Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets

Abstract

Three allosteric glycolytic enzymes, phosphofructokinase, glyceraldehyde-3 phosphate dehydrogenase and pyruvate kinase, associated with bacterial, parasitic and human species, were explored to identify potential allosteric sites that would be used as prime targets for species-specific drug design purposes using a newly developed approach which incorporates solvent mapping, elastic network modeling, sequence and structural alignments. The majority of binding sites detected by solvent mapping overlapped with the interface regions connecting the subunits, thus appeared as promising target sites for allosteric regulation. Each binding site was then evaluated by its ability to alter the global dynamics of the receptor defined by the percentage change in the frequencies of the lowest-frequency modes most significantly and as anticipated, the most effective ones were detected in the vicinity of the well-reported catalytic and allosteric sites. Furthermore, some of our proposed regions intersected with experimentally resolved sites which are known to be critical for activity regulation, which further validated our approach. Despite the high degree of structural conservation encountered between bacterial/parasitic and human glycolytic enzymes, the majority of the newly presented allosteric sites exhibited a low degree of sequence conservation which further increased their likelihood to be used as species-specific target regions for drug design studies.

Exploring the Allosteric Territory of Protein Function

“…The model allows one to observe the causality and to quantify the energetics of allosteric communication upon ligand binding and/or mutations in a protein, to identify potential regulatory exosites through a reverse perturbation of allosteric communication, and to obtain a comprehensive picture, allosteric signaling map (ASM), of per-residue allosteric signaling in proteins. The SBSMMA was thoroughly benchmarked in our previous works, , and it was successfully used in experimental , and theoretical − projects as a predictive and analytical tool. These works describe allosteric effects of mutations, ,, regulation of protein–protein interactions, prediction of druggable sites, and effects of the ligand binding, to name a few.…”

“…The SBSMMA was thoroughly benchmarked in our previous works, , and it was successfully used in experimental , and theoretical − projects as a predictive and analytical tool. These works describe allosteric effects of mutations, ,, regulation of protein–protein interactions, prediction of druggable sites, and effects of the ligand binding, to name a few. The SBSMMA is implemented in web resources, the server AlloSigMA , and database AlloMAPS, which are proven to be instrumental in elucidation of allosteric mechanisms and actions of allosteric effectors.…”

Predicting allosteric pockets in protein biological assemblages

“…Moreover, APOP can also detect alternative allosteric pockets as high-ranked pockets, indicating its potential utility for designing ways to alter protein activity by targeting newly identified ligand-binding pockets. Prediction of alternate allosteric pockets can facilitate the effective drug targeting of enzymes such as Phosphofructokinase, Glyceraldehyde-3 phosphate dehydrogenase, and Pyruvate kinase ( Ayyildiz et al 2020 ). APOP can also predict the known allosteric ligand-binding pockets as the top-ranked pockets in different protein conformational states.…”

Engineering an Allosteric Control of Protein Function

“…They found that functional sites possess increased communication propensities and secondary structures are quite efficient in mediating allosteric communications. Recently, Ayyildiz et al incorporated elastic network modeling with solvent mapping and sequential and structural alignments to identify species-specific allosteric sites in glycolytic enzymes of bacteria, parasites, and humans. Ota et al used anisotropic thermal diffusion, a nonequilibrium MD simulation method, , to study the intramolecular signaling pathways in PDZ domain proteins.…”