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Jansson AM, Więckowska A, Björkelid C, Yahiaoui S, Sooriyaarachchi S, Lindh M, Bergfors T, Dharavath S, Desroses M, Suresh S, Andaloussi M, Nikhil R, Sreevalli S, Srinivasa BR, Larhed M, Jones TA, Karlén A, Mowbray SL. DXR Inhibition by Potent Mono- and Disubstituted Fosmidomycin Analogues. J Med Chem 2013; 56:6190-9. [DOI: 10.1021/jm4006498] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna M. Jansson
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Anna Więckowska
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Christofer Björkelid
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Samir Yahiaoui
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Sanjeewani Sooriyaarachchi
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Martin Lindh
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Terese Bergfors
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Shyamraj Dharavath
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Matthieu Desroses
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Surisetti Suresh
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Mounir Andaloussi
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Rautela Nikhil
- AstraZeneca India Private Limited, Bellary Road, Hebbal, Bangalore 560024,
India
| | - Sharma Sreevalli
- AstraZeneca India Private Limited, Bellary Road, Hebbal, Bangalore 560024,
India
| | | | - Mats Larhed
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - T. Alwyn Jones
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Sherry L. Mowbray
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Björkelid C, Bergfors T, Unge T, Mowbray SL, Jones TA. Structural studies on Mycobacterium tuberculosis DXR in complex with the antibiotic FR-900098. Acta Crystallogr D Biol Crystallogr 2012; 68:134-43. [PMID: 22281742 DOI: 10.1107/s0907444911052231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 12/03/2011] [Indexed: 11/10/2022]
Abstract
A number of pathogens, including the causative agents of tuberculosis and malaria, synthesize the essential isoprenoid precursor isopentenyl diphosphate via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway rather than the classical mevalonate pathway that is found in humans. As part of a structure-based drug-discovery program against tuberculosis, DXR, the enzyme that carries out the second step in the MEP pathway, has been investigated. This enzyme is the target for the antibiotic fosmidomycin and its active acetyl derivative FR-900098. The structure of DXR from Mycobacterium tuberculosis in complex with FR-900098, manganese and the NADPH cofactor has been solved and refined. This is a new crystal form that diffracts to a higher resolution than any other DXR complex reported to date. Comparisons with other ternary complexes show that the conformation is that of the enzyme in an active state: the active-site flap is well defined and the cofactor-binding domain has a conformation that brings the NADPH into the active site in a manner suitable for catalysis. The substrate-binding site is highly conserved in a number of pathogens that use this pathway, so any new inhibitor that is designed for the M. tuberculosis enzyme is likely to exhibit broad-spectrum activity.
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Affiliation(s)
- Christofer Björkelid
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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Nordqvist A, Björkelid C, Andaloussi M, Jansson AM, Mowbray SL, Karlén A, Larhed M. Synthesis of functionalized cinnamaldehyde derivatives by an oxidative Heck reaction and their use as starting materials for preparation of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase inhibitors. J Org Chem 2011; 76:8986-98. [PMID: 21936546 PMCID: PMC3203620 DOI: 10.1021/jo201715x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [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] [Indexed: 11/05/2022]
Abstract
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Cinnamaldehyde derivatives were synthesized in good to excellent yields in one step by a mild and selective, base-free palladium(II)-catalyzed oxidative Heck reaction starting from acrolein and various arylboronic acids. Prepared α,β-unsaturated aldehydes were used for synthesis of novel α-aryl substituted fosmidomycin analogues, which were evaluated for their inhibition of Mycobacterium tuberculosis 1-deoxy-d-xylulose 5-phosphate reductoisomerase. IC50 values between 0.8 and 27.3 μM were measured. The best compound showed activity comparable to that of the most potent previously reported α-aryl substituted fosmidomycin-class inhibitor.
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Affiliation(s)
- Anneli Nordqvist
- Division of Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751 23 Uppsala, Sweden
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Andaloussi M, Lindh M, Björkelid C, Suresh S, Wieckowska A, Iyer H, Karlén A, Larhed M. Substitution of the phosphonic acid and hydroxamic acid functionalities of the DXR inhibitor FR900098: An attempt to improve the activity against Mycobacterium tuberculosis. Bioorg Med Chem Lett 2011; 21:5403-7. [DOI: 10.1016/j.bmcl.2011.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Revised: 06/30/2011] [Accepted: 07/03/2011] [Indexed: 10/17/2022]
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Björkelid C, Bergfors T, Henriksson LM, Stern AL, Unge T, Mowbray SL, Jones TA. Structural and functional studies of mycobacterial IspD enzymes. Acta Crystallogr D Biol Crystallogr 2011; 67:403-14. [PMID: 21543842 DOI: 10.1107/s0907444911006160] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/18/2011] [Indexed: 11/10/2022]
Abstract
A number of pathogens, including the causative agents of tuberculosis and malaria, synthesize isopentenyl diphosphate via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway rather than the classical mevalonate pathway found in humans. As part of a structure-based drug-discovery program against tuberculosis, IspD, the enzyme that carries out the third step in the MEP pathway, was targeted. Constructs of both the Mycobacterium smegmatis and the Mycobacterium tuberculosis enzymes that were suitable for structural and inhibitor-screening studies were engineered. Two crystal structures of the M. smegmatis enzyme were produced, one in complex with CTP and the other in complex with CMP. In addition, the M. tuberculosis enzyme was crystallized in complex with CTP. Here, the structure determination and crystallographic refinement of these crystal forms and the enzymatic characterization of the M. tuberculosis enzyme construct are reported. A comparison with known IspD structures allowed the definition of the structurally conserved core of the enzyme. It indicates potential flexibility in the enzyme and in particular in areas close to the active site. These well behaved constructs provide tools for future target-based screening of potential inhibitors. The conserved nature of the extended active site suggests that any new inhibitor will potentially exhibit broad-spectrum activity.
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Affiliation(s)
- Christofer Björkelid
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-75124 Uppsala, Sweden
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Henriksson LM, Björkelid C, Mowbray SL, Unge T. The 1.9 Å resolution structure ofMycobacterium tuberculosis1-deoxy-D-xylulose 5-phosphate reductoisomerase, a potential drug target. Acta Crystallogr D Biol Crystallogr 2006; 62:807-13. [PMID: 16790937 DOI: 10.1107/s0907444906019196] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Accepted: 05/23/2006] [Indexed: 11/10/2022]
Abstract
1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzes the NADPH-dependent rearrangement and reduction of 1-deoxy-D-xylulose 5-phosphate to form 2-C-methyl-D-erythritol 4-phosphate, as the second step of the deoxyxylulose 5-phosphate/methylerythritol 4-phosphate pathway found in many bacteria and plants. The end product, isopentenyl diphosphate, is the precursor of various isoprenoids vital to all living organisms. The pathway is not found in humans; the mevalonate pathway is instead used for the formation of isopentenyl diphosphate. This difference, combined with its essentiality, makes the reductoisomerase an excellent drug target in a number of pathogenic organisms. The structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Mycobacterium tuberculosis (Rv2870c) was solved by molecular replacement and refined to a resolution of 1.9 A. The enzyme exhibited an estimated kcat of 5.3 s-1 and Km and kcat/Km values of 7.2 microM and 7.4x10(5) M-1 s-1 for NADPH and 340 microM and 1.6x10(4) M-1 s-1 for 1-deoxy-D-xylulose 5-phosphate. In the structure, a sulfate is bound at the expected site of the phosphate moiety of the sugar substrate. The M. tuberculosis enzyme displays a similar fold to the previously published structures from Escherichia coli and Zymomonas mobilis. Comparisons offer suggestions for the design of specific drugs. Furthermore, the new structure represents an intermediate conformation between the open apo form and the closed holo form observed previously, giving insights into the conformational changes associated with catalysis.
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Affiliation(s)
- Lena M Henriksson
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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Suarez Covarrubias A, Larsson AM, Högbom M, Lindberg J, Bergfors T, Björkelid C, Mowbray SL, Unge T, Jones TA. Structure and Function of Carbonic Anhydrases from Mycobacterium tuberculosis. J Biol Chem 2005; 280:18782-9. [PMID: 15753099 DOI: 10.1074/jbc.m414348200] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to form bicarbonate. This activity is universally required for fatty acid biosynthesis as well as for the production of a number of small molecules, pH homeostasis, and other functions. At least three different carbonic anhydrase families are known to exist, of which the alpha-class found in humans has been studied in most detail. In the present work, we describe the structures of two of the three beta-class carbonic anhydrases that have been identified in Mycobacterium tuberculosis, i.e. Rv1284 and Rv3588c. Both structures were solved by molecular replacement and then refined to resolutions of 2.0 and 1.75 A, respectively. The active site of Rv1284 is small and almost completely shielded from solvent, whereas that of Rv3588c is larger and quite open to solution. Differences in coordination of the active site metal are also observed. In Rv3588c, an aspartic acid side chain displaces a water molecule and coordinates directly to the zinc ion, thereby closing the zinc coordination sphere and breaking the salt link to a nearby arginine that is a feature of Rv1284. The two carbonic anhydrases thus exhibit both of the metal coordination geometries that have previously been observed for structures in this family. Activity studies demonstrate that Rv3588c is a completely functional carbonic anhydrase. The apparent lack of activity of Rv1284 in the present assay system is likely exacerbated by the observed depletion of zinc in the preparation.
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