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

Molecules ◽  
2020 ◽  
Vol 25 (10) ◽  
pp. 2384
Author(s):  
Ali R. Elnaas ◽  
Darren Grice ◽  
Jianying Han ◽  
Yunjiang Feng ◽  
Angela Di Capua ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mycobacterium Tuberculosis ◽  
Drug Discovery ◽  
Drug Target ◽  
Inhibitory Concentration ◽  
Native Mass Spectrometry ◽  
Cellular Activity ◽  
Future Drug ◽  
Mycobacterial Protein

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.

scholarly journals A New Native Mass Spectrometry Platform Identifies Inhibitors of the HSP90 – HOP Protein-Protein Interaction

2020 ◽  
Author(s):  
Clinton Veale ◽  
Mateos-Jimenez, Maria ◽  
Michaelone Vaaltyn ◽  
Ronel Müller ◽  
Matodzi Makhubu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Drug Discovery ◽  
Protein Interaction ◽  
Drug Target ◽  
Native Mass Spectrometry ◽  
Cancer Drug ◽  
Protein Protein Interaction ◽  
Cancer Drug Discovery ◽  
First Time

This communication discusses for the first time, the use of mass spectrometry as a platform for screening for PPI inhibitors, without protein tethering or labeling. Furthermore, in the context of cancer drug discovery, this study demonstrates the ligandability and therefore the potential druggability of HOP, whose PPI with HSP90 has been routinely discussed as a difficult to drug target of substantial potential.

scholarly journals A New Native Mass Spectrometry Platform Identifies Inhibitors of the HSP90 – HOP Protein-Protein Interaction

2020 ◽  
Author(s):  
Clinton Veale ◽  
Mateos-Jimenez, Maria ◽  
Michaelone Vaaltyn ◽  
Ronel Müller ◽  
Matodzi Makhubu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Drug Discovery ◽  
Protein Interaction ◽  
Drug Target ◽  
Native Mass Spectrometry ◽  
Cancer Drug ◽  
Protein Protein Interaction ◽  
Cancer Drug Discovery ◽  
First Time

This communication discusses for the first time, the use of mass spectrometry as a platform for screening for PPI inhibitors, without protein tethering or labeling. Furthermore, in the context of cancer drug discovery, this study demonstrates the ligandability and therefore the potential druggability of HOP, whose PPI with HSP90 has been routinely discussed as a difficult to drug target of substantial potential.

scholarly journals Structural insights into the EthR–DNA interaction using native mass spectrometry

2017 ◽  
Vol 53 (25) ◽  
pp. 3527-3530 ◽  
Author(s):  
Daniel Shiu-Hin Chan ◽  
Wei-Guang Seetoh ◽  
Brendan N. McConnell ◽  
Dijana Matak-Vinković ◽  
Sherine E. Thomas ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mycobacterium Tuberculosis ◽  
Dna Interaction ◽  
Native Mass Spectrometry ◽  
Operator Dna ◽  
Structural Insights

The interaction between Mycobacterium tuberculosis EthR and its operator DNA has been studied by native mass spectrometry, revealing an interesting stoichiometry.

scholarly journals Multiplexed screening of thousands of natural products for protein-ligand binding in native mass spectrometry

2021 ◽  
Author(s):  
Giang Nguyen ◽  
Jack Bennett ◽  
Sherrie Liu ◽  
Sarah Hancock ◽  
Daniel Winter ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Natural Products ◽  
Drug Discovery ◽  
Small Molecules ◽  
Natural Product ◽  
Drug Targets ◽  
Structural Diversity ◽  
Native Mass Spectrometry ◽  
Protein Targets ◽  
Rapid Measurement

The structural diversity of natural products offers unique opportunities for drug discovery, but challenges associated with their isolation and screening can hinder the identification of drug-like molecules from complex natural product extracts. Here we introduce a mass spectrometry-based approach that integrates untargeted metabolomics with multistage, high-resolution native mass spectrometry to rapidly identify natural products that bind to therapeutically relevant protein targets. By directly screening crude natural product extracts containing thousands of drug-like small molecules using a single, rapid measurement, novel natural product ligands of human drug targets could be identified without fractionation. This method should significantly increase the efficiency of target-based natural product drug discovery workflows.

scholarly journals Antimicrobial Lavandulylated Flavonoids from a Sponge-Derived Streptomyces sp. G248 in East Vietnam Sea

Marine Drugs ◽  
2019 ◽  
Vol 17 (9) ◽  
pp. 529 ◽  
Author(s):  
Cao ◽  
Trinh ◽  
Mai ◽  
Vu ◽  
Le ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Antimicrobial Activity ◽  
Mycobacterium Tuberculosis ◽  
Spectroscopic Data ◽  
Inhibitory Concentration ◽  
Culture Broth ◽  
Ionization Mass ◽  
Streptomyces Sp ◽  
Mycobacterium Tuberculosis H37rv

Three new lavandulylated flavonoids, (2S,2′’S)-6-lavandulyl-7,4′-dimethoxy-5,2′-dihydroxylflavanone (1), (2S,2′’S)-6-lavandulyl-5,7,2′,4′-tetrahydroxylflavanone (2), and (2′’S)-5′-lavandulyl-2′-methoxy-2,4,4′,6′-tetrahydroxylchalcone (3), along with seven known compounds 4–10 were isolated from culture broth of Streptomyces sp. G248. Their structures were established by spectroscopic data analysis, including 1D and 2D nuclear magnetic resonance (NMR), and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS). The absolute configurations of 1–3 were resolved by comparison of their experimental and calculated electronic circular dichroism spectra. Compounds 1–3 exhibited remarkable antimicrobial activity. Whereas, two known compounds 4 and 5 exhibited inhibitory activity against Mycobacterium tuberculosis H37Rv with minimum inhibitory concentration (MIC) values of 6.0 µg/mL and 11.1 µg/mL, respectively.

Multiplexed screening of thousands of natural products for protein-ligand binding in native mass spectrometry

2021 ◽  
Author(s):  
Giang Nguyen ◽  
Jack Bennett ◽  
Sherrie Liu ◽  
Sarah Hancock ◽  
Daniel Winter ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Natural Products ◽  
Drug Discovery ◽  
Small Molecules ◽  
Natural Product ◽  
Drug Targets ◽  
Structural Diversity ◽  
Native Mass Spectrometry ◽  
Protein Targets ◽  
Rapid Measurement

The structural diversity of natural products offers unique opportunities for drug discovery, but challenges associated with their isolation and screening can hinder the identification of drug-like molecules from complex natural product extracts. Here we introduce a mass spectrometry-based approach that integrates untargeted metabolomics with multistage, high-resolution native mass spectrometry to rapidly identify natural products that bind to therapeutically relevant protein targets. By directly screening crude natural product extracts containing thousands of drug-like small molecules using a single, rapid measurement, novel natural product ligands of human drug targets could be identified without fractionation. This method should significantly increase the efficiency of target-based natural product drug discovery workflows.

scholarly journals Mycobacterium tuberculosis Gyrase Inhibitors as a New Class of Antitubercular Drugs

2015 ◽  
Vol 59 (4) ◽  
pp. 1868-1875 ◽  
Author(s):  
Delia Blanco ◽  
Esther Perez-Herran ◽  
Mónica Cacho ◽  
Lluís Ballell ◽  
Julia Castro ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Discovery ◽  
Oral Absorption ◽  
Cell Activity ◽  
Cross Resistance ◽  
Drug Candidate ◽  
Antibacterial Drug ◽  
Gyrase Inhibitors

ABSTRACTOne way to speed up the TB drug discovery process is to search for antitubercular activity among compound series that already possess some of the key properties needed in anti-infective drug discovery, such as whole-cell activity and oral absorption. Here, we present MGIs, a new series ofMycobacterium tuberculosisgyrase inhibitors, which stem from the long-term efforts GSK has dedicated to the discovery and development of novel bacterial topoisomerase inhibitors (NBTIs). The compounds identified were found to be devoid of fluoroquinolone (FQ) cross-resistance and seem to operate through a mechanism similar to that of the previously described NBTI GSK antibacterial drug candidate. The remarkablein vitroandin vivoantitubercular profiles showed by the hits has prompted us to further advance the MGI project to full lead optimization.

scholarly journals 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase (IspC) from Mycobacterium tuberculosis: towards Understanding Mycobacterial Resistance to Fosmidomycin

2005 ◽  
Vol 187 (24) ◽  
pp. 8395-8402 ◽  
Author(s):  
Rakesh K. Dhiman ◽  
Merrill L. Schaeffer ◽  
Ann Marie Bailey ◽  
Charles A. Testa ◽  
Hataichanok Scherman ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Target ◽  
Pathogenic Bacteria ◽  
Biosynthetic Pathway ◽  
Inhibitory Concentration ◽  
Forward Direction ◽  
Gram Negative Bacteria ◽  
Isopentenyl Diphosphate ◽  
Intrinsic Properties ◽  
Specificity Constant

ABSTRACT 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (IspC) catalyzes the first committed step in the mevalonate-independent isopentenyl diphosphate biosynthetic pathway and is a potential drug target in some pathogenic bacteria. The antibiotic fosmidomycin has been shown to inhibit IspC in a number of organisms and is active against most gram-negative bacteria but not gram positives, including Mycobacterium tuberculosis, even though the mevalonate-independent pathway is the sole isopentenyl diphosphate biosynthetic pathway in this organism. Therefore, the enzymatic properties of recombinant IspC from M. tuberculosis were characterized. Rv2870c from M. tuberculosis converts 1-deoxy-d-xylulose 5-phosphate to 2-C-methyl-d-erythritol 4-phosphate in the presence of NADPH. The enzymatic activity is dependent on the presence of Mg2+ ions and exhibits optimal activity between pH 7.5 and 7.9; the Km for 1-deoxyxylulose 5-phosphate was calculated to be 47.1 μM, and the Km for NADPH was 29.7 μM. The specificity constant of Rv2780c in the forward direction is 1.5 × 106 M−1 min−1, and the reaction is inhibited by fosmidomycin, with a 50% inhibitory concentration of 310 nM. In addition, Rv2870c complements an inactivated chromosomal copy of IspC in Salmonella enterica, and the complemented strain is sensitive to fosmidomycin. Thus, M. tuberculosis resistance to fosmidomycin is not due to intrinsic properties of Rv2870c, and the enzyme appears to be a valid drug target in this pathogen.

scholarly journals Insights into glycan import by a prominent gut symbiont

2020 ◽  
Author(s):  
Declan A. Gray ◽  
Joshua B. R. White ◽  
Abraham O. Oluwole ◽  
Parthasarathi Rath ◽  
Amy J. Glenwright ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Transport Mechanism ◽  
Protein Complexes ◽  
Native Mass Spectrometry ◽  
Structural Features ◽  
Titration Calorimetry ◽  
Binding Cavity ◽  
Shed Light

AbstractIn Bacteroidetes, one of the dominant phyla of the mammalian gut, active uptake of large nutrients across the outer membrane is mediated by SusCD protein complexes via a “pedal bin” transport mechanism. However, many features of SusCD function in glycan uptake remain unclear, including ligand binding, the role of the SusD lid and the size limit for substrate transport. Here we characterise the β2,6 fructo-oligosaccharide (FOS) importing SusCD from Bacteroides thetaiotaomicron (Bt1762-Bt1763) to shed light on SusCD function. Co-crystal structures reveal residues involved in glycan recognition and suggest that the large binding cavity can accommodate several substrate molecules, each up to ∼2.5 kDa in size, a finding supported by native mass spectrometry and isothermal titration calorimetry. Mutational studies in vivo provide functional insights into the key structural features of the SusCD apparatus and cryo-EM of the intact dimeric SusCD complex reveals several distinct states of the transporter, directly visualising the dynamics of the pedal bin transport mechanism.

scholarly journals HAP40 orchestrates huntingtin structure for differential interaction with polyglutamine expanded exon 1

2021 ◽  
Author(s):  
Rachel J. Harding ◽  
Justin C. Deme ◽  
Johannes F. Hevler ◽  
Sem Tamara ◽  
Alexander Lemak ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Huntington's Disease ◽  
Huntington’S Disease ◽  
Domain Architecture ◽  
Native Mass Spectrometry ◽  
Polyglutamine Expansion ◽  
X Ray Scattering ◽  
Exon 1 ◽  
Functional Relevance

AbstractHuntington’s disease results from expansion of a glutamine-coding CAG tract in the huntingtin (HTT) gene, producing an aberrantly functioning form of HTT. Both wildtype and disease-state HTT form a hetero-dimer with HAP40 of unknown functional relevance. We demonstrate in vivo that HTT and HAP40 cellular abundance are coupled. Integrating data from a 2.6 Å cryo-electron microscopy structure, cross-linking mass spectrometry, small-angle X-ray scattering, and modeling, we provide a near-atomic-level view of HTT, its molecular interaction surfaces and compacted domain architecture, orchestrated by HAP40. Native mass-spectrometry reveals a remarkably stable hetero-dimer, potentially explaining the cellular inter-dependence of HTT and HAP40. The polyglutamine tract containing N-terminal exon 1 region of HTT is dynamic, but shows greater conformational variety in the mutant than wildtype exon 1. By providing novel insight into the structural consequences of HTT polyglutamine expansion, our data provide a foundation for future functional and drug discovery studies targeting Huntington’s disease.

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