Along the allostery stream: Recent advances in computational methods for allosteric drug discovery

D Ni, Z Chai, Y Wang, M Li, Z Yu, Y Liu… - Wiley …, 2022 - Wiley Online Library
Allostery is a universal, biological phenomenon in which orthosteric sites are fine‐tuned by
topologically distal allosteric sites triggered by perturbations, such as ligand binding, residue …

Harnessing reversed allosteric communication: a novel strategy for allosteric drug discovery

J Fan, Y Liu, R Kong, D Ni, Z Yu, S Lu… - Journal of Medicinal …, 2021 - ACS Publications
Allostery is a fundamental and extensive mechanism of intramolecular signal transmission.
Allosteric drugs possess several unique pharmacological advantages over traditional …

Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy

D Ni, J Wei, X He, AU Rehman, X Li, Y Qiu, J Pu… - Chemical …, 2021 - pubs.rsc.org
Allostery, which is one of the most direct and efficient methods to fine-tune protein functions,
has gained increasing recognition in drug discovery. However, there are several challenges …

AlloReverse: multiscale understanding among hierarchical allosteric regulations

J Zha, Q Li, X Liu, W Lin, T Wang, J Wei… - Nucleic acids …, 2023 - academic.oup.com
Increasing data in allostery are requiring analysis of coupling relationships among different
allosteric sites on a single protein. Here, based on our previous efforts on reversed allosteric …

[HTML][HTML] D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19

Y Shi, X Zhang, K Mu, C Peng, Z Zhu, X Wang… - … Pharmaceutica Sinica B, 2020 - Elsevier
A highly effective medicine is urgently required to cure coronavirus disease 2019 (COVID-
19). For the purpose, we developed a molecular docking based webserver, namely …

New techniques and strategies in drug discovery

J Du, J Guo, D Kang, Z Li, G Wang, J Wu, Z Zhang… - Chinese Chemical …, 2020 - Elsevier
Great success has been witnessed in last decades, some new techniques and strategies
have been widely used in drug discovery. In this roadmap, several representative …

Untangling dual-targeting therapeutic mechanism of epidermal growth factor receptor (EGFR) based on reversed allosteric communication

Y Qiu, X Yin, X Li, Y Wang, Q Fu, R Huang, S Lu - Pharmaceutics, 2021 - mdpi.com
Dual-targeting therapeutics by coadministration of allosteric and orthosteric drugs is drawing
increased attention as a revolutionary strategy for overcoming the drug-resistance problems …

Computational insights into the conformational accessibility and binding strength of SARS-CoV-2 spike protein to human angiotensin-converting enzyme 2

C Peng, Z Zhu, Y Shi, X Wang, K Mu… - The journal of …, 2020 - ACS Publications
The spike protein of SARS-CoV-2 (CoV-2-S) mediates the virus entry into human cells.
Experimental studies have shown the stronger binding affinity of the RBD (receptor binding …

Mechanistic insights into the long-range allosteric regulation of KRAS via neurofibromatosis type 1 (NF1) scaffold upon SPRED1 loading

M Li, Y Wang, J Fan, H Zhuang, Y Liu, D Ji… - Journal of Molecular …, 2022 - Elsevier
Allosteric regulation is the most direct and efficient way of regulating protein function,
wherein proteins transmit the perturbations at one site to another distinct functional site …

Computational elucidation of allosteric communication in proteins for allosteric drug design

D Ni, Y Liu, R Kong, Z Yu, S Lu, J Zhang - Drug Discovery Today, 2022 - Elsevier
Highlights•Allosteric signals underlie the functional mechanisms of allosteric
drugs.•Elucidation of allosteric signals facilitates rational allosteric drug discovery.• …