1
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Bhuyan R, Seal A. Exploration and validation of diphosphate-based Plasmodium
LytB inhibitors using computational approaches. J Mol Recognit 2018; 32:e2762. [PMID: 30191613 DOI: 10.1002/jmr.2762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Rajabrata Bhuyan
- BIF Centre, Department of Biochemistry & Biophysics; University of Kalyani; Kalyani West Bengal India
| | - Alpana Seal
- BIF Centre, Department of Biochemistry & Biophysics; University of Kalyani; Kalyani West Bengal India
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2
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Wang T, Yuan XS, Wu MB, Lin JP, Yang LR. The advancement of multidimensional QSAR for novel drug discovery - where are we headed? Expert Opin Drug Discov 2017; 12:769-784. [PMID: 28562095 DOI: 10.1080/17460441.2017.1336157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION The Multidimensional quantitative structure-activity relationship (multidimensional-QSAR) method is one of the most popular computational methods employed to predict interesting biochemical properties of existing or hypothetical molecules. With continuous progress, the QSAR method has made remarkable success in various fields, such as medicinal chemistry, material science and predictive toxicology. Areas covered: In this review, the authors cover the basic elements of multidimensional -QSAR including model construction, validation and application. It includes and emphasizes the very recent developments of multidimensional -QSAR such as: HQSAR, G-QSAR, MIA-QSAR, multi-target QSAR. The advantages and disadvantages of each method are also discussed and typical examples of their application are detailed. Expert opinion: Although there are defects in multidimensional-QSAR modeling, it is still of enormous help to chemists, biologists and other researchers in various fields. In the authors' opinion, the latest more precise and feasible QSAR models should be further developed by integrating new descriptors, algorithms and other relevant computational techniques. Apart from being applied in traditional fields (e.g. lead optimization and predictive risk assessment), QSAR should be used more widely as a routine method in other emerging research fields including the modeling of nanoparticles(NPs), mixture toxicity and peptides.
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Affiliation(s)
- Tao Wang
- a School of biological science , Jining Medical University , Jining , China.,b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Xin-Song Yuan
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Mian-Bin Wu
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Jian-Ping Lin
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
| | - Li-Rong Yang
- b Department of Chemical and Biological Engineering , Zhejiang University , Hangzhou , China
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3
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de Ruyck J, Brysbaert G, Blossey R, Lensink MF. Molecular docking as a popular tool in drug design, an in silico travel. Adv Appl Bioinform Chem 2016; 9:1-11. [PMID: 27390530 PMCID: PMC4930227 DOI: 10.2147/aabc.s105289] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism-or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Second, we present recent advances in anti-infectious agents' synthesis driven by structural insights. At the end, we focus on larger biological complexes made by protein-protein interactions and discuss their relevance in drug design. This review provides information on how these large systems, even in the presence of the solvent, can be investigated with the outlook of drug discovery.
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Affiliation(s)
| | | | - Ralf Blossey
- University Lille, CNRS UMR8576 UGSF, Lille, France
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4
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Nguyen GTT, Erlenkamp G, Jäck O, Küberl A, Bott M, Fiorani F, Gohlke H, Groth G. Chalcone-based Selective Inhibitors of a C4 Plant Key Enzyme as Novel Potential Herbicides. Sci Rep 2016; 6:27333. [PMID: 27263468 PMCID: PMC4893628 DOI: 10.1038/srep27333] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/18/2016] [Indexed: 11/08/2022] Open
Abstract
Weeds are a challenge for global food production due to their rapidly evolving resistance against herbicides. We have identified chalcones as selective inhibitors of phosphoenolpyruvate carboxylase (PEPC), a key enzyme for carbon fixation and biomass increase in the C4 photosynthetic pathway of many of the world's most damaging weeds. In contrast, many of the most important crop plants use C3 photosynthesis. Here, we show that 2',3',4',3,4-Pentahydroxychalcone (IC50 = 600 nM) and 2',3',4'-Trihydroxychalcone (IC50 = 4.2 μM) are potent inhibitors of C4 PEPC but do not affect C3 PEPC at a same concentration range (selectivity factor: 15-45). Binding and modeling studies indicate that the active compounds bind at the same site as malate/aspartate, the natural feedback inhibitors of the C4 pathway. At the whole plant level, both substances showed pronounced growth-inhibitory effects on the C4 weed Amaranthus retroflexus, while there were no measurable effects on oilseed rape, a C3 plant. Growth of selected soil bacteria was not affected by these substances. Our chalcone compounds are the most potent and selective C4 PEPC inhibitors known to date. They offer a novel approach to combat C4 weeds based on a hitherto unexplored mode of allosteric inhibition of a C4 plant key enzyme.
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Affiliation(s)
- G. T. T. Nguyen
- Biochemical Plant Physiology, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
| | - G. Erlenkamp
- Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
| | - O. Jäck
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - A. Küberl
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - M. Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - F. Fiorani
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich and Bioeconomy Science Center (BioSC), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - H. Gohlke
- Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
| | - G. Groth
- Biochemical Plant Physiology, Heinrich Heine University Düsseldorf and Bioeconomy Science Center (BioSC), Universitätsstr.1, 40225 Düsseldorf, Germany
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5
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Fernandes JF, Lell B, Agnandji ST, Obiang RM, Bassat Q, Kremsner PG, Mordmüller B, Grobusch MP. Fosmidomycin as an antimalarial drug: a meta-analysis of clinical trials. Future Microbiol 2015; 10:1375-90. [PMID: 26228767 DOI: 10.2217/fmb.15.60] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
With first indications of resistance against artemisinin compounds, the development of novel alternative antimalarials remains an urgent need. One candidate is fosmidomycin (Fos), a phosphonic acid derivative. This PRISMA guideline-adhering and PROSPERO-registered systematic review and meta-analysis provides an overview of the state-of-the-art of the clinical development of Fos as an antimalarial. Pooling six clinical trials of Fos against uncomplicated malaria in African children yielded an overall day 28 cure rate of 85% (95% CI: 71-98%); a parasite clearance time of 39 h; and a fever clearance time of 30 h. In four adult cohorts, the corresponding values were 70% (95% CI: 40-100%), 49 and 42 h, respectively. Data suggest that besides the partner drug, formulation determines efficacy. We advocate further clinical development of Fos-combinations. PROSPERO registration number: CRD42014013688.
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Affiliation(s)
- Jose Francisco Fernandes
- Institut für Tropenmedizin, University of Tübingen, Wilhelmstraße 27, D-72074 Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, BP 118 Lambaréné, Gabon.,Center of Tropical Medicine & Travel Medicine, Department of Infectious Diseases, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Bertrand Lell
- Institut für Tropenmedizin, University of Tübingen, Wilhelmstraße 27, D-72074 Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, BP 118 Lambaréné, Gabon
| | - Selidji Todagbe Agnandji
- Institut für Tropenmedizin, University of Tübingen, Wilhelmstraße 27, D-72074 Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, BP 118 Lambaréné, Gabon
| | - Regis Maurin Obiang
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, BP 118 Lambaréné, Gabon
| | - Quique Bassat
- Barcelona Center for International Health Research (CRESIB, Hospital Clíníc-Universitat de Barcelona), Barcelona, Spain.,Centro de investigação em saúde de Manhiça (CISM), Maputo, Mozambique
| | - Peter Gottfried Kremsner
- Institut für Tropenmedizin, University of Tübingen, Wilhelmstraße 27, D-72074 Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, BP 118 Lambaréné, Gabon
| | - Benjamin Mordmüller
- Institut für Tropenmedizin, University of Tübingen, Wilhelmstraße 27, D-72074 Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, BP 118 Lambaréné, Gabon
| | - Martin Peter Grobusch
- Institut für Tropenmedizin, University of Tübingen, Wilhelmstraße 27, D-72074 Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital, BP 118 Lambaréné, Gabon.,Center of Tropical Medicine & Travel Medicine, Department of Infectious Diseases, Academic Medical Center, University of Amsterdam, The Netherlands
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6
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Chofor R, Sooriyaarachchi S, Risseeuw MDP, Bergfors T, Pouyez J, Johny C, Haymond A, Everaert A, Dowd CS, Maes L, Coenye T, Alex A, Couch RD, Jones TA, Wouters J, Mowbray SL, Van Calenbergh S. Synthesis and Bioactivity of β-Substituted Fosmidomycin Analogues Targeting 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase. J Med Chem 2015; 58:2988-3001. [DOI: 10.1021/jm5014264] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- René Chofor
- Laboratory
for Medicinal Chemistry (FFW), Universiteit Gent, Ottergemsesteenweg
460, B-9000 Gent, Belgium
| | - Sanjeewani Sooriyaarachchi
- Department
of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Martijn D. P. Risseeuw
- Laboratory
for Medicinal Chemistry (FFW), Universiteit Gent, Ottergemsesteenweg
460, B-9000 Gent, Belgium
| | - Terese Bergfors
- Department
of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Jenny Pouyez
- Department
of Chemistry, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Chinchu Johny
- Department
of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20110, United States
| | - Amanda Haymond
- Department
of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20110, United States
| | - Annelien Everaert
- Laboratory
of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Cynthia S. Dowd
- Department
of Chemistry, George Washington University, Washington, D.C. 20052, United States
| | - Louis Maes
- Laboratory
for Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical,
Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein
1, B-2610 Antwerp, Belgium
| | - Tom Coenye
- Laboratory
of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Alexander Alex
- Evenor Consulting Ltd., The
New Barn, Mill Lane, Eastry, Kent CT13 0JW, United Kingdom
| | - Robin D. Couch
- Department
of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20110, United States
| | - T. Alwyn Jones
- Department
of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Wouters
- Department
of Chemistry, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Sherry L. Mowbray
- Department
of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Serge Van Calenbergh
- Laboratory
for Medicinal Chemistry (FFW), Universiteit Gent, Ottergemsesteenweg
460, B-9000 Gent, Belgium
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7
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Exploring Drug Targets in Isoprenoid Biosynthetic Pathway for Plasmodium falciparum. Biochem Res Int 2014; 2014:657189. [PMID: 24864210 PMCID: PMC4017727 DOI: 10.1155/2014/657189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 02/07/2014] [Accepted: 02/07/2014] [Indexed: 12/28/2022] Open
Abstract
Emergence of rapid drug resistance to existing antimalarial drugs in Plasmodium falciparum has created the need for prediction of novel targets as well as leads derived from original molecules with improved activity against a validated drug target. The malaria parasite has a plant plastid-like apicoplast. To overcome the problem of falciparum malaria, the metabolic pathways in parasite apicoplast have been used as antimalarial drug targets. Among several pathways in apicoplast, isoprenoid biosynthesis is one of the important pathways for parasite as its multiplication in human erythrocytes requires isoprenoids. Therefore targeting this pathway and exploring leads with improved activity is a highly attractive approach. This report has explored progress towards the study of proteins and inhibitors of isoprenoid biosynthesis pathway. For more comprehensive analysis, antimalarial drug-protein interaction has been covered.
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8
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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] [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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9
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Bodill T, Conibear AC, Mutorwa MK, Goble JL, Blatch GL, Lobb KA, Klein R, Kaye PT. Exploring DOXP-reductoisomerase binding limits using phosphonated N-aryl and N-heteroarylcarboxamides as DXR inhibitors. Bioorg Med Chem 2013; 21:4332-41. [DOI: 10.1016/j.bmc.2013.04.076] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
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10
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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.
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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
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11
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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.
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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
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12
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He Y, Niu C, Wen X, Xi Z. Biomacromolecular 3D-QSAR to Decipher Molecular Herbicide Resistance in Acetohydroxyacid Synthases. Mol Inform 2013; 32:139-44. [PMID: 27481275 DOI: 10.1002/minf.201200144] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 01/05/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Yinwu He
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University, NO 94, Weijin Road, Tianjin, 300071, P. R. China fax: (+86) 022-23504782
| | - Congwei Niu
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University, NO 94, Weijin Road, Tianjin, 300071, P. R. China fax: (+86) 022-23504782
| | - Xin Wen
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University, NO 94, Weijin Road, Tianjin, 300071, P. R. China fax: (+86) 022-23504782
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University, NO 94, Weijin Road, Tianjin, 300071, P. R. China fax: (+86) 022-23504782.
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13
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San Jose G, Jackson ER, Uh E, Johny C, Haymond A, Lundberg L, Pinkham C, Kehn-Hall K, Boshoff HI, Couch RD, Dowd CS. Design of Potential Bisubstrate Inhibitors against Mycobacterium tuberculosis (Mtb) 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr)-Evidence of a Novel Binding Mode. MEDCHEMCOMM 2013; 4:1099-1104. [PMID: 23914289 DOI: 10.1039/c3md00085k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In most bacteria, the nonmevalonate pathway is used to synthesize isoprene units. Dxr, the second step in the pathway, catalyzes the NADPH-dependent reductive isomerization of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol-4-phosphate (MEP). Dxr is inhibited by natural products fosmidomycin and FR900098, which bind in the DXP binding site. These compounds, while potent inhibitors of Dxr, lack whole cell activity against Mycobacterium tuberculosis (Mtb) due to their polarity. Our goal was to use the Mtb Dxr-fosmidomycin co-crystal structure to design bisubstrate ligands to bind to both the DXP and NADPH sites. Such compounds would be expected to demonstrate improved whole cell activity due to increased lipophilicity. Two series of compounds were designed and synthesized. Compounds from both series inhibited Mtb Dxr. The most potent compound (8) has an IC50 of 17.8 µM. Analysis shows 8 binds to Mtb Dxr via a novel, non-bisubstrate mechanism. Further, the diethyl ester of 8 inhibits Mtb growth making this class of compounds interesting lead molecules in the search for new antitubercular agents.
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Affiliation(s)
- Géraldine San Jose
- Department of Chemistry, George Washington University, Washington DC 20052, USA. ; Tel: 01 202 994 8405
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14
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Gertzen CGW, Gohlke H. From Hansch-Fujita Analysis to AFMoC: A Road to Structure-Based QSAR. Mol Inform 2012; 31:698-704. [PMID: 27476451 DOI: 10.1002/minf.201200015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 07/10/2012] [Indexed: 11/05/2022]
Abstract
Since the pioneering effort of Hansch and Fujita, quantitative structure-activity relationships (QSAR) have proved valuable in optimizing lead structures. Enriching classical 3D-QSAR analysis, which exploits the three-dimensional structure of ligands, with structural information of the target has helped to improve the interpretability of the derived models and to increase their predictive power. One such method is the Adaption of Fields for Molecular Comparison (AFMoC) approach where protein-specifically adapted knowledge-based pair-potentials are tailored to one particular protein by considering additional structural and energetic information about ligands. Here, we summarize applications of AFMoC, describe recent developments, and provide an outlook on how to improve the method.
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Affiliation(s)
- Christoph G W Gertzen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf fax: +49-211-8113847
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf fax: +49-211-8113847.
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15
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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.
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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
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16
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Ghasemi JB, Tavakoli H. Improvement of the Prediction Power of the CoMFA and CoMSIA Models on Histamine H3 Antagonists by Different Variable Selection Methods. Sci Pharm 2012; 80:547-66. [PMID: 23008805 PMCID: PMC3447613 DOI: 10.3797/scipharm.1204-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 05/24/2012] [Indexed: 11/22/2022] Open
Abstract
The aim of this study is to enhance the predictivity power of CoMFA and CoMSIA models by means of different variable selection algorithms. The genetic algorithm (GA), successive projection algorithm (SPA), stepwise multiple linear regression (SW-MLR), and the enhanced replacement method (ERM) were used and tested as variable selection algorithms. Then, the selected variables were used to generate a simple and predictive model by the multilinear regression algorithm. A set of 74 histamine H3 antagonists were split into 40 compounds as a training set, and 17 compounds as a test set, by the Kennard-Stone algorithm. Before splitting the data, 17 compounds were randomly selected from the pool of the whole data set as an evaluation set without any supervision, pretreatment, or visual inspection. Among applied variable selection algorithms, ERM had noticeable improvement on the statistical parameters. The r2 values of training, test, and evaluation sets for the ERM-MLR model using CoMFA fields were 0.9560, 0.8630, and 0.8460 and using the CoMSIA fields were 0.9800, 0.8521, and 0.9080, respectively. In this study, the principles of organization for economic cooperation and development (OECD) for regulatory acceptability of QSARs are considered.
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Affiliation(s)
- Jahan B Ghasemi
- Department of chemistry, faculty of sciences, K. N. Toosi University of Technology, Tehran, Iran
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17
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Behrendt CT, Kunfermann A, Illarionova V, Matheeussen A, Pein MK, Gräwert T, Kaiser J, Bacher A, Eisenreich W, Illarionov B, Fischer M, Maes L, Groll M, Kurz T. Reverse Fosmidomycin Derivatives against the Antimalarial Drug Target IspC (Dxr). J Med Chem 2011; 54:6796-802. [DOI: 10.1021/jm200694q] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christoph T. Behrendt
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Andrea Kunfermann
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Victoria Illarionova
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - An Matheeussen
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Groenenborgerlaan 171, 2020 Wilrijk, Belgium
| | - Miriam K. Pein
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tobias Gräwert
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Johannes Kaiser
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Adelbert Bacher
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Groenenborgerlaan 171, 2020 Wilrijk, Belgium
| | - Michael Groll
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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18
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Andaloussi M, Henriksson LM, Wiȩckowska A, Lindh M, Björkelid C, Larsson AM, Suresh S, Iyer H, Srinivasa BR, Bergfors T, Unge T, Mowbray SL, Larhed M, Jones TA, Karlén A. Design, Synthesis, and X-ray Crystallographic Studies of α-Aryl Substituted Fosmidomycin Analogues as Inhibitors ofMycobacterium tuberculosis1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase. J Med Chem 2011; 54:4964-76. [DOI: 10.1021/jm2000085] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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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.
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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.
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20
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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.
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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
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21
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Bodill T, Conibear AC, Blatch GL, Lobb KA, Kaye PT. Synthesis and evaluation of phosphonated N-heteroarylcarboxamides as DOXP-reductoisomerase (DXR) inhibitors. Bioorg Med Chem 2011; 19:1321-7. [DOI: 10.1016/j.bmc.2010.11.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 11/22/2010] [Accepted: 11/25/2010] [Indexed: 11/29/2022]
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22
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Fidelak J, Juraszek J, Branduardi D, Bianciotto M, Gervasio FL. Free-energy-based methods for binding profile determination in a congeneric series of CDK2 inhibitors. J Phys Chem B 2010; 114:9516-24. [PMID: 20593892 DOI: 10.1021/jp911689r] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Free-energy pathway methods show great promise in computing the mode of action and the free energy profile associated with the binding of small molecules with proteins, but are generally very computationally demanding. Here we apply a novel approach based on metadynamics and path collective variables. We show that this combination is able to find an optimal reaction coordinate and the free energy profile of binding with explicit solvent and full flexibility, while minimizing human intervention and computational costs. We apply it to predict the binding affinity of a congeneric series of 5 CDK2 inhibitors. The predicted binding free energy profiles are in accordance with experiment.
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Affiliation(s)
- Jérémy Fidelak
- Chemical and Analytical Sciences/In Silico Sciences, Sanofi-Aventis SA, 195 route d'Espagne, Toulouse, France
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23
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Behrendt CT, Kunfermann A, Illarionova V, Matheeussen A, Gräwert T, Groll M, Rohdich F, Bacher A, Eisenreich W, Fischer M, Maes L, Kurz T. Synthesis and Antiplasmodial Activity of Highly Active Reverse Analogues of the Antimalarial Drug Candidate Fosmidomycin. ChemMedChem 2010; 5:1673-6. [DOI: 10.1002/cmdc.201000276] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Roy K, Ojha PK. Advances in quantitative structure–activity relationship models of antimalarials. Expert Opin Drug Discov 2010; 5:751-78. [DOI: 10.1517/17460441.2010.497812] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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25
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Sippl W. 3D-QSAR – Applications, Recent Advances, and Limitations. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9783-6_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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26
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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
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27
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Grimberg BT, Jaworska MM, Hough LB, Zimmerman PA, Phillips JG. Addressing the malaria drug resistance challenge using flow cytometry to discover new antimalarials. Bioorg Med Chem Lett 2009; 19:5452-7. [PMID: 19666223 PMCID: PMC3131497 DOI: 10.1016/j.bmcl.2009.07.095] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 07/16/2009] [Accepted: 07/20/2009] [Indexed: 10/20/2022]
Abstract
A new flow cytometry method that uses an optimized DNA and RNA staining strategy to monitor the growth and development of the Plasmodium falciparum strain W2mef has been used in a pilot study and has identified Bay 43-9006 1, SU 11274 2, and TMC 125 5 as compounds that exhibit potent (<1 microM) overall and ring stage in vitro antimalarial activity.
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Affiliation(s)
- Brian T Grimberg
- Center for Global Health & Diseases, Case Western Reserve University, Cleveland, OH 44106-7286, USA
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28
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Giessmann D, Heidler P, Haemers T, Van Calenbergh S, Reichenberg A, Jomaa H, Weidemeyer C, Sanderbrand S, Wiesner J, Link A. 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. Chem Biodivers 2008; 5:643-56. [PMID: 18421757 DOI: 10.1002/cbdv.200890060] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The conversion of 1-deoxy-D-xylulose-5-phosphate (DOXP) to 2-C-methyl-D-erythritol-4-phosphate (MEP) is effectively blocked by 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) inhibitors such as the natural antibiotic fosmidomycin. Prediction of binding affinities for closely related Dxr ligands as well as estimation of the affinities of structurally more distinct inhibitors within this class of non-hydrolyzable phosphate mimics relies on the synthesis of fosmidomycin derivatives with a broad range of target affinity. Maintaining the phosphonic acid moiety, linear modifications of the lead structure were carried out in an effort to expand the SAR of this physicochemically challenging class of compounds. Synthetic access to a set of phosphonic acids with inhibitory activity (IC(50)) in the range from 1 to >30 microM vs. E. coli Dxr and 0.4 to 20 microM against P. falciparum Dxr is reported.
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Affiliation(s)
- Dirk Giessmann
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Strasse 17, D-17487 Greifswald
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29
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Sotriffer CA, Sanschagrin P, Matter H, Klebe G. SFCscore: Scoring functions for affinity prediction of protein-ligand complexes. Proteins 2008; 73:395-419. [PMID: 18442132 DOI: 10.1002/prot.22058] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christoph A Sotriffer
- Department of Pharmaceutical Chemistry, Philipps-Universität Marburg, D-35032 Marburg, Germany
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30
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Breu B, Silber K, Gohlke H. Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions. J Chem Inf Model 2007; 47:2383-400. [DOI: 10.1021/ci7002472] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin Breu
- Department of Biological Sciences, J.W. Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany, and Department of Pharmacy, Philipps-University, Marburg, Germany
| | - Katrin Silber
- Department of Biological Sciences, J.W. Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany, and Department of Pharmacy, Philipps-University, Marburg, Germany
| | - Holger Gohlke
- Department of Biological Sciences, J.W. Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany, and Department of Pharmacy, Philipps-University, Marburg, Germany
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31
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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.
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Affiliation(s)
- Regina Ortmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
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32
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Ershov YV. 2-C-methylerythritol phosphate pathway of isoprenoid biosynthesis as a target in identifying new antibiotics, herbicides, and immunomodulators: A review. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807020019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Hillebrecht A, Supuran CT, Klebe G. Integrated approach using protein and ligand information to analyze selectivity- and affinity-determining features of carbonic anhydrase isozymes. ChemMedChem 2006; 1:839-53. [PMID: 16902938 DOI: 10.1002/cmdc.200600083] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The application and comparison of selected protein- and ligand-based approaches to elucidate factors important for affinity and selectivity towards the carbonic anhydrase isozymes I, II, and IV are described. Carbonic anhydrases are abundant in pro- and eukaryotes. These enzymes catalyze the reversible hydration of carbon dioxide to bicarbonate and H(+) ions and are thus involved in many important physiological and pathophysiological processes. Due to the fact that the human carbonic anhydrase family consists of 16 closely related isozymes, the design of selective inhibitors is a special challenge for medicinal chemists. In order to extract selectivity-determining features, we applied purely ligand-based 3D QSAR techniques as well as qualitative comparative molecular field analyses of the targets' binding sites using consensus principal component analysis (CPCA). The dataset for the QSAR studies was deliberately compiled from 1,748 inhibitors and comprises about 140 ligands, mainly of the sulfonamide type. Additionally, we employed the novel AFMoC approach, which intrinsically combines protein and ligand information. The simultaneous use of these different techniques gives deeper insight into selectivity and affinity-determining features and provides quantitative models for prediction.
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Affiliation(s)
- Alexander Hillebrecht
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Singh N, Chevé G, Avery MA, McCurdy CR. Comparative protein modeling of 1-deoxy-D-xylulose-5-phosphate reductoisomerase enzyme from Plasmodium falciparum: a potential target for antimalarial drug discovery. J Chem Inf Model 2006; 46:1360-70. [PMID: 16711755 DOI: 10.1021/ci050523w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Pf-DXR) is a potential target for antimalarial chemotherapy. The three-dimensional model (3D) of this enzyme was determined by means of comparative modeling through multiple alignment followed by intensive optimization, minimization, and validation. The resulting model demonstrates a reasonable topology as gauged from the Ramachandran plot and acceptable three-dimensional structure compatibility as assessed by the Profiles-3D score. The modeled monomeric subunit consists of three domains: (1) N-terminal NADPH binding domain, (2) connective or linker domain (with most of the active site residues located in this domain), and (3) a C-terminal domain. This structure proved to be consistent with known DXR crystal structures from other species. The predicted active site compared favorably with those of the templates and appears to have an active site with a highly conserved architecture. Additionally, the model explains several site-directed mutagenesis data. Besides using several protein structure-checking programs to validate the model, a set of known inhibitors of DXR were also docked into the active site of the modeled Pf-DXR. The docked scores correlated reasonably well with experimental pIC50 values with a regression coefficient (R2) equal to 0.84. Results of the current study should prove useful in the early design and development of inhibitors by either de novo drug design or virtual screening of large small-molecule databases leading to development of new antimalarial agents.
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Affiliation(s)
- Nidhi Singh
- Department of Medicinal Chemistry, Laboratory for Applied Drug Design and Synthesis, University of Mississippi, University, Mississippi 38677-1848, USA
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Woo YH, Fernandes RPM, Proteau PJ. Evaluation of fosmidomycin analogs as inhibitors of the Synechocystis sp. PCC6803 1-deoxy-d-xylulose 5-phosphate reductoisomerase. Bioorg Med Chem 2006; 14:2375-85. [PMID: 16310360 DOI: 10.1016/j.bmc.2005.11.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 11/05/2005] [Accepted: 11/08/2005] [Indexed: 11/17/2022]
Abstract
Analogs of the antibiotic fosmidomycin, an inhibitor of the methylerythritol phosphate pathway to isoprenoids, were synthesized and evaluated against the recombinant Synechocystis sp. PCC6803 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR). Fosfoxacin, the phosphate analog of fosmidomycin, and its acetyl congener were found to be more potent inhibitors of DXR than fosmidomycin.
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Affiliation(s)
- Youn-Hi Woo
- Department of Pharmaceutical Sciences, College of Pharmacy, Pharmacy Bldg. Rm. 203, Oregon State University, Corvallis, OR 97331-3507, USA
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Devreux V, Wiesner J, Goeman JL, Van der Eycken J, Jomaa H, Van Calenbergh S. Synthesis and Biological Evaluation of Cyclopropyl Analogues of Fosmidomycin as Potent Plasmodium falciparum Growth Inhibitors. J Med Chem 2006; 49:2656-60. [PMID: 16610809 DOI: 10.1021/jm051177c] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of fosmidomycin analogues featuring restricted conformational mobility has been synthesized and evaluated as inhibitors of 1-deoxy-D-xylulose 5-phosphate (DOXP) reductoisomerase and as growth inhibitors of P. falciparum. The enantiomerically pure trans-cyclopropyl N-acetyl analogue 3b showed comparable inhibitory activity as fosmidomycin toward E. coli DOXP reductoisomerase and proved equally active when tested in vitro for P. falciparum growth inhibition. Conversely, the alpha-phenyl cis-cyclopropyl analogue 4 showed virtually no inhibition of the enzyme.
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Affiliation(s)
- Vincent Devreux
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Gent, Belgium
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Walker JR, Poulter CD. Synthesis and Evaluation of 1-Deoxy-d-xylulose 5-Phosphate Analogues as Chelation-Based Inhibitors of Methylerythritol Phosphate Synthase. J Org Chem 2005; 70:9955-9. [PMID: 16292827 DOI: 10.1021/jo0516786] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structures: see text] A series of 1-deoxy-D-xylulose 5-phosphate (DXP) analogues were synthesized and evaluated as inhibitors of E. coli methylerythritol phosphate (MEP) synthase. In analogues 1-4, the methyl group in DXP was replaced by hydroxyl, hydroxylamino, methoxy, and amino moieties, respectively. In analogues 5 and 6, the acetyl moiety in DXP was replaced by hydroxymethyl and aminomethyl groups. These compounds were designed to coordinate to the active site divalent metal in MEP synthase. The carboxylate (1), methyl ester (3), amide (4), and alcohol (5) analogues were inhibitors with IC50's ranging from 0.25 to 1.0 mM. The hydroxamic acid (2) and amino (6) analogues did not inhibit the enzyme.
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Affiliation(s)
- Joel R Walker
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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