AlphaFold, artificial intelligence (AI), and allostery

R Nussinov, M Zhang, Y Liu, H Jang - The Journal of Physical …, 2022 - ACS Publications
AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of
biological sequence data and artificial intelligence (AI). AlphaFold has appended projects …

[HTML][HTML] AlphaFold, allosteric, and orthosteric drug discovery: Ways forward

R Nussinov, M Zhang, Y Liu, H Jang - Drug discovery today, 2023 - Elsevier
Highlights•AlphaFold models have rigid protein structures.•Advanced deep algorithms fed
relevant data can accurately predict structures.•Algorithmic advances can harness …

Mapping the energetic and allosteric landscapes of protein binding domains

AJ Faure, J Domingo, JM Schmiedel… - Nature, 2022 - nature.com
Allosteric communication between distant sites in proteins is central to biological regulation
but still poorly characterized, limiting understanding, engineering and drug development …

ASD2023: towards the integrating landscapes of allosteric knowledgebase

J He, X Liu, C Zhu, J Zha, Q Li, M Zhao… - Nucleic Acids …, 2024 - academic.oup.com
Allosteric regulation, induced by perturbations at an allosteric site topographically distinct
from the orthosteric site, is one of the most direct and efficient ways to fine-tune …

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 …

Insulin‐degrading enzyme: an ally against metabolic and neurodegenerative diseases

L Sousa, M Guarda, MJ Meneses… - The Journal of …, 2021 - Wiley Online Library
Insulin‐degrading enzyme (IDE) function goes far beyond its known proteolytic role as a
regulator of insulin levels. IDE has a wide substrate promiscuity, degrading several proteins …

[HTML][HTML] Enzyme kinetics by isothermal titration calorimetry: Allostery, inhibition, and dynamics

Y Wang, G Wang, N Moitessier… - Frontiers in molecular …, 2020 - frontiersin.org
Isothermal titration calorimetry (ITC) involves accurately measuring the heat that is released
or absorbed in real time when one solution is titrated into another. This technique is usually …

[HTML][HTML] Allostery: allosteric cancer drivers and innovative allosteric drugs

R Nussinov, M Zhang, R Maloney, Y Liu, CJ Tsai… - Journal of molecular …, 2022 - Elsevier
Here, we discuss the principles of allosteric activating mutations, propagation downstream of
the signals that they prompt, and allosteric drugs, with examples from the Ras signaling …

Designing drugs and chemical probes with the dualsteric approach

J Zha, J He, C Wu, M Zhang, X Liu… - Chemical Society Reviews, 2023 - pubs.rsc.org
Traditionally, drugs are monovalent, targeting only one site on the protein surface. This
includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric …

[HTML][HTML] Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators

S Lu, Y Chen, J Wei, M Zhao, D Ni, X He… - … Pharmaceutica Sinica B, 2021 - Elsevier
The recent discovery of activator compounds binding to an allosteric site on the NAD+-
dependent protein lysine deacetylase, sirtuin 6 (SIRT6) has attracted interest and presents a …