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Front. Chem. | doi: 10.3389/fchem.2018.00564

GPU accelerated Quantum Virtual Screening: Application for the natural inhibitors of New Dehli Metalloprotein (NDM-1)

Mingsong Shi1,  Dingguo Xu1* and  Jun Zeng2
  • 1Sichuan University, China
  • 2MedChemSoft Solutions, Australia

Quantum mechanical approaches for the massive computation on large biological system such as virtual screening in drug design and development have presented a challenge to computational chemists for many years. In this study, we demonstrated that by taking advantage of rapid growth of GPU-based hardware and software (i.e. teraChem), it is feasible to perform virtual screening of a refined chemical library at quantum mechanical level in order to identify the lead compounds with improved accuracy, especially for the drug targets such as metalloproteins in which significant charge transfer and polarization occur amongst the metal ions and their coordinated amino acids. Our calculations predicted four nature compounds (i.e. Curcumin, Catechin, menthol, and Ferulic acid) as the suitable inhibitors for antibiotics resistance against New Delhi Metallo--lactamase-1 (NDM-1). Molecular orbitals (MOs) of the QM region of metal ions and their coordinated residues indicate that the bridged hydroxide ion delocalized the electron over the Zn-OH-Zn group at HOMO, different from MOs when the OH- is not presented in NDM-1. This indicates that the bridged hydroxide ion plays an important role in the design of antibiotics and other inhibitors targeting the metalloproteins.

Keywords: Virtual Screening, QM/MM, gpu, NDM-1, Natural inhibitors

Received: 09 Oct 2018; Accepted: 31 Oct 2018.

Edited by:

Yong Wang, Ningbo University, China

Reviewed by:

Jun Gao, Huazhong Agricultural University, China
Qing-Chuan Zheng, Jilin University, China
Fei Xia, East China Normal University, China  

Copyright: © 2018 Shi, Xu and Zeng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Dingguo Xu, Sichuan University, Chengdu, 610065, Sichuan Province, China, dgxu@scu.edu.cn