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Bahl A, Rakshit R, Pandey S, Tripathi D. Genome wide screening to discover novel toxin-antitoxin modules in Mycobacterium indicus pranii; perspective on gene acquisition during mycobacterial evolution. Biotechnol Appl Biochem 2025; 72:116-137. [PMID: 39113212 DOI: 10.1002/bab.2651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 07/24/2024] [Indexed: 02/06/2025]
Abstract
Mycobacterium indicus pranii (MIP), a benign saprophyte with potent immunomodulatory attributes, holds a pivotal position in mycobacterial evolution, potentially serving as the precursor to the pathogenic Mycobacterium avium complex (MAC). Despite its established immunotherapeutic efficacy against leprosy and notable outcomes in gram-negative sepsis and COVID-19 cases, the genomic and biochemical features of MIP remain largely elusive. This study explores the uncharted territory of toxin-antitoxin (TA) systems within MIP, hypothesizing their role in mycobacterial pathogenicity regulation. Genome-wide screening, employing diverse databases, unveils putative TA modules in MIP, setting the stage for a comparative analysis with known modules in Mycobacterium tuberculosis, Mycobacterium smegmatis, Escherichia coli, and Vibrio cholerae. The study further delves into the TA network of MAC and Mycobacterium intracellulare, unraveling interactive properties and family characteristics of identified TA modules in MIP. This comprehensive exploration seeks to illuminate the contribution of TA modules in regulating virulence, habitat diversification, and the evolutionary pathogenicity of mycobacteria. The insights garnered from this investigation not only enhance our understanding of MIP's potential as a vaccine candidate but also hold promise in optimizing tuberculosis drug regimens for expedited recovery.
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Affiliation(s)
- Aayush Bahl
- Microbial Pathogenesis and Microbiome Lab, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Roopshali Rakshit
- Microbial Pathogenesis and Microbiome Lab, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Saurabh Pandey
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, Delhi, India
| | - Deeksha Tripathi
- Microbial Pathogenesis and Microbiome Lab, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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2
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Kingdon ADH, Alderwick LJ. Structure-based in silico approaches for drug discovery against Mycobacterium tuberculosis. Comput Struct Biotechnol J 2021; 19:3708-3719. [PMID: 34285773 PMCID: PMC8258792 DOI: 10.1016/j.csbj.2021.06.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of TB and was estimated to cause 1.4 million death in 2019, alongside 10 million new infections. Drug resistance is a growing issue, with multi-drug resistant infections representing 3.3% of all new infections, hence novel antimycobacterial drugs are urgently required to combat this growing health emergency. Alongside this, increased knowledge of gene essentiality in the pathogenic organism and larger compound databases can aid in the discovery of new drug compounds. The number of protein structures, X-ray based and modelled, is increasing and now accounts for greater than > 80% of all predicted M. tuberculosis proteins; allowing novel targets to be investigated. This review will focus on structure-based in silico approaches for drug discovery, covering a range of complexities and computational demands, with associated antimycobacterial examples. This includes molecular docking, molecular dynamic simulations, ensemble docking and free energy calculations. Applications of machine learning onto each of these approaches will be discussed. The need for experimental validation of computational hits is an essential component, which is unfortunately missing from many current studies. The future outlooks of these approaches will also be discussed.
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Key Words
- CV, collective variable
- Docking
- Drug discovery
- In silico
- LIE, Linear Interaction Energy
- MD, Molecular Dynamic
- MDR, multi-drug resistant
- MMPB(GB)SA, Molecular Mechanics with Poisson Boltzmann (or generalised Born) and Surface Area solvation
- Machine learning
- Mt, Mycobacterium tuberculosis
- Mycobacterium tuberculosis
- PTC, peptidyl transferase centre
- RMSD, root-mean square-deviation
- Tuberculosis, TB
- cMD, Classical Molecular Dynamic
- cryo-EM, cryogenic electron microscopy
- ns, nanosecond
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Affiliation(s)
- Alexander D H Kingdon
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Luke J Alderwick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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3
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Beckham KSH, Staack S, Wilmanns M, Parret AHA. The pMy vector series: A versatile cloning platform for the recombinant production of mycobacterial proteins in Mycobacterium smegmatis. Protein Sci 2020; 29:2528-2537. [PMID: 33006405 PMCID: PMC7679961 DOI: 10.1002/pro.3962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 12/16/2022]
Abstract
Structural and biophysical characterization of molecular mechanisms of disease‐causing pathogens, such as Mycobacterium tuberculosis, often requires recombinant expression of large amounts highly pure protein. For the production of mycobacterial proteins, overexpression in the fast‐growing and non‐pathogenic species Mycobacterium smegmatis has several benefits over the standard Escherichia coli expression strains. However, unlike for E. coli, the range of expression vectors currently available is limited. Here we describe the development of the pMy vector series, a set of expression plasmids for recombinant production of single proteins and protein complexes in M. smegmatis. By incorporating an alternative selection marker, we show that these plasmids can also be used for co‐expression studies. All vectors in the pMy vector series are available in the Addgene repository (www.addgene.com).
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Affiliation(s)
| | - Sonja Staack
- Hamburg Unit, European Molecular Biology Laboratory, Hamburg, Germany
| | - Matthias Wilmanns
- Hamburg Unit, European Molecular Biology Laboratory, Hamburg, Germany.,University Hamburg Clinical Centre Hamburg-Eppendorf, Hamburg, Germany
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4
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Raj P, Karthik S, Arif SM, Varshney U, Vijayan M. Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1. Acta Crystallogr D Struct Biol 2020; 76:982-992. [PMID: 33021500 DOI: 10.1107/s2059798320010992] [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: 05/25/2020] [Accepted: 08/11/2020] [Indexed: 11/10/2022] Open
Abstract
Mycobacterium smegmatis MutT1 (MsMutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of MsMutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes MsMutT1 a versatile enzyme.
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Affiliation(s)
- Prateek Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India
| | - S Karthik
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India
| | - S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India
| | - U Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560 012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560 012, India
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5
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Pediatric Tuberculosis: The Impact of "Omics" on Diagnostics Development. Int J Mol Sci 2020; 21:ijms21196979. [PMID: 32977381 PMCID: PMC7582311 DOI: 10.3390/ijms21196979] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) is a major public health concern for all ages. However, the disease presents a larger challenge in pediatric populations, partially owing to the lack of reliable diagnostic standards for the early identification of infection. Currently, there are no biomarkers that have been clinically validated for use in pediatric TB diagnosis. Identification and validation of biomarkers could provide critical information on prognosis of disease, and response to treatment. In this review, we discuss how the “omics” approach has influenced biomarker discovery and the advancement of a next generation rapid point-of-care diagnostic for TB, with special emphasis on pediatric disease. Limitations of current published studies and the barriers to their implementation into the field will be thoroughly reviewed within this article in hopes of highlighting future avenues and needs for combating the problem of pediatric tuberculosis.
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Abstract
After several years of limited success, an effective regimen for the treatment of both drug-sensitive and multiple-drug-resistant tuberculosis is in place. However, this success is still incomplete, as we need several more novel combinations to treat extensively drug-resistant tuberculosis, as well newer emerging resistance. Additionally, the goal of a shortened therapy continues to evade us. A systematic analysis of the tuberculosis drug discovery approaches employed over the last two decades shows that the lead identification path has been largely influenced by the improved understanding of the biology of the pathogen Mycobacterium tuberculosis. Interestingly, the drug discovery efforts can be grouped into a few defined approaches that predominated over a period of time. This review delineates the key drivers during each of these periods. While doing so, the author’s experiences at AstraZeneca R&D, Bangalore, India, on the discovery of new antimycobacterial candidate drugs are used to exemplify the concept. Finally, the review also discusses the value of validated targets, promiscuous targets, the current anti-TB pipeline, the gaps in it, and the possible way forward.
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7
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Structure-Based Drug Design for Tuberculosis: Challenges Still Ahead. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-based and computer-aided drug design approaches are commonly considered to have been successful in the fields of cancer and antiviral drug discovery but not as much for antibacterial drug development. The search for novel anti-tuberculosis agents is indeed an emblematic example of this trend. Although huge efforts, by consortiums and groups worldwide, dramatically increased the structural coverage of the Mycobacterium tuberculosis proteome, the vast majority of candidate drugs included in clinical trials during the last decade were issued from phenotypic screenings on whole mycobacterial cells. We developed here three selected case studies, i.e., the serine/threonine (Ser/Thr) kinases—protein kinase (Pkn) B and PknG, considered as very promising targets for a long time, and the DNA gyrase of M. tuberculosis, a well-known, pharmacologically validated target. We illustrated some of the challenges that rational, target-based drug discovery programs in tuberculosis (TB) still have to face, and, finally, discussed the perspectives opened by the recent, methodological developments in structural biology and integrative techniques.
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8
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Paul A, Mishra A, Surolia A, Vijayan M. Structural studies on
M. tuberculosis
argininosuccinate lyase and its liganded complex: Insights into catalytic mechanism. IUBMB Life 2019; 71:643-652. [DOI: 10.1002/iub.2000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Anju Paul
- Molecular Biophysics UnitIndian Institute of Science Bangalore India
| | - Archita Mishra
- Molecular Biophysics UnitIndian Institute of Science Bangalore India
| | - Avadhesha Surolia
- Molecular Biophysics UnitIndian Institute of Science Bangalore India
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9
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Chandran AV, Srikalaivani R, Paul A, Vijayan M. Biochemical characterization of Mycobacterium tuberculosisLexA and structural studies of its C-terminal segment. Acta Crystallogr D Struct Biol 2019; 75:41-55. [DOI: 10.1107/s2059798318016066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/13/2018] [Indexed: 03/21/2023] Open
Abstract
LexA is a protein that is involved in the SOS response. The protein fromMycobacterium tuberculosisand its mutants have been biochemically characterized and the structures of their catalytic segments have been determined. The protein is made up of an N-terminal segment, which includes the DNA-binding domain, and a C-terminal segment encompassing much of the catalytic domain. The two segments are defined by a cleavage site. Full-length LexA, the two segments, two point mutants involving changes in the active-site residues (S160A and K197A) and another mutant involving a change at the cleavage site (G126D) were cloned and purified. The wild-type protein autocleaves at basic pH, while the mutants do not. The wild-type and the mutant proteins dimerize and bind DNA with equal facility. The C-terminal segment also dimerizes, and it also shows a tendency to form tetramers. The C-terminal segment readily crystallized. The crystals obtained from attempts involving the full-length protein and its mutants contained only the C-terminal segment including the catalytic core and a few residues preceding it, in a dimeric or tetrameric form, indicating protein cleavage during the long period involved in crystal formation. Modes of tetramerization of the full-length protein similar to those observed for the catalytic core are feasible. A complex ofM. tuberculosisLexA and the cognate SOS box could be modeled in which the mutual orientation of the two N-terminal domains differs from that in theEscherichia coliLexA–DNA complex. These results represent the first thorough characterization ofM. tuberculosisLexA and provide definitive information on its structure and assembly. They also provide leads for further exploration of this important protein.
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10
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Chikhale RV, Barmade MA, Murumkar PR, Yadav MR. Overview of the Development of DprE1 Inhibitors for Combating the Menace of Tuberculosis. J Med Chem 2018; 61:8563-8593. [PMID: 29851474 DOI: 10.1021/acs.jmedchem.8b00281] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1), a vital enzyme for cell wall synthesis, plays a crucial role in the formation of lipoarabinomannan and arabinogalactan. It was first reported as a druggable target on the basis of inhibitors discovered in high throughput screening of a drug library. Since then, inhibitors with different types of chemical scaffolds have been reported for their activity against this enzyme. Formation of a covalent or noncovalent bond by the interacting ligand with the enzyme causes loss of its catalytic activity which ultimately leads to the death of the mycobacterium. This Perspective describes various DprE1 inhibitors as anti-TB agents reported to date.
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Affiliation(s)
- Rupesh V Chikhale
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India.,School of Health Sciences, Division of Pharmacy and Optometry , University of Manchester , Manchester M13 9PL , U.K
| | - Mahesh A Barmade
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India
| | - Mange Ram Yadav
- Faculty of Pharmacy, Kalabhavan Campus , The Maharaja Sayajirao University of Baroda , Vadodara 390 001 , India
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11
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Barros-Álvarez X, Turley S, Ranade RM, Gillespie JR, Duster NA, Verlinde CLMJ, Fan E, Buckner FS, Hol WGJ. The crystal structure of the drug target Mycobacterium tuberculosis methionyl-tRNA synthetase in complex with a catalytic intermediate. Acta Crystallogr F Struct Biol Commun 2018; 74:245-254. [PMID: 29633973 PMCID: PMC5893993 DOI: 10.1107/s2053230x18003151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/23/2018] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis is a pathogenic bacterial infectious agent that is responsible for approximately 1.5 million human deaths annually. Current treatment requires the long-term administration of multiple medicines with substantial side effects. Lack of compliance, together with other factors, has resulted in a worrisome increase in resistance. New treatment options are therefore urgently needed. Here, the crystal structure of methionyl-tRNA synthetase (MetRS), an enzyme critical for protein biosynthesis and therefore a drug target, in complex with its catalytic intermediate methionyl adenylate is reported. Phenylalanine 292 of the M. tuberculosis enzyme is in an `out' conformation and barely contacts the adenine ring, in contrast to other MetRS structures where ring stacking occurs between the adenine and a protein side-chain ring in the `in' conformation. A comparison with human cytosolic MetRS reveals substantial differences in the active site as well as regarding the position of the connective peptide subdomain 1 (CP1) near the active site, which bodes well for arriving at selective inhibitors. Comparison with the human mitochondrial enzyme at the amino-acid sequence level suggests that arriving at inhibitors with higher affinity for the mycobacterial enzyme than for the mitochondrial enzyme might be achievable.
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Affiliation(s)
- Ximena Barros-Álvarez
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de los Andes, Mérida, Venezuela
| | - Stewart Turley
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Ranae M. Ranade
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, Washington, USA
| | - J. Robert Gillespie
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Nicole A. Duster
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Frederick S. Buckner
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Wim G. J. Hol
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
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12
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Tatum NJ, Liebeschuetz JW, Cole JC, Frita R, Herledan A, Baulard AR, Willand N, Pohl E. New active leads for tuberculosis booster drugs by structure-based drug discovery. Org Biomol Chem 2018; 15:10245-10255. [PMID: 29182187 DOI: 10.1039/c7ob00910k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The transcriptional repressor EthR from Mycobacterium tuberculosis, a member of the TetR family of prokaryotic homo-dimeric transcription factors, controls the expression of the mycobacterial mono-oxygenase EthA. EthA is responsible for the bio-activation of the second-line tuberculosis pro-drug ethionamide, and consequently EthR inhibitors boost drug efficacy. Here, we present a comprehensive in silico structure-based screening protocol that led to the identification of a number of novel scaffolds of EthR inhibitors in subsequent biophysical screening by thermal shift assay. Growth inhibition assays demonstrated that five of the twenty biophysical hits were capable of boosting ethionamide activity in vitro, with the best novel scaffold displaying an EC50 of 34 μM. In addition, the co-crystal structures of EthR with four new ligands at resolution ranging from 2.1 to 1.4 Å confirm the binding and inactivation mode, and will enable future lead development.
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Affiliation(s)
- Natalie J Tatum
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK.
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13
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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.
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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
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14
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Arif SM, Varshney U, Vijayan M. Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1. J Struct Biol 2017; 199:165-176. [PMID: 28705712 DOI: 10.1016/j.jsb.2017.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 10/19/2022]
Abstract
Diadenosine polyphosphates (ApnA, n=2-6), particularly Ap4A, are involved in several important physiological processes. The substantial sequence identity of the Nudix hydrolase domain (domain 1) of Mycobacterium smegmatis MutT1 (MsMutT1) with a known Ap4A hydrolase suggested that MsMutT1 could also hydrolyse diadenosine polyphosphates. Biochemical experiments yielded results in conformity with this suggestion, with Ap4A as the best among the substrates. ATP is a product in all experiments; small amounts of ADP were also observed in the experiments involving Ap4A and Ap6A. Hydrolysis was inhibited by fluoride ions in all cases. The mechanism of action and its inhibition in relation to ApnA were explored through the X-ray analysis of the crystals of the MsMutT1 complexes with Ap5A; Ap5A and MnCl2; Ap4A; ATP; and ATP.NaF.MgCl2. The aggregation pattern of molecules in the first four crystals is similar to that found in a majority of MsMutT1-NTP crystals. Substrate molecules occupy the primary binding site and ATP occupies a site at an intermolecular interface, in the first two. ATP occupies both the sites in the third and fourth crystal. The protein-ligand interactions observed in these crystal structures lead to an explanation of the molecular mechanism of hydrolysis of ApnA by MsMutT1. The fifth crystal exhibits a new packing arrangement. The structure of the complex provides an explanation for the fluoride inhibition of the activity of the enzyme. It would thus appear that MutT1 has a major role involving the hydrolysis of diadenosine polyphosphates, which could be elucidated at the molecular level.
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Affiliation(s)
- S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - U 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.
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15
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Arif SM, Patil AG, Varshney U, Vijayan M. Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:349-364. [PMID: 28375146 DOI: 10.1107/s2059798317002534] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/14/2017] [Indexed: 01/12/2023]
Abstract
Mycobacterium smegmatis MutT1, which is made up of a Nudix domain (domain 1) and a histidine phosphatase domain (domain 2), efficiently hydrolyses 8-oxo-GTP and 8-oxo-dGTP to the corresponding nucleoside diphosphates and phosphate in the presence of magnesium ions. Domain 1 alone hydrolyses nucleoside triphosphates less efficiently. Under high concentrations and over long periods, the full-length enzyme as well as domain 1 catalyses the hydrolysis of the nucleoside triphosphates to the respective nucleoside monophosphates and pyrophosphate. The role of domain 2 appears to be limited to speeding up the reaction. Crystal structures of the apoenzyme and those of ligand-bound enzyme prepared in the presence of 8-oxo-GTP or 8-oxo-dGTP and different concentrations of magnesium were determined. In all of the structures except one, the molecules arrange themselves in a head-to-tail fashion in which domain 1 is brought into contact with domain 2 (trans domain 2) of a neighbouring molecule. The binding site for NTP (site A) is almost exclusively made up of residues from domain 1, while those for NDP (site B) and NMP (site C) are at the interface between domain 1 and trans domain 2 in an unusual instance of intermolecular interactions leading to binding sites. Protein-ligand interactions at site A lead to a proposal for the mechanism of hydrolysis of NTP to NDP and phosphate. A small modification in site A in the crystal which does not exhibit the head-to-tail arrangement appears to facilitate the production of NMP and pyrophosphate from NTP. The two arrangements could be in dynamic equilibrium in the cellular milieu.
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Affiliation(s)
- S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A G Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - U 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
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16
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Chandran AV, Jayanthi S, Vijayan M. Structure and interactions of RecA: plasticity revealed by molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:98-111. [PMID: 28049371 DOI: 10.1080/07391102.2016.1268975] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Eleven independent simulations, each involving three consecutive molecules in the RecA filament, carried out on the protein from Mycobacterium tuberculosis, Mycobacterium smegmatis and Escherichia coli and their Adenosine triphosphate (ATP) complexes, provide valuable information which is complementary to that obtained from crystal structures, in addition to confirming the robust common structural framework within which RecA molecules from different eubacteria function. Functionally important loops, which are largely disordered in crystal structures, appear to adopt in each simulation subsets of conformations from larger ensembles. The simulations indicate the possibility of additional interactions involving the P-loop which remains largely invariant. The phosphate tail of the ATP is firmly anchored on the loop while the nucleoside moiety exhibits substantial structural variability. The most important consequence of ATP binding is the movement of the 'switch' residue. The relevant simulations indicate the feasibility of a second nucleotide binding site, but the pathway between adjacent molecules in the filament involving the two nucleotide binding sites appears to be possible only in the mycobacterial proteins.
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Affiliation(s)
- Anu V Chandran
- a Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - S Jayanthi
- a Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - M Vijayan
- a Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
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17
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Recent advancements in the development of anti-tuberculosis drugs. Bioorg Med Chem Lett 2016; 27:370-386. [PMID: 28017531 DOI: 10.1016/j.bmcl.2016.11.084] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/16/2016] [Accepted: 11/27/2016] [Indexed: 01/09/2023]
Abstract
Modern chemotherapy has significantly improved patient outcomes against drug-sensitive tuberculosis. However, the rapid emergence of drug-resistant tuberculosis, together with the bacterium's ability to persist and remain latent present a major public health challenge. To overcome this problem, research into novel anti-tuberculosis targets and drug candidates is thus of paramount importance. This review article provides an overview of tuberculosis highlighting the recent advances and tools that are employed in the field of anti-tuberculosis drug discovery. The predominant focus is on anti-tuberculosis agents that are currently in the pipeline, i.e. clinical trials.
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18
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Gazi MA, Kibria MG, Mahfuz M, Islam MR, Ghosh P, Afsar MNA, Khan MA, Ahmed T. Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets. Gene 2016; 591:442-55. [PMID: 27374154 DOI: 10.1016/j.gene.2016.06.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/27/2016] [Accepted: 06/28/2016] [Indexed: 01/11/2023]
Abstract
The global control of tuberculosis (TB) remains a great challenge from the standpoint of diagnosis, detection of drug resistance, and treatment. Major serodiagnostic limitations include low sensitivity and high cost in detecting TB. On the other hand, treatment measures are often hindered by low efficacies of commonly used drugs and resistance developed by the bacteria. Hence, there is a need to look into newer diagnostic and therapeutic targets. The proteome information available suggests that among the 3906 proteins in Mycobacterium tuberculosis H37Rv, about quarter remain classified as hypothetical uncharacterized set. This study involves a combination of a number of bioinformatics tools to analyze those hypothetical proteins (HPs). An entire set of 999 proteins was primarily screened for protein sequences having conserved domains with high confidence using a combination of the latest versions of protein family databases. Subsequently, 98 of such potential target proteins were extensively analyzed by means of physicochemical characteristics, protein-protein interaction, sub-cellular localization, structural similarity and functional classification. Next, we predicted antigenic proteins from the entire set and identified B and T cell epitopes of these proteins in M. tuberculosis H37Rv. We predicted the function of these HPs belong to various classes of proteins such as enzymes, transporters, receptors, structural proteins, transcription regulators and other proteins. However, the structural similarity prediction of the annotated proteins substantiated the functional classification of those proteins. Consequently, based on higher antigenicity score and sub-cellular localization, we choose two (NP_216420.1, NP_216903.1) of the antigenic proteins to exemplify B and T cell epitope prediction approach. Finally we found 15 epitopes those located partially or fully in the linear epitope region. We found 21 conformational epitopes by using Ellipro server as well. In silico methodology used in this study and the data thus generated for HPs of M. tuberculosis H37Rv may facilitate swift experimental identification of potential serodiagnostic and therapeutic targets for treatment and control.
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Affiliation(s)
- Md Amran Gazi
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Mohammad Golam Kibria
- Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Mustafa Mahfuz
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Md Rezaul Islam
- International Max Planck Research School, Grisebachstraße 5, 37077 Göttingen, Germany.
| | - Prakash Ghosh
- Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Md Nure Alam Afsar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Md Arif Khan
- Bio-Bio-1 Research Foundation, Sangskriti Bikash Kendra Bhaban, 1/E/1, Poribag, Dhaka 1000, Bangladesh.
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
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19
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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: 10] [Impact Index Per Article: 1.0] [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.
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Affiliation(s)
- Anu V Chandran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012
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20
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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: 1.2] [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.
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21
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Bashiri G, Baker EN. Production of recombinant proteins in Mycobacterium smegmatis for structural and functional studies. Protein Sci 2014; 24:1-10. [PMID: 25303009 DOI: 10.1002/pro.2584] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 11/11/2022]
Abstract
Protein production using recombinant DNA technology has a fundamental impact on our understanding of biology through providing proteins for structural and functional studies. Escherichia coli (E. coli) has been traditionally used as the default expression host to over-express and purify proteins from many different organisms. E. coli does, however, have known shortcomings for obtaining soluble, properly folded proteins suitable for downstream studies. These shortcomings are even more pronounced for the mycobacterial pathogen Mycobacterium tuberculosis, the bacterium that causes tuberculosis, with typically only one third of proteins expressed in E. coli produced as soluble proteins. Mycobacterium smegmatis (M. smegmatis) is a closely related and non-pathogenic species that has been successfully used as an expression host for production of proteins from various mycobacterial species. In this review, we describe the early attempts to produce mycobacterial proteins in alternative expression hosts and then focus on available expression systems in M. smegmatis. The advantages of using M. smegmatis as an expression host, its application in structural biology and some practical aspects of protein production are also discussed. M. smegmatis provides an effective expression platform for enhanced understanding of mycobacterial biology and pathogenesis and for developing novel and better therapeutics and diagnostics.
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Affiliation(s)
- Ghader Bashiri
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1010, New Zealand
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22
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Selvaraj M, Govindan A, Seshadri A, Dubey B, Varshney U, Vijayan M. Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: an exploration involving mutants. J Biosci 2014; 38:845-55. [PMID: 24296887 DOI: 10.1007/s12038-013-9381-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Internal mobility of the two domain molecule of ribosome recycling factor (RRF) is known to be important for its action. Mycobacterium tuberculosis RRF does not complement E. coli for its deficiency of RRF (in the presence of E. coli EF-G alone). Crystal structure had revealed higher rigidity of the M. tuberculosis RRF due to the presence of additional salt bridges between domains. Two inter-domain salt bridges and one between the linker region and the domain containing C-terminal residues were disrupted by appropriate mutations. Except for a C-terminal deletion mutant, all mutants showed RRF activity in E. coli when M. tuberculosis EF-G was also co-expressed. The crystal structures of the point mutants, that of the C-terminal deletion mutant and that of the protein grown in the presence of a detergent, were determined. The increased mobility resulting from the disruption of the salt bridge involving the hinge region allows the appropriate mutant to weakly complement E. coli for its deficiency of RRF even in the absence of simultaneous expression of the mycobacterial EF-G. The loss of activity of the C-terminal deletion mutant appears to be partly due to the rigidification of the molecule consequent to changes in the hinge region.
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Affiliation(s)
- M Selvaraj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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23
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Tomioka H, Tatano Y, Yasumoto K, Shimizu T. Recent advances in antituberculous drug development and novel drug targets. Expert Rev Respir Med 2014; 2:455-71. [DOI: 10.1586/17476348.2.4.455] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Liu X, Zang Y, Sun B, Yin Y. Optimization of phage heptapeptide library-screening process for developing inhibitors of the isocitrate lyase homologue from Mycobacterium tuberculosis. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0845-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Abuhammad A, Lowe ED, McDonough MA, Shaw Stewart PD, Kolek SA, Sim E, Garman EF. Structure of arylamineN-acetyltransferase fromMycobacterium tuberculosisdetermined by cross-seeding with the homologous protein fromM. marinum: triumph over adversity. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1433-46. [DOI: 10.1107/s0907444913015126] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 05/31/2013] [Indexed: 11/10/2022]
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26
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Cipriani F, Röwer M, Landret C, Zander U, Felisaz F, Márquez JA. CrystalDirect: a new method for automated crystal harvesting based on laser-induced photoablation of thin films. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1393-9. [DOI: 10.1107/s0907444912031459] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/10/2012] [Indexed: 11/10/2022]
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27
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Selvaraj S, Sambandam V, Sardar D, Anishetty S. In silico analysis of DosR regulon proteins of Mycobacterium tuberculosis. Gene 2012; 506:233-41. [DOI: 10.1016/j.gene.2012.06.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 03/01/2012] [Accepted: 06/18/2012] [Indexed: 11/28/2022]
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28
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Shingnapurkar D, Dandawate P, Anson CE, Powell AK, Afrasiabi Z, Sinn E, Pandit S, Venkateswara Swamy K, Franzblau S, Padhye S. Synthesis and characterization of pyruvate–isoniazid analogs and their copper complexes as potential ICL inhibitors. Bioorg Med Chem Lett 2012; 22:3172-6. [DOI: 10.1016/j.bmcl.2012.03.047] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 03/01/2012] [Accepted: 03/12/2012] [Indexed: 01/11/2023]
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29
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Synthesis and biological evaluation of chalcones and acetyl pyrazoline derivatives comprising furan nucleus as an antitubercular agents. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9857-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Arora A, Chandra NR, Das A, Gopal B, Mande SC, Prakash B, Ramachandran R, Sankaranarayanan R, Sekar K, Suguna K, Tyagi AK, Vijayan M. Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts. Tuberculosis (Edinb) 2011; 91:456-68. [DOI: 10.1016/j.tube.2011.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 03/15/2011] [Accepted: 03/16/2011] [Indexed: 01/23/2023]
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31
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Stacy R, Begley DW, Phan I, Staker BL, Van Voorhis WC, Varani G, Buchko GW, Stewart LJ, Myler PJ. Structural genomics of infectious disease drug targets: the SSGCID. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:979-84. [PMID: 21904037 PMCID: PMC3169389 DOI: 10.1107/s1744309111029204] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 07/19/2011] [Indexed: 11/29/2022]
Abstract
The Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium of researchers at Seattle BioMed, Emerald BioStructures, the University of Washington and Pacific Northwest National Laboratory that was established to apply structural genomics approaches to drug targets from infectious disease organisms. The SSGCID is currently funded over a five-year period by the National Institute of Allergy and Infectious Diseases (NIAID) to determine the three-dimensional structures of 400 proteins from a variety of Category A, B and C pathogens. Target selection engages the infectious disease research and drug-therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. The protein-expression systems, purified proteins, ligand screens and three-dimensional structures produced by SSGCID constitute a valuable resource for drug-discovery research, all of which is made freely available to the greater scientific community. This issue of Acta Crystallographica Section F, entirely devoted to the work of the SSGCID, covers the details of the high-throughput pipeline and presents a series of structures from a broad array of pathogenic organisms. Here, a background is provided on the structural genomics of infectious disease, the essential components of the SSGCID pipeline are discussed and a survey of progress to date is presented.
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Affiliation(s)
- Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
| | - Darren W. Begley
- Seattle Structural Genomics Center for Infectious Disease, USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Box 357185, Seattle, WA 98195, USA
| | - Gabriele Varani
- Seattle Structural Genomics Center for Infectious Disease, USA
- Departments of Chemistry and Biochemistry, University of Washington, Box 351700, Seattle, WA 98185, USA
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease, USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
- Departments of Global Health and Medical Education and Biomedical Informatics, University of Washington, Box 357238, Seattle, WA 98195, USA
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32
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Shabbeer A, Ozcaglar C, Yener B, Bennett KP. Web tools for molecular epidemiology of tuberculosis. INFECTION GENETICS AND EVOLUTION 2011; 12:767-81. [PMID: 21903179 DOI: 10.1016/j.meegid.2011.08.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/14/2011] [Accepted: 08/19/2011] [Indexed: 01/03/2023]
Abstract
In this study we explore publicly available web tools designed to use molecular epidemiological data to extract information that can be employed for the effective tracking and control of tuberculosis (TB). The application of molecular methods for the epidemiology of TB complement traditional approaches used in public health. DNA fingerprinting methods are now routinely employed in TB surveillance programs and are primarily used to detect recent transmissions and in outbreak investigations. Here we present web tools that facilitate systematic analysis of Mycobacterium tuberculosis complex (MTBC) genotype information and provide a view of the genetic diversity in the MTBC population. These tools help answer questions about the characteristics of MTBC strains, such as their pathogenicity, virulence, immunogenicity, transmissibility, drug-resistance profiles and host-pathogen associativity. They provide an integrated platform for researchers to use molecular epidemiological data to address current challenges in the understanding of TB dynamics and the characteristics of MTBC.
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Affiliation(s)
- Amina Shabbeer
- Department of Mathematical Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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33
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Yin J, Garen CR, Bateman K, Yu M, Alipio Lyon EZ, Habel J, Kim H, Hung LW, Kim CY, James MNG. Expression, purification and preliminary crystallographic analysis of O-acetylhomoserine sulfhydrylase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:959-63. [PMID: 21821905 PMCID: PMC3151138 DOI: 10.1107/s1744309111017611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/10/2011] [Indexed: 11/11/2022]
Abstract
The gene product of the open reading frame Rv3340 from Mycobacterium tuberculosis is annotated as encoding a probable O-acetylhomoserine (OAH) sulfhydrylase (MetC), an enzyme that catalyzes the last step in the biosynthesis of methionine, which is an essential amino acid in bacteria and plants. Following overexpression in Escherichia coli, the M. tuberculosis MetC enzyme was purified and crystallized using the hanging-drop vapor-diffusion method. Native diffraction data were collected from crystals belonging to space group P2(1) and were processed to a resolution of 2.1 Å.
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Affiliation(s)
- Jiang Yin
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig R. Garen
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Katherine Bateman
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Minmin Yu
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Emily Z. Alipio Lyon
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jeff Habel
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Heungbok Kim
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Li-wei Hung
- E. O. Lawrence Berkeley National Laboratory, University of California at Berkeley, California 94720, USA
| | - Chang-Yub Kim
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Michael N. G. James
- Protein Structure and Function Group, Department of Biochemistry, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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34
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Sharma D, Surolia A. Computational tools to study and understand the intricate biology of mycobacteria. Tuberculosis (Edinb) 2011; 91:273-6. [PMID: 21398182 DOI: 10.1016/j.tube.2011.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 02/07/2011] [Accepted: 02/08/2011] [Indexed: 11/19/2022]
Abstract
The field of mycobacteriology is currently an area of intense research. To deal with the copious amount of data being generated, numerous web servers and databases have been developed. However, these are available at disparate sites and there exists no single source/platform which provides information about their utility and access. Therefore, a comprehensive compilation of various bioinformatics tools/resources dedicated to mycobacteria is presented in this article.
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Affiliation(s)
- Deepak Sharma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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35
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Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim CY, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung LW, Baker EN, Lott JS, James MNG, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. The TB Structural Genomics Consortium: a decade of progress. Tuberculosis (Edinb) 2011; 91:155-72. [PMID: 21247804 DOI: 10.1016/j.tube.2010.11.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/19/2010] [Accepted: 11/26/2010] [Indexed: 01/03/2023]
Abstract
The TB Structural Genomics Consortium is a worldwide organization of collaborators whose mission is the comprehensive structural determination and analyses of Mycobacterium tuberculosis proteins to ultimately aid in tuberculosis diagnosis and treatment. Congruent to the overall vision, Consortium members have additionally established an integrated facilities core to streamline M. tuberculosis structural biology and developed bioinformatics resources for data mining. This review aims to share the latest Consortium developments with the TB community, including recent structures of proteins that play significant roles within M. tuberculosis. Atomic resolution details may unravel mechanistic insights and reveal unique and novel protein features, as well as important protein-protein and protein-ligand interactions, which ultimately lead to a better understanding of M. tuberculosis biology and may be exploited for rational, structure-based therapeutics design.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
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36
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Ekins S, Freundlich JS, Choi I, Sarker M, Talcott C. Computational databases, pathway and cheminformatics tools for tuberculosis drug discovery. Trends Microbiol 2010; 19:65-74. [PMID: 21129975 DOI: 10.1016/j.tim.2010.10.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/15/2010] [Accepted: 10/29/2010] [Indexed: 01/31/2023]
Abstract
We are witnessing the growing menace of both increasing cases of drug-sensitive and drug-resistant Mycobacterium tuberculosis strains and the challenge to produce the first new tuberculosis (TB) drug in well over 40 years. The TB community, having invested in extensive high-throughput screening efforts, is faced with the question of how to optimally leverage these data to move from a hit to a lead to a clinical candidate and potentially, a new drug. Complementing this approach, yet conducted on a much smaller scale, cheminformatic techniques have been leveraged and are examined in this review. We suggest that these computational approaches should be optimally integrated within a workflow with experimental approaches to accelerate TB drug discovery.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, 601 Runnymede Avenue, Jenkintown, PA 19046, USA.
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37
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Willand N, Desroses M, Toto P, Dirié B, Lens Z, Villeret V, Rucktooa P, Locht C, Baulard A, Deprez B. Exploring drug target flexibility using in situ click chemistry: application to a mycobacterial transcriptional regulator. ACS Chem Biol 2010; 5:1007-13. [PMID: 20704273 DOI: 10.1021/cb100177g] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In situ click chemistry has been successfully applied to probe the ligand binding domain of EthR, a mycobacterial transcriptional regulator known to control the sensitivity of Mycobacterium tuberculosis to several antibiotics. Specific protein-templated ligands were generated in situ from one azide and six clusters of 10 acetylenic fragments. Comparative X-ray structures of EthR complexed with either clicked ligand BDM14950 or its azide precursor showed ligand-dependent conformational impacts on the protein architecture. This approach revealed two mobile phenylalanine residues that control the access to a previously hidden hydrophobic pocket that can be further exploited for the development of structurally diverse EthR inhibitors. This report shows that protein-directed in situ chemistry allows medicinal chemists to explore the conformational space of a ligand-binding pocket and is thus a valuable tool to guide drug design in the complex path of hit-to-lead processes.
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Affiliation(s)
- Nicolas Willand
- Univ Lille Nord de France, F-59000 Lille, France
- Biostructures and Drug Discovery, INSERM U761, F-59000 Lille, France and UDSL, F-59000 Lille, France
- IPL, F-59000 Lille, France
- PRIM, F-59000 Lille, France
| | - Matthieu Desroses
- Univ Lille Nord de France, F-59000 Lille, France
- Biostructures and Drug Discovery, INSERM U761, F-59000 Lille, France and UDSL, F-59000 Lille, France
- IPL, F-59000 Lille, France
- PRIM, F-59000 Lille, France
| | - Patrick Toto
- Univ Lille Nord de France, F-59000 Lille, France
- Biostructures and Drug Discovery, INSERM U761, F-59000 Lille, France and UDSL, F-59000 Lille, France
- IPL, F-59000 Lille, France
- PRIM, F-59000 Lille, France
| | - Bertrand Dirié
- Univ Lille Nord de France, F-59000 Lille, France
- Biostructures and Drug Discovery, INSERM U761, F-59000 Lille, France and UDSL, F-59000 Lille, France
- IPL, F-59000 Lille, France
- PRIM, F-59000 Lille, France
| | - Zoé Lens
- Univ Lille Nord de France, F-59000 Lille, France
- IRI, USR 3078 CNRS, F-59658 Villeneuve d’Ascq, France
- Laboratory of Molecular Virology, IBBM, ULB, 6041 Gosselies, Belgium
| | - Vincent Villeret
- Univ Lille Nord de France, F-59000 Lille, France
- IRI, USR 3078 CNRS, F-59658 Villeneuve d’Ascq, France
| | - Prakash Rucktooa
- Univ Lille Nord de France, F-59000 Lille, France
- IRI, USR 3078 CNRS, F-59658 Villeneuve d’Ascq, France
| | - Camille Locht
- Univ Lille Nord de France, F-59000 Lille, France
- IPL, F-59000 Lille, France
- INSERM U1019, F-59000 Lille, France and CNRS UMR8204, F-59021 Lille, France and Center for Infection and Immunity, F-59019 Lille, France
| | - Alain Baulard
- Univ Lille Nord de France, F-59000 Lille, France
- IPL, F-59000 Lille, France
- PRIM, F-59000 Lille, France
- INSERM U1019, F-59000 Lille, France and CNRS UMR8204, F-59021 Lille, France and Center for Infection and Immunity, F-59019 Lille, France
| | - Benoit Deprez
- Univ Lille Nord de France, F-59000 Lille, France
- Biostructures and Drug Discovery, INSERM U761, F-59000 Lille, France and UDSL, F-59000 Lille, France
- IPL, F-59000 Lille, France
- PRIM, F-59000 Lille, France
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Kinnings SL, Xie L, Fung KH, Jackson RM, Xie L, Bourne PE. The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol 2010; 6:e1000976. [PMID: 21079673 PMCID: PMC2973814 DOI: 10.1371/journal.pcbi.1000976] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 09/24/2010] [Indexed: 11/26/2022] Open
Abstract
We report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. The approach has been applied to the genome of Mycobacterium tuberculosis (M.tb), the causative agent of one of today's most widely spread infectious diseases. The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’. The TB-drugome reveals that approximately one-third of the drugs examined have the potential to be repositioned to treat tuberculosis and that many currently unexploited M.tb receptors may be chemically druggable and could serve as novel anti-tubercular targets. Furthermore, a detailed analysis of the TB-drugome has shed new light on the controversial issues surrounding drug-target networks [1]–[3]. Indeed, our results support the idea that drug-target networks are inherently modular, and further that any observed randomness is mainly caused by biased target coverage. The TB-drugome (http://funsite.sdsc.edu/drugome/TB) has the potential to be a valuable resource in the development of safe and efficient anti-tubercular drugs. More generally the methodology may be applied to other pathogens of interest with results improving as more of their structural proteomes are determined through the continued efforts of structural biology/genomics. The worldwide increase in multi-drug resistant TB poses a great threat to human health and highlights the need to identify new anti-tubercular agents. We have developed a computational strategy to link the structural proteome of Mycobacterium tuberculosis, the causative agent of tuberculosis, to all structurally characterized approved drugs, and hence construct a proteome-wide drug-target network – the TB-drugome. The TB-drugome has the potential to be a valuable resource in the development of safe and efficient anti-tubercular drugs. More generally, the proteome-wide and multi-scale view of target and drug space may facilitate a systematic drug discovery process, which concurrently takes into account the disease mechanism and druggability of targets, the drug-likeness and ADMET properties of chemical compounds, and the genetic dispositions of individuals. Ultimately it may help to reduce the high attrition rate in drug development through a better understanding of drug-receptor interactions on a large scale.
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Affiliation(s)
- Sarah L. Kinnings
- Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America
| | - Li Xie
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kingston H. Fung
- Bioinformatics Program, University of California, San Diego, La Jolla, California, United States of America
| | - Richard M. Jackson
- Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Lei Xie
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (LX); (PEB)
| | - Philip E. Bourne
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail: (LX); (PEB)
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Lew JM, Kapopoulou A, Jones LM, Cole ST. TubercuList--10 years after. Tuberculosis (Edinb) 2010; 91:1-7. [PMID: 20980199 DOI: 10.1016/j.tube.2010.09.008] [Citation(s) in RCA: 310] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 09/06/2010] [Accepted: 09/30/2010] [Indexed: 01/10/2023]
Abstract
TubercuList (http://tuberculist.epfl.ch/), the relational database that presents genome-derived information about H37Rv, the paradigm strain of Mycobacterium tuberculosis, has been active for ten years and now presents its twentieth release. Here, we describe some of the recent changes that have resulted from manual annotation with information from the scientific literature. Through manual curation, TubercuList strives to provide current gene-based information and is thus distinguished from other online sources of genome sequence data for M. tuberculosis. New, mostly small, genes have been discovered and the coordinates of some existing coding sequences have been changed when bioinformatics or experimental data suggest that this is required. Nucleotides that are polymorphic between different sources of H37Rv are annotated and gene essentiality data have been updated. A host of functional information has been gleaned from the literature and many new activities of proteins and RNAs have been included. To facilitate basic and translational research, TubercuList also provides links to other specialized databases that present diverse datasets such as 3D-structures, expression profiles, drug development criteria and drug resistance information, in addition to direct access to PubMed articles pertinent to particular genes. TubercuList has been and remains a highly valuable tool for the tuberculosis research community with >75,000 visitors per month.
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Affiliation(s)
- Jocelyne M Lew
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Station 19, CH-1015 Lausanne, Switzerland.
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Jatana N, Jangid S, Khare G, Tyagi AK, Latha N. Molecular modeling studies of Fatty acyl-CoA synthetase (FadD13) from Mycobacterium tuberculosis--a potential target for the development of antitubercular drugs. J Mol Model 2010; 17:301-13. [PMID: 20454815 DOI: 10.1007/s00894-010-0727-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 04/20/2010] [Indexed: 11/29/2022]
Abstract
Tuberculosis (TB) is a global health problem and the situation has become more precarious due to the advent of HIV infections and continuous rise in the number of multi-drug resistant strains of Mycobacterium tuberculosis (M. tb). Biochemical studies on Fatty Acyl-CoA Synthetases (FadD13), one of the gene products of mymA operon, have provided insights into the involvement of this protein in the activation of fatty acids. Due to non-availability of the crystal structure of FadD13, we have employed in silico approaches to resolve and characterize the structure of this important protein of M. tb. A three dimensional model of M. tb FadD13 was predicted by a de novo structure prediction server that integrates fragment assembly with SimFold energy function. With the aid of molecular mechanics and dynamics methods, the final model was obtained and assessed subsequently for global and local accuracy by various assessment programs. With this model, a flexible docking study with the substrates was performed. Results of ligand interactions with key amino acids in the binding site are also summarized. The molecular model for the M. tb FadD13 obtained sheds light on the topographical features of the binding pocket of the protein and provides atomic insight into the possible modes of substrate recognition. The three-dimensional model of FadD13 presented here would be helpful in guiding both enzymatic studies as well as design of specific inhibitors.
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Affiliation(s)
- Nidhi Jatana
- Bioinformatics Infrastructure Facility, Sri Venkateswara College, New Delhi, India
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41
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Grabowski M, Chruszcz M, Zimmerman MD, Kirillova O, Minor W. Benefits of structural genomics for drug discovery research. Infect Disord Drug Targets 2009; 9:459-74. [PMID: 19594422 PMCID: PMC2866842 DOI: 10.2174/187152609789105704] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 06/15/2009] [Indexed: 11/22/2022]
Abstract
While three dimensional structures have long been used to search for new drug targets, only a fraction of new drugs coming to the market has been developed with the use of a structure-based drug discovery approach. However, the recent years have brought not only an avalanche of new macromolecular structures, but also significant advances in the protein structure determination methodology only now making their way into structure-based drug discovery. In this paper, we review recent developments resulting from the Structural Genomics (SG) programs, focusing on the methods and results most likely to improve our understanding of the molecular foundation of human diseases. SG programs have been around for almost a decade, and in that time, have contributed a significant part of the structural coverage of both the genomes of pathogens causing infectious diseases and structurally uncharacterized biological processes in general. Perhaps most importantly, SG programs have developed new methodology at all steps of the structure determination process, not only to determine new structures highly efficiently, but also to screen protein/ligand interactions. We describe the methodologies, experience and technologies developed by SG, which range from improvements to cloning protocols to improved procedures for crystallographic structure solution that may be applied in "traditional" structural biology laboratories particularly those performing drug discovery. We also discuss the conditions that must be met to convert the present high-throughput structure determination pipeline into a high-output structure-based drug discovery system.
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Affiliation(s)
- Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
- Center for Structural Genomics of Infectious Diseases
| | - Maksymilian Chruszcz
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
- Center for Structural Genomics of Infectious Diseases
| | - Matthew D. Zimmerman
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
- Center for Structural Genomics of Infectious Diseases
| | - Olga Kirillova
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Midwest Center for Structural Genomics
- Center for Structural Genomics of Infectious Diseases
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42
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Sankaranarayanan R, Garen CR, Cherney MM, Yuan M, Lee C, James MNG. Preliminary X-ray crystallographic analysis of ornithine acetyltransferase (Rv1653) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:173-6. [PMID: 19194014 PMCID: PMC2635878 DOI: 10.1107/s1744309109000360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 01/05/2009] [Indexed: 11/11/2022]
Abstract
The gene product of open reading frame Rv1653 from Mycobacterium tuberculosis is annotated as encoding a probable ornithine acetyltransferase (OATase; EC 2.3.1.35), an enzyme that catalyzes two steps in the arginine-biosynthesis pathway. It transfers an acetyl group from N-acetylornithine to L-glutamate to produce N-acetylglutamate and L-ornithine. Rv1653 was crystallized using the sitting-drop vapour-diffusion method. The native crystals diffracted to a resolution of 1.7 A and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 60.1, b = 99.7, c = 155.3 A. The preliminary X-ray study showed the presence of a dimer in the asymmetric unit of the crystals, which had a Matthews coefficient V(M) of 2.8 A(3) Da(-1).
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Affiliation(s)
- R. Sankaranarayanan
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - C. R. Garen
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. M. Cherney
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. Yuan
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - C. Lee
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. N. G. James
- Protein Structure and Function Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Raman K, Yeturu K, Chandra N. targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC SYSTEMS BIOLOGY 2008; 2:109. [PMID: 19099550 PMCID: PMC2651862 DOI: 10.1186/1752-0509-2-109] [Citation(s) in RCA: 197] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Accepted: 12/19/2008] [Indexed: 01/19/2023]
Abstract
Background Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are critical steps in drug discovery, which are at present major bottle-necks. A majority of drugs in current clinical use for many diseases have been designed without the knowledge of the targets, perhaps because standard methodologies to identify such targets in a high-throughput fashion do not really exist. With different kinds of 'omics' data that are now available, computational approaches can be powerful means of obtaining short-lists of possible targets for further experimental validation. Results We report a comprehensive in silico target identification pipeline, targetTB, for Mycobacterium tuberculosis. The pipeline incorporates a network analysis of the protein-protein interactome, a flux balance analysis of the reactome, experimentally derived phenotype essentiality data, sequence analyses and a structural assessment of targetability, using novel algorithms recently developed by us. Using flux balance analysis and network analysis, proteins critical for survival of M. tuberculosis are first identified, followed by comparative genomics with the host, finally incorporating a novel structural analysis of the binding sites to assess the feasibility of a protein as a target. Further analyses include correlation with expression data and non-similarity to gut flora proteins as well as 'anti-targets' in the host, leading to the identification of 451 high-confidence targets. Through phylogenetic profiling against 228 pathogen genomes, shortlisted targets have been further explored to identify broad-spectrum antibiotic targets, while also identifying those specific to tuberculosis. Targets that address mycobacterial persistence and drug resistance mechanisms are also analysed. Conclusion The pipeline developed provides rational schema for drug target identification that are likely to have high rates of success, which is expected to save enormous amounts of money, resources and time in the drug discovery process. A thorough comparison with previously suggested targets in the literature demonstrates the usefulness of the integrated approach used in our study, highlighting the importance of systems-level analyses in particular. The method has the potential to be used as a general strategy for target identification and validation and hence significantly impact most drug discovery programmes.
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Affiliation(s)
- Karthik Raman
- Supercomputer Education and Research Centre and Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India.
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44
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Reddy TBK, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res 2008; 37:D499-508. [PMID: 18835847 PMCID: PMC2686437 DOI: 10.1093/nar/gkn652] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of biomarkers of clinical status. The promise of the genomics era for TB control is substantial, but has been hindered by the lack of a central repository that collects and integrates genomic and experimental data about this organism in a way that can be readily accessed and analyzed. The Tuberculosis Database (TBDB) is an integrated database providing access to TB genomic data and resources, relevant to the discovery and development of TB drugs, vaccines and biomarkers. The current release of TBDB houses genome sequence data and annotations for 28 different Mycobacterium tuberculosis strains and related bacteria. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives. TBDB currently hosts data for nearly 1500 public tuberculosis microarrays and 260 arrays for Streptomyces. In addition, TBDB provides access to a suite of comparative genomics and microarray analysis software. By bringing together M. tuberculosis genome annotation and gene-expression data with a suite of analysis tools, TBDB (http://www.tbdb.org/) provides a unique discovery platform for TB research.
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Affiliation(s)
- T B K Reddy
- Department of Biochemistry, Stanford University, CA 94305, USA.
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Gupta V, Gupta RK, Khare G, Salunke DM, Tyagi AK. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of bacterioferritin A from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:398-401. [PMID: 18453710 PMCID: PMC2376407 DOI: 10.1107/s1744309108007240] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Accepted: 03/18/2008] [Indexed: 11/11/2022]
Abstract
Bacterioferritins (Bfrs) comprise a subfamily of the ferritin superfamily of proteins that play an important role in bacterial iron storage and homeostasis. Bacterioferritins differ from ferritins in that they have additional noncovalently bound haem groups. To assess the physiological role of this subfamily of ferritins, a greater understanding of the structural details of bacterioferritins from various sources is required. The gene encoding bacterioferritin A (BfrA) from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The recombinant protein product was purified by affinity chromatography on a Strep-Tactin column and crystallized with sodium chloride as a precipitant at pH 8.0 using the vapour-diffusion technique. The crystals diffracted to 2.1 A resolution and belonged to space group P4(2), with unit-cell parameters a = 123.0, b = 123.0, c = 174.6 A.
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Affiliation(s)
- Vibha Gupta
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Rakesh K. Gupta
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
- Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi 110021, India
| | - Garima Khare
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Dinakar M. Salunke
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anil K. Tyagi
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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Tomioka H. Development of new antituberculous agents based on new drug targets and structure–activity relationship. Expert Opin Drug Discov 2007; 3:21-49. [DOI: 10.1517/17460441.3.1.21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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47
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Sankaranarayanan R, Cherney MM, Cherney LT, Garen CR, Moradian F, James MNG. The crystal structures of ornithine carbamoyltransferase from Mycobacterium tuberculosis and its ternary complex with carbamoyl phosphate and L-norvaline reveal the enzyme's catalytic mechanism. J Mol Biol 2007; 375:1052-63. [PMID: 18062991 DOI: 10.1016/j.jmb.2007.11.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 11/06/2007] [Accepted: 11/09/2007] [Indexed: 11/27/2022]
Abstract
Mycobacterium tuberculosis ornithine carbamoyltransferase (Mtb OTC) catalyzes the sixth step in arginine biosynthesis; it produces citrulline from carbamoyl phosphate (CP) and ornithine (ORN). Here, we report the crystal structures of Mtb OTC in orthorhombic (form I) and hexagonal (form II) space groups. The molecules in form II are complexed with CP and l-norvaline (NVA); the latter is a competitive inhibitor of OTC. The asymmetric unit in form I contains a pseudo hexamer with 32 point group symmetry. The CP and NVA in form II induce a remarkable conformational change in the 80s and the 240s loops with the displacement of these loops towards the active site. The displacement of these loops is strikingly different from that seen in other OTC structures. In addition, the ligands induce a domain closure of 4.4 degrees in form II. Sequence comparison of active-site residues of Mtb OTC with several other OTCs of known structure reveals that they are virtually identical. The interactions involving the active-site residues of Mtb OTC with CP and NVA and a modeling study of ORN in the form II structure strongly rule out an earlier proposed mechanistic role of Cys264 in catalysis and suggest a possible mechanism for OTC. Our results strongly support the view that ORN with an already deprotonated N(epsilon) atom is the species that binds to the enzyme and that one of the phosphate oxygen atoms of CP is likely to be involved in accepting a proton from the doubly protonated N(epsilon) atom of ORN. We have interpreted this deprotonation as part of the collapse of the transition state of the reaction.
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Affiliation(s)
- Ramasamy Sankaranarayanan
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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48
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Kim SM, Bowers PM, Pal D, Strong M, Terwilliger TC, Kaufmann M, Eisenberg D. Functional linkages can reveal protein complexes for structure determination. Structure 2007; 15:1079-89. [PMID: 17850747 DOI: 10.1016/j.str.2007.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 05/25/2007] [Accepted: 06/01/2007] [Indexed: 11/19/2022]
Abstract
In the study of protein complexes, is there a computational method for inferring which combinations of proteins in an organism are likely to form a crystallizable complex? Here we attempt to answer this question, using the Protein Data Bank (PDB) to assess the usefulness of inferred functional protein linkages from the Prolinks database. We find that of the 242 nonredundant prokaryotic protein complexes shared between the current PDB and Prolinks, 44% (107/242) contain proteins linked at high confidence by one or more methods of computed functional linkages. Similarly, high-confidence linkages detect 47% of known Escherichia coli protein complexes, with 45% accuracy. Together these findings suggest that functional linkages will be useful in defining protein complexes for structural studies, including for structural genomics. We offer a database of inferred linkages corresponding to likely protein complexes for some 629,952 pairs of proteins in 154 prokaryotes and archaea.
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Affiliation(s)
- Sul-Min Kim
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA
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49
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Baker EN. Structural genomics as an approach towards understanding the biology of tuberculosis. ACTA ACUST UNITED AC 2007; 8:57-65. [PMID: 17668294 DOI: 10.1007/s10969-007-9020-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 07/09/2007] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) is a devastating disease of worldwide importance. The availability of the genome sequence of Mycobacterium tuberculosis (Mtb), the causative agent, has stimulated a large variety of genome-scale initiatives. These include international structural genomics efforts which have the dual aim of characterising potential new drug targets and addressing key aspects of the biology of Mtb. This review highlights the various ways in which structural analysis has illuminated the biological activities of Mtb gene products, which were previously of unknown or uncertain function. Key information comes from the protein fold, from bound ligands, solvent molecules, ions etc. or from unexpectedly modified amino acid residues. Most importantly, the three dimensional structure of a protein permits the integration of data from many sources, both bioinformatic and experimental, to develop testable functional hypotheses. This has led to many new insights into TB biology.
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Affiliation(s)
- Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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50
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Hatzopoulos GN, Mueller-Dieckmann J. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of initiation factor 1 from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:183-6. [PMID: 17329809 PMCID: PMC2330178 DOI: 10.1107/s174430910700437x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 01/26/2007] [Indexed: 11/11/2022]
Abstract
Initiation factor 1 (IF-1; Rv3462c) from Mycobacterium tuberculosis, a component of the 30S initiation complex, was cloned and heterologously expressed in Escherichia coli. The protein was purified by affinity and size-exclusion chromatography and crystallized. A complete data set has been collected to high resolution. The crystals belonged to space group P2(1)2(1)2, with two molecules per asymmetric unit which are related by translational symmetry.
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