CIPDB: A biological structure databank for studying cation and π interactions

Jing-Fang Yang; Fan Wang; Meng-Yao Wang; Di Wang; Zhong-Shi Zhou; Ge-Fei Hao; Qing X Li; Guang-Fu Yang

doi:10.1016/j.drudis.2023.103546

CIPDB: A biological structure databank for studying cation and π interactions

Drug Discov Today. 2023 May;28(5):103546. doi: 10.1016/j.drudis.2023.103546. Epub 2023 Mar 5.

Authors

Jing-Fang Yang¹, Fan Wang², Meng-Yao Wang², Di Wang², Zhong-Shi Zhou³, Ge-Fei Hao⁴, Qing X Li⁵, Guang-Fu Yang⁶

Affiliations

¹ Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
² Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China.
³ State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
⁴ Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China; State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, PR China. Electronic address: gefei_hao@foxmail.com.
⁵ Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA. Electronic address: qingl@hawaii.edu.
⁶ Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, PR China. Electronic address: gfyang@mail.ccnu.edu.cn.

PMID: 36871844
DOI: 10.1016/j.drudis.2023.103546

Abstract

As major forces for modulating protein folding and molecular recognition, cation and π interactions are extensively identified in protein structures. They are even more competitive than hydrogen bonds in molecular recognition, thus, are vital in numerous biological processes. In this review, we introduce the methods for the identification and quantification of cation and π interactions, provide insights into the characteristics of cation and π interactions in the natural state, and reveal their biological function together with our developed database (Cation and π Interaction in Protein Data Bank; CIPDB; http://chemyang.ccnu.edu.cn/ccb/database/CIPDB). This review lays the foundation for the in-depth study of cation and π interactions and will guide the use of molecular design for drug discovery.

Keywords: biological; cation-π; dataset; drug; function; noncovalent interaction; pesticide; structure.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Cations / chemistry
Drug Discovery*
Models, Molecular
Proteins* / metabolism

Substances

Proteins
Cations