Mycobacterium tuberculosis PanD structure-function analysis and identification of a potent pyrazinoic acid-derived enzyme inhibitor
A common strategy employed in antibacterial drug discovery is targeting of biosynthetic processes which are essential and specific for the pathogen. Specificity in particular avoids undesirable interactions with potential enzymatic counterparts in the human host, and ensures on-target toxicity. S...
| Main Authors: | , , , , , , , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2022
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/155645 |
| _version_ | 1826125635753345024 |
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| author | Ragunathan, Priya Cole, Malcolm Latka, Chitra Aragaw, Wassihun Wedajo Hegde, Pooja Shin, Joon Manimekalai, Malathy Sony Subramanian Rishikesan, Sankaranarayanan Aldrich, Courtney C. Dick, Thomas Grüber, Gerhard |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Ragunathan, Priya Cole, Malcolm Latka, Chitra Aragaw, Wassihun Wedajo Hegde, Pooja Shin, Joon Manimekalai, Malathy Sony Subramanian Rishikesan, Sankaranarayanan Aldrich, Courtney C. Dick, Thomas Grüber, Gerhard |
| author_sort | Ragunathan, Priya |
| collection | NTU |
| description | A common strategy employed in antibacterial drug discovery is targeting of biosynthetic processes
which are essential and specific for the pathogen. Specificity in particular avoids undesirable
interactions with potential enzymatic counterparts in the human host, and ensures on-target
toxicity. Synthesis of pantothenate (Vitamine B5), a precursor of the acyl carrier coenzyme A, is
an example of such a pathway. In Mycobacterium tuberculosis (Mtb), the causative agent of
tuberculosis (TB), pantothenate is formed by pantothenate synthase, utilizing D-pantoate and βAla as substrates. β-Ala is mainly formed by the decarboxylation of L-aspartate, generated by the
decarboxylase PanD, a homo-oliogomer in solution. Pyrazinoic acid (POA), 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 analogs with modifications at position 3 of the
pyrazine ring. Analog 2, incorporating a bulky naphthamido group at this position, displayed a
1,000-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. |
| first_indexed | 2024-10-01T06:39:54Z |
| format | Journal Article |
| id | ntu-10356/155645 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T06:39:54Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | ntu-10356/1556452023-02-28T17:09:08Z Mycobacterium tuberculosis PanD structure-function analysis and identification of a potent pyrazinoic acid-derived enzyme inhibitor Ragunathan, Priya Cole, Malcolm Latka, Chitra Aragaw, Wassihun Wedajo Hegde, Pooja Shin, Joon Manimekalai, Malathy Sony Subramanian Rishikesan, Sankaranarayanan Aldrich, Courtney C. Dick, Thomas Grüber, Gerhard School of Biological Sciences Science::Biological sciences::Biochemistry Science::Chemistry::Analytical chemistry Tuberculosis Mycobacteria Pyrazinamide; Pyrazinoic Acid Coenzyme A Aspartate Decarboxylase A common strategy employed in antibacterial drug discovery is targeting of biosynthetic processes which are essential and specific for the pathogen. Specificity in particular avoids undesirable interactions with potential enzymatic counterparts in the human host, and ensures on-target toxicity. Synthesis of pantothenate (Vitamine B5), a precursor of the acyl carrier coenzyme A, is an example of such a pathway. In Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), pantothenate is formed by pantothenate synthase, utilizing D-pantoate and βAla as substrates. β-Ala is mainly formed by the decarboxylation of L-aspartate, generated by the decarboxylase PanD, a homo-oliogomer in solution. Pyrazinoic acid (POA), 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 analogs with modifications at position 3 of the pyrazine ring. Analog 2, incorporating a bulky naphthamido group at this position, displayed a 1,000-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. Ministry of Education (MOE) National Research Foundation (NRF) Submitted/Accepted version Research reported in this publication is supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Number R01AI106398 (T.D., C.A., G.G.) the National Research Foundation (NRF) Singapore, NRF Competitive Research Programme (CRP), Grant Award Number NRF–CRP18– 2017–01) to G.G., and the Singapore Ministry of Education Academic Research Fund Tier 1 (RG107/20) to GG. 2022-03-11T06:51:48Z 2022-03-11T06:51:48Z 2021 Journal Article Ragunathan, P., Cole, M., Latka, C., Aragaw, W. W., Hegde, P., Shin, J., Manimekalai, M. S. S., Rishikesan, S., Aldrich, C. C., Dick, T. & Grüber, G. (2021). Mycobacterium tuberculosis PanD structure-function analysis and identification of a potent pyrazinoic acid-derived enzyme inhibitor. ACS Chemical Biology, 16(6), 1030-1039. https://dx.doi.org/10.1021/acschembio.1c00131 1554-8929 https://hdl.handle.net/10356/155645 10.1021/acschembio.1c00131 6 16 1030 1039 en NRF-CRP18-2017-01 RG107/20 R01AI106398 ACS Chemical Biology This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Chemical Biology, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acschembio.1c00131. application/pdf |
| spellingShingle | Science::Biological sciences::Biochemistry Science::Chemistry::Analytical chemistry Tuberculosis Mycobacteria Pyrazinamide; Pyrazinoic Acid Coenzyme A Aspartate Decarboxylase Ragunathan, Priya Cole, Malcolm Latka, Chitra Aragaw, Wassihun Wedajo Hegde, Pooja Shin, Joon Manimekalai, Malathy Sony Subramanian Rishikesan, Sankaranarayanan Aldrich, Courtney C. Dick, Thomas Grüber, Gerhard Mycobacterium tuberculosis PanD structure-function analysis and identification of a potent pyrazinoic acid-derived enzyme inhibitor |
| title | Mycobacterium tuberculosis PanD structure-function analysis and identification of a potent pyrazinoic acid-derived enzyme inhibitor |
| title_full | Mycobacterium tuberculosis PanD structure-function analysis and identification of a potent pyrazinoic acid-derived enzyme inhibitor |
| title_fullStr | Mycobacterium tuberculosis PanD structure-function analysis and identification of a potent pyrazinoic acid-derived enzyme inhibitor |
| title_full_unstemmed | Mycobacterium tuberculosis PanD structure-function analysis and identification of a potent pyrazinoic acid-derived enzyme inhibitor |
| title_short | Mycobacterium tuberculosis PanD structure-function analysis and identification of a potent pyrazinoic acid-derived enzyme inhibitor |
| title_sort | mycobacterium tuberculosis pand structure function analysis and identification of a potent pyrazinoic acid derived enzyme inhibitor |
| topic | Science::Biological sciences::Biochemistry Science::Chemistry::Analytical chemistry Tuberculosis Mycobacteria Pyrazinamide; Pyrazinoic Acid Coenzyme A Aspartate Decarboxylase |
| url | https://hdl.handle.net/10356/155645 |
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