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Theoretical and practical study of the cefoxitin‐Escherichia coli PBP5 complex interaction by molecular dynamics to obtain computational prototype of antimicrobial susceptibility to Gram negative bacteria
Chemical Biology & Drug Design ( IF 3 ) Pub Date : 2018-06-25 , DOI: 10.1111/cbdd.13358
Thaís Boulhosa Barros da Silva 1 , Marta Chagas Monteiro 1 , Rosivaldo Dos Santos Borges 2 , Tainá Guimarães Barros 3 , Agnaldo da Silva Carneiro 3 , Carlos Augusto Lima Barros 3
Affiliation  

The penicillin‐binding proteins (PBPs) are important biological target for new antibacterial drugs development. This study focused on molecular interaction between cefoxitin and the Escherichia coli PBP5 by molecular dynamics (MD) using hybrid quantum mechanics/molecular mechanics (QM/MM) simulations approach, searching to develop a computational simulations prototype method on antimicrobial susceptibility of gram‐negative bacteria against antibiotics. Escherichia coli ATCC 8739 strain susceptibility for the drugs used in the antimicrobial susceptibility testing and selection of bioactive molecules against resistant strain. The protonation revealed a deprotonate state for His146, His151, His216, and His320 residues. The complex was stabilized after 0.6 ns of MD simulation. The global interaction means for inhibition zone diameters of E. coli ATCC8739 strain and cefoxitin were 24.33 mm no showing significant difference between computational and experimental methods. Our computational simulation method can reliably be performed as a molecular modeling prototype for gram‐negative antimicrobial susceptibility testing bacteria.

中文翻译:

头孢西丁-大肠杆菌PBP5复合物相互作用的分子动力学理论和实践研究,以得到对革兰氏阴性细菌敏感的抗菌药物的计算原型

青霉素结合蛋白(PBPs)是开发新抗菌药物的重要生物学靶标。这项研究集中在头孢西丁与大肠杆菌PBP5之间的分子相互作用上,采用混合量子力学/分子力学(QM / MM)模拟方法,通过分子动力学(MD),寻求开发一种计算革兰氏阴性菌抗菌敏感性的计算机模拟原型方法。对抗抗生素。大肠杆菌ATCC 8739菌株的药敏性用于药物的药敏试验和抗药性选择的生物活性分子。质子化显示His146,His151,His216和His320残基处于质子化状态。MD模拟0.6 ns后,复合物稳定。大肠杆菌ATCC8739菌株和头孢西丁抑制区直径的整体相互作用方式为24.33 mm,在计算和实验方法之间没有显着差异。我们的计算模拟方法可以作为革兰氏阴性抗菌药敏感性测试细菌的分子建模原型可靠地执行。
更新日期:2018-06-25
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