Design, synthesis, and X-ray crystallographic studies of α-aryl substituted fosmidomycin analogues as inhibitors of Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase.

The natural antibiotic fosmidomycin acts via inhibition of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), an essential enzyme in the non-mevalonate pathway of isoprenoid biosynthesis. Fosmidomycin is active on Mycobacterium tuberculosis DXR (MtDXR), but it lacks antibacterial activity probably because of poor uptake. α-Aryl substituted fosmidomycin analogues have more favorable physicochemical properties and are also more active in inhibiting malaria parasite growth. We have solved crystal structures of MtDXR in complex with 3,4-dichlorophenyl substituted fosmidomycin analogues; these show important differences compared to our previously described forsmidomycin-DXR complex. Our best inhibitor has an IC(50) = 0.15 μM on MtDXR but still lacked activity in a mycobacterial growth assay (MIC > 32 μg/mL). The combined results, however, provide insights into how DXR accommodates the new inhibitors and serve as an excellent starting point for the design of other novel and more potent inhibitors, particularly against pathogens where uptake is less of a problem, such as the malaria parasite.

[1]  J. Wiesner,et al.  Fosmidomycin plus Clindamycin for Treatment of Pediatric Patients Aged 1 to 14 Years with Plasmodium falciparum Malaria , 2006, Antimicrobial Agents and Chemotherapy.

[2]  Shunji Takahashi,et al.  Fosmidomycin, a specific inhibitor of 1-deoxy-d-xylulose 5-phosphate reductoisomerase in the nonmevalonate pathway for terpenoid biosynthesis , 1998 .

[3]  S. Furukawa,et al.  Fosmidomycin Resistance in Adenylate Cyclase Deficient (cya) Mutants of Escherichia coli , 2003, Bioscience, biotechnology, and biochemistry.

[4]  J. Wiesner,et al.  In Vitro and In Vivo Synergy of Fosmidomycin, a Novel Antimalarial Drug, with Clindamycin , 2002, Antimicrobial Agents and Chemotherapy.

[5]  Y. Tu,et al.  A RhCl(PPh 3) 3/BF 3·OEt 2 co-promoted direct C–C cross-coupling of alcohols at β-position with aldehydes , 2009 .

[6]  Shunji Takahashi,et al.  Direct formation of 2-C-methyl-d-erythritol 4-phosphate from 1-deoxy-d-xylulose 5-phosphate by 1-deoxy-d-xylulose 5-phosphate reductoisomerase, a new enzyme in the non-mevalonate pathway to isopentenyl diphosphate , 1998 .

[7]  T. Parish,et al.  Bmc Microbiology , 2022 .

[8]  Gerhard Klebe,et al.  AFMoC enhances predictivity of 3D QSAR: a case study with DOXP-reductoisomerase. , 2005, Journal of medicinal chemistry.

[9]  Torsten Unge,et al.  The 1.9 A resolution structure of Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase, a potential drug target. , 2006, Acta crystallographica. Section D, Biological crystallography.

[10]  J. Wiesner,et al.  Acyloxyalkyl ester prodrugs of FR900098 with improved in vivo anti-malarial activity. , 2003, Bioorganic & medicinal chemistry letters.

[11]  J. Wiesner,et al.  Divergent strategy for the synthesis of α-aryl-substituted fosmidomycin analogues , 2007 .

[12]  Y. Shigi,et al.  Inhibition of bacterial isoprenoid synthesis by fosmidomycin, a phosphonic acid-containing antibiotic. , 1989, The Journal of antimicrobial chemotherapy.

[13]  S. Ehrlich,et al.  Essential Bacillus subtilis genes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[14]  H. Lichtenthaler,et al.  Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. , 1999, Science.

[15]  Hartmut K. Lichtenthaler,et al.  THE 1-DEOXY-D-XYLULOSE-5-PHOSPHATE PATHWAY OF ISOPRENOID BIOSYNTHESIS IN PLANTS. , 1999, Annual review of plant physiology and plant molecular biology.

[16]  W. Doolittle,et al.  The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways , 2000, Molecular microbiology.

[17]  Nimi Marcel,et al.  Evaluation of Killing Kinetics of Anti-Tuberculosis Drugs on Mycobacterium tuberculosis Using a Bacteriophage-Based Assay , 2008, Chemotherapy.

[18]  J. Sacchettini,et al.  Creating Isoprenoid Diversity , 1997, Science.

[19]  M. Rohmer,et al.  Isoprenoid biosynthesis via the methylerythritol phosphate pathway: structural variations around phosphonate anchor and spacer of fosmidomycin, a potent inhibitor of deoxyxylulose phosphate reductoisomerase. , 2010, The Journal of organic chemistry.

[20]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[21]  S. Takahashi,et al.  A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[22]  B. Lell,et al.  Randomized Controlled Trial of Fosmidomycin-Clindamycin versus Sulfadoxine-Pyrimethamine in the Treatment of Plasmodium falciparum Malaria , 2007, Antimicrobial Agents and Chemotherapy.

[23]  Jochen Wiesner,et al.  Fosmidomycin for malaria , 2002, The Lancet.

[24]  W. Delano.  The PyMOL Molecular Graphics System (2002) , 2002 .

[25]  Gerhard Klebe,et al.  Crystal Structure of 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase, a Crucial Enzyme in the Non-mevalonate Pathway of Isoprenoid Biosynthesis* , 2002, The Journal of Biological Chemistry.

[26]  D. Crick,et al.  1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase (IspC) from Mycobacterium tuberculosis: towards Understanding Mycobacterial Resistance to Fosmidomycin , 2005, Journal of bacteriology.

[27]  A. Hallberg,et al.  Microwave-Promoted Palladium-Catalyzed Coupling Reactions. , 1997 .

[28]  J. Wiesner,et al.  Diaryl ester prodrugs of FR900098 with improved in vivo antimalarial activity. , 2001, Bioorganic & medicinal chemistry letters.

[29]  M. Rohmer,et al.  Genetic evidence of branching in the isoprenoid pathway for the production of isopentenyl diphosphate and dimethylallyl diphosphate in Escherichia coli , 2000, FEBS letters.

[30]  J. Schwender,et al.  Inhibition of the Non-Mevalonate 1-Deoxy-ᴅ-xylulose-5-phosphate Pathway of Plant Isoprenoid Biosynthesis by Fosmidomycin , 1998 .

[31]  M Harris,et al.  Molray--a web interface between O and the POV-Ray ray tracer. , 2001, Acta crystallographica. Section D, Biological crystallography.

[32]  J. Wiesner,et al.  Synthesis of α-aryl-substituted and conformationally restricted fosmidomycin analogues as promising antimalarials , 2006 .

[33]  J. Wiesner,et al.  Fosmidomycin-clindamycin for Plasmodium falciparum Infections in African children. , 2004, The Journal of infectious diseases.

[34]  Jens Carlsson,et al.  Structures of Mycobacterium tuberculosis 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase Provide New Insights into Catalysis* , 2007, Journal of Biological Chemistry.

[35]  N. Botting,et al.  Synthesis of [4-13C]-Isoflavonoid Phytoestrogens , 2000 .

[36]  J. Porter,et al.  Biosynthesis of Isoprenoid Compounds , 1983 .

[37]  P. Proteau,et al.  Evaluation of fosmidomycin analogs as inhibitors of the Synechocystis sp. PCC6803 1-deoxy-D-xylulose 5-phosphate reductoisomerase. , 2006, Bioorganic & medicinal chemistry.

[38]  B. Samuelsson,et al.  Two-carbon-elongated HIV-1 protease inhibitors with a tertiary-alcohol-containing transition-state mimic. , 2008, Journal of medicinal chemistry.

[39]  S. van Calenbergh,et al.  Synthesis and evaluation of alpha-halogenated analogues of 3-(acetylhydroxyamino)propylphosphonic acid (FR900098) as antimalarials. , 2010, Journal of medicinal chemistry.

[40]  H. Sahm,et al.  Isoprenoid biosynthesis in bacteria: a novel pathway for the early steps leading to isopentenyl diphosphate. , 1993, The Biochemical journal.

[41]  M. Larhed,et al.  Efficient palladium(II) catalysis under air. Base-free oxidative heck reactions at room temperature or with microwave heating. , 2007, The Journal of organic chemistry.

[42]  R. Read.  Improved Fourier Coefficients for Maps Using Phases from Partial Structures with Errors , 1986 .

[43]  J. Wiesner,et al.  Synthesis of α-Substituted Fosmidomycin Analogues as Highly Potent Plasmodium falciparum Growth Inhibitors. , 2006 .

[44]  Ricardo L. Mancera,et al.  Including Tightly-Bound Water Molecules in de Novo Drug Design. Exemplification through the in Silico Generation of Poly(ADP-ribose)polymerase Ligands , 2005, J. Chem. Inf. Model..

[45]  J. Wiesner,et al.  Towards New Antimalarial Drugs: Synthesis of Non‐Hydrolyzable Phosphate Mimics as Feed for a Predictive QSAR Study on 1‐Deoxy‐D‐xylulose‐5‐phosphate Reductoisomerase Inhibitors , 2008, Chemistry & biodiversity.

[46]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[47]  Jochen Wiesner,et al.  Fosmidomycin, a Novel Chemotherapeutic Agent for Malaria , 2003, Antimicrobial Agents and Chemotherapy.

[48]  M. Rohmer.  The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. , 1999, Natural product reports.

[49]  G. Klebe,et al.  Studies Addressing the Importance of Charge in the Binding of Fosmidomycin‐Like Molecules to Deoxyxylulosephosphate Reductoisomerase , 2008, ChemMedChem.