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Updated: Sep 29, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Computational elucidation of allosteric communication in proteins for allosteric drug design
Duan Ni1, Yaqin Liu2, Ren Kong3
1College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China; State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China; The Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia.
Abstract:
Allosteric modulators target topologically distal allosteric sites in order to modulate orthosteric sites, providing enhanced specificity and physiochemical properties. Harnessing allostery for drug discovery is an emerging paradigm in modern pharmaceutics. Allosteric regulation substantially depends on the propagation of allosteric signaling. Delineating allosteric signaling pathways is therefore one of the leading prerequisites for allosteric drug discovery. Allosteric signal transduction is subtle and dynamic, posing challenges for characterization through traditional experimental techniques, but computational strategies promise to provide a solution to this problem. Here, we comprehensively review bioinformatic methods for elucidating allosteric communication, along with their successful applications in allosteric drug design. Current challenges and future perspectives are also discussed. We aim to provide guidance for the future application and optimization of these computational strategies, thereby promoting rational allosteric drug discovery.
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