1
|
Brown KL, Krekhno JMC, Xing S, Huan T, Eltis LD. Cholesterol-Mediated Coenzyme A Depletion in Catabolic Mutants of Mycobacteria Leads to Toxicity. ACS Infect Dis 2024; 10:107-119. [PMID: 38054469 DOI: 10.1021/acsinfecdis.3c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Cholesterol is a critical growth substrate for Mycobacterium tuberculosis (Mtb) during infection, and the cholesterol catabolic pathway has been targeted for the development of new antimycobacterial agents. A key metabolite in cholesterol catabolism is 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indanedione (HIP). Many of the HIP metabolites are acyl-coenzyme A (CoA) thioesters, whose accumulation in deletion mutants can cause cholesterol-mediated toxicity. We used LC-MS/MS analysis to demonstrate that deletion of genes involved in HIP catabolism leads to acyl-CoA accumulation with concomitant depletion of free CoASH, leading to dysregulation of central metabolic pathways. CoASH and acyl-CoAs inhibited PanK, the enzyme that catalyzes the first step in the transformation of pantothenate to CoASH. Inhibition was competitive with respect to ATP with Kic values ranging from 9 μM for CoASH to 57 μM for small acyl-CoAs and 180 ± 30 μM for cholesterol-derived acyl-CoA. These findings link two critical metabolic pathways and suggest that therapeutics targeting cholesterol catabolic enzymes could both prevent the utilization of an important growth substrate and simultaneously sequester CoA from essential cellular processes, leading to bacterial toxicity.
Collapse
Affiliation(s)
- Kirstin L Brown
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Jessica M C Krekhno
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Shipei Xing
- Department of Chemistry, The University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Tao Huan
- Department of Chemistry, The University of British Columbia, Vancouver V6T 1Z1, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| |
Collapse
|
2
|
Butman HS, Kotzé TJ, Dowd CS, Strauss E. Vitamin in the Crosshairs: Targeting Pantothenate and Coenzyme A Biosynthesis for New Antituberculosis Agents. Front Cell Infect Microbiol 2020; 10:605662. [PMID: 33384970 PMCID: PMC7770189 DOI: 10.3389/fcimb.2020.605662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Despite decades of dedicated research, there remains a dire need for new drugs against tuberculosis (TB). Current therapies are generations old and problematic. Resistance to these existing therapies results in an ever-increasing burden of patients with disease that is difficult or impossible to treat. Novel chemical entities with new mechanisms of action are therefore earnestly required. The biosynthesis of coenzyme A (CoA) has long been known to be essential in Mycobacterium tuberculosis (Mtb), the causative agent of TB. The pathway has been genetically validated by seminal studies in vitro and in vivo. In Mtb, the CoA biosynthetic pathway is comprised of nine enzymes: four to synthesize pantothenate (Pan) from l-aspartate and α-ketoisovalerate; five to synthesize CoA from Pan and pantetheine (PantSH). This review gathers literature reports on the structure/mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway. In addition to traditional inhibition of a single enzyme, the CoA pathway offers an antimetabolite strategy as a promising alternative. In this review, we provide our assessment of what appear to be the best targets, and, thus, which CoA pathway enzymes present the best opportunities for antitubercular drug discovery moving forward.
Collapse
Affiliation(s)
- Hailey S. Butman
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Timothy J. Kotzé
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
3
|
Su Z, Wei Y, Kang XF. Simultaneous High-Resolution Detection of Bioenergetic Molecules using Biomimetic-Receptor Nanopore. Anal Chem 2019; 91:15255-15259. [PMID: 31665602 DOI: 10.1021/acs.analchem.9b04268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel artificial receptor, heptakis-[6-deoxy-6-(2-hydroxy-3-trimethylammonion-propyl) amino]-beta-cyclomaltoheptaose, with similar functions of mitochondrial ADP/ATP carrier protein, was synthesized and harbored in the engineered α-HL (M113R)7 nanopore, forming a single-molecule biosensor for sensing bioenergetic molecules and their transformations. The strategy significantly elevates both selectivity and signal-to-noise, which enables simultaneous recognition and detection of ATP, ADP, and AMP by real-time single-molecule measurement.
Collapse
Affiliation(s)
- Zhuoqun Su
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science , Northwest University , Xi'an 710069 , P. R. China
| | - Yongfeng Wei
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science , Northwest University , Xi'an 710069 , P. R. China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science , Northwest University , Xi'an 710069 , P. R. China
| |
Collapse
|
4
|
Duncan D, Auclair K. The coenzyme A biosynthetic pathway: A new tool for prodrug bioactivation. Arch Biochem Biophys 2019; 672:108069. [PMID: 31404525 DOI: 10.1016/j.abb.2019.108069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 11/29/2022]
Abstract
Prodrugs account for more than 5% of pharmaceuticals approved worldwide. Over the past decades several prodrug design strategies have been firmly established; however, only a few functional groups remain amenable to this approach. The aim of this overview is to highlight the use of coenzyme A (CoA) biosynthetic enzymes as a recently explored bioactivation scheme and provide information about its scope of utility. This emerging tool is likely to have a strong impact on future medicinal and biological studies as it offers promiscuity, orthogonal selectivity, and the capability of assembling exceptionally large molecules.
Collapse
Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.
| |
Collapse
|
5
|
Puranik N, Srivastava P, Swami S, Choudhari A, Sarkar D. Molecular modeling studies and in vitro screening of dihydrorugosaflavonoid and its derivatives against Mycobacterium tuberculosis. RSC Adv 2018; 8:10634-10643. [PMID: 35540494 PMCID: PMC9078922 DOI: 10.1039/c8ra00636a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 02/28/2018] [Indexed: 11/21/2022] Open
Abstract
Novel drug regimens against tuberculosis (TB) are urgently needed and may be developed by targeting essential enzymes of Mtb that sustain the pathogenicity of tuberculosis. Dihydrorugosaflavonoid interacted with the active pocket of MabA and PanK.
Collapse
Affiliation(s)
- Ninad V. Puranik
- Bioprospecting Group
- Agharkar Research Institute
- Pune 411004
- India
- Savitribai Phule Pune University
| | - Pratibha Srivastava
- Bioprospecting Group
- Agharkar Research Institute
- Pune 411004
- India
- Savitribai Phule Pune University
| | - Sagar Swami
- Organic Chemistry Division
- National Chemical Laboratory
- Pune-411008
- India
| | - Amit Choudhari
- Organic Chemistry Division
- National Chemical Laboratory
- Pune-411008
- India
| | - Dhiman Sarkar
- Organic Chemistry Division
- National Chemical Laboratory
- Pune-411008
- India
| |
Collapse
|
6
|
Paul A, Kumar P, Surolia A, Vijayan M. Biochemical and structural studies of mutants indicate concerted movement of the dimer interface and ligand-binding region of Mycobacterium tuberculosis pantothenate kinase. Acta Crystallogr F Struct Biol Commun 2017; 73:635-643. [PMID: 29095158 PMCID: PMC5683034 DOI: 10.1107/s2053230x17015667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/27/2017] [Indexed: 11/11/2022] Open
Abstract
Two point mutants and the corresponding double mutant of Mycobacterium tuberculosis pantothenate kinase have been prepared and biochemically and structurally characterized. The mutants were designed to weaken the affinity of the enzyme for the feedback inhibitor CoA. The mutants exhibit reduced activity, which can be explained in terms of their structures. The crystals of the mutants are not isomorphous to any of the previously analysed crystals of the wild-type enzyme or its complexes. The mycobacterial enzyme and its homologous Escherichia coli enzyme exhibit structural differences in their nucleotide complexes in the dimer interface and the ligand-binding region. In three of the four crystallographically independent mutant molecules the structure is similar to that in the E. coli enzyme. Although the mutants involve changes in the CoA-binding region, the dimer interface and the ligand-binding region move in a concerted manner, an observation which might be important in enzyme action. This work demonstrates that the structure of the mycobacterial enzyme can be transformed into a structure similar to that of the E. coli enzyme through minor perturbations without external influences such as those involving ligand binding.
Collapse
Affiliation(s)
- A. Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - P. Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A. Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
7
|
Chandran AV, Prabu JR, Nautiyal A, Patil KN, Muniyappa K, Vijayan M. Structural studies on Mycobacterium tuberculosis RecA: molecular plasticity and interspecies variability. J Biosci 2015; 40:13-30. [PMID: 25740138 DOI: 10.1007/s12038-014-9497-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures of crystals of Mycobacterium tuberculosis RecA, grown and analysed under different conditions, provide insights into hitherto underappreciated details of molecular structure and plasticity. In particular, they yield information on the invariant and variable features of the geometry of the P-loop, whose binding to ATP is central for all the biochemical activities of RecA. The strengths of interaction of the ligands with the P-loop reveal significant differences. This in turn affects the magnitude of the motion of the 'switch' residue, Gln195 in M. tuberculosis RecA, which triggers the transmission of ATP-mediated allosteric information to the DNA binding region. M. tuberculosis RecA is substantially rigid compared with its counterparts from M. smegmatis and E. coli, which exhibit concerted internal molecular mobility. The interspecies variability in the plasticity of the two mycobacterial proteins is particularly surprising as they have similar sequence and 3D structure. Details of the interactions of ligands with the protein, characterized in the structures reported here, could be useful for design of inhibitors against M. tuberculosis RecA.
Collapse
Affiliation(s)
- Anu V Chandran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012
| | | | | | | | | | | |
Collapse
|
8
|
Arif SM, Geethanandan K, Mishra P, Surolia A, Varshney U, Vijayan M. Structural plasticity inMycobacterium tuberculosisuracil-DNA glycosylase (MtUng) and its functional implications. ACTA ACUST UNITED AC 2015; 71:1514-27. [DOI: 10.1107/s1399004715009311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/15/2015] [Indexed: 12/29/2022]
Abstract
17 independent crystal structures of family I uracil-DNA glycosylase fromMycobacterium tuberculosis(MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 5′ position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.
Collapse
|
9
|
Recent advances in targeting coenzyme A biosynthesis and utilization for antimicrobial drug development. Biochem Soc Trans 2015; 42:1080-6. [PMID: 25110006 DOI: 10.1042/bst20140131] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The biosynthesis and utilization of CoA (coenzyme A), the ubiquitous and essential acyl carrier in all organisms, have long been regarded as excellent targets for the development of new antimicrobial drugs. Moreover, bioinformatics and biochemical studies have highlighted significant differences between several of the bacterial enzyme targets and their human counterparts, indicating that selective inhibition of the former should be possible. Over the past decade, a large amount of structural and mechanistic data has been gathered on CoA metabolism and the CoA biosynthetic enzymes, and this has facilitated the discovery and development of several promising candidate antimicrobial agents. These compounds include both target-specific inhibitors, as well as CoA antimetabolite precursors that can reduce CoA levels and interfere with processes that are dependent on this cofactor. In the present mini-review we provide an overview of the most recent of these studies that, taken together, have also provided chemical validation of CoA biosynthesis and utilization as viable targets for antimicrobial drug development.
Collapse
|
10
|
Paul A, Mishra A, Surolia A, Vijayan M. Cloning, expression, purification, crystallization and preliminary X-ray studies of argininosuccinate lyase (Rv1659) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1422-4. [PMID: 24316845 PMCID: PMC3855735 DOI: 10.1107/s1744309113031138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 11/12/2013] [Indexed: 11/10/2022]
Abstract
The last enzyme in the arginine-biosynthesis pathway, argininosuccinate lyase, from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized, and preliminary X-ray studies have been carried out on the crystals. The His-tagged tetrameric enzyme with a subunit molecular weight of 50.9 kDa crystallized with two tetramers in the asymmetric unit of the orthorhombic unit cell, space group P2(1)2(1)2(1). Molecular-replacement calculations and self-rotation calculations confirmed the space group and the tetrameric nature of the molecule.
Collapse
Affiliation(s)
- A. Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A. Mishra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A. Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
11
|
Björkelid C, Bergfors T, Raichurkar AKV, Mukherjee K, Malolanarasimhan K, Bandodkar B, Jones TA. Structural and biochemical characterization of compounds inhibiting Mycobacterium tuberculosis pantothenate kinase. J Biol Chem 2013; 288:18260-70. [PMID: 23661699 DOI: 10.1074/jbc.m113.476473] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis, the bacterial causative agent of tuberculosis, currently affects millions of people. The emergence of drug-resistant strains makes development of new antibiotics targeting the bacterium a global health priority. Pantothenate kinase, a key enzyme in the universal biosynthesis of the essential cofactor CoA, was targeted in this study to find new tuberculosis drugs. The biochemical characterizations of two new classes of compounds that inhibit pantothenate kinase from M. tuberculosis are described, along with crystal structures of their enzyme-inhibitor complexes. These represent the first crystal structures of this enzyme with engineered inhibitors. Both classes of compounds bind in the active site of the enzyme, overlapping with the binding sites of the natural substrate and product, pantothenate and phosphopantothenate, respectively. One class of compounds also interferes with binding of the cofactor ATP. The complexes were crystallized in two crystal forms, one of which is in a new space group for this enzyme and diffracts to the highest resolution reported for any pantothenate kinase structure. These two crystal forms allowed, for the first time, modeling of the cofactor-binding loop in both open and closed conformations. The structures also show a binding mode of ATP different from that previously reported for the M. tuberculosis enzyme but similar to that in the pantothenate kinases of other organisms.
Collapse
Affiliation(s)
- Christofer Björkelid
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden.
| | | | | | | | | | | | | |
Collapse
|
12
|
Chetnani B, Kumar P, Abhinav KV, Chhibber M, Surolia A, Vijayan M. Location and conformation of pantothenate and its derivatives in Mycobacterium tuberculosis pantothenate kinase: insights into enzyme action. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:774-83. [PMID: 21904030 DOI: 10.1107/s0907444911024462] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/22/2011] [Indexed: 11/10/2022]
Abstract
Previous studies of complexes of Mycobacterium tuberculosis PanK (MtPanK) with nucleotide diphosphates and nonhydrolysable analogues of nucleoside triphosphates in the presence or the absence of pantothenate established that the enzyme has dual specificity for ATP and GTP, revealed the unusual movement of ligands during enzyme action and provided information on the effect of pantothenate on the location and conformation of the nucleotides at the beginning and the end of enzyme action. The X-ray analyses of the binary complexes of MtPanK with pantothenate, pantothenol and N-nonylpantothenamide reported here demonstrate that in the absence of nucleotide these ligands occupy, with a somewhat open conformation, a location similar to that occupied by phosphopantothenate in the `end' complexes, which differs distinctly from the location of pantothenate in the closed conformation in the ternary `initiation' complexes. The conformation and the location of the nucleotide were also different in the initiation and end complexes. An invariant arginine appears to play a critical role in the movement of ligands that takes place during enzyme action. The work presented here completes the description of the locations and conformations of nucleoside diphosphates and triphosphates and pantothenate in different binary and ternary complexes, and suggests a structural rationale for the movement of ligands during enzyme action. The present investigation also suggests that N-alkylpantothenamides could be phosphorylated by the enzyme in the same manner as pantothenate.
Collapse
Affiliation(s)
- Bhaskar Chetnani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
| | | | | | | | | | | |
Collapse
|
13
|
Kaushal PS, Talawar RK, Varshney U, Vijayan M. Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:887-92. [PMID: 20693660 PMCID: PMC2917283 DOI: 10.1107/s1744309110023043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 06/15/2010] [Indexed: 11/10/2022]
Abstract
Uracil N-glycosylase (Ung) is the most thoroughly studied of the group of uracil DNA-glycosylase (UDG) enzymes that catalyse the first step in the uracil excision-repair pathway. The overall structure of the enzyme from Mycobacterium tuberculosis is essentially the same as that of the enzyme from other sources. However, differences exist in the N- and C-terminal stretches and some catalytic loops. Comparison with appropriate structures indicate that the two-domain enzyme closes slightly when binding to DNA, while it opens slightly when binding to the proteinaceous inhibitor Ugi. The structural changes in the catalytic loops on complexation reflect the special features of their structure in the mycobacterial protein. A comparative analysis of available sequences of the enzyme from different sources indicates high conservation of amino-acid residues in the catalytic loops. The uracil-binding pocket in the structure is occupied by a citrate ion. The interactions of the citrate ion with the protein mimic those of uracil, in addition to providing insights into other possible interactions that inhibitors could be involved in.
Collapse
Affiliation(s)
- Prem Singh Kaushal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ramappa K. Talawar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|
14
|
Lou Z, Zhang X. Protein targets for structure-based anti-Mycobacterium tuberculosis drug discovery. Protein Cell 2010; 1:435-42. [PMID: 21203958 DOI: 10.1007/s13238-010-0057-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 05/01/2010] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis, which belongs to the genus Mycobacterium, is the pathogenic agent for most tuberculosis (TB). As TB remains one of the most rampant infectious diseases, causing morbidity and death with emergence of multi-drug-resistant and extensively-drug-resistant forms, it is urgent to identify new drugs with novel targets to ensure future therapeutic success. In this regards, the structural genomics of M. tuberculosis provides important information to identify potential targets, perform biochemical assays, determine crystal structures in complex with potential inhibitor(s), reveal the key sites/residues for biological activity, and thus validate drug targets and discover novel drugs. In this review, we will discuss the recent progress on novel targets for structure-based anti-M. tuberculosis drug discovery.
Collapse
Affiliation(s)
- Zhiyong Lou
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.
| | | |
Collapse
|
15
|
Chetnani B, Kumar P, Surolia A, Vijayan M. M. tuberculosis pantothenate kinase: dual substrate specificity and unusual changes in ligand locations. J Mol Biol 2010; 400:171-85. [PMID: 20451532 DOI: 10.1016/j.jmb.2010.04.064] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 04/29/2010] [Accepted: 04/30/2010] [Indexed: 12/19/2022]
Abstract
Kinetic measurements of enzyme activity indicate that type I pantothenate kinase from Mycobacterium tuberculosis has dual substrate specificity for ATP and GTP, unlike the enzyme from Escherichia coli, which shows a higher specificity for ATP. A molecular explanation for the difference in the specificities of the two homologous enzymes is provided by the crystal structures of the complexes of the M. tuberculosis enzyme with (1) GMPPCP and pantothenate, (2) GDP and phosphopantothenate, (3) GDP, (4) GDP and pantothenate, (5) AMPPCP, and (6) GMPPCP, reported here, and the structures of the complexes of the two enzymes involving coenzyme A and different adenyl nucleotides reported earlier. The explanation is substantially based on two critical substitutions in the amino acid sequence and the local conformational change resulting from them. The structures also provide a rationale for the movement of ligands during the action of the mycobacterial enzyme. Dual specificity of the type exhibited by this enzyme is rare. The change in locations of ligands during action, observed in the case of the M. tuberculosis enzyme, is unusual, so is the striking difference between two homologous enzymes in the geometry of the binding site, locations of ligands, and specificity. Furthermore, the dual specificity of the mycobacterial enzyme appears to have been caused by a biological necessity.
Collapse
Affiliation(s)
- Bhaskar Chetnani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | | | | |
Collapse
|