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

Guang-Hui Ma; Yan Ye; Dan Zhang; Xin Xu; Pei Si; Jian-Long Peng; Yong-Long Xiao; Rui-Yuan Cao; Yu-Ling Yin; Jing Chen; Lin-Xiang Zhao; Yu Zhou; Wu Zhong; Hong Liu; Xiao-Min Luo; Li-Li Chen; Xu Shen

doi:10.1016/j.ejmech.2016.10.019

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

Eur J Med Chem. 2016 Nov 29:124:981-991. doi: 10.1016/j.ejmech.2016.10.019. Epub 2016 Oct 11.

Authors

Guang-Hui Ma¹, Yan Ye², Dan Zhang³, Xin Xu⁴, Pei Si⁵, Jian-Long Peng⁶, Yong-Long Xiao⁴, Rui-Yuan Cao⁷, Yu-Ling Yin⁴, Jing Chen⁴, Lin-Xiang Zhao⁸, Yu Zhou⁹, Wu Zhong⁷, Hong Liu⁴, Xiao-Min Luo¹⁰, Li-Li Chen¹¹, Xu Shen⁴

Affiliations

¹ Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Rd, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd, Pudong, Shanghai 201210, China.
² Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Rd, Beijing 100191, China; University of Chinese Academy of Sciences, No.19A Yuquan Rd, Beijing 100049, China.
³ Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, 103 Culture Rd, Shenyang 110016, China.
⁴ Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
⁵ Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; College of Life and Environmental Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai 200234, China.
⁶ Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
⁷ Beijing Institute of Pharmacology and Toxicology, 27 Taiping Rd., Beijing 100850, China.
⁸ Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, 103 Culture Rd, Shenyang 110016, China.
⁹ Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China. Electronic address: zhouyu@simm.ac.cn.
¹⁰ Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Rd, Beijing 100191, China. Electronic address: xmluo@simm.ac.cn.
¹¹ Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China. Electronic address: lilichen@simm.ac.cn.

PMID: 27776325
DOI: 10.1016/j.ejmech.2016.10.019

Abstract

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 3C^pro 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 3C^pro inhibitors by docking-based virtual screening. Totally 50 compounds were selected to test their inhibitory activity against EV71 3C^pro. 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 3C^pro 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 3C^pro. 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.

Keywords: EV71 3C(pro); HFMD; Non-peptidyl inhibitor; Virtual screening.

MeSH terms

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*
Humans
Molecular Docking Simulation
Molecular Dynamics Simulation
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

Substances

Antiviral Agents
DC07090
Oxazoles
Pyridines
Viral Proteins
Cysteine Endopeptidases
3C Viral Proteases