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Farr DC, Haselhorst T, Tan L, Furness J, Strong E, Grice ID, West NP, Houston TA. Reassessing the putative molecular Target(s) of potent antitubercular 2-(Alkylsulfonyl)acetamides. Eur J Med Chem 2024; 264:115983. [PMID: 38048695 DOI: 10.1016/j.ejmech.2023.115983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/11/2023] [Accepted: 11/19/2023] [Indexed: 12/06/2023]
Abstract
Simple alkyl-sulfonylacetamides have potent antitubercular activity and significantly decrease mycolic acid levels in mycobacteria. Although these compounds were originally designed to inhibit the ketoacyl synthase domain of fatty acid synthase, structure-activity relationships and biochemical evidence do not fully support fatty acid synthase as the target. In 2004, an enzyme family involved in the activation and transfer of fatty acids as acyl-adenylates was identified in mycobacteria, separate from the universal acetyl-CoA carrier mechanism. These fatty acyl-AMP ligases (FAAL), encoded by the FadD family play important roles in the biosynthesis of mycolic acids along with fatty acid metabolism and are hypothesised here to be the molecular target of the sulfonylacetamides. Due to structural similarities with the ligase's natural substrate, it is believed these compounds are exerting action via competitive inhibition of these highly potent molecular targets. The primary aim of this investigation was to synthesize an extended library of sulfonylacetamide derivatives, building upon existing structural activity relations to validate the molecular mechanism with the aid of molecular modelling, while also attempting to explore novel structural isosteres for further drug design and development. Sulfonylacetamide derivatives were modified based on the putative molecular target resulting in derivatives with improved activities towards Mycobacteriumtuberculosis (H37Rv). The most active novel derivatives reported were 19, 22b, 22c and 46 displaying MIC90 levels of 1.4, 16.0, 13.0 and 5.9 μg/mL, respectively.
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Affiliation(s)
- Dylan C Farr
- Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Juanelle Furness
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Emily Strong
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - I Darren Grice
- Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia; School of Pharmacy and Medical Science, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Todd A Houston
- Institute for Glycomics, Griffith University, Gold Coast, QLD, 4222, Australia.
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2
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Yan M, Ma M, Chen R, Cao Y, Zhang W, Liu X. Structural basis for the development of potential inhibitors targeting FadD23 from Mycobacterium tuberculosis. Acta Crystallogr F Struct Biol Commun 2023; 79:208-216. [PMID: 37522751 PMCID: PMC10416763 DOI: 10.1107/s2053230x23005836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Sulfolipid-1 (SL-1) is a lipid that is abundantly found in the cell wall of Mycobacterium tuberculosis (Mtb). MtbFadD23 is crucial in the SL-1 synthesis pathway. Previously, 5'-O-[N-(11-phenoxyundecanoyl)sulfamoyl]adenosine (PhU-AMS) has been shown to be a general inhibitor of fatty-acid-adenylating enzymes (FadDs) in Mtb. However, the fatty acyl-AMP ligase (FAAL) class of FadDs, which includes MtbFadD23, appears to be functionally nonredundant in the production of multiple fatty acids. In this study, the ability of PhU-AMS to bind to MtbFadD23 was examined under in vitro conditions. The crystal structure of the MtbFadD23-PhU-AMS complex was determined at a resolution of 2.64 Å. Novel features were identified by structural analysis and comparison. Although PhU-AMS could bind to MtbFadD23, it did not inhibit the FAAL adenylation activity of MtbFadD23. However, PhU-AMS improved the main Tm value in a differential scanning fluorimetry assay, and a structural comparison of MtbFadD23-PhU-AMS with FadD32 and PA1221 suggested that PhU-AMS blocks the loading of the acyl chain onto Pks2. This study sheds light on the structure-based design of specific inhibitors of MtbFadD23 and general inhibitors of FAALs.
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Affiliation(s)
- Mengrong Yan
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Mengyuan Ma
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Rong Chen
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
| | - Yangzi Cao
- College of Pharmacy, Nankai University, Tianjin, People’s Republic of China
| | - Wei Zhang
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, People’s Republic of China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, People’s Republic of China
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3
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Yan M, Cao L, Zhao L, Zhou W, Liu X, Zhang W, Rao Z. The Key Roles of Mycobacterium tuberculosis FadD23 C-terminal Domain in Catalytic Mechanisms. Front Microbiol 2023; 14:1090534. [PMID: 36896429 PMCID: PMC9989471 DOI: 10.3389/fmicb.2023.1090534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Sulfolipid-1 (SL-1) is located in the Mycobacterium tuberculosis (M. tb) cell wall, and is essential for pathogen virulence and intracellular growth. Multiple proteins (e.g., Pks2, FadD23, PapA1, and MmpL8) in the SL-1 synthesis pathway can be treated as drug targets, but, to date, their structures have not been solved. The crystal structures of FadD23 bound to ATP or hexadecanoyl adenylate was determined in this study. We have also investigated long-chain saturated fatty acids as biological substrates of FadD23 through structural, biological, and chemical analyses. The mutation at the active site of FadD23 greatly influences enzymatic activity. Meanwhile, the FadD23 N-terminal domain alone cannot bind palmitic acid without C-terminal domain facilitation since it is almost inactive after removing the C-terminal domain. FadD23 is the first protein in the SL-1 synthesis pathway whose structure has been solved. These results reveal the importance of the C-terminal domain in the catalytic mechanism.
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Affiliation(s)
- Mengrong Yan
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Lin Cao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Li Zhao
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Weihong Zhou
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Wei Zhang
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.,Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China.,Shanghai Institute for Advanced Immunochemical Studies and School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
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4
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Di Capua CB, Belardinelli JM, Carignano HA, Buchieri MV, Suarez CA, Morbidoni HR. Unveiling the Biosynthetic Pathway for Short Mycolic Acids in Nontuberculous Mycobacteria: Mycobacterium smegmatis MSMEG_4301 and Its Ortholog Mycobacterium abscessus MAB_1915 Are Essential for the Synthesis of α'-Mycolic Acids. Microbiol Spectr 2022; 10:e0128822. [PMID: 35862962 PMCID: PMC9431677 DOI: 10.1128/spectrum.01288-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/09/2022] [Indexed: 11/20/2022] Open
Abstract
Mycolic acids, a hallmark of the genus Mycobacterium, are unique branched long-chain fatty acids produced by a complex biosynthetic pathway. Due to their essentiality and involvement in various aspects of mycobacterial pathogenesis, the synthesis of mycolic acids-and the identification of the enzymes involved-is a valuable target for drug development. Although most of the core pathway is comparable between species, subtle structure differences lead to different structures delineating the mycolic acid repertoire of tuberculous and some nontuberculous mycobacteria. We here report the characterization of an α'-mycolic acid-deficient Mycobacterium smegmatis mutant obtained by chemical mutagenesis. Whole-genome sequencing and bioinformatic analysis identified a premature stop codon in MSMEG_4301, encoding an acyl-CoA synthetase. Orthologs of MSMEG_4301 are present in all mycobacterial species containing α'-mycolic acids. Deletion of the Mycobacterium abscessus ortholog MAB_1915 abrogated synthesis of α'-mycolic acids; likewise, deletion of MSMEG_4301 in an otherwise wild-type M. smegmatis background also caused loss of these short mycolates. IMPORTANCE Mycobacterium abscessus is a nontuberculous mycobacterium responsible for an increasing number of hard-to-treat infections due to the impervious nature of its cell envelope, a natural barrier to several antibiotics. Mycolic acids are key components of that envelope; thus, their synthesis is a valuable target for drug development. Our results identify the first enzyme involved in α'-mycolic acids, a short-chain member of mycolic acids, loss of which greatly affects growth of this opportunistic pathogen.
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Affiliation(s)
- Cecilia B. Di Capua
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Juan M. Belardinelli
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Hugo A. Carignano
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María V. Buchieri
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Cristian A. Suarez
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Héctor R. Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
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5
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Le NH, Constant P, Tranier S, Nahoum V, Guillet V, Maveyraud L, Daffé M, Mourey L, Verhaeghe P, Marrakchi H. Drug screening approach against mycobacterial fatty acyl-AMP ligase FAAL32 renews the interaest of the salicylanilide pharmacophore in the fight against tuberculosis. Bioorg Med Chem 2022; 71:116938. [DOI: 10.1016/j.bmc.2022.116938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/24/2022] [Accepted: 07/12/2022] [Indexed: 11/02/2022]
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6
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Rajakumara E, Abhishek S, Nitin K, Saniya D, Bajaj P, Schwaneberg U, Davari MD. Structure and Cooperativity in Substrate-Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design. ACS Chem Biol 2022; 17:266-280. [PMID: 35041385 DOI: 10.1021/acschembio.1c00500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure-function relationship, cooperativity in binding of substrates, and dynamics of substrate-enzyme-cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure-activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes' structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Kulhar Nitin
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Dubey Saniya
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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7
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Chen R, Yuan J, Shi X, Tang W, Liu X. Crystal structures of FadD32 and pks13-ACP domain from Corynebacterium diphtheriae. Biochem Biophys Res Commun 2022; 590:152-157. [PMID: 34974304 DOI: 10.1016/j.bbrc.2021.12.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/02/2022]
Abstract
Mycolic acids (MAs) are unique components of cell envelope of Mycobacterium or Corynebacterium and are key factors of their virulence to human. In order to develop new anti-Tuberculosis (TB) drugs, many efforts have paid on investigation of structures and functions of proteins involved in the biosynthesis pathway of MAs. FadD32 and polyketide synthase 13 (pks13) catalyze the last step of MAs synthesis. Here we present the crystal structures of FadD32 with substrates and holo-form of ACP-domain from Corynebacterium diphtheriae. The crystal structures and in vitro biochemical assays provide new insights into the assembly of FadD32 and pks13.
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Affiliation(s)
- Rong Chen
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Jingting Yuan
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Xiaoqian Shi
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Wenjian Tang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071, Tianjin, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071, Tianjin, China.
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8
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In Silico Drug Repurposing Approach: Investigation of Mycobacterium tuberculosis FadD32 Targeted by FDA-Approved Drugs. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030668. [PMID: 35163931 PMCID: PMC8840176 DOI: 10.3390/molecules27030668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/27/2021] [Accepted: 01/09/2022] [Indexed: 12/17/2022]
Abstract
Background: Despite the enormous efforts made towards combating tuberculosis (TB), the disease remains a major global threat. Hence, new drugs with novel mechanisms against TB are urgently needed. Fatty acid degradation protein D32 (FadD32) has been identified as a promising drug target against TB, the protein is required for the biosynthesis of mycolic acids, hence, essential for the growth and multiplication of the mycobacterium. However, the FadD32 mechanism upon the binding of FDA-approved drugs is not well established. Herein, we applied virtual screening (VS), molecular docking, and molecular dynamic (MD) simulation to identify potential FDA-approved drugs against FadD32. Methodology/Results: VS technique was found promising to identify four FDA-approved drugs (accolate, sorafenib, mefloquine, and loperamide) with higher molecular docking scores, ranging from -8.0 to -10.0 kcal/mol. Post-MD analysis showed that the accolate hit displayed the highest total binding energy of -45.13 kcal/mol. Results also showed that the accolate hit formed more interactions with FadD32 active site residues and all active site residues displayed an increase in total binding contribution. RMSD, RMSF, Rg, and DCCM analysis further supported that the presence of accolate exhibited more structural stability, lower bimolecular flexibility, and more compactness into the FadD32 protein. Conclusions: Our study revealed accolate as the best potential drug against FadD32, hence a prospective anti-TB drug in TB therapy. In addition, we believe that the approach presented in the current study will serve as a cornerstone to identifying new potential inhibitors against a wide range of biological targets.
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9
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Patil GS, Kinatukara P, Mondal S, Shambhavi S, Patel KD, Pramanik S, Dubey N, Narasimhan S, Madduri MK, Pal B, Gokhale RS, Sankaranarayanan R. A universal pocket in fatty acyl-AMP ligases ensures redirection of fatty acid pool away from coenzyme A-based activation. eLife 2021; 10:70067. [PMID: 34490847 PMCID: PMC8460268 DOI: 10.7554/elife.70067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/06/2021] [Indexed: 12/29/2022] Open
Abstract
Fatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4′-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and accept holo-ACP unlike other members of the ANL superfamily remains elusive. We show that FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3′,5′-bisphosphate-containing CoA from holo-ACP and thus FAALs can distinguish between CoA and holo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organizations. The universal distribution of FAALs suggests that they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.
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Affiliation(s)
- Gajanan S Patil
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - Sudipta Mondal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sakshi Shambhavi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ketan D Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Surabhi Pramanik
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Noopur Dubey
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Biswajit Pal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Rajan Sankaranarayanan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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10
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Shyam M, Shilkar D, Verma H, Dev A, Sinha BN, Brucoli F, Bhakta S, Jayaprakash V. The Mycobactin Biosynthesis Pathway: A Prospective Therapeutic Target in the Battle against Tuberculosis. J Med Chem 2020; 64:71-100. [PMID: 33372516 DOI: 10.1021/acs.jmedchem.0c01176] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The alarming rise in drug-resistant clinical cases of tuberculosis (TB) has necessitated the rapid development of newer chemotherapeutic agents with novel mechanisms of action. The mycobactin biosynthesis pathway, conserved only among the mycolata family of actinobacteria, a group of intracellularly surviving bacterial pathogens that includes Mycobacterium tuberculosis, generates a salicyl-capped peptide mycobactin under iron-stress conditions in host macrophages to support the iron demands of the pathogen. This in vivo essentiality makes this less explored mycobactin biosynthesis pathway a promising endogenous target for novel lead-compounds discovery. In this Perspective, we have provided an up-to-date account of drug discovery efforts targeting selected enzymes (MbtI, MbtA, MbtM, and PPTase) from the mbt gene cluster (mbtA-mbtN). Furthermore, a succinct discussion on non-specific mycobactin biosynthesis inhibitors and the Trojan horse approach adopted to impair iron metabolism in mycobacteria has also been included in this Perspective.
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Affiliation(s)
- Mousumi Shyam
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India.,Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Harshita Verma
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Abhimanyu Dev
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Barij Nayan Sinha
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Federico Brucoli
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, U.K
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
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11
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Baran M, Grimes KD, Sibbald PA, Fu P, Boshoff HIM, Wilson DJ, Aldrich CC. Development of small-molecule inhibitors of fatty acyl-AMP and fatty acyl-CoA ligases in Mycobacterium tuberculosis. Eur J Med Chem 2020; 201:112408. [PMID: 32574901 DOI: 10.1016/j.ejmech.2020.112408] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/07/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022]
Abstract
Lipid metabolism in Mycobacterium tuberculosis (Mtb) relies on 34 fatty acid adenylating enzymes (FadDs) that can be grouped into two classes: fatty acyl-CoA ligases (FACLs) involved in lipid and cholesterol catabolism and long chain fatty acyl-AMP ligases (FAALs) involved in biosynthesis of the numerous essential and virulence-conferring lipids found in Mtb. The precise biochemical roles of many FACLs remain poorly characterized while the functionally non-redundant FAALs are much better understood. Here we describe the systematic investigation of 5'-O-[N-(alkanoyl)sulfamoyl]adenosine (alkanoyl adenosine monosulfamate, alkanoyl-AMS) analogs as potential multitarget FadD inhibitors for their antitubercular activity and biochemical selectivity towards representative FAAL and FACL enzymes. We identified several potent compounds including 12-azidododecanoyl-AMS 28, 11-phenoxyundecanoyl-AMS 32, and nonyloxyacetyl-AMS 36 with minimum inhibitory concentrations (MICs) against M. tuberculosis ranging from 0.098 to 3.13 μM. Compound 32 was notable for its impressive biochemical selectivity against FAAL28 (apparent Ki = 0.7 μM) versus FACL19 (Ki > 100 μM), and uniform activity against a panel of multidrug and extensively drug-resistant TB strains with MICs ranging from 3.13 to 12.5 μM in minimal (GAST) and rich (7H9) media. The SAR analysis provided valuable insights for further optimization of 32 and also identified limitations to overcome.
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Affiliation(s)
- Marzena Baran
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States
| | - Kimberly D Grimes
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Paul A Sibbald
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Peng Fu
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Helena I M Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, United States
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States; Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States.
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12
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Marchetti PM, Kelly V, Simpson JP, Ward M, Campopiano DJ. The carbon chain-selective adenylation enzyme TamA: the missing link between fatty acid and pyrrole natural product biosynthesis. Org Biomol Chem 2019; 16:2735-2740. [PMID: 29594310 PMCID: PMC5939613 DOI: 10.1039/c8ob00441b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
TamA is the adenylating enzyme that selects and activates fatty acids for tambjamine biosynthesis.
The marine bacterium Pseudoalteromonas tunicata produces the bipyrrole antibiotic tambjamine YP1. This natural product is built from common amino acid and fatty acid building blocks in a biosynthetic pathway that is encoded in the tam operon which contains 19 genes. The exact role that each of these Tam proteins plays in tambjamine biosynthesis is not known. Here, we provide evidence that TamA initiates the synthesis and controls the chain length of the essential tambjamine fatty amine tail. Sequence analysis suggests the unusual TamA is comprised of an N-terminal adenylation (ANL) domain fused to a C-terminal acyl carrier protein (ACP). Mass spectrometry analysis of recombinant TamA revealed the surprising presence of bound C11 and C12 acyl-adenylate intermediates. Acylation of the ACP domain was observed upon attachment of the phosphopantetheine (4′-PP) arm to the ACP. We also show that TamA can transfer fatty acids ranging in chain length from C6–C13 to an isolated ACP domain. Thus TamA bridges the gap between primary and secondary metabolism by linking fatty acid and pyrrole biosynthetic pathways.
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Affiliation(s)
- Piera M Marchetti
- EaStCHEM School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
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13
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Fang C, Lee KK, Nietupski R, Bates RH, Fernandez-Menendez R, Lopez-Roman EM, Guijarro-Lopez L, Yin Y, Peng Z, Gomez JE, Fisher S, Barros-Aguirre D, Hubbard BK, Serrano-Wu MH, Hung DT. Discovery of heterocyclic replacements for the coumarin core of anti-tubercular FadD32 inhibitors. Bioorg Med Chem Lett 2018; 28:3529-3533. [PMID: 30316633 DOI: 10.1016/j.bmcl.2018.09.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/20/2018] [Accepted: 09/27/2018] [Indexed: 11/27/2022]
Abstract
Previous work established a coumarin scaffold as a starting point for inhibition of Mycobacterium tuberculosis (Mtb) FadD32 enzymatic activity. After further profiling of the coumarin inhibitor 4 revealed chemical instability, we discovered that a quinoline ring circumvented this instability and had the advantage of offering additional substitution vectors to further optimize. Ensuing SAR studies gave rise to quinoline-2-carboxamides with potent anti-tubercular activity. Further optimization of ADME/PK properties culminated in 21b that exhibited compelling in vivo efficacy in a mouse model of Mtb infection.
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Affiliation(s)
- Chao Fang
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA
| | - Katie K Lee
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Department of Molecular Biology and Center for Integrative and Computational Biology, Massachusetts General Hospital, 185 Cambridge St, Boston, MA 02114, USA
| | - Raymond Nietupski
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA
| | - Robert H Bates
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | | | - Eva Maria Lopez-Roman
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Laura Guijarro-Lopez
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Yunxing Yin
- WuXi AppTec, 168 Nanhai Rd, Tianjin Economic-Technological Development Area (TEDA), Tianjin 300457, China
| | - Zuozhong Peng
- WuXi AppTec, 288 Fute Zhong Rd, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - James E Gomez
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Department of Molecular Biology and Center for Integrative and Computational Biology, Massachusetts General Hospital, 185 Cambridge St, Boston, MA 02114, USA
| | - Stewart Fisher
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA
| | - David Barros-Aguirre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Brian K Hubbard
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA
| | | | - Deborah T Hung
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA 02142, USA; Department of Molecular Biology and Center for Integrative and Computational Biology, Massachusetts General Hospital, 185 Cambridge St, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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14
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Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria: a systematic review and meta-analysis. Sci Rep 2018. [PMID: 29515167 PMCID: PMC5841357 DOI: 10.1038/s41598-018-22642-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium species are a significant cause of morbidity and mortality worldwide. The present study was carried out to systematically evaluate the accuracy of Matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF MS) for the identification of clinical pathogenic mycobacteria. After a rigid selection process, 19 articles involving 2,593 mycobacteria isolates were included. The pooled result agreed with the reference method identification for 85% of the isolates to genus level, with 71% (95% CI of 69% to 72%) correct to the species level. The MALDI-TOF MS correctly identified 92% of the M.tuberculosis isolates (95% CI of 0.87 to 0.96), and 68% of M. bovisisolates (95% CI of 27% to 100%) to the species level. Mycobacterium tuberculosis complex in solid media with reference strains using augmented database showing more accurate identification. The identifying accuracy rate of bioMérieuxVitek MS was slight higher than Bruker MALDI Biotyper (75% vs 72%). However, opposite results were obtained in identifications of M. fortuitum, M. kansasii, M. marinum, and M. terrae with these two systems. In summary, our results demonstrate that application of MALDI-TOF MS in clinical pathogenic mycobacteria identification is less satisfactory to date. Increasing need for improvement is important especially at species level.
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15
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Barisch C, Soldati T. Mycobacterium marinum Degrades Both Triacylglycerols and Phospholipids from Its Dictyostelium Host to Synthesise Its Own Triacylglycerols and Generate Lipid Inclusions. PLoS Pathog 2017; 13:e1006095. [PMID: 28103313 PMCID: PMC5245797 DOI: 10.1371/journal.ppat.1006095] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/28/2016] [Indexed: 12/21/2022] Open
Abstract
During a tuberculosis infection and inside lipid-laden foamy macrophages, fatty acids (FAs) and sterols are the major energy and carbon source for Mycobacterium tuberculosis. Mycobacteria can be found both inside a vacuole and the cytosol, but how this impacts their access to lipids is not well appreciated. Lipid droplets (LDs) store FAs in form of triacylglycerols (TAGs) and are energy reservoirs of prokaryotes and eukaryotes. Using the Dictyostelium discoideum/Mycobacterium marinum infection model we showed that M. marinum accesses host LDs to build up its own intracytosolic lipid inclusions (ILIs). Here, we show that host LDs aggregate at regions of the bacteria that become exposed to the cytosol, and appear to coalesce on their hydrophobic surface leading to a transfer of diacylglycerol O-acyltransferase 2 (Dgat2)-GFP onto the bacteria. Dictyostelium knockout mutants for both Dgat enzymes are unable to generate LDs. Instead, the excess of exogenous FAs is esterified predominantly into phospholipids, inducing uncontrolled proliferation of the endoplasmic reticulum (ER). Strikingly, in absence of host LDs, M. marinum alternatively exploits these phospholipids, resulting in rapid reversal of ER-proliferation. In addition, the bacteria are unable to restrict their acquisition of lipids from the dgat1&2 double knockout leading to vast accumulation of ILIs. Recent data indicate that the presence of ILIs is one of the characteristics of dormant mycobacteria. During Dictyostelium infection, ILI formation in M. marinum is not accompanied by a significant change in intracellular growth and a reduction in metabolic activity, thus providing evidence that storage of neutral lipids does not necessarily induce dormancy.
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Affiliation(s)
- Caroline Barisch
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, Geneva, Switzerland
- * E-mail:
| | - Thierry Soldati
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, Geneva, Switzerland
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16
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Le NH, Molle V, Eynard N, Miras M, Stella A, Bardou F, Galandrin S, Guillet V, André-Leroux G, Bellinzoni M, Alzari P, Mourey L, Burlet-Schiltz O, Daffé M, Marrakchi H. Ser/Thr Phosphorylation Regulates the Fatty Acyl-AMP Ligase Activity of FadD32, an Essential Enzyme in Mycolic Acid Biosynthesis. J Biol Chem 2016; 291:22793-22805. [PMID: 27590338 DOI: 10.1074/jbc.m116.748053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
Mycolic acids are essential components of the mycobacterial cell envelope, and their biosynthetic pathway is a well known source of antituberculous drug targets. Among the promising new targets in the pathway, FadD32 is an essential enzyme required for the activation of the long meromycolic chain of mycolic acids and is essential for mycobacterial growth. Following the in-depth biochemical, biophysical, and structural characterization of FadD32, we investigated its putative regulation via post-translational modifications. Comparison of the fatty acyl-AMP ligase activity between phosphorylated and dephosphorylated FadD32 isoforms showed that the native protein is phosphorylated by serine/threonine protein kinases and that this phosphorylation induced a significant loss of activity. Mass spectrometry analysis of the native protein confirmed the post-translational modifications and identified Thr-552 as the phosphosite. Phosphoablative and phosphomimetic FadD32 mutant proteins confirmed both the position and the importance of the modification and its correlation with the negative regulation of FadD32 activity. Investigation of the mycolic acid condensation reaction catalyzed by Pks13, involving FadD32 as a partner, showed that FadD32 phosphorylation also impacts the condensation activity. Altogether, our results bring to light FadD32 phosphorylation by serine/threonine protein kinases and its correlation with the enzyme-negative regulation, thus shedding a new horizon on the mycolic acid biosynthesis modulation and possible inhibition strategies for this promising drug target.
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Affiliation(s)
- Nguyen-Hung Le
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Virginie Molle
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université de Montpellier, CNRS UMR 5235, Place Eugène Bataillon, 34095 Montpellier Cedex 05, and
| | - Nathalie Eynard
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Mathieu Miras
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Alexandre Stella
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Fabienne Bardou
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Ségolène Galandrin
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Valérie Guillet
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Gwenaëlle André-Leroux
- the Institut Pasteur, Unité de Microbiologie Structurale, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marco Bellinzoni
- the Institut Pasteur, Unité de Microbiologie Structurale, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Pedro Alzari
- the Institut Pasteur, Unité de Microbiologie Structurale, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Lionel Mourey
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Odile Burlet-Schiltz
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS
| | - Mamadou Daffé
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS,
| | - Hedia Marrakchi
- From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS,
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17
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Quémard A. New Insights into the Mycolate-Containing Compound Biosynthesis and Transport in Mycobacteria. Trends Microbiol 2016; 24:725-738. [DOI: 10.1016/j.tim.2016.04.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/14/2016] [Accepted: 04/29/2016] [Indexed: 12/15/2022]
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18
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Kuhn ML, Alexander E, Minasov G, Page HJ, Warwrzak Z, Shuvalova L, Flores KJ, Wilson DJ, Shi C, Aldrich CC, Anderson WF. Structure of the Essential Mtb FadD32 Enzyme: A Promising Drug Target for Treating Tuberculosis. ACS Infect Dis 2016; 2:579-591. [PMID: 27547819 DOI: 10.1021/acsinfecdis.6b00082] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mycolic acids are indispensible lipids of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), and contribute to the distinctive architecture and impermeability of the mycobacterial cell envelope. FadD32 plays a pivotal role in mycolic acid biosynthesis by functionally linking fatty acid synthase (FAS) and polyketide synthase (PKS) biosynthetic pathways. FadD32, a fatty acyl-AMP ligase (FAAL), represents one of the best genetically and chemically validated new TB drug targets. We have determined the three-dimensional crystal structure of Mtb FadD32 in complex with a ligand specifically designed to stabilize the catalytically active adenylate-conformation, which provides a foundation for structure-based drug design efforts against this essential protein. The structure also captures the unique interactions of a FAAL-specific insertion sequence and provides insight into the specificity and mechanism of fatty acid transfer.
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Affiliation(s)
- Misty L. Kuhn
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | | | - George Minasov
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Holland J. Page
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, United States
| | - Zdzislaw Warwrzak
- LS-CAT,
Synchrotron Research Center, Northwestern University, Argonne, Illinois 60439, United States
| | - Ludmilla Shuvalova
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Kristin J. Flores
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | | | | | | | - Wayne F. Anderson
- Center for Structural
Genomics of Infectious Diseases, Department of Biochemistry and Molecular
Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
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