Identification and biochemical characterization of DC07090 as a novel potent small molecule inhibitor against human enterovirus 71 3C protease by structure-based virtual screening

• Published in: European journal of medicinal chemistry 2016-11, Vol.124, p.981-991
• Main Authors: Ma, Guang-Hui, Ye, Yan, Zhang, Dan, Xu, Xin, Si, Pei, Peng, Jian-Long, Xiao, Yong-Long, Cao, Rui-Yuan, Yin, Yu-Ling, Chen, Jing, Zhao, Lin-Xiang, Zhou, Yu, Zhong, Wu, Liu, Hong, Luo, Xiao-Min, Chen, Li-Li, Shen, Xu
• Format: Article
• Language: English
• Subjects: 3C Viral Proteases; Antiviral Agents - chemistry; Antiviral Agents - metabolism; Antiviral Agents - pharmacology; Binding Sites; Cysteine Endopeptidases - chemistry; Cysteine Endopeptidases - metabolism; Drug Evaluation, Preclinical; Enterovirus A, Human - drug effects; Enterovirus A, Human - enzymology; EV71 3Cpro; HFMD; Humans; Molecular Docking Simulation; Molecular Dynamics Simulation; Non-peptidyl inhibitor; Oxazoles - chemistry; Oxazoles - metabolism; Oxazoles - pharmacology; Protein Conformation; Pyridines - chemistry; Pyridines - metabolism; Pyridines - pharmacology; Structure-Activity Relationship; User-Computer Interface; Viral Proteins - antagonists & inhibitors; Viral Proteins - chemistry; Viral Proteins - metabolism; Virtual screening
• ISSN: 0223-5234; 1768-3254
• DOI: 10.1016/j.ejmech.2016.10.019

Hand, foot and mouth disease (HFMD) is a serious, highly contagious disease. HFMD caused by Enterovirus 71 (EV71), results in severe complications and even death. The pivotal role of EV71 3Cpro in the viral life cycle makes it an attractive target for drug discovery and development to treat HFMD. In this study, we identified novel EV71 3Cpro inhibitors by docking-based virtual screening. Totally 50 compounds were selected to test their inhibitory activity against EV71 3Cpro. The best inhibitor DC07090 exhibited the inhibition potency with an IC50 value of 21.72 ± 0.95 μM without apparent toxicity (CC50 > 200 μM). To explore structure-activity relationship of DC07090, 15 new derivatives were designed, synthesized and evaluated in vitro enzyme assay accordingly. Interestingly, four compounds showed inhibitory activities against EV71 3Cpro and only DC07090 inhibited EV71 replication with an EC50 value of 22.09 ± 1.07 μM. Enzyme inhibition kinetic experiments showed that the compound was a reversible and competitive inhibitor. The Ki value was determined to be 23.29 ± 12.08 μM. Further molecular docking, MD simulation and mutagenesis studies confirmed the binding mode of DC07090 and EV71 3Cpro. Besides, DC07090 could also inhibit coxsackievirus A16 (CVA16) replication with an EC50 value of 27.76 ± 0.88 μM. Therefore, DC07090 represents a new non-peptidyl small molecule inhibitor for further development of antiviral therapy against EV71 or other picornaviruses. DC07090 as a novel potent small molecule inhibitor against human enterovirus 71 3C protease was identified with the combination of virtual screening and in vitro assays. Molecular docking, MD simulation and mutagenesis studies confirmed that DC07090 forms stable hydrogen-bonding interaction with the main chain of S128, G145, G164 and hydrophobic interaction with F25, L125, L127 and F170. [Display omitted] •A novel non-peptidyl small molecule inhibitor against EV71 was identified.•The compound might have broader activity against other entero/picornaviruses.•Some amino acid residues of EV71 3Cpro might be involved in substrate recognition.