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Puranik NV, Swami S, Misar AV, Mamgain R, Gulawani SS, Dhiman, Sarkar, Srivastava P. The first synthesis of podocarflavone A and its analogs and evaluation of their antimycobacterial potential against Mycobacterium tuberculosis with the support of virtual screening. Nat Prod Res 2021; 36:3879-3886. [PMID: 33663286 DOI: 10.1080/14786419.2021.1893317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The first synthetic route developed for Podocarflavone A reported from Podocarpus macrophyllus and its analogs in 7 steps. Computational analysis for binding with the pantothenate kinase (3AVO) of Mycobacterium tuberculosis showed their docking score (ds) in the range of -8.9 to -9.3 Kcal/mol. MD simulations delineated the stability of the protein-ligand complexes in the TIP3P model. MMGBSA and MMPBSA values of 8d were -42.46 Kcal/mol and -14.58 Kcal/mol, respectively. Further in-vitro antitubercular screening of compounds 8a, 8d, and 8e against M. tuberculosis H37Ra using XRMA protocol exhibited promising antimycobacterial activity with IC50 values 21.82 µg/mL, 15.55 µg/mL, and 16.56 µg/mL, respectively. Compounds 8a, 8d, and 8e showed antibacterial activity with IC50 values 41.56 µg/mL, 24.72 µg/mL, and 72.45 µg/mL respectively against the Staphylococcus aureus. 8a and 8d showed inhibition with IC50 values 39.6 µg/mL and 27.64 µg/mL, respectively, against Bacillus subtilis. The present study could help in the further development of lead molecules against tuberculosis.
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Affiliation(s)
- Ninad V Puranik
- Bioprospecting Group, Agharkar Research Institute, Pune, Maharashtra, India.,Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Sagar Swami
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Combi-Chem Bio-Resource Center, Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Ashwini V Misar
- Bioprospecting Group, Agharkar Research Institute, Pune, Maharashtra, India
| | - Ritu Mamgain
- Bioprospecting Group, Agharkar Research Institute, Pune, Maharashtra, India
| | | | | | - Sarkar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Combi-Chem Bio-Resource Center, Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Pratibha Srivastava
- Bioprospecting Group, Agharkar Research Institute, Pune, Maharashtra, India.,Savitribai Phule Pune University, Pune, Maharashtra, India
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Butman HS, Kotzé TJ, Dowd CS, Strauss E. Vitamin in the Crosshairs: Targeting Pantothenate and Coenzyme A Biosynthesis for New Antituberculosis Agents. Front Cell Infect Microbiol 2020; 10:605662. [PMID: 33384970 PMCID: PMC7770189 DOI: 10.3389/fcimb.2020.605662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Despite decades of dedicated research, there remains a dire need for new drugs against tuberculosis (TB). Current therapies are generations old and problematic. Resistance to these existing therapies results in an ever-increasing burden of patients with disease that is difficult or impossible to treat. Novel chemical entities with new mechanisms of action are therefore earnestly required. The biosynthesis of coenzyme A (CoA) has long been known to be essential in Mycobacterium tuberculosis (Mtb), the causative agent of TB. The pathway has been genetically validated by seminal studies in vitro and in vivo. In Mtb, the CoA biosynthetic pathway is comprised of nine enzymes: four to synthesize pantothenate (Pan) from l-aspartate and α-ketoisovalerate; five to synthesize CoA from Pan and pantetheine (PantSH). This review gathers literature reports on the structure/mechanism, inhibitors, and vulnerability of each enzyme in the CoA pathway. In addition to traditional inhibition of a single enzyme, the CoA pathway offers an antimetabolite strategy as a promising alternative. In this review, we provide our assessment of what appear to be the best targets, and, thus, which CoA pathway enzymes present the best opportunities for antitubercular drug discovery moving forward.
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Affiliation(s)
- Hailey S. Butman
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Timothy J. Kotzé
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington, DC, United States
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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Duncan D, Auclair K. The coenzyme A biosynthetic pathway: A new tool for prodrug bioactivation. Arch Biochem Biophys 2019; 672:108069. [PMID: 31404525 DOI: 10.1016/j.abb.2019.108069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 11/29/2022]
Abstract
Prodrugs account for more than 5% of pharmaceuticals approved worldwide. Over the past decades several prodrug design strategies have been firmly established; however, only a few functional groups remain amenable to this approach. The aim of this overview is to highlight the use of coenzyme A (CoA) biosynthetic enzymes as a recently explored bioactivation scheme and provide information about its scope of utility. This emerging tool is likely to have a strong impact on future medicinal and biological studies as it offers promiscuity, orthogonal selectivity, and the capability of assembling exceptionally large molecules.
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Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.
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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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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: 80] [Impact Index Per Article: 10.0] [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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Recent advances in targeting coenzyme A biosynthesis and utilization for antimicrobial drug development. Biochem Soc Trans 2015; 42:1080-6. [PMID: 25110006 DOI: 10.1042/bst20140131] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The biosynthesis and utilization of CoA (coenzyme A), the ubiquitous and essential acyl carrier in all organisms, have long been regarded as excellent targets for the development of new antimicrobial drugs. Moreover, bioinformatics and biochemical studies have highlighted significant differences between several of the bacterial enzyme targets and their human counterparts, indicating that selective inhibition of the former should be possible. Over the past decade, a large amount of structural and mechanistic data has been gathered on CoA metabolism and the CoA biosynthetic enzymes, and this has facilitated the discovery and development of several promising candidate antimicrobial agents. These compounds include both target-specific inhibitors, as well as CoA antimetabolite precursors that can reduce CoA levels and interfere with processes that are dependent on this cofactor. In the present mini-review we provide an overview of the most recent of these studies that, taken together, have also provided chemical validation of CoA biosynthesis and utilization as viable targets for antimicrobial drug development.
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Paul A, Mishra A, Surolia A, Vijayan M. Cloning, expression, purification, crystallization and preliminary X-ray studies of argininosuccinate lyase (Rv1659) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1422-4. [PMID: 24316845 PMCID: PMC3855735 DOI: 10.1107/s1744309113031138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 11/12/2013] [Indexed: 11/10/2022]
Abstract
The last enzyme in the arginine-biosynthesis pathway, argininosuccinate lyase, from Mycobacterium tuberculosis has been cloned, expressed, purified and crystallized, and preliminary X-ray studies have been carried out on the crystals. The His-tagged tetrameric enzyme with a subunit molecular weight of 50.9 kDa crystallized with two tetramers in the asymmetric unit of the orthorhombic unit cell, space group P2(1)2(1)2(1). Molecular-replacement calculations and self-rotation calculations confirmed the space group and the tetrameric nature of the molecule.
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Affiliation(s)
- A. Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A. Mishra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A. Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Björkelid C, Bergfors T, Raichurkar AKV, Mukherjee K, Malolanarasimhan K, Bandodkar B, Jones TA. Structural and biochemical characterization of compounds inhibiting Mycobacterium tuberculosis pantothenate kinase. J Biol Chem 2013; 288:18260-70. [PMID: 23661699 DOI: 10.1074/jbc.m113.476473] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis, the bacterial causative agent of tuberculosis, currently affects millions of people. The emergence of drug-resistant strains makes development of new antibiotics targeting the bacterium a global health priority. Pantothenate kinase, a key enzyme in the universal biosynthesis of the essential cofactor CoA, was targeted in this study to find new tuberculosis drugs. The biochemical characterizations of two new classes of compounds that inhibit pantothenate kinase from M. tuberculosis are described, along with crystal structures of their enzyme-inhibitor complexes. These represent the first crystal structures of this enzyme with engineered inhibitors. Both classes of compounds bind in the active site of the enzyme, overlapping with the binding sites of the natural substrate and product, pantothenate and phosphopantothenate, respectively. One class of compounds also interferes with binding of the cofactor ATP. The complexes were crystallized in two crystal forms, one of which is in a new space group for this enzyme and diffracts to the highest resolution reported for any pantothenate kinase structure. These two crystal forms allowed, for the first time, modeling of the cofactor-binding loop in both open and closed conformations. The structures also show a binding mode of ATP different from that previously reported for the M. tuberculosis enzyme but similar to that in the pantothenate kinases of other organisms.
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Affiliation(s)
- Christofer Björkelid
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden.
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