Aug 2026· Nature Communications· Vol 17· 0 citations· 72 references
TL;DR
Dynamical network analysis is used to identify key residues involved in a dynamic allostery between the N- and C-lobes that connects the major functional units of the MAP kinase p38α, providing mechanistic insight into p38α allostery and suggesting viable opportunities for the rational design of allosteric modulators of MAP kinases.
Abstract
Kinases are major drug targets especially in cancer therapy. However, the high degree of conservation of their active sites hinders the development of selective inhibitors, motivating a deeper understanding of kinase conformational ensembles and allosteric communication pathways. Here, we use dynamical network analysis to identify key residues involved in a dynamic allostery between the N- and C-lobes that connects the major functional units of the MAP kinase p38α. By combining NMR spectroscopy, activity assays, and in silico analysis of wildtype protein and mutants in the presence or absence of an active-site inhibitor, we experimentally validate the obtained architecture with respect to global protein motion and long-range allosteric modulation. Notably, the identified network highlights communication pathways across several functional sites, prominently involving the allosteric site, the activation loop, and even the lipid-binding domain with its embedded cryptic pocket in the C-lobe. These findings provide mechanistic insight into p38α allostery and suggest viable opportunities for the rational design of allosteric modulators of MAP kinases. Here, the authors apply dynamic network analysis, alongside a set of experimental validations, to probe correlated motions within p38α kinase. The data corroborate communication between its N- and C-lobes, including in particular the lipid pocket.
This work highlights how distinct inhibitors exploit different conformational states of cKIT and demonstrates the value of integrating structural analyses, biophysical measurements, calculations and molecular simulations to define the mechanism of kinase inhibition.
Irene Cipollone, Carmen Gratteri, C. Talarico et al.· International Journal of Bio...· 0 citations
The conformational plasticity of protein kinases poses a challenge for inhibitor design, motivating the use of molecular dynamics (MD) simulations to study their dynamic binding processes. While conformational changes are increasingly discussed, the impact of drug compound flexibility remains underexplored because of experimental limitations. In this study, we employ two-dimensional replica-exchange MD simulations to investigate how c-Src kinase binds to PP1, a small inhibitor, and to dasatinib, a larger, more flexible inhibitor. Simulations totaling 600 μs revealed frequent binding and unbinding events, yielding statistically converged information about the binding pathways. While both inhibitors follow multiple binding pathways, a notable difference emerges in their binding mechanisms on the free-energy profiles: PP1 is rigid along the binding path, whereas dasatinib substantially changes its conformation at different stages in the pathway to the canonical pose. Conformational analysis reveals distinct conformers of dasatinib, including a hidden intermediate, which helps to avoid trapping at the salt-bridge pair linking the β3 strand and the αC-helix of the c-Src kinase. These results, distinct from previous computational studies, demonstrate that inhibitor size and flexibility affect binding mechanisms and have implications on kinetics.
A. Shinobu, Suyong Re, Hiraku Oshima et al.· Journal of Physical Chemistr...· 0 citations
The activity and abundance of >160,000 variants are quantify the activity and abundance of >160,000 variants to construct complete maps of the energetic and allosteric architectures of five human kinase domains: SRC, FGR, JNK2/MAPK9, ZAK/MAP3K20, and TSSK2.
Carla Folgado, Antoni Beltran, Ben Lehner· bioRxiv· 0 citations
Understanding how allosteric modulators influence protein dynamics is essential for guiding drug design. This work analyses a total of 45 μs of classical molecular dynamics simulations for four class A G-protein-coupled receptors (GPCRs), namely the Complement C5a receptor (C5AR1), the Purinergic Receptor P2Y (P2RY1), and the Cannabinoid Receptors 1 and 2 (CNR1/CNR2). Protein dynamics is essential to detect the shallow extrahelical binding sites, such as the one found in P2RY1. Current methods for computing Allosteric Communication Networks (ACNs) produce complex outputs requiring expert interpretation. To address this, we focus on the shortest paths of information transfer between the orthosteric and G-protein binding sites in Class A GPCRs. Our retrospective analysis reveals state- and bias ligand-dependent residue interactions along these communication pathways. Furthermore, focusing on the predicted binding site of allosteric modulator EC21a at cannabinoid receptors, the ACN framework was used to prioritize two residues for mutational analysis that may contribute to allosteric communication.
S. Peter, G. Chalhoub, Peter J. McCormick et al.· Journal of Chemical Informat...· 0 citations
This study provides potential lead compounds for the design of small-molecule allosteric drugs targeting class B1 GPCRs and performs conformational sampling and combined dynamic pocket detection algorithms, MDpocket and FTMove, to identify six characteristic cryptic pockets within the dynamic trajectories.
Zhi Dong, Long Cheng, Qingxin Shi et al.· International Journal of Bio...· 0 citations
The SARS-CoV-2 main protease (MPro) is an essential enzyme for viral replication and a primary target for antiviral drug development. Despite extensive structural and biochemical characterization, the allosteric mechanisms by which dimerization informs conformational changes at active site lack an explicit comparison across the different states that identify key residues that connect substrate binding, dimerization, and catalytic activation. Here, we integrate microsecond time scale all-atom molecular dynamics (MD) simulations with dynamical network analysis to characterize how ligand binding and dimerization modulate the allosteric communication landscape of MPro. We performed triplicate 1-μs simulations of MPro in the monomer and dimer states. For each of these states, we simulated MPro in the apo state, as well as bound to a natural peptide substrate (nsp 15/16), the covalent inhibitor nirmatrelvir (Paxlovid) and the noncovalent inhibitor ensitrelvir (Xocova). Dynamical network analyses from the resulting simulations reveal that dimerization redirects the highest correlated motions from the interdomain loop towards the domain II and III interface. At the dimer interface, we identified N-terminal and domain II β-hairpin residues that act as central communication hubs creating networks that connect both chains in the dimer. Small molecule binding to the active site further modulates these networks in distinct ways: nirmatrelvir and peptide substrate binding results in the formation of allosteric networks within the oxyanion loop, while ensitrelvir-bound monomeric MPro results in a dimer-like network, suggesting an inhibitory "allosteric switch" mechanism that may hinder dimerization upon binding. Across all systems, domain III emerges as an allosteric "pivot", providing a platform that allows the most relevant networks to connect inter-chain communication to the active site upon dimerization. Together, these findings define how correlated motion networks couple active-site dynamics to dimerization and ligand binding, providing molecular insight into the principles governing allosteric regulation in MPro. This framework highlights potential avenues for developing antivirals that target not only the catalytic site but also the communication pathways sustaining dimer stability and enzymatic function.
Javier O. Sanlley Hernandez, Carla Calvó-Tusell, Fiona L. Kearns et al.· Biophysical Journal· 0 citations
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