In-silico identification and optimization of MMP-9 inhibitors for cerebral ischemia using structure based virtual screening, MD simulation, and binding free energy calculations

Jian Zhang; Beibei Zhang; Haisong Feng; Chongxiao Sheng

doi:10.1371/journal.pone.0346627

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Open Access

Peer-reviewed

Research Article

In-silico identification and optimization of MMP-9 inhibitors for cerebral ischemia using structure based virtual screening, MD simulation, and binding free energy calculations

Jian Zhang ,

Contributed equally to this work with: Jian Zhang, Beibei Zhang

Roles Data curation, Writing – original draft

Affiliations Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei, China, Hubei Key Laboratory of theory and application research of liver and kidney in traditional Chinese Medicine, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, Hubei, China
⨯
Beibei Zhang ,

Contributed equally to this work with: Jian Zhang, Beibei Zhang

Roles Methodology, Writing – original draft

Affiliations Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei, China, Hubei Key Laboratory of theory and application research of liver and kidney in traditional Chinese Medicine, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, Hubei, China
⨯
Haisong Feng ,

Roles Validation, Visualization, Writing – review & editing

* E-mail: chongsheng996@gmail.com (CS); fenghaisong1986@163.com (HF)

Affiliations Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei, China, Hubei Key Laboratory of theory and application research of liver and kidney in traditional Chinese Medicine, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, Hubei, China
⨯
Chongxiao Sheng

Roles Conceptualization, Supervision, Validation, Writing – review & editing

* E-mail: chongsheng996@gmail.com (CS); fenghaisong1986@163.com (HF)

Affiliations Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei, China, Hubei Key Laboratory of theory and application research of liver and kidney in traditional Chinese Medicine, Affiliated Hospital of Hubei University of Chinese Medicine, Wuhan, Hubei, China

https://orcid.org/0009-0007-4158-8874

⨯

In-silico identification and optimization of MMP-9 inhibitors for cerebral ischemia using structure based virtual screening, MD simulation, and binding free energy calculations

Jian Zhang,
Beibei Zhang,
Haisong Feng,
Chongxiao Sheng

Published: May 14, 2026
https://doi.org/10.1371/journal.pone.0346627

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