒”的两个短视频。
5-氨基-1-(2H-[1,2,4]三嗪并[5,6-b]吲哚-3-基)-1H-吡唑-4-甲腈，编号为MCULE-1352214421-0-56，与细菌CTX-M-15酶显示出最有效的结合。该筛选出的分子通过13个氨基酸残基与CTX-M-15显著相互作用。值得注意的是，发现9个氨基酸残基与阿维巴坦结合（参考配体）相同。轨迹分析产生了410个快照。RMSD图显示，在约26纳秒时达到平衡，此后复合物保持相当稳定。在26纳秒及之后直到102.25纳秒期间，主链RMSD波动被限制在0.8 - 1.4埃的范围内。
5-氨基-1-(2H-[1,2,4]三嗪并[5,6-b]吲哚-3-基)-1H-吡唑-4-甲腈可能成为CTX-M-15抑制剂设计中有前景的种子分子。它满足ADMET特性并显示出令人鼓舞的“模拟结果”。通过轨迹分析获得的高级图表预测了所提出的蛋白质-配体复合物的稳定性。需要进行实际的湿实验室验证。
