Discovery of a Natural Product That Binds to the Mycobacterium tuberculosis Protein Rv1466 Using Native Mass Spectrometry

Abstract

Elucidation of the mechanism of action of compounds with cellular bioactivity is important for progressing compounds into future drug development. In recent years, phenotype-based drug discovery has become the dominant approach to drug discovery over target-based drug discovery, which relies on the knowledge of a specific drug target of a disease. Still, when targeting an infectious disease via a high throughput phenotypic assay it is highly advantageous to identifying the compound’s cellular activity. A fraction derived from the plant Polyalthia sp. showed activity against Mycobacterium tuberculosis at 62.5 μge/μL. A known compound, altholactone, was identified from this fraction that showed activity towards M. tuberculosis at an minimum inhibitory concentration (MIC) of 64 μM. Retrospective analysis of a target-based screen against a TB proteome panel using native mass spectrometry established that the active fraction was bound to the mycobacterial protein Rv1466 with an estimated pseudo-Kd of 42.0 ± 6.1 µM. Our findings established Rv1466 as the potential molecular target of altholactone, which is responsible for the observed in vivo toxicity towards M. tuberculosis.

Identification of Potential Drug Targets of Broad-Spectrum Inhibitors with a Michael Acceptor Moiety Using Shotgun Proteomics

“…As a powerful technique, several studies have used MS-based proteomics to study the interaction of drugs and their targets in a simple setting, and none have been reported for antiviral-target interactions. Liu et al employed a label-free native MS approach to analyze the multiple charges of purified mycobacterial proteins in their native states by using nondenaturing ESI [ 87 ]. This mild electrospray method can be used to identify both noncovalent and covalent protein–ligand complexes.…”

Antimicrobial Benzyltetrahydroisoquinoline-Derived Alkaloids from the Leaves of Doryphora aromatica

“…Compounds were evaluated for their antimycobacterial activities against M. smegmatis strain mc 2 155 (ATCC 70084), 20 M. tuberculosis mc 2 6220 biosafety level 2 (BSL2) strain, and M. tuberculosis H37Rv. 21 All the experiments were performed in triplicate.…”

A natural product compound inhibits coronaviral replication in vitro by binding to the conserved Nsp9 SARS-CoV-2 protein

“…To identify small-molecules that bind to Nsp9COV19, recombinant protein was produced as described (21), and screened by native mass spectrometry against an in-house natural product library of 1614 molecules with drug-like physicochemical properties. Native MS screening using high-resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS) is a fast, label-free, accurate method that allows direct detection of covalent and noncovalent protein−ligand complexes (29).…”