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bioRxiv · 10.1101/2025.07.03.662948

Molecular insights into inhibitor action on a key bacterial metabolic enzyme Cystathionine β-Synthase

Polepalli, S.·Roy, A.·Mondal, B.·Singh, A.·Dutta, S.
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Abstract

Tuberculosis (TB) remains a major global health threat, with Mycobacterium tuberculosis (Mtb) infecting nearly a quarter of the global population. Drug-resistant TB and HIV-TB co- infections emphasize the need for novel therapeutic approaches targeting essential metabolic pathways. Here, we investigated Mtb cystathionine {beta}-synthase (MtbCBS), a PLP-dependent enzyme critical for sulfur metabolism and redox regulation, owing its potential as a therapeutic target. We present the first high-resolution cryo-EM structure of MtbCBS bound to aminooxyacetic acid (AOAA), and employed molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) calculations, and comparative inhibition studies to reveal the molecular basis and determinants governing irreversible PLP-enzyme inhibition. Our Cryo-EM structural analysis revealed two highly conserved active-site residues, T75 and Q147, critically stabilizing the inhibitor complex. Through molecular mimic studies, we demonstrated the precise structural factors and electronic features critical for inhibition efficiency. These findings provide the first mechanistic rationale for PLP enzyme inhibition and offer a generalizable framework for designing covalent inhibitors targeting PLP-dependent enzymes implicated in infectious diseases, cancer, and neurological disorders. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/662948v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@195c7c7org.highwire.dtl.DTLVardef@6ee0c8org.highwire.dtl.DTLVardef@1679dfborg.highwire.dtl.DTLVardef@1b4e000_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO Proposed mechanism of MtbCBS inhibition by AOAA. Proposed mechanism of action of AOAA illustrated through a graphical representation. The cartoon shows the domains of MtbCBS. Tetrameric structure of MtbCBS with active site highlighted (in red dashes). Enlarged view indicating the PLP-AOAA blocked intermediate interacting with residue Q147. Reaction scheme depicting the previous missing understanding of active site residue role in -elimination. Schematic representation of AOAA inhibition mechanism in the catalytic cycle of MtbCBS. Reactions were drawn using ChemDraw. The proposed scheme highlights that AOAA (highlighted Red) binding is stabilized by nearby residues Q147 and T75, leading to the formation of PLP-AOAA covalent adduct, and substrates (highlighted green) were incapable of reverting the suicidal inhibition. The directionality and reversibility were mentioned for each step. C_FIG

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Polepalli, S., Roy, A., Mondal, B., Singh, A., Dutta, S.. 2025-07-05. Molecular insights into inhibitor action on a key bacterial metabolic enzyme Cystathionine β-Synthase. https://doi.org/10.1101/2025.07.03.662948

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