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Talapati SR, Goyal M, Nataraj V, Pothuganti M, R SM, Gore S, Ramachandra M, Antony T, More SS, Rao NK. Structural and binding studies of cyclin-dependent kinase 2 with NU6140 inhibitor. Chem Biol Drug Des 2021; 98:857-868. [PMID: 34423559 DOI: 10.1111/cbdd.13941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/21/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Abstract
Cyclin-dependent kinase 2 (CDK2) is an established target protein for therapeutic intervention in various diseases, including cancer. Reported inhibitors of CDK2 target the ATP-binding pocket to inhibit the kinase activity. Many small molecule CDK2 inhibitors have been discovered, and their crystal structure with CDK2 or CDK2-cyclin A complex has been published. NU6140 is a CDK2 inhibitor with moderate potency and selectivity. Herein, we report the cocrystal structure determination of NU6140 in complex with CDK2 and confirmation of the binding using various biophysical methods. Our data show that NU6140 binds to CDK2 with a Kd of 800 nM as determined by SPR and stabilizes the protein against thermal denaturation (ΔTm -5°C). The cocrystal structure determined in our study shows that NU6140 binds in the ATP-binding pocket as expected for this class of compounds and interacts with Leu83 and Glu81 with regular hydrogen bonds and with Asp145 via water-mediated H-bond. Based on these data, we propose structural modifications of NU6140 to introduce new interactions with CDK2 that can improve its potency while retaining the selectivity.
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Affiliation(s)
- Sumalatha Rani Talapati
- Aurigene Discovery Technologies Ltd, Bangalore, India.,School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
| | - Megha Goyal
- Aurigene Discovery Technologies Ltd, Bangalore, India
| | | | | | - Sreevidya M R
- Aurigene Discovery Technologies Ltd, Bangalore, India
| | - Suraj Gore
- Aurigene Discovery Technologies Ltd, Bangalore, India
| | | | - Thomas Antony
- Aurigene Discovery Technologies Ltd, Bangalore, India
| | - Sunil S More
- School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
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Talapati SR, Nataraj V, Pothuganti M, Gore S, Ramachandra M, Antony T, More SS, Krishnamurthy NR. Structure of cyclin-dependent kinase 2 (CDK2) in complex with the specific and potent inhibitor CVT-313. Acta Crystallogr F Struct Biol Commun 2020; 76:350-356. [PMID: 32744246 PMCID: PMC7397463 DOI: 10.1107/s2053230x20009243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/07/2020] [Indexed: 01/18/2023] Open
Abstract
CVT-313 is a potent CDK2 inhibitor that was identified by screening a purine-analogue library and is currently in preclinical studies. Since this molecule has the potential to be developed as a CDK2 inhibitor for cancer therapy, the potency of CVT-313 to bind and stabilize CDK2 was evaluated, together with its ability to inhibit aberrant cell proliferation. CVT-313 increased the melting temperature of CDK2 by 7°C in thermal stabilization studies, thus indicating its protein-stabilizing effect. CVT-313 inhibited the growth of human lung carcinoma cell line A549 in a dose-dependent manner, with an IC50 of 1.2 µM, which is in line with the reported biochemical potency of 0.5 µM. To support the further chemical modification of CVT-313 and to improve its biochemical and cellular potency, a crystal structure was elucidated in order to understand the molecular interaction of CVT-313 and CDK2. The crystal structure of CDK2 bound to CVT-313 was determined to a resolution of 1.74 Å and clearly demonstrated that CVT-313 binds in the ATP-binding pocket, interacting with Leu83, Asp86 and Asp145 directly, and the binding was further stabilized by a water-mediated interaction with Asn132. Based on the crystal structure, further modifications of CVT-313 are proposed to provide additional interactions with CDK2 in the active site, which may significantly increase the biochemical and cellular potency of CVT-313.
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Affiliation(s)
- Sumalatha Rani Talapati
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Vijayashankar Nataraj
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Manoj Pothuganti
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Suraj Gore
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Murali Ramachandra
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Thomas Antony
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
| | - Sunil Shivaji More
- School of Basic and Applied Sciences, Dayananada Sagar University, Shavige Malleshawara Hills, Kumaraswamy Layout, Bangalore 560 078, India
| | - Narasimha Rao Krishnamurthy
- Aurigene Discovery Technologies Ltd, 39-40 KIADB Industrial Area, Electronic City Phase II, Hosur Road, Bangalore 560 100, India
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Rao NK, Nataraj V, Ravi M, Panchariya L, Palai K, Talapati SR, Lakshminarasimhan A, Ramachandra M, Antony T. Ternary complex formation of AFN-1252 with Acinetobacter baumannii FabI and NADH: Crystallographic and biochemical studies. Chem Biol Drug Des 2020; 96:704-713. [PMID: 32227402 DOI: 10.1111/cbdd.13686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/08/2020] [Accepted: 01/25/2020] [Indexed: 01/22/2023]
Abstract
Acinetobacter baumannii is an opportunistic Gram-negative bacterial pathogen, associated mostly with hospital-acquired infections. The emergence of drug resistance strains made it necessary to explore new pathways for the development of more effective antibiotics. Enoyl CoA reductase (FabI), a key enzyme in the fatty acid biosynthesis (FAS) pathway, has emerged as a potential target for antibacterial drug development. Earlier reports show that the lead SaFabI inhibitor AFN-1252 can inhibit FabI from other organisms including Escherichia coli and Burkholderia pseudomallei, but with differential potency. In the present work, we show that AFN-1252 is a moderate inhibitor of AbFabI with an IC50 of 216 nM. AFN-1252 stabilized AbFabI with a 4.2°C increase in the melting temperature (Tm ) and, interestingly, the stabilization effect was significantly increased in presence of the cofactor NADH (∆Tm = 17°C), suggesting the formation of a ternary complex AbFabI: AFN-1252: NADH. X-ray crystallography studies of AbFabI co-crystalized with AFN-1252 and NADH confirmed the ternary complex formation. The critical interactions of AFN-1252 with AbFabI and NADH identified from the co-crystal structure may facilitate the design and development of new drugs against A. baumannii infections by targeting the FAS pathway.
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Affiliation(s)
| | | | - Mohan Ravi
- Aurigene Discovery Technologies Ltd, Bangalore, India
| | - Love Panchariya
- International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | | | | | | | | | - Thomas Antony
- Aurigene Discovery Technologies Ltd, Bangalore, India
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Jankute M, Nataraj V, Lee OYC, Wu HHT, Ridell M, Garton NJ, Barer MR, Minnikin DE, Bhatt A, Besra GS. The role of hydrophobicity in tuberculosis evolution and pathogenicity. Sci Rep 2017; 7:1315. [PMID: 28465507 PMCID: PMC5431016 DOI: 10.1038/s41598-017-01501-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/29/2017] [Indexed: 12/24/2022] Open
Abstract
The evolution of tubercle bacilli parallels a route from environmental Mycobacterium kansasii, through intermediate "Mycobacterium canettii", to the modern Mycobacterium tuberculosis complex. Cell envelope outer membrane lipids change systematically from hydrophilic lipooligosaccharides and phenolic glycolipids to hydrophobic phthiocerol dimycocerosates, di- and pentaacyl trehaloses and sulfoglycolipids. Such lipid changes point to a hydrophobic phenotype for M. tuberculosis sensu stricto. Using Congo Red staining and hexadecane-aqueous buffer partitioning, the hydrophobicity of rough morphology M. tuberculosis and Mycobacterium bovis strains was greater than smooth "M. canettii" and M. kansasii. Killed mycobacteria maintained differential hydrophobicity but defatted cells were similar, indicating that outer membrane lipids govern overall hydrophobicity. A rough M. tuberculosis H37Rv ΔpapA1 sulfoglycolipid-deficient mutant had significantly diminished Congo Red uptake though hexadecane-aqueous buffer partitioning was similar to H37Rv. An M. kansasii, ΔMKAN27435 partially lipooligosaccharide-deficient mutant absorbed marginally more Congo Red dye than the parent strain but was comparable in partition experiments. In evolving from ancestral mycobacteria, related to "M. canettii" and M. kansasii, modern M. tuberculosis probably became more hydrophobic by increasing the proportion of less polar lipids in the outer membrane. Importantly, such a change would enhance the capability for aerosol transmission, affecting virulence and pathogenicity.
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Affiliation(s)
- Monika Jankute
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Vijayashankar Nataraj
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Malin Ridell
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Natalie J Garton
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Michael R Barer
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Apoorva Bhatt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
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Cox JAG, Abrahams KA, Alemparte C, Ghidelli-Disse S, Rullas J, Angulo-Barturen I, Singh A, Gurcha SS, Nataraj V, Bethell S, Remuiñán MJ, Encinas L, Jervis PJ, Cammack NC, Bhatt A, Kruse U, Bantscheff M, Fütterer K, Barros D, Ballell L, Drewes G, Besra GS. THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria. Nat Microbiol 2016; 1:15006. [DOI: 10.1038/nmicrobiol.2015.6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/02/2015] [Indexed: 01/18/2023]
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Nataraj V, Bakhshi S, Khan S, Rastogi S, Agarwala S. 3442 Timing of relapse and Surgery post relapse is predictive of survival in relapsed osteosarcoma patients - an observational study. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31915-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nataraj V, Varela C, Javid A, Singh A, Besra GS, Bhatt A. Mycolic acids: deciphering and targeting the Achilles' heel of the tubercle bacillus. Mol Microbiol 2015; 98:7-16. [PMID: 26135034 PMCID: PMC4949712 DOI: 10.1111/mmi.13101] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2015] [Indexed: 12/31/2022]
Abstract
Mycolic acids are unique long chain fatty acids found in the lipid-rich cell walls of mycobacteria including the tubercle bacillus Mycobacterium tuberculosis. Essential for viability and virulence, enzymes involved in the biosynthesis of mycolic acids represent novel targets for drug development. This is particularly relevant to the impact on global health given the rise of multidrug resistant and extensively drug resistant strains of M. tuberculosis. In this review, we discuss recent advances in our understanding of how mycolic acid are synthesised, especially the potential role of specialised fatty acid synthase complexes. Also, we examine the role of a recently reported mycolic acid transporter MmpL3 with reference to several reports of the targeting of this transporter by diverse compounds with anti-M. tuberculosis activity. Additionally, we consider recent findings that place mycolic acid biosynthesis in the context of the cell biology of the bacterium, viz its localisation and co-ordination with the bacterial cytoskeleton, and its role beyond maintaining cell envelope integrity.
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Affiliation(s)
- Vijayashankar Nataraj
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Cristian Varela
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Asma Javid
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Albel Singh
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Gurdyal S Besra
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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Nataraj V, Pang PC, Haslam SM, Veerapen N, Minnikin DE, Dell A, Besra GS, Bhatt A. MKAN27435 is required for the biosynthesis of higher subclasses of lipooligosaccharides in Mycobacterium kansasii. PLoS One 2015; 10:e0122804. [PMID: 25893968 PMCID: PMC4403928 DOI: 10.1371/journal.pone.0122804] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/13/2015] [Indexed: 11/18/2022] Open
Abstract
Lipooligosaccharides are glycolipids found in the cell wall of many mycobacterial species including the opportunistic pathogen Mycobacterium kansasii. The genome of M. kansasii ATCC12478 contains a cluster with genes orthologous to Mycobacterium marinum LOS biosynthesis genes. To initiate a genetic dissection of this cluster and demonstrate its role in LOS biosynthesis in M. kansasii, we chose MKAN27435, a gene encoding a putative glycosyltransferase. Using Specialized Transduction, a phage-based gene knockout tool previously used to generate null mutants in other mycobacteria, we generated a MKAN27435 null mutant. The mutant strain was found to be defective in the biosynthesis of higher LOS subspecies, viz LOS-IV, LOS-V, LOS-VI and LOS-VII. Additionally, a range of low abundance species were detected in the mutant strain and mass spectroscopic analysis indicated that these were shunt products generated from LOS-III by the addition of up to six molecules of a pentose.
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Affiliation(s)
- Vijayashankar Nataraj
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Poh-choo Pang
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Stuart M. Haslam
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Natacha Veerapen
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - David E. Minnikin
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Anne Dell
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Gurdyal S. Besra
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- * E-mail:
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Minnikin DE, Lee OYC, Wu HHT, Besra GS, Bhatt A, Nataraj V, Rothschild BM, Spigelman M, Donoghue HD. Ancient mycobacterial lipids: Key reference biomarkers in charting the evolution of tuberculosis. Tuberculosis (Edinb) 2015; 95 Suppl 1:S133-9. [PMID: 25736170 DOI: 10.1016/j.tube.2015.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mycobacterium tuberculosis has a cell envelope incorporating a peptidoglycan-linked arabinogalactan esterified by long-chain mycolic acids. A range of "free" lipids are associated with the "bound" mycolic acids, producing an effective envelope outer membrane. The distribution of these lipids is discontinuous among mycobacteria and such lipids have proven potential for biomarker use in tracing the evolution of tuberculosis. A plausible evolutionary scenario involves progression from an environmental organism, such as Mycobacterium kansasii, through intermediate "smooth" tubercle bacilli, labelled "Mycobacterium canettii"; cell envelope lipid composition possibly correlates with such a progression. M. kansasii and "M. canettii" have characteristic lipooligosaccharides, associated with motility and biofilms, and glycosyl phenolphthiocerol dimycocerosates ("phenolic glycolipids"). Both these lipid classes are absent in modern M. tuberculosis sensu stricto, though simplified phenolic glycolipids remain in certain current biotypes. Dimycocerosates of the phthiocerol family are restricted to smaller phthiodiolone diesters in M. kansasii. Diacyl and pentaacyl trehaloses are present in "M. canettii" and M. tuberculosis, accompanied in the latter by related sulfated acyl trehaloses. In comparison with environmental mycobacteria, subtle modifications in mycolic acid structures in "M. canettii" and M. tuberculosis are notable. The probability of essential tuberculosis evolution taking place in Pleistocene megafauna, rather than Homo sapiens, is reemphasised.
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Affiliation(s)
- David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Apoorva Bhatt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Vijayashankar Nataraj
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Bruce M Rothschild
- Biodiversity Institute and Departments of Anthropology and Geology, University of Kansas, Lawrence, KS 66045, USA.
| | - Mark Spigelman
- Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, Hebrew University, Jerusalem, Israel.
| | - Helen D Donoghue
- Centres for Clinical Microbiology and the History of Medicine, University College London, London, UK.
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