1
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Levendosky K, Janisch N, Quadri LEN. Comprehensive essentiality analysis of the Mycobacterium kansasii genome by saturation transposon mutagenesis and deep sequencing. mBio 2023; 14:e0057323. [PMID: 37350613 PMCID: PMC10470612 DOI: 10.1128/mbio.00573-23] [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: 03/07/2023] [Accepted: 05/01/2023] [Indexed: 06/24/2023] Open
Abstract
Mycobacterium kansasii (Mk) is an opportunistic pathogen that is frequently isolated from urban water systems, posing a health risk to susceptible individuals. Despite its ability to cause tuberculosis-like pulmonary disease, very few studies have probed the genetics of this opportunistic pathogen. Here, we report a comprehensive essentiality analysis of the Mk genome. Deep sequencing of a high-density library of Mk Himar1 transposon mutants revealed that 86.8% of the chromosomal thymine-adenine (TA) dinucleotide target sites were permissive to insertion, leaving 13.2% TA sites unoccupied. Our analysis identified 394 of the 5,350 annotated open reading frames (ORFs) as essential. The majority of these essential ORFs (84.8%) share essential mutual orthologs with Mycobacterium tuberculosis (Mtb). A comparative genomics analysis identified 139 Mk essential ORFs that share essential orthologs in four other species of mycobacteria. Thirteen Mk essential ORFs share orthologs in all four species that were identified as being not essential, while only two Mk essential ORFs are absent in all species compared. We used the essentiality data and a comparative genomics analysis reported here to highlight differences in essentiality between candidate Mtb drug targets and the corresponding Mk orthologs. Our findings suggest that the Mk genome encodes redundant or additional pathways that may confound validation of potential Mtb drugs and drug target candidates against the opportunistic pathogen. Additionally, we identified 57 intergenic regions containing four or more consecutive unoccupied TA sites. A disproportionally large number of these regions were located upstream of pe/ppe genes. Finally, we present an essentiality and orthology analysis of the Mk pRAW-like plasmid, pMK1248. IMPORTANCE Mk is one of the most common nontuberculous mycobacterial pathogens associated with tuberculosis-like pulmonary disease. Drug resistance emergence is a threat to the control of Mk infections, which already requires long-term, multidrug courses. A comprehensive understanding of Mk biology is critical to facilitate the development of new and more efficacious therapeutics against Mk. We combined transposon-based mutagenesis with analysis of insertion site identification data to uncover genes and other genomic regions required for Mk growth. We also compared the gene essentiality data set of Mk to those available for several other mycobacteria. This analysis highlighted key similarities and differences in the biology of Mk compared to these other species. Altogether, the genome-wide essentiality information generated and the results of the cross-species comparative genomics analysis represent valuable resources to assist the process of identifying and prioritizing potential Mk drug target candidates and to guide future studies on Mk biology.
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Affiliation(s)
- Keith Levendosky
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, New York, USA
- Biology Program, Graduate Center, Biology Program, Graduate Center, City University of New York, New York, New York, USA
| | - Niklas Janisch
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, New York, USA
- Biology Program, Graduate Center, Biology Program, Graduate Center, City University of New York, New York, New York, USA
| | - Luis E. N. Quadri
- Department of Biology, Brooklyn College, City University of New York, Brooklyn, New York, USA
- Biology Program, Graduate Center, Biology Program, Graduate Center, City University of New York, New York, New York, USA
- Biochemistry Program, Graduate Center, City University of New York, New York, New York, USA
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2
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Kanvatirth P, Jeeves RE, Bacon J, Besra GS, Alderwick LJ. Utilisation of the Prestwick Chemical Library to identify drugs that inhibit the growth of mycobacteria. PLoS One 2019; 14:e0213713. [PMID: 30861059 PMCID: PMC6414029 DOI: 10.1371/journal.pone.0213713] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/27/2019] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis (TB) is an infectious bacterial disease that kills approximately 1.3 million people every year. Despite global efforts to reduce both the incidence and mortality associated with TB, the emergence of drug resistant strains has slowed any progress made towards combating the spread of this deadly disease. The current TB drug regimen is inadequate, takes months to complete and poses significant challenges when administering to patients suffering from drug resistant TB. New treatments that are faster, simpler and more affordable are urgently required. Arguably, a good strategy to discover new drugs is to start with an old drug. Here, we have screened a library of 1200 FDA approved drugs from the Prestwick Chemical library using a GFP microplate assay. Drugs were screened against GFP expressing strains of Mycobacterium smegmatis and Mycobacterium bovis BCG as surrogates for Mycobacterium tuberculosis, the causative agent of TB in humans. We identified several classes of drugs that displayed antimycobacterial activity against both M. smegmatis and BCG, however each organism also displayed some selectivity towards certain drug classes. Variant analysis of whole genomes sequenced for resistant mutants raised to florfenicol, vanoxerine and pentamidine highlight new pathways that could be exploited in drug repurposing programmes.
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Affiliation(s)
- Panchali Kanvatirth
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rose E. Jeeves
- TB Research Group, National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Joanna Bacon
- TB Research Group, National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Luke J. Alderwick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail:
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3
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Bythrow GV, Mohandas P, Guney T, Standke LC, Germain GA, Lu X, Ji C, Levendosky K, Chavadi SS, Tan DS, Quadri LEN. Kinetic Analyses of the Siderophore Biosynthesis Inhibitor Salicyl-AMS and Analogues as MbtA Inhibitors and Antimycobacterial Agents. Biochemistry 2019; 58:833-847. [PMID: 30582694 DOI: 10.1021/acs.biochem.8b01153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
There is a paramount need for expanding the drug armamentarium to counter the growing problem of drug-resistant tuberculosis. Salicyl-AMS, an inhibitor of salicylic acid adenylation enzymes, is a first-in-class antibacterial lead compound for the development of tuberculosis drugs targeting the biosynthesis of salicylic-acid-derived siderophores. In this study, we determined the Ki of salicyl-AMS for inhibition of the salicylic acid adenylation enzyme MbtA from Mycobacterium tuberculosis (MbtAtb), designed and synthesized two new salicyl-AMS analogues to probe structure-activity relationships (SAR), and characterized these two analogues alongside salicyl-AMS and six previously reported analogues in biochemical and cell-based studies. The biochemical studies included determination of kinetic parameters ( Kiapp, konapp, koff, and tR) and analysis of the mechanism of inhibition. For these studies, we optimized production and purification of recombinant MbtAtb, for which Km and kcat values were determined, and used the enzyme in conjunction with an MbtAtb-optimized, continuous, spectrophotometric assay for MbtA activity and inhibition. The cell-based studies provided an assessment of the antimycobacterial activity and postantibiotic effect of the nine MbtAtb inhibitors. The antimycobacterial properties were evaluated using a strain of nonpathogenic, fast-growing Mycobacterium smegmatis that was genetically engineered for MbtAtb-dependent susceptibility to MbtA inhibitors. This convenient model system greatly facilitated the cell-based studies by bypassing the methodological complexities associated with the use of pathogenic, slow-growing M. tuberculosis. Collectively, these studies provide new information on the mechanism of inhibition of MbtAtb by salicyl-AMS and eight analogues, afford new SAR insights for these inhibitors, and highlight several suitable candidates for future preclinical evaluation.
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Affiliation(s)
- Glennon V Bythrow
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Poornima Mohandas
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Tezcan Guney
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Lisa C Standke
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Gabrielle A Germain
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Xuequan Lu
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Cheng Ji
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Keith Levendosky
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Sivagami Sundaram Chavadi
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States.,Pharmacology Program, Weill Cornell Graduate School of Medical Sciences , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States.,Tri-Institutional Research Program , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Luis E N Quadri
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States.,Biochemistry Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
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4
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Pattanashetty SH, Hosamani K, Barretto DA. Microwave assisted synthesis, computational study and biological evaluation of novel quinolin-2(1H)-one based pyrazoline hybrids. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.cdc.2018.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Abstract
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Current tuberculosis
(TB) drug development efforts are not sufficient
to end the global TB epidemic. Recent efforts have focused on the
development of whole-cell screening assays because biochemical, target-based
inhibitor screens during the last two decades have not delivered new
TB drugs. Mycobacterium tuberculosis (Mtb), the causative
agent of TB, encounters diverse microenvironments and can be found
in a variety of metabolic states in the human host. Due to the complexity
and heterogeneity of Mtb infection, no single model can fully recapitulate
the in vivo conditions in which Mtb is found in TB patients, and there
is no single “standard” screening condition to generate
hit compounds for TB drug development. However, current screening
assays have become more sophisticated as researchers attempt to mirror
the complexity of TB disease in the laboratory. In this review, we
describe efforts using surrogates and engineered strains of Mtb to
focus screens on specific targets. We explain model culture systems
ranging from carbon starvation to hypoxia, and combinations thereof,
designed to represent the microenvironment which Mtb encounters in
the human body. We outline ongoing efforts to model Mtb infection
in the lung granuloma. We assess these different models, their ability
to generate hit compounds, and needs for further TB drug development,
to provide direction for future TB drug discovery.
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Affiliation(s)
- Tianao Yuan
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University , Stellenbosch 7600, South Africa
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6
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Sellamuthu S, Singh M, Kumar A, Singh SK. Type-II NADH Dehydrogenase (NDH-2): a promising therapeutic target for antitubercular and antibacterial drug discovery. Expert Opin Ther Targets 2017; 21:559-570. [PMID: 28472892 DOI: 10.1080/14728222.2017.1327577] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Tuberculosis (TB) is highly dangerous due to the development of resistance to first-line drugs. Moreover, Mycobacterium tuberculosis (Mtb) has also developed resistance to newly approved antitubercular drug bedaquiline. This necessitates the search for drugs acting on newer molecular targets. The energy metabolism of mycobacteria is the prime focus for the discovery of novel antitubercular drugs. Targeting type-2 NADH dehydrogenase (NDH-2) involved in the production of respiratory ATP could, therefore, be effective in treating the disease. Areas covered: This review describes the energetics of mycobacteria and the role of NDH-2 in ATP synthesis. Special attention has been given for genetic and chemical validations of NDH-2 as a molecular target. The reported kinetics and crystal structures of NDH-2 have been given in detail for better understanding of the enzyme. Expert opinion: NDH-2 is an essential enzyme for ATP synthesis and has a potential role in dormancy and persistence of Mtb. The human counterpart lacks this enzyme and hence NDH-2 inhibitors could have more clinical importance. Phenothiazines are potent inhibitor of NDH-2 and are effective against both drug-susceptible and drug-resistant Mtb. Thus, it is highly desirable to optimize phenothiazine class of compounds for the development of next generation anti-TB drugs.
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Affiliation(s)
- Satheeshkumar Sellamuthu
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
| | - Meenakshi Singh
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
| | - Ashok Kumar
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
| | - Sushil Kumar Singh
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
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7
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Dhumal ST, Deshmukh AR, Bhosle MR, Khedkar VM, Nawale LU, Sarkar D, Mane RA. Synthesis and antitubercular activity of new 1,3,4-oxadiazoles bearing pyridyl and thiazolyl scaffolds. Bioorg Med Chem Lett 2016; 26:3646-51. [PMID: 27301367 DOI: 10.1016/j.bmcl.2016.05.093] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/28/2016] [Accepted: 05/31/2016] [Indexed: 12/31/2022]
Abstract
In search of more potent and safe new antitubercular agents, here new 2-pyridinyl substituted thiazolyl-5-aryl-1,3,4-oxadiazoles (6a-o), have been designed and synthesized using thionicotinamide as a starting, following novel multistep synthetic route. An intermediate, pyridinyl substituted thiazolyl acid hydrazide (4) when condensed with benzoic acids/nicotinic acids (5a-o) in the presence of silica supported POCl3 yielded better to excellent yields of the title compounds. All the synthesized compounds (6a-o) and intermediate acid hydrazide (4) have been screened for their in vitro antitubercular activity against Mycobacterium tuberculosis H37Ra (MTB) and Mycobacterium bovis BCG. Amongst them, 6f, 6j, 6l and 6o have revealed promising activity against M. bovis BCG at concentrations less than 3μg/mL. These compounds have shown low cytotoxicity (CC50: >100μg/mL) towards four human cancer cell lines. Molecular docking study has also been performed against mycobacterial enoyl reductase (InhA) enzyme to gain an insight into the binding modes of these molecules and recorded good binding affinity. The ADME properties the title products have also been analyzed.
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Affiliation(s)
- Sambhaji T Dhumal
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad 431004, India
| | - Amarsinh R Deshmukh
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad 431004, India
| | - Manisha R Bhosle
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad 431004, India
| | - Vijay M Khedkar
- Combi Chem-Bio Resource Centre, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Laxman U Nawale
- Combi Chem-Bio Resource Centre, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Dhiman Sarkar
- Combi Chem-Bio Resource Centre, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Ramrao A Mane
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad 431004, India.
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8
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Perspective: Challenges and opportunities in TB drug discovery from phenotypic screening. Bioorg Med Chem 2014; 23:5087-97. [PMID: 25577708 DOI: 10.1016/j.bmc.2014.12.031] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 02/06/2023]
Abstract
Tuberculosis poses a major global health problem and multi-drug resistant strains are increasingly prevalent. Hence there is an urgent need to discover new TB drugs. Cell based phenotypic screening represents a powerful approach to identify anti-mycobacterial compounds and elucidate novel targets. Three high throughput phenotypic screens were performed at NITD against mycobacterium. Hits were identified and chemical series selected for optimisation. This produced compounds with good in vitro anti-mycobacterial activity and pharmacokinetic properties. Some compounds displayed oral activity in mouse efficacy models of TB. Herein, we review the TB discovery efforts at NITD and share experiences in optimisation of phenotypic hits, describing challenges encountered and lessons learned. We also offer perspectives to facilitate future selection and advancement of phenotypic hits.
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9
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Morayya S, Awasthy D, Yadav R, Ambady A, Sharma U. Revisiting the essentiality of glutamate racemase in Mycobacterium tuberculosis. Gene 2014; 555:269-76. [PMID: 25447907 DOI: 10.1016/j.gene.2014.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/04/2014] [Accepted: 11/10/2014] [Indexed: 01/25/2023]
Abstract
Glutamate racemase (MurI) converts l-glutamate into d-glutamate which is an essential component of peptidoglycan in bacteria. The gene encoding glutamate racemase, murI has been shown to be essential for the growth of a number of bacterial species including Escherichia coli. However, in some Gram-positive species d-amino acid transaminase (Dat) can also convert l-glutamate into d-glutamate thus rendering MurI non-essential for growth. In a recent study the murI gene of Mycobacterium tuberculosis was shown to be non-essential. As d-glutamate is an essential component of peptidoglycan of M. tuberculosis, either Dat or MurI has to be essential for its survival. Since, a Dat encoding gene has not been reported in M. tuberculosis genome sequence, the reported non-essentiality of murI was unexplainable. In order to resolve this dilemma we tried to knockout murI in the presence of single and two copies of murI, in wild type and merodiploid strains respectively. It was found that murI could not be inactivated in the wild type background indicating that it could be an essential gene. Also, inactivation of murI could not be achieved in the presence of externally supplied d-glutamate in 7H9 medium suggesting that M. tuberculosis is unable to take up d-glutamate under the conditions tested. However we could generate murI knockout strains at high frequency when two copies of the gene were present indicating that at least one murI gene is required for cellular viability. The essential nature of MurI in M. tuberculosis H37Rv suggests that it could be a potential drug target.
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Affiliation(s)
- Sapna Morayya
- Present address: Biocon Bristol Myer squib R&D Centre, Biocon Park, Jigani Link Road, Bommasandra, Bangalore, India
| | - Disha Awasthy
- Present address: Strand Center for Genomics & Personalized Medicine, Strand Life Sciences Pvt. Ltd., Veterinary College Campus, Bellary Road, Bangalore, India
| | - Reena Yadav
- AstraZeneca India Pvt. Ltd., "Avishkar", Bellary Road, Hebbal, Bangalore, India
| | - Anisha Ambady
- Present address: Biocon Bristol Myer squib R&D Centre, Biocon Park, Jigani Link Road, Bommasandra, Bangalore, India
| | - Umender Sharma
- Present address: GangaGen Biotechnologies Pvt. Ltd, No 12, 5th Cross, Raghavendra Layout, Tumkur Road, Yeshwantpur, Bangalore, India.
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10
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Awasthy D, Ambady A, Narayana A, Morayya S, Sharma U. Roles of the two type II NADH dehydrogenases in the survival of Mycobacterium tuberculosis in vitro. Gene 2014; 550:110-6. [PMID: 25128581 DOI: 10.1016/j.gene.2014.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/11/2014] [Accepted: 08/12/2014] [Indexed: 12/21/2022]
Abstract
Most bacteria are able to generate sufficient amounts of ATP from substrate level phosphorylation, thus rendering the respiratory oxidative phosphorylation non-critical. In mycobacteria, including Mycobacterium tuberculosis, ATP generation by oxidative phosphorylation is an essential process. Of the two types of NADH dehydrogenases (type I and type II), the type II NADH dehydrogenase (Ndh) which is inhibited by phenothiazines has been thought to be essential. In M. tuberculosis there are two Ndh isozymes (Ndh and NdhA) coded by ndh and ndhA genes respectively. Ndh and NdhA share a high degree of amino acid similarity. Both the enzymes have been shown to be enzymatically active and are inhibited by phenothiazines, suggesting a functional similarity between the two. We attempted gene knockout of ndh and ndhA genes in wild type and merodiploid backgrounds. It was found that ndh gene cannot be inactivated in a wild type background, though it was possible to do so when an additional copy of ndh was provided. This showed that in spite of its apparent functional equivalence, NdhA cannot complement the loss of Ndh in M. tuberculosis. We also showed that NdhA is not essential in M. tuberculosis as the ndhA gene could be deleted in a wild type strain of M. tuberculosis without causing any adverse effects in vitro. RT-PCR analysis of in vitro grown M. tuberculosis showed that ndhA gene is actively transcribed. This study suggests that despite being biochemically similar, Ndh and NdhA play different roles in the physiology of M. tuberculosis.
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Affiliation(s)
- Disha Awasthy
- AstraZeneca India Pvt Ltd., Infection iMed, "Avishkar", Bellary Road, Hebbal, Bangalore, India
| | - Anisha Ambady
- AstraZeneca India Pvt Ltd., Infection iMed, "Avishkar", Bellary Road, Hebbal, Bangalore, India
| | - Ashwini Narayana
- AstraZeneca India Pvt Ltd., Infection iMed, "Avishkar", Bellary Road, Hebbal, Bangalore, India
| | - Sapna Morayya
- AstraZeneca India Pvt Ltd., Infection iMed, "Avishkar", Bellary Road, Hebbal, Bangalore, India
| | - Umender Sharma
- AstraZeneca India Pvt Ltd., Infection iMed, "Avishkar", Bellary Road, Hebbal, Bangalore, India.
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11
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Chauhan K, Sharma M, Trivedi P, Chaturvedi V, Chauhan PMS. New class of methyl tetrazole based hybrid of (Z)-5-benzylidene-2-(piperazin-1-yl)thiazol-4(%H)-one as potent antitubercular agents. Bioorg Med Chem Lett 2014; 24:4166-70. [PMID: 25127167 DOI: 10.1016/j.bmcl.2014.07.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 11/30/2022]
Abstract
In search of potential therapeutics for tuberculosis, we describe here the synthesis and in vitro antitubercular activity of a novel series of thiazolone piperazine tetrazole derivatives. Among all the synthesized derivatives, four compounds (10, 14, 20 and 33) exhibited more potent activity (MIC=3.08, 3.01, 2.62 and 2.51 μM) than ethambutol (MIC=9.78 μM) and pyrazinamide (MIC=101.53 μM) against Mycobacterium tuberculosis. Furthermore, they displayed no toxicity against Vero cells (C1008) and mouse bone marrow derived macrophages (MBMDMϕ). These investigated analogues have emerged as possible lead molecule to enlarge the scope of the study.
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Affiliation(s)
- Kuldeep Chauhan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India
| | - Moni Sharma
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India
| | - Priyanka Trivedi
- Drug Target Discovery and Development Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Vinita Chaturvedi
- Drug Target Discovery and Development Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Prem M S Chauhan
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Sitapur Road, Lucknow 226031, U.P., India.
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12
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Hameed P S, Patil V, Solapure S, Sharma U, Madhavapeddi P, Raichurkar A, Chinnapattu M, Manjrekar P, Shanbhag G, Puttur J, Shinde V, Menasinakai S, Rudrapatana S, Achar V, Awasthy D, Nandishaiah R, Humnabadkar V, Ghosh A, Narayan C, Ramya VK, Kaur P, Sharma S, Werngren J, Hoffner S, Panduga V, Kumar CNN, Reddy J, Kumar KN M, Ganguly S, Bharath S, Bheemarao U, Mukherjee K, Arora U, Gaonkar S, Coulson M, Waterson D, Sambandamurthy VK, de Sousa SM. Novel N-Linked Aminopiperidine-Based Gyrase Inhibitors with Improved hERG and in Vivo Efficacy against Mycobacterium tuberculosis. J Med Chem 2014; 57:4889-905. [DOI: 10.1021/jm500432n] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michelle Coulson
- Safety
Assessment, AstraZeneca, Alderley Park, Macclesfield, U.K
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13
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Shaikh MS, Palkar MB, Patel HM, Rane RA, Alwan WS, Shaikh MM, Shaikh IM, Hampannavar GA, Karpoormath R. Design and synthesis of novel carbazolo–thiazoles as potential anti-mycobacterial agents using a molecular hybridization approach. RSC Adv 2014. [DOI: 10.1039/c4ra11752b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A series of novel carbazolo–thiazoles was synthesized and evaluated for in vitro anti-mycobacterial activity.
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Affiliation(s)
- Mahamadhanif S. Shaikh
- Department of Pharmaceutical Chemistry
- Discipline of Pharmaceutical Sciences
- College of Health Sciences
- University of KwaZulu-Natal
- Durban-4000, South Africa
| | - Mahesh B. Palkar
- Department of Pharmaceutical Chemistry
- Discipline of Pharmaceutical Sciences
- College of Health Sciences
- University of KwaZulu-Natal
- Durban-4000, South Africa
| | - Harun M. Patel
- Department of Pharmaceutical Chemistry
- Discipline of Pharmaceutical Sciences
- College of Health Sciences
- University of KwaZulu-Natal
- Durban-4000, South Africa
| | - Rajesh A. Rane
- Department of Pharmaceutical Chemistry
- Discipline of Pharmaceutical Sciences
- College of Health Sciences
- University of KwaZulu-Natal
- Durban-4000, South Africa
| | - Wesam S. Alwan
- Department of Pharmaceutical Chemistry
- Discipline of Pharmaceutical Sciences
- College of Health Sciences
- University of KwaZulu-Natal
- Durban-4000, South Africa
| | - Mahidansha M. Shaikh
- Department of Pharmaceutical Chemistry
- Discipline of Pharmaceutical Sciences
- College of Health Sciences
- University of KwaZulu-Natal
- Durban-4000, South Africa
| | - Iqbal M. Shaikh
- Department of Pharmaceutical Chemistry
- Discipline of Pharmaceutical Sciences
- College of Health Sciences
- University of KwaZulu-Natal
- Durban-4000, South Africa
| | - Girish A. Hampannavar
- Department of Pharmaceutical Chemistry
- Discipline of Pharmaceutical Sciences
- College of Health Sciences
- University of KwaZulu-Natal
- Durban-4000, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry
- Discipline of Pharmaceutical Sciences
- College of Health Sciences
- University of KwaZulu-Natal
- Durban-4000, South Africa
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14
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Cooper CB. Development of Mycobacterium tuberculosis whole cell screening hits as potential antituberculosis agents. J Med Chem 2013; 56:7755-60. [PMID: 23927683 DOI: 10.1021/jm400381v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The global pandemic of drug sensitive tuberculosis (TB) as well as the increasing threat from various multidrug resistant forms of TB drives the quest for newer, safer, more effective TB treatment options. The general lack of success in progressing novel chemical matter from high throughput screens of Mycobacterium tuberculosis (M.tb) biochemical targets has prompted resurgence in interest and efforts in prosecuting mycobacterial phenotypic screens. Whole cell active compounds identified from such screens offer significant intrinsic advantages over biochemical screening hits, and derivatives of many of these have proven invaluable in helping to fill the current TB drug development pipeline. Modern techniques for "de-orphaning" such screening hits (i.e., determining their specific biological mechanism of action) offer the possibility of ultimately identifying improved next-generation chemical series by screening these essential, pharmacologically validated biochemical targets as well.
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Affiliation(s)
- Christopher B Cooper
- Global Alliance for TB Drug Development (TB Alliance) , 40 Wall Street, 24th Floor, New York, New York 10005, United States
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15
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Ramachandran V, Singh R, Yang X, Tunduguru R, Mohapatra S, Khandelwal S, Patel S, Datta S. Genetic and chemical knockdown: a complementary strategy for evaluating an anti-infective target. Adv Appl Bioinform Chem 2013; 6:1-13. [PMID: 23413046 PMCID: PMC3572760 DOI: 10.2147/aabc.s39198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Indexed: 11/23/2022] Open
Abstract
The equity of a drug target is principally evaluated by its genetic vulnerability with tools ranging from antisense- and microRNA-driven knockdowns to induced expression of the target protein. In order to upgrade the process of antibacterial target identification and discern its most effective type of inhibition, an in silico toolbox that evaluates its genetic and chemical vulnerability leading either to stasis or cidal outcome was constructed and validated. By precise simulation and careful experimentation using enolpyruvyl shikimate-3-phosphate synthase and its specific inhibitor glyphosate, it was shown that genetic knockdown is distinct from chemical knockdown. It was also observed that depending on the particular mechanism of inhibition, viz competitive, uncompetitive, and noncompetitive, the antimicrobial potency of an inhibitor could be orders of magnitude different. Susceptibility of Escherichia coli to glyphosate and the lack of it in Mycobacterium tuberculosis could be predicted by the in silico platform. Finally, as predicted and simulated in the in silico platform, the translation of growth inhibition to a cidal effect was able to be demonstrated experimentally by altering the carbon source from sorbitol to glucose.
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16
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Munack S, Leroux V, Roderer K, Ökvist M, van Eerde A, Gundersen LL, Krengel U, Kast P. When Inhibitors Do Not Inhibit: Critical Evaluation of Rational Drug Design Targeting Chorismate Mutase fromMycobacterium tuberculosis. Chem Biodivers 2012; 9:2507-27. [DOI: 10.1002/cbdv.201200322] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Indexed: 12/16/2022]
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17
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Ambady A, Awasthy D, Yadav R, Basuthkar S, Seshadri K, Sharma U. Evaluation of CoA biosynthesis proteins of Mycobacterium tuberculosis as potential drug targets. Tuberculosis (Edinb) 2012; 92:521-8. [PMID: 22954585 DOI: 10.1016/j.tube.2012.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/30/2012] [Accepted: 08/02/2012] [Indexed: 01/05/2023]
Abstract
Coenzyme A biosynthesis pathway proteins are potential targets for developing inhibitors against bacteria including Mycobacterium tuberculosis. We have evaluated two enzymes in this pathway: phosphopantetheine adenylyltransferase (CoaD) and dephospho CoA kinase (CoaE) for essentiality and selectivity. Based on the previous transposon mutagenesis studies, coaD had been predicted to be a non-essential gene in M. tuberculosis. Our bioinformatics analysis showed that there is no other functional homolog of this enzyme in M. tuberculosis, which suggests that coaD should be an essential gene. In order to get an unambiguous answer on the essentiality of coaD, we attempted inactivation of coaD in wild type and merodiploid backgrounds. It was found that coaD could only be inactivated in the presence of an additional gene copy, confirming it to be an essential gene. Using a similar approach we found that CoaE was also essential for the survival of M. tuberculosis. RT-PCR analysis showed that both coaD and coaE were transcribed in M. tuberculosis. Amino acids alignment and phylogenetic analysis showed CoaD to be distantly related to the human counterpart while CoaE was found to be relatively similar to the human enzyme. Analysis of CoaD and CoaE structures at molecular level allowed us to identify unique residues in the Mtb proteins, thus providing a selectivity handle. The essentiality and selectivity analysis combined with the published biochemical characterization of CoaD and CoaE makes them suitable targets for developing inhibitors against M. tuberculosis.
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Affiliation(s)
- Anisha Ambady
- AstraZeneca R & D, Infection iMed, Avishkar, Bellary Road, Hebbal, Bangalore, India
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18
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Patpi SR, Pulipati L, Yogeeswari P, Sriram D, Jain N, Sridhar B, Murthy R, Anjana Devi T, Kalivendi SV, Kantevari S. Design, synthesis, and structure-activity correlations of novel dibenzo[b,d]furan, dibenzo[b,d]thiophene, and N-methylcarbazole clubbed 1,2,3-triazoles as potent inhibitors of Mycobacterium tuberculosis. J Med Chem 2012; 55:3911-22. [PMID: 22449006 DOI: 10.1021/jm300125e] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A molecular hybridization approach is an emerging structural modification tool to design new molecules with improved pharmacophoric properties. In this study, 1,2,3-triazole-based Mycobacterium tuberculosis inhibitors and synthetic and natural product-based tricyclic (carbazole, dibenzo[b,d]furan, and dibenzo[b,d]thiophene) antimycobacterial agents were integrated in one molecular platform to prepare various novel clubbed 1,2,3-triazole hybrids using click chemistry. Structure-activity correlations and in vitro activity against M. tuberculosis strain H37Rv of new analogues revealed the order: dibenzo[b,d]thiophene > dibenzo[b,d]furan > 9-methyl-9H-carbazole series. Two of the most potent M. tuberculosis inhibitors 13h and 13q with MIC = 0.78 μg/mL (∼1.9 μM) displayed a low cytotoxicity and high selectivity index (50-255) against four different human cancer cell lines. These results together provided the potential importance of molecular hybridization and the development of triazole clubbed dibenzo[b,d]thiophene-based lead candidates to treat mycobacterial infections.
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Affiliation(s)
- Santhosh Reddy Patpi
- Organic Chemistry (CPC) Division-II, Indian Institute of Chemical Technology, Hyderabad-500607, India
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