Identification of novel pyrazolo[4,3-c]pyridine and diazepane derivatives as potent inhibitors of Mycobacterium tuberculosis protein tyrosine phosphatase B

TL;DR

This study identifies new chemical compounds that strongly inhibit a key protein in tuberculosis bacteria, offering potential for new treatments.

Contribution

Novel pyrazolo[4,3-c]pyridine and diazepane derivatives are identified as potent and selective inhibitors of Mycobacterium tuberculosis PtpB-Mtb.

Findings

Two compounds showed IC₅₀ values of 14.4 µM and 32.6 µM against PtpB-Mtb.

Biolayer interferometry confirmed strong binding with Kd values of 0.012 µM and 0.57 µM.

The compounds represent promising scaffolds for next-generation anti-tubercular drugs.

Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), continues to pose a critical global health threat as a leading infectious cause of mortality. Therapeutic efficacy is increasingly compromised by the emergence of multidrug-resistant strains and the limitations of existing regimens, which necessitate treatment durations of six months or longer. Protein tyrosine phosphatase B from Mtb (PtpB-Mtb) has been recognized as a critical virulence factor, representing a promising target for novel antitubercular therapies due to its unique structural and functional properties. In this study, a comprehensive structure-based virtual screening approach was employed to identify novel small-molecule scaffolds with inhibitory potential against PtpB-Mtb. The ChemBridge compound library was curated and filtered for drug-like properties, followed by hierarchical molecular docking and molecular dynamics simulations to prioritize candidates with high predicted affinity and stability within the PtpB-Mtb active site. Quantum mechanical calculations further characterized the electronic properties of top hits. Recombinant PtpB-Mtb was expressed and purified to homogeneity, and in vitro enzymatic assays were performed to evaluate the inhibitory potency and selectivity of shortlisted compounds. Two derivatives bearing pyrazolo[4,3-c]pyridine and 1,4-diazepane ring nuclei demonstrated significant inhibition of PtpB-Mtb activity, exhibiting IC₅₀ values of 14.4 µM and 32.6 µM, respectively. Biolayer interferometry confirmed strong and specific binding to PtpB-Mtb, with dissociation constants (Kd) of 0.012 µM and 0.57 µM. The integrated workflow presented herein highlights the potential of these novel scaffolds as starting points for the development of selective, cell-permeable PtpB-Mtb inhibitors, offering a promising avenue for next-generation anti-tubercular drug discovery.

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