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Mycobacterium tuberculosis AND drug use and [keywords]
- [Purification and chemical characterization of antimicrobial compounds from a new soil isolate Streptomyces rimosus MTCC 10792]. [English Abstract, Journal Article]
- Prikl Biokhim Mikrobiol 2013 Sep-Oct; 49(5):467-75.
A new isolate of Streptomyces sp. from soil of state Chhattisgarh (India) having broad spectrum antibacterial and antifungal activity was obtained. The active strain was identified as Streptomyces rimosus subsp. rimosus with accession number MTCC 10792 based on physiological, biochemical characteristics and 16S rRNA sequence homology studies. Antimicrobial compound produced by S. rimosus was tested against the drug resistance pathogens by the Bauer and Kirby method. The crude active metabolite was extracted using solvent n-butanol and purified by silica column chromatography and HPLC method. The physicochemical characteristics of the one purified compound viz. color, melting point, solubility, elemental analysis; ESIMS, IR,UV, 1HNMR, 13CNMR and chemical reactions have been investigated. Purified antimicrobial compound produced by S. rimosus MTCC 10792 at concentration 25 μg/ml showed antitubercular activity against Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis H37Ra as well as broad activity against all tested bacterial and fungal pathogens.
- Structure based virtual screening to identify inhibitors against MurE Enzyme of Mycobacterium tuberculosis using AutoDock Vina. [Journal Article]
- Bioinformation 2014; 10(11):697-702.
The Mur E enzyme of Mur pathway of Mycobacterium tuberculosis is an attractive drug target as it is unique to bacteria and is absent in mammalian cells. The virtual screening of large libraries of drug like molecules against a protein target is a common strategy used to identify novel inhibitors. However, the method has a large number of pitfalls, with large variations in accuracy caused in part by inaccurate protocols, use of improper standards and libraries, and system dependencies such as the potential for nonspecific docking from large active-site cavities. The screening of drug-like small molecules from diversity sets can, however, be used to short-list potential fragments as building blocks to generate leads with improved specificity. We describe a protocol to implement this strategy, which involves an analysis of the active site and known inhibitors to identify orthospecific determinants, virtual screening of a drug-like diversity library to identify potential drug primitives, and inspection of the potential docked fragments for both binding potential and toxicity. The protocol is implemented on the M.tb Mur E protein which has a large active site with poor enrichment of known positives and a set of drug-like molecules that meets this criteria is presented for further analysis.MTB - Mycobacterium tuberculosis, NCI - National Cancer Institute, PDB - Protein Databank.
- From workstations to workbenches: Towards predicting physicochemically viable protein-protein interactions across a host and a pathogen. [JOURNAL ARTICLE]
- IUBMB Life 2014 Dec 15.
The understanding of protein-protein interactions is indispensable in comprehending most of the biological processes in a cell. Small-scale experiments as well as large-scale high-throughput techniques over the past few decades have facilitated identification and analysis of protein-protein interactions which form the basis of much of our knowledge on functional and regulatory aspects of proteins. However, such rich catalog of interaction data should be used with caution when establishing protein-protein interactions in silico, as the high-throughput datasets are prone to false positives. Numerous computational means developed to pursue genome-wide studies on protein-protein interactions at times overlook the mechanistic and molecular details, thus questioning the reliability of predicted protein-protein interactions. We review the development, advantages, and shortcomings of varied approaches and demonstrate that by providing a structural viewpoint in terms of shape complementarity and interaction energies at protein-protein interfaces coupled with information on expression and localization of proteins homologous to an interacting pair, it is possible to assess the credibility of predicted interactions in biological context. With a focus on human pathogen Mycobacterium tuberculosis H37Rv, we show that such scrupulous use of details at the molecular level can predict physicochemically viable protein-protein interactions across host and pathogen. Such predicted interactions have the potential to provide molecular basis of probable mechanisms of pathogenesis and hence open up ways to explore their usefulness as targets in the light of drug discovery. © 2014 IUBMB Life, 2014.
- Case Report Tuberculoma masked by glioma: a case report. [Journal Article]
- Genet Mol Res 2014; 13(4):10450-3.
Tuberculous meningitis (TM), a common infectious disease of the central nervous system that is also seen in other types of tuberculosis infections, has higher mortality rates in young and middle-aged patients. TM is difficult to diagnose and treat owing to its non-specific clinical features and often atypical cerebrospinal fluid changes. Patients who present with focal neurologic signs, cough, low-grade fever and illness duration of more than 5 days, have intracalvarial abnormalities, and do not meet Thwaites' criterion findings should be diagnosed using computed tomography or magnetic resonance imaging. Mycobacterium infections can also be diagnosed by acid-fast staining of smears, cerebrospinal fluid culture, diagnostic polymerase chain reaction for Mycobacterium tuberculosis, and purified protein derivative test. To prevent TM misdiagnosis, clinicians must have sufficient knowledge of the clinical manifestations of tuberculosis. Appropriate application of tuberculosis chemotherapy drug principles, including early diagnosis and treatment, combination therapies, and consistent administration of treatment at appropriate dosages, can greatly reduce TM mortality rates and improve satisfactory treatment outcomes.
- Multi-drug resistant tuberculosis among category I treatment failures--a retrospective study. [Journal Article]
- Indian J Tuberc 2014 Apr; 61(2):148-51.
Tuberculosis (TB) remains a major global health problem and ranks as the second leading cause of death worldwide. An important cause of TB epidemic is the emergence of multi drug resistant (MDR) strains of Mycobacterium tuberculosis. Despite the availability of treatment that is expected to cure most cases of TB, levels of MDR-TB remain worryingly high in India.This study was carried out to ascertain the prevalence of MDR-TB among category I pulmonary TB treatment failure patients.This was a retrospective study involving 750 pulmonary tuberculosis patients enrolled at six district centres of Delhi State under RNTCP who failed to respond to CAT I treatment and whose sputum samples were submitted for culture and drug sensitivity testing (DST) over a period of three years (2009-2012). MDR-TB was defined as TB caused by bacilli showing resistance to at least isoniazid and rifampicin.Out of the total 750 patients included in the study, 470 (62.6 %) were culture positive. Of these, 377 (80.2%) were subjected to DST and rest 93 (19.7%) were excluded. Ultimately, DST result was available for 353 (93.6 %) cases. 239 (68%) cases were detected as multi drug resistant TB.High proportion of MDR-TB (68%) among culture positive CAT I treatment failure cases highlights the need for rapid diagnostic tests which will enable the detection of MDR-TB at an early stage and will thus minimize the risk of transmission as well as the possible errors associated with the treatment.
- Novel mutation detection IN rpoB OF rifampicin-resistant Mycobacterium Tuberculosis using pyroseouencing. [Journal Article, Research Support, Non-U.S. Gov't]
- Southeast Asian J Trop Med Public Health 2014 Jul; 45(4):843-52.
Tuberculosis (TB) remains a major global public health problem particularly severe in parts of Asia and Africa, where often it is present in HIV-AIDS patients. Although rifampicin-resistant (RIFr) TB is slow to emerge due to the low rate of mutation of its target leading to RIFE being a marker of TB that is already resistant to other anti-TB drugs, and such cases are prone to treatment failure. More than 95% of rifampicin resistance is associated with mutations in Mycobacterium tuberculosis (MTB) rpoB, with 97% of mutations occurring within the 81 bp rifampicin-resistant determining region (RRDR) of this gene. In this study, we employed pyrosequencing technique to identify mutations in RRDR and 5 codons beyond of 39 MTB strains, comprising of 14 multi-drug resistance TB (MDRTB) and 3 RIF susceptible (RIFs) MTB from the Center of Disease Control (CDC), Ratchaburi Province, and 19 mono RIFr MTB, 1 MDRTB and 2 poly-drug resistant MTB from the Chest Institute, Ministry of Public Health, Thailand. Mu- tations in 8/22 samples from the Chest Institute and 13/14 from CDC were able to be identified. Six point mutations were detected, with Ser531Leu mutation accounting for 13, the silent mutation at Gly536 for 4, deletion of Gly523 for 2, combination of His526Cys and novel Leu533Arg for 1, and a novel Leu538Arg for 1. Mutation analysis of the 81 bp fragment and 5 codons beyond in MTB rpoB using pyrosequencing provides a useful approach in predicting RIFr phenotype allowing early diagnosis and appropriate drug therapy.
- Diversity-Oriented Synthesis for Novel, Selective and Drug-like Inhibitors for a Phosphatase from Mycobacterium Tuberculosis. [JOURNAL ARTICLE]
- Medchemcomm 2014 Oct; 5(10):1496-1499.
Mycobacterium protein tyrosine phosphatase B (mPTPB) is a potential drug target of Tuberculosis (TB). Small molecule inhibitors of mPTPB could be a treatment to overcome emerging TB drug resistance. Using a Diversity-Oriented Synthesis (DOS) strategy, we successfully developed a salicylic acid based and drug-like mPTPB inhibitor with an IC50 of 2 μM and >20-fold specificity over many human PTPs, making it an excellent lead molecule for anti-TB drug discovery. In addition, DOS generated bicyclic salicylic acids are also promising starting points for acquiring inhibitors targeting other PTPs.
- Evaluation of Point Mutation Detection in Mycobacterium tuberculosis with Isoniazid Resistance Using Real-Time PCR and TaqMan Probe Assay. [JOURNAL ARTICLE]
- Appl Biochem Biotechnol 2014 Dec 12.
Rapid methods for diagnosis of Mycobacterium tuberculosis (Mtb) drug resistance and choosing appropriate antibiotic treatment are pivotal. Thirty isoniazid (INH)-resistant and 30 INH-susceptible Mtb isolates were evaluated using minimum inhibitory concentration (MIC) method followed by multiplex real-time PCR (RT-PCR). Amplification refractory mutation system (ARMS) for detection of mutation in 315 codon of katG gene and single-nucleotide polymorphism (SNP) for detection of mutation in -15 (C>T) in the regulatory zone of mabA-inhA were carried out using the TaqMan method. Primers and probe were used for IS6110 region of Mtb as an internal amplification control. The sensitivity and specificity of the RT-PCR TaqMan probe for detection of Mtb complex were 100 %. Detection of INH-resistant Mtb using the ARMS method for KatG had 69 % sensitivity and 100 % specificity. The sensitivity and specificity of SNP in mabA-inhA fragment for detection of INH-resistant Mtb were 53 and 100 %, respectively. Furthermore, considering both regions, the sensitivity of RT-PCR has increased to 75 %. This study revealed that the qPCR-TaqMan method can be used as a standard tool for diagnosis of Mtb. Moreover, ARMS and SNP RT-PCR TaqMan methods can be used as rapid screening methods for detection of INH-resistant Mtb.
- Study of Mycobacterium tuberculosis Complex Genotypic Diversity in Malaysia Reveals a Predominance of Ancestral East-African-Indian Lineage with a Malaysia-Specific Signature. [JOURNAL ARTICLE]
- PLoS One 2014; 9(12):e114832.
Tuberculosis (TB) still constitutes a major public health problem in Malaysia. The identification and genotyping based characterization of Mycobacterium tuberculosis complex (MTBC) isolates causing the disease is important to determine the effectiveness of the control and surveillance programs.This study intended a first assessment of spoligotyping-based MTBC genotypic diversity in Malaysia followed by a comparison of strains with those prevailing in neighboring countries by comparison with an international MTBC genotyping database.Spoligotyping was performed on a total of 220 M. tuberculosis clinical isolates collected in Kelantan and Kuala Lumpur. The results were compared with the SITVIT2 international database of the Pasteur Institute of Guadeloupe.Spoligotyping revealed 77 different patterns: 22 corresponded to orphan patterns while 55 patterns containing 198 isolates were assigned a Spoligo International Type (SIT) designation in the database (the latter included 6 newly created SITs). The eight most common SITs grouped 141 isolates (5 to 56 strains per cluster) as follows: SIT1/Beijing, n = 56, 25.5%; SIT745/EAI1-SOM, n = 33, 15.0%; SIT591/EAI6-BGD1, n = 13, 5.9%; SIT256/EAI5, n = 12, 5.5%; SIT236/EAI5, n = 10, 4.6%; SIT19/EAI2-Manila, n = 9, 4.1%; SIT89/EAI2-Nonthaburi, n = 5, 2.3%; and SIT50/H3, n = 3, 1.4%. The association between city of isolation and lineages was statistically significant; Haarlem and T lineages being higher in Kuala Lumpur (p<0.01). However, no statistically significant differences were noted when comparing drug resistance vs. major lineages, nor between gender and clades.The ancestral East-African-Indian (EAI) lineage was most predominant followed by the Beijing lineage. A comparison of strains with those prevailing in neighboring countries in South Asia, East Asia and South East Asia underlined the phylogeographical specificity of SIT745 for Malaysia, and its probable ongoing evolution with locally evolved strains sharing a specific signature characterized by absence of spacers 37, 38, and 40. Pending complementary genotyping confirmation, we propose that SIT745/EAI-SOM is tentatively reclassified as SIT745/EAI-MYS.
- HGV&TB: a comprehensive online resource on human genes and genetic variants associated with tuberculosis. [Journal Article]
- Database (Oxford) 2014.
Tuberculosis (TB) is an infectious disease caused by fastidious pathogen Mycobacterium tuberculosis. TB has emerged as one of the major causes of mortality in the developing world. Role of host genetic factors that modulate disease susceptibility have not been studied widely. Recent studies have reported few genetic loci that provide impetus to this area of research. The availability of tools has enabled genome-wide scans for disease susceptibility loci associated with infectious diseases. Till now, information on human genetic variations and their associated genes that modulate TB susceptibility have not been systematically compiled. In this work, we have created a resource: HGV&TB, which hosts genetic variations reported to be associated with TB susceptibility in humans. It currently houses information on 307 variations in 98 genes. In total, 101 of these variations are exonic, whereas 78 fall in intronic regions. We also analysed the pathogenicity of the genetic variations, their phenotypic consequences and ethnic origin. Using various computational analyses, 30 variations of the 101 exonic variations were predicted to be pathogenic. The resource is freely available at http://genome.igib.res.in/hgvtb/index.html. Using integrative analysis, we have shown that the disease associated variants are selectively enriched in the immune signalling pathways which are crucial in the pathophysiology of TB. Database URL: http://genome.igib.res.in/hgvtb/index.html.