Mycobacterium tuberculosis PanD Structure-Function Analysis and Identification of a Potent Pyrazinoic Acid-Derived Enzyme Inhibitor

Priya Ragunathan, Malcolm Cole, Chitra Latka, Wassihun Wedajo Aragaw, Pooja Hegde, Joon Shin, Malathy Sony Subramanian Manimekalai, Sankaranarayanan Rishikesan, Courtney C. Aldrich, Thomas Dick, Gerhard Grüber

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

A common strategy employed in antibacterial drug discovery is the targeting of biosynthetic processes that are essential and specific for the pathogen. Specificity in particular avoids undesirable interactions with potential enzymatic counterparts in the human host, and it ensures on-target toxicity. Synthesis of pantothenate (Vitamine B5), which is a precursor of the acyl carrier coenzyme A, is an example of such a pathway. In Mycobacterium tuberculosis (Mtb), which is the causative agent of tuberculosis (TB), pantothenate is formed by pantothenate synthase, utilizing D-pantoate and β-Ala as substrates. β-Ala is mainly formed by the decarboxylation of l-aspartate, generated by the decarboxylase PanD, which is a homo-oliogomer in solution. Pyrazinoic acid (POA), which is the bioactive form of the TB prodrug pyrazinamide, binds and inhibits PanD activity weakly. Here, we generated a library of recombinant Mtb PanD mutants based on structural information and PZA/POA resistance mutants. Alterations in oligomer formation, enzyme activity, and/or POA binding were observed in respective mutants, providing insights into essential amino acids for Mtb PanD's proper structural assembly, decarboxylation activity and drug interaction. This information provided the platform for the design of novel POA analogues with modifications at position 3 of the pyrazine ring. Analogue 2, which incorporates a bulky naphthamido group at this position, displayed a 1000-fold increase in enzyme inhibition, compared to POA, along with moderately improved antimycobacterial activity. The data demonstrate that an improved understanding of mechanistic and enzymatic features of key metabolic enzymes can stimulate design of more-potent PanD inhibitors.

Original languageEnglish (US)
Pages (from-to)1030-1039
Number of pages10
JournalACS Chemical Biology
Volume16
Issue number6
DOIs
StatePublished - Jun 18 2021

Bibliographical note

Funding Information:
Research reported in this publication is supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health, Award No. R01AI106398 (T.D., C.A., G.G.) the National Research Foundation (NRF) Singapore, NRF Competitive Research Programme (CRP), Grant Award No. NRF-CRP18-2017-01) to G.G., and the Singapore Ministry of Education Academic Research Fund Tier 1 (No. RG107/20) to G.G.

Publisher Copyright:
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PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

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