1
|
Over 40 Years of Fosmidomycin Drug Research: A Comprehensive Review and Future Opportunities. Pharmaceuticals (Basel) 2022; 15:ph15121553. [PMID: 36559004 PMCID: PMC9782300 DOI: 10.3390/ph15121553] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
To address the continued rise of multi-drug-resistant microorganisms, the development of novel drugs with new modes of action is urgently required. While humans biosynthesize the essential isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) via the established mevalonate pathway, pathogenic protozoa and certain pathogenic eubacteria use the less well-known methylerythritol phosphate pathway for this purpose. Important pathogens using the MEP pathway are, for example, Plasmodium falciparum, Mycobacterium tuberculosis, Pseudomonas aeruginosa and Escherichia coli. The enzymes of that pathway are targets for antiinfective drugs that are exempt from target-related toxicity. 2C-Methyl-D-erythritol 4-phosphate (MEP), the second enzyme of the non-mevalonate pathway, has been established as the molecular target of fosmidomycin, an antibiotic that has so far failed to be approved as an anti-infective drug. This review describes the development and anti-infective properties of a wide range of fosmidomycin derivatives synthesized over the last four decades. Here we discuss the DXR inhibitor pharmacophore, which comprises a metal-binding group, a phosphate or phosphonate moiety and a connecting linker. Furthermore, non-fosmidomycin-based DXRi, bisubstrate inhibitors and several prodrug concepts are described. A comprehensive structure-activity relationship (SAR) of nearly all inhibitor types is presented and some novel opportunities for further drug development of DXR inhibitors are discussed.
Collapse
|
2
|
Seno Y, Matsushita T, Marhbubul HM, Ali MI, Mahmud MM, Mandai T, Nemoto H. Storable protection-free BGL reagents possessing a bioorthogonal functional group at apex. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
3
|
Non-hydroxamate inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): A critical review and future perspective. Eur J Med Chem 2020; 213:113055. [PMID: 33303239 DOI: 10.1016/j.ejmech.2020.113055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/22/2022]
Abstract
1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the second step of the non-mevalonate (or MEP) pathway that functions in several organisms and plants for the synthesis of isoprenoids. DXR is essential for the survival of multiple pathogenic bacteria/parasites, including those that cause tuberculosis and malaria in humans. DXR function is inhibited by fosmidomycin (1), a natural product, which forms a chelate with the active site divalent metal (Mg2+/Mn2+) through its hydroxamate metal-binding group (MBG). Most of the potent DXR inhibitors are structurally similar to 1 and retain hydroxamate despite the unfavourable pharmacokinetic and toxicity profile of the latter. We provide our perspective on the lack of non-hydroxamate DXR inhibitors. We also highlight the fundamental flaws in the design of MBG in these molecules, primarily responsible for their failure to inhibit DXR. We also suggest that for designing next-generation non-hydroxamate DXR inhibitors, approaches followed for other metalloenzymes targets may be exploited.
Collapse
|
4
|
Megarity CF, Abdel‐Aal Bettley H, Caraher MC, Scott KA, Whitehead RC, Jowitt TA, Gutierrez A, Bryce RA, Nolan KA, Stratford IJ, Timson DJ. Negative Cooperativity in NAD(P)H Quinone Oxidoreductase 1 (NQO1). Chembiochem 2019; 20:2841-2849. [DOI: 10.1002/cbic.201900313] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Clare F. Megarity
- School of Biological SciencesQueen's University BelfastMedical Biology Centre 97 Lisburn Road Belfast BT9 7BL UK
| | - Hoda Abdel‐Aal Bettley
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - M. Clare Caraher
- School of Biological SciencesQueen's University BelfastMedical Biology Centre 97 Lisburn Road Belfast BT9 7BL UK
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Katherine A. Scott
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Roger C. Whitehead
- Department of ChemistryThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Thomas A. Jowitt
- The Faculty of Life ScienceManchester Cancer Research Centre and the University of Manchester Oxford Road Manchester M13 9PT UK
| | - Aldo Gutierrez
- School of Science and TechnologyNottingham Trent University Clifton Campus Nottingham NG11 8NS UK
| | - Richard A. Bryce
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Karen A. Nolan
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - Ian J. Stratford
- Manchester Pharmacy SchoolThe University of Manchester Oxford Road Manchester M13 9PL UK
| | - David J. Timson
- School of Biological SciencesQueen's University BelfastMedical Biology Centre 97 Lisburn Road Belfast BT9 7BL UK
- School of Pharmacy and Biomolecular Sciences, Huxley BuildingUniversity of Brighton Lewes Road Brighton BN2 4GJ UK
| |
Collapse
|
5
|
Janczewski Ł, Gajda A, Braszczyńska J, Gajda T. Microwave-assisted synthesis of dialkyl ω-azidoalkylphosphonates. SYNTHETIC COMMUN 2016. [DOI: 10.1080/00397911.2016.1221114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Łukasz Janczewski
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Anna Gajda
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Julia Braszczyńska
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| | - Tadeusz Gajda
- Institute of Organic Chemistry, Lodz University of Technology, Łódź, Poland
| |
Collapse
|
6
|
Rygielska-Tokarska D, Andrei G, Schols D, Snoeck R, Głowacka IE. Synthesis, antiviral, cytotoxic and cytostatic evaluation of N 1-(phosphonoalkyl)uracil derivatives. MONATSHEFTE FUR CHEMIE 2016; 147:1081-1090. [PMID: 32214481 PMCID: PMC7087680 DOI: 10.1007/s00706-016-1701-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/09/2016] [Indexed: 11/20/2022]
Abstract
Abstract A series of N1-(phosphonoalkyl)uracils was prepared in a two-step reaction sequence from ω-aminoalkylphosphonates and (E)-3-ethoxyacryloyl isocyanate followed by the uracil ring closure. Under standard conditions (NCS; NBS; I2/CAN) all N1-(phosphonoalkyl)uracils were transformed into the respective 5-halogeno derivatives to be later benzoylated at N3. All compounds were evaluated in vitro for activity against a broad variety of DNA and RNA viruses. One compound was slightly active against human cytomegalovirus in HEL cell cultures (EC50 = 45 μM) while another showed weak activity against varicella-zoster virus (TK+ VZV strain OKA and TK− VZV strain 07-1) with EC50 = 43 and 53 µM, respectively. In addition, several compounds exhibited noticeable inhibitory effects on the proliferation of human cervical carcinoma cells (HeLa) at a concentration lower than 200 μM. Graphical abstract ![]()
Collapse
Affiliation(s)
- Dorota Rygielska-Tokarska
- 1Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland
| | - Graciela Andrei
- 2Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Louvain, Belgium
| | - Dominique Schols
- 2Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Louvain, Belgium
| | - Robert Snoeck
- 2Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Louvain, Belgium
| | - Iwona E Głowacka
- 1Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland
| |
Collapse
|
7
|
Mechanism and inhibition of 1-deoxy-d-xylulose-5-phosphate reductoisomerase. Bioorg Chem 2014; 57:171-185. [DOI: 10.1016/j.bioorg.2014.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 12/23/2022]
|
8
|
Dehe D, Wang L, Müller MK, Dörr G, Zhou Z, Klupp-Taylor RN, Sun Y, Ernst S, Hartmann M, Bauer M, Thiel WR. A Rhodium Triphenylphosphine Catalyst for Alkene Hydrogenation Supported on Neat Superparamagnetic Iron Oxide Nanoparticles. ChemCatChem 2014. [DOI: 10.1002/cctc.201402615] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
9
|
Rabasso N, Fadel A. Cyclopropanation of 1,2-dibromoethylphosphonate: a synthesis of β-aminocyclopropylphosphonic acid and derivatives. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.09.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
10
|
Cai G, Deng L, Xue J, Moreno SN, Striepen B, Song Y. Expression, characterization and inhibition of Toxoplasma gondii 1-deoxy-D-xylulose-5-phosphate reductoisomerase. Bioorg Med Chem Lett 2013; 23:2158-61. [PMID: 23428849 PMCID: PMC3602143 DOI: 10.1016/j.bmcl.2013.01.097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 01/14/2013] [Accepted: 01/22/2013] [Indexed: 10/27/2022]
Abstract
The apicomplexan parasite Toxoplasma gondii, the causative agent of toxoplasmosis, is an important human pathogen. 1-Deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) in the non-mevalonate isoprene biosynthesis pathway is essential to the organism and therefore a target for developing anti-toxoplasmosis drugs. In order to find potent inhibitors, we expressed and purified recombinant T. gondii DXR (TgDXR). Biochemical properties of this enzyme were characterized and an enzyme activity/inhibition assay was developed. A collection of 11 compounds with a broad structural diversity were tested against TgDXR and several potent inhibitors were identified with Ki values as low as 48 nM. Analysis of the results as well as those of Escherichia coli and Plasmodium falciparum DXR enzymes revealed a different structure-activity relationship profile for the inhibition of TgDXR.
Collapse
Affiliation(s)
- Guobin Cai
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States
| | - Lisheng Deng
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States
| | - Jian Xue
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States
| | - Silvia N.J. Moreno
- Department of Cellular Biology, University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602
| | - Boris Striepen
- Department of Cellular Biology, University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602
| | - Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, United States
| |
Collapse
|
11
|
Xue J, Diao J, Cai G, Deng L, Zheng B, Yao Y, Song Y. Antimalarial and Structural Studies of Pyridine-containing Inhibitors of 1-Deoxyxylulose-5-phosphate Reductoisomerase. ACS Med Chem Lett 2013; 4:278-282. [PMID: 23795240 PMCID: PMC3685428 DOI: 10.1021/ml300419r] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 12/11/2012] [Indexed: 11/29/2022] Open
Abstract
1-Deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) in the non-mevalonate isoprene biosynthesis pathway is a target for developing antimalarial drugs. Fosmidomycin, a potent DXR inhibitor, showed safety as well as efficacy against P. falciparum malaria in clinical trials. Based on our previous quantitative structure activity relationship (QSAR) and crystallographic studies, several novel pyridine-containing fosmidomycin derivatives were designed, synthesized and found to be highly potent inhibitors of P. falciparum DXR (PfDXR) having Ki values of 1.9 - 13 nM, with the best one being ~11× more active than fosmidomycin. These compounds also potently block the proliferation of multi-drug resistant P. falciparum with EC50 values as low as 170 nM. A 2.3 Å crystal structure of PfDXR in complex with one of the inhibitors is reported, showing the flexible loop of the protein undergoes conformational changes upon ligand binding and a hydrogen bond and favorable hydrophobic interactions between the pyridine group and PfDXR account for the enhanced activity.
Collapse
Affiliation(s)
| | | | | | - Lisheng Deng
- Department of Pharmacology, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Baisong Zheng
- Department of Pharmacology, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Yuan Yao
- Department of Pharmacology, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Yongcheng Song
- Department of Pharmacology, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| |
Collapse
|
12
|
McNulty J, Calzavara J. Tandem oxidative radical fragmentation–rearrangement of 2-amino-1,3-benzylidene acetals: a short entry to densely functionalised fully differentiated oxazolidinones. RSC Adv 2013. [DOI: 10.1039/c3ra40218e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
13
|
Yamamoto I, Absalom N, Carland JE, Doddareddy M, Gavande N, Johnston GAR, Hanrahan JR, Chebib M. Differentiating enantioselective actions of GABOB: a possible role for threonine 244 in the binding site of GABA(C) ρ(1) receptors. ACS Chem Neurosci 2012; 3:665-73. [PMID: 23019493 PMCID: PMC3447397 DOI: 10.1021/cn3000229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/26/2012] [Indexed: 01/20/2023] Open
Abstract
Designing potent and subtype-selective ligands with therapeutic value requires knowledge about how endogenous ligands interact with their binding site. 4-Amino-3-hydroxybutanoic acid (GABOB) is an endogenous ligand found in the central nervous system in mammals. It is a metabolic product of GABA, the major inhibitory neurotransmitter. Homology modeling of the GABA(C) ρ(1) receptor revealed a potential H-bond interaction between the hydroxyl group of GABOB and threonine 244 (T244) located on loop C of the ligand binding site of the ρ(1) subunit. Using site-directed mutagenesis, we examined the effect of mutating T244 on the efficacy and pharmacology of GABOB and various ligands. It was found that mutating T244 to amino acids that lacked a hydroxyl group in their side chains produced GABA insensitive receptors. Only by mutating ρ(1)T244 to serine (ρ(1)T244S) produced a GABA responsive receptor, albeit 39-fold less sensitive to GABA than ρ(1)wild-type. We also observed changes in the activities of the GABA(C) receptor partial agonists, muscimol and imidazole-4-acetic acid (I4AA). At the concentrations we tested, the partial agonists antagonized GABA-induced currents at ρ(1)T244S mutant receptors (Muscimol: ρ(1)wild-type, EC(50) = 1.4 μM; ρ(1)T244S, IC(50) = 32.8 μM. I4AA: ρ(1)wild-type, EC(50) = 8.6 μM; ρ(1)T244S, IC(50) = 21.4 μM). This indicates that T244 is predominantly involved in channel gating. R-(-)-GABOB and S-(+)-GABOB are full agonists at ρ(1)wild-type receptors. In contrast, R-(-)-GABOB was a weak partial agonist at ρ(1)T244S (1 mM activates 26% of the current produced by GABA EC(50) versus ρ(1)wild-type, EC(50) = 19 μM; I(max) 100%), and S-(+)-GABOB was a competitive antagonist at ρ(1)T244S receptors (ρ(1)wild-type, EC(50) = 45 μM versus ρ(1)T244S, IC(50) = 417.4 μM, K(B) = 204 μM). This highlights that the interaction of GABOB with T244 is enantioselective. In contrast, the potencies of a range of antagonists tested, 3-aminopropyl(methyl)phosphinic acid (3-APMPA), 3-aminopropylphosphonic acid (3-APA), S- and R-(3-amino-2-hydroxypropyl)methylphosphinic acid (S-(-)-CGP44532 and R-(+)-CGP44533), were not altered. This suggests that T244 is not critical for antagonist binding. Receptor gating is dynamic, and this study highlights the role of loop C in agonist-evoked receptor activation, coupling agonist binding to channel gating.
Collapse
Affiliation(s)
- Izumi Yamamoto
- Faculty of
Pharmacy, The University of Sydney, Sydney,
NSW 2006, Australia
| | - Nathan Absalom
- Faculty of
Pharmacy, The University of Sydney, Sydney,
NSW 2006, Australia
| | - Jane E. Carland
- Department
of Pharmacology, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Navnath Gavande
- Faculty of
Pharmacy, The University of Sydney, Sydney,
NSW 2006, Australia
| | | | - Jane R. Hanrahan
- Faculty of
Pharmacy, The University of Sydney, Sydney,
NSW 2006, Australia
| | - Mary Chebib
- Faculty of
Pharmacy, The University of Sydney, Sydney,
NSW 2006, Australia
| |
Collapse
|
14
|
Cai G, Deng L, Fryszczyn BG, Brown NG, Liu Z, Jiang H, Palzkill T, Song Y. Thermodynamic Investigation of Inhibitor Binding to 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase. ACS Med Chem Lett 2012; 3:496-500. [PMID: 23050057 PMCID: PMC3462030 DOI: 10.1021/ml300071w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 05/07/2012] [Indexed: 11/29/2022] Open
Abstract
Isothermal titration calorimetry (ITC) was used to investigate the binding of six inhibitors to 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), a target for developing novel anti-infectives. The binding of hydroxamate inhibitors to E. coli DXR is Mg(2+)-dependent, highly endothermic (ΔH: 22.7-24.3 kJ/mol) and entropy-driven, while that of non-hydroxamate compounds is metal ion independent and exothermic (ΔH: -19.4- -13.8 kJ/mol), showing hydration/dehydration of the enzyme metal ion binding pocket account for the drastic ΔH change. However, for DXRs from Plasmodium falciparum and Mycobacterium tuberculosis, the binding of all inhibitors is exothermic (ΔH: -24.9 - -9.2 kJ/mol), suggesting the metal ion binding sites of these two enzymes are considerably less hydrated. The dissociation constants measured by ITC are well correlated with those obtained by enzyme inhibition assays (R(2) = 0.75). Given the rapid rise of antibiotic resistance, this work is of interest since it provides novel structural implications for rational development of potent DXR inhibitors.
Collapse
Affiliation(s)
- Guobin Cai
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Lisheng Deng
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Bartlomiej G. Fryszczyn
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Nicholas G. Brown
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Zhen Liu
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Hong Jiang
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| | - Yongcheng Song
- Department
of Pharmacology and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor
Plaza, Houston, Texas 77030, United States
| |
Collapse
|
15
|
Queffélec C, Petit M, Janvier P, Knight DA, Bujoli B. Surface modification using phosphonic acids and esters. Chem Rev 2012; 112:3777-807. [PMID: 22530923 DOI: 10.1021/cr2004212] [Citation(s) in RCA: 551] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Clémence Queffélec
- LUNAM Université, CNRS, UMR, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation, UFR Sciences et Techniques, Nantes, France
| | | | | | | | | |
Collapse
|
16
|
Deng L, Diao J, Chen P, Pujari V, Yao Y, Cheng G, Crick DC, Venkataram Prasad BV, Song Y. Inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase by lipophilic phosphonates: SAR, QSAR, and crystallographic studies. J Med Chem 2011; 54:4721-34. [PMID: 21561155 PMCID: PMC3601441 DOI: 10.1021/jm200363d] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
1-Deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) is a novel target for developing new antibacterial (including antituberculosis) and antimalaria drugs. Forty-one lipophilic phosphonates, representing a new class of DXR inhibitors, were synthesized, among which 5-phenylpyridin-2-ylmethylphosphonic acid possesses the most activity against E. coli DXR (EcDXR) with a K(i) of 420 nM. Structure-activity relationships (SAR) are discussed, which can be rationalized using our EcDXR:inhibitor structures, and a predictive quantitative SAR (QSAR) model is also developed. Since inhibition studies of DXR from Mycobacterium tuberculosis (MtDXR) have not been performed well, 48 EcDXR inhibitors with a broad chemical diversity were found, however, to generally exhibit considerably reduced activity against MtDXR. The crystal structure of a MtDXR:inhibitor complex reveals the flexible loop containing the residues 198-208 has no strong interactions with the 3,4-dichlorophenyl group of the inhibitor, representing a structural basis for the reduced activity. Overall, these results provide implications in the future design and development of potent DXR inhibitors.
Collapse
Affiliation(s)
- Lisheng Deng
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030
| | - Jiasheng Diao
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030
| | - Pinhong Chen
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030
| | - Venugopal Pujari
- Department of Microbiology, Colorado State University, 1682 Campus Delivery, Ft. Collins, CO 80523
| | - Yuan Yao
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030
| | - Gang Cheng
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030
| | - Dean C. Crick
- Department of Microbiology, Colorado State University, 1682 Campus Delivery, Ft. Collins, CO 80523
| | - B. V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030
| | - Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030,To whom correspondence should be addressed. Address: Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030. Tel: 713-798-7415.
| |
Collapse
|
17
|
de Ruyck J, Wouters J, Poulter CD. Inhibition Studies on Enzymes Involved in Isoprenoid Biosynthesis: Focus on Two Potential Drug Targets: DXR and IDI-2 Enzymes. ACTA ACUST UNITED AC 2011; 7. [PMID: 24339799 DOI: 10.2174/157340811796575317] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic compounds that play important roles in all living organisms. Despite the diversity of their structures, this plethora of natural products arises from only two 5-carbon precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This review will discuss the enzymes in the mevalonate (MVA) and methylerythritol phosphate (MEP) biosynthetic pathways leading to IPP and DMAPP with a particular focus on MEP synthase (DXR) and IPP isomerase (IDI), which are potential targets for the development of antibiotic compounds. DXR is the second enzyme in the MEP pathway and the only one for which inhibitors with antimicrobial activity at pharmaceutically relevant concentrations are known. All of the published DXR inhibitors are fosmidomycin analogues, except for a few bisphosphonates with moderate inhibitory activity. These far, there are no other candidates that target DXR. IDI was first identified and characterised over 40 years ago (IDI-1) and a second convergently evolved isoform (IDI-2) was discovered in 2001. IDI-1 is a metalloprotein found in Eukarya and many species of Bacteria. Its mechanism has been extensively studied. In contrast, IDI-2 requires reduced flavin mononucleotide as a cofactor. The mechanism of action for IDI-2 is less well defined. This review will describe how lead inhibitors are being improved by structure-based drug design and enzymatic assays against DXR to lead to new drug families and how mechanistic probes are being used to address questions about the mechanisms of the isomerases.
Collapse
Affiliation(s)
- Jérôme de Ruyck
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112, USA
| | | | | |
Collapse
|
18
|
Deng L, Endo K, Kato M, Cheng G, Yajima S, Song Y. Structures of 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase/Lipophilic Phosphonate Complexes. ACS Med Chem Lett 2011; 2:165-170. [PMID: 21379374 PMCID: PMC3046873 DOI: 10.1021/ml100243r] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 11/15/2010] [Indexed: 11/28/2022] Open
Abstract
Fosmidomycin, a potent inhibitor of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), has antibacterial and antimalaria activity. Due to its poor pharmacokinetics, more lipophilic DXR inhibitors are needed. However, the hydrophobic binding site(s) in DXR remains elusive. Here, pyridine/quinoline containing phosphonates are identified to be DXR inhibitors with IC(50) values as low as 840 nM. We also report three DXR:inhibitor structures, revealing a novel binding mode. The indole group of Trp211 is found to move ~4.6 Å to open up a mainly hydrophobic pocket, where the pyridine/quinoline rings of the inhibitors are located and have strong π-π stacking/charge-transfer interactions with the indole. Docking studies demonstrate our structures could be used to predict the binding modes of other lipophilic DXR inhibitors. Overall, this work shows an important role of Trp211 in inhibitor recognition and provides a structural basis for future drug design and development.
Collapse
Affiliation(s)
- Lisheng Deng
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Kiwamu Endo
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masahiro Kato
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Gang Cheng
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Shunsuke Yajima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| |
Collapse
|
19
|
Zinglé C, Kuntz L, Tritsch D, Grosdemange-Billiard C, Rohmer M. Isoprenoid biosynthesis via the methylerythritol phosphate pathway: structural variations around phosphonate anchor and spacer of fosmidomycin, a potent inhibitor of deoxyxylulose phosphate reductoisomerase. J Org Chem 2010; 75:3203-7. [PMID: 20429517 DOI: 10.1021/jo9024732] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fosmidomycin and its analogue FR-900098 are potent inhibitors of 1-deoxy-d-xylulose 5-phosphate reducto-isomerase (DXR), the second enzyme of the MEP pathway for the biosynthesis of isoprenoids. This paper describes the synthesis of analogues of the two reverse phosphonohydroxamic acids 3 and 4, in which the length of the carbon spacer is modified, the N-methyl group of 3 is replaced by an ethyl group, and the phosphate group is replaced by potential isosteric moieties, i.e., sulfonate or carboxylate functionalities. The potential of the synthesized analogues to inhibit the E. coli DXR was evaluated.
Collapse
Affiliation(s)
- Catherine Zinglé
- Université de Strasbourg/CNRS, Strasbourg, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67070 Strasbourg, France
| | | | | | | | | |
Collapse
|
20
|
Deng L, Sundriyal S, Rubio V, Shi ZZ, Song Y. Coordination Chemistry Based Approach to Lipophilic Inhibitors of 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase. J Med Chem 2009; 52:6539-42. [DOI: 10.1021/jm9012592] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lisheng Deng
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030
| | - Sandeep Sundriyal
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030
| | - Valentina Rubio
- Department of Radiology, The Methodist Hospital Research Institute, 6565 Fannin Street, Houston, Texas 77030
| | - Zheng-zheng Shi
- Department of Radiology, The Methodist Hospital Research Institute, 6565 Fannin Street, Houston, Texas 77030
| | - Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030
| |
Collapse
|
21
|
Ortmann R, Wiesner J, Silber K, Klebe G, Jomaa H, Schlitzer M. Novel Deoxyxylulosephosphate-Reductoisomerase Inhibitors: Fosmidomycin Derivatives with Spacious Acyl Residues. Arch Pharm (Weinheim) 2007; 340:483-90. [PMID: 17806130 DOI: 10.1002/ardp.200700149] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) represents an essential enzyme of the mevalonate-independent pathway of the isoprenoid biosynthesis. Using fosmidomycin as a specific inhibitor of Dxr, this enzyme was previously validated as target for the treatment of malaria and bacterial infections. The replacement of the formyl residue of fosmidomycin by spacious acyl residues yielded inhibitors active in the micromolar range. As predicted by flexible docking, evidence was obtained for the formation of a hydrogen bond between an appropriately placed carbonyl group in the acyl residue and the main-chain NH of Met214 located in the flexible catalytic loop of the enzyme.
Collapse
Affiliation(s)
- Regina Ortmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | | | | | | | | |
Collapse
|
22
|
Wong U, Cox RJ. The Chemical Mechanism ofD-1-Deoxyxylulose-5-phosphate Reductoisomerase fromEscherichia coli. Angew Chem Int Ed Engl 2007; 46:4926-9. [PMID: 17516600 DOI: 10.1002/anie.200700647] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ursula Wong
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | | |
Collapse
|
23
|
Wong U, Cox R. The Chemical Mechanism ofD-1-Deoxyxylulose-5-phosphate Reductoisomerase fromEscherichia coli. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700647] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|