1
|
Garia A, Grover J, Jain N. Metal‐Free Synthesis of Anthranils by PhIO Mediated Heterocyclization of
ortho
‐Carbonyl Anilines. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alankrita Garia
- Department of Chemistry Indian Institute of Technology New Delhi 110016 India
| | - Jatin Grover
- Department of Chemistry Indian Institute of Technology New Delhi 110016 India
| | - Nidhi Jain
- Department of Chemistry Indian Institute of Technology New Delhi 110016 India
| |
Collapse
|
2
|
Structural and biophysical characterization of the Burkholderia pseudomallei IspF inhibitor L-tryptophan hydroxamate. Bioorg Med Chem Lett 2021; 48:128273. [PMID: 34298132 DOI: 10.1016/j.bmcl.2021.128273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 11/23/2022]
Abstract
The enzyme 2-methylerythritol 2,4-cyclodiphosphate synthase, IspF, is essential for the biosynthesis of isoprenoids in most bacteria, some eukaryotic parasites, and the plastids of plant cells. The development of inhibitors that target IspF may lead to novel classes of anti-infective agents or herbicides. Enantiomers of tryptophan hydroxamate were synthesized and evaluated for binding to Burkholderia pseudomallei (Bp) IspF. The L-isomer possessed the highest potency, binding BpIspF with a KD of 36 µM and inhibited BpIspF activity 55% at 120 µM. The high-resolution crystal structure of the L-tryptophan hydroxamate (3)/BpIspF complex revealed a non-traditional mode of hydroxamate binding where the ligand interacts with the active site zinc ion through the primary amine. In addition, two hydrogen bonds are formed with active site groups, and the indole group is buried within the hydrophobic pocket composed of side chains from the 60 s/70 s loop. Along with the co-crystal structure, STD NMR studies suggest the methylene group and indole ring are potential positions for optimization to enhance binding potency.
Collapse
|
3
|
Mah S, Jang J, Song D, Shin Y, Latif M, Jung Y, Hong S. Discovery of fluorescent 3-heteroarylcoumarin derivatives as novel inhibitors of anaplastic lymphoma kinase. Org Biomol Chem 2019; 17:186-194. [DOI: 10.1039/c8ob02874e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coumarin-based ALK inhibitors were identified as a new template for the development of novel fluorescent ALK inhibitors, which can be tracked using microscopy techniques.
Collapse
Affiliation(s)
- Shinmee Mah
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations
| | - Jaebong Jang
- Center for Catalytic Hydrocarbon Functionalizations
- Institute for Basic Science (IBS)
- Daejeon 34141
- Republic of Korea
| | - Daesun Song
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Republic of Korea
| | - Yongje Shin
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations
| | - Muhammad Latif
- Center for Catalytic Hydrocarbon Functionalizations
- Institute for Basic Science (IBS)
- Daejeon 34141
- Republic of Korea
- Centre for Genetics and Inherited Diseases (CGID)
| | - Yongwon Jung
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Republic of Korea
| | - Sungwoo Hong
- Department of Chemistry
- Korea Advanced Institute of Science and Technology (KAIST)
- Daejeon 34141
- Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations
| |
Collapse
|
4
|
Root K, Barylyuk K, Schwab A, Thelemann J, Illarionov B, Geist JG, Gräwert T, Bacher A, Fischer M, Diederich F, Zenobi R. Aryl bis-sulfonamides bind to the active site of a homotrimeric isoprenoid biosynthesis enzyme IspF and extract the essential divalent metal cation cofactor. Chem Sci 2018; 9:5976-5986. [PMID: 30079212 PMCID: PMC6050538 DOI: 10.1039/c8sc00814k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/17/2018] [Indexed: 12/22/2022] Open
Abstract
Characterizing the mode of action of non-covalent inhibitors in multisubunit enzymes often presents a great challenge. Most of the conventionally used methods are based on ensemble measurements of protein-ligand binding in bulk solution. They often fail to accurately describe multiple binding processes occurring in such systems. Native electrospray ionization mass spectrometry (ESI-MS) of intact protein complexes is a direct, label-free approach that can render the entire distribution of ligand-bound states in multimeric protein complexes. Here we apply native ESI-MS to comprehensively characterize the isoprenoid biosynthesis enzyme IspF from Arabidopsis thaliana, an example of a homomeric protein complex with multiple binding sites for several types of ligands, including a metal cofactor and a synthetic inhibitor. While standard biophysical techniques failed to reveal the mode of action of recently discovered aryl-sulfonamide-based inhibitors of AtIspF, direct native ESI-MS titrations of the protein with the ligands and ligand competition assays allowed us to accurately capture the solution-phase protein-ligand binding equilibria in full complexity and detail. Based on these combined with computational modeling, we propose a mechanism of AtIspF inhibition by aryl bis-sulfonamides that involves both the competition with the substrate for the ligand-binding pocket and the extraction of Zn2+ from the enzyme active site. This inhibition mode is therefore mixed competitive and non-competitive, the latter exerting a key inhibitory effect on the enzyme activity. The results of our study deliver a profound insight into the mechanisms of AtIspF action and inhibition, open new perspectives for designing inhibitors of this important drug target, and demonstrate the applicability and value of the native ESI-MS approach for deep analysis of complex biomolecular binding equilibria.
Collapse
Affiliation(s)
- Katharina Root
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Anatol Schwab
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Jonas Thelemann
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Boris Illarionov
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - Julie G Geist
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Tobias Gräwert
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - Adelbert Bacher
- Department of Chemistry , Technical University of Munich , Garching , Germany
| | - Markus Fischer
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - François Diederich
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| |
Collapse
|
5
|
Watkins SM, Hagen TJ, Perkins TS, Zheng C. ( Z)-4-Chloro- N-{3-[(4-chlorophenyl)sulfonyl]-2,3-dihydrobenzo[ d]thiazol-2-ylidene}benzene-sulfonamide. IUCRDATA 2017; 2:x170865. [PMID: 29445777 PMCID: PMC5808994 DOI: 10.1107/s2414314617008653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/09/2017] [Indexed: 11/10/2022] Open
Abstract
The title compound, C19H12Cl2N2O4S3, is related to a ditosylated 2-iminobenzothiazole with the two methyl groups on the two phenyl rings replaced by chlorine. There is a weak intramolecular π-π contact between the two phenyl rings, with a centroid-to-centroid distance of 4.004 (2) Å. The dihedral angle between the rings is 9.96 (13)°. An intramolecular C-H⋯O hydrogen bond stabilizes the molecular conformation.
Collapse
Affiliation(s)
- Sydney M. Watkins
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Timothy J. Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Timothy S. Perkins
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Chong Zheng
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| |
Collapse
|
6
|
Saggu GS, Pala ZR, Garg S, Saxena V. New Insight into Isoprenoids Biosynthesis Process and Future Prospects for Drug Designing in Plasmodium. Front Microbiol 2016; 7:1421. [PMID: 27679614 PMCID: PMC5020098 DOI: 10.3389/fmicb.2016.01421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/26/2016] [Indexed: 12/20/2022] Open
Abstract
The MEP (Methyl Erythritol Phosphate) isoprenoids biosynthesis pathway is an attractive drug target to combat malaria, due to its uniqueness and indispensability for the parasite. It is functional in the apicoplast of Plasmodium and its products get transported to the cytoplasm, where they participate in glycoprotein synthesis, electron transport chain, tRNA modification and several other biological processes. Several compounds have been tested against the enzymes involved in this pathway and amongst them Fosmidomycin, targeted against IspC (DXP reductoisomerase) enzyme and MMV008138 targeted against IspD enzyme have shown good anti-malarial activity in parasite cultures. Fosmidomycin is now-a-days prescribed clinically, however, less absorption, shorter half-life, and toxicity at higher doses, limits its use as an anti-malarial. The potential of other enzymes of the pathway as candidate drug targets has also been determined. This review details the various drug molecules tested against these targets with special emphasis to Plasmodium. We corroborate that MEP pathway functional within the apicoplast of Plasmodium is a major drug target, especially during erythrocytic stages. However, the major bottlenecks, bioavailability and toxicity of the new molecules needs to be addressed, before considering any new molecule as a potent antimalarial.
Collapse
Affiliation(s)
- Gagandeep S Saggu
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| | - Zarna R Pala
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| | - Shilpi Garg
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| | - Vishal Saxena
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| |
Collapse
|
7
|
Thelemann J, Illarionov B, Barylyuk K, Geist J, Kirchmair J, Schneider P, Anthore L, Root K, Trapp N, Bacher A, Witschel M, Zenobi R, Fischer M, Schneider G, Diederich F. Aryl Bis-Sulfonamide Inhibitors of IspF from Arabidopsis thaliana and Plasmodium falciparum. ChemMedChem 2015; 10:2090-8. [PMID: 26435072 DOI: 10.1002/cmdc.201500382] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Indexed: 01/23/2023]
Abstract
2-Methylerythritol 2,4-cyclodiphosphate synthase (IspF) is an essential enzyme for the biosynthesis of isoprenoid precursors in plants and many human pathogens. The protein is an attractive target for the development of anti-infectives and herbicides. Using a photometric assay, a screen of 40 000 compounds on IspF from Arabidopsis thaliana afforded symmetrical aryl bis-sulfonamides that inhibit IspF from A. thaliana (AtIspF) and Plasmodium falciparum (PfIspF) with IC50 values in the micromolar range. The ortho-bis-sulfonamide structural motif is essential for inhibitory activity. The best derivatives obtained by parallel synthesis showed IC50 values of 1.4 μm against PfIspF and 240 nm against AtIspF. Substantial herbicidal activity was observed at a dose of 2 kg ha(-1) . Molecular modeling studies served as the basis for an in silico search targeted at the discovery of novel, non-symmetrical sulfonamide IspF inhibitors. The designed compounds were found to exhibit inhibitory activities in the double-digit micromolar IC50 range.
Collapse
Affiliation(s)
- Jonas Thelemann
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Konstantin Barylyuk
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Julie Geist
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Johannes Kirchmair
- Zentrum für Bioinformatik, Universität Hamburg, Bundesstr. 43, 20146, Hamburg, Germany
| | - Petra Schneider
- Institut für Pharmazeutische Wissenschaften, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Lucile Anthore
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Katharina Root
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Adelbert Bacher
- Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergerstr. 4, 85748, Garching, Germany
| | | | - Renato Zenobi
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland.
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany.
| | - Gisbert Schneider
- Institut für Pharmazeutische Wissenschaften, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland.
| |
Collapse
|
8
|
Heller K, Ochtrop P, Albers MF, Zauner FB, Itzen A, Hedberg C. Kovalente Proteinmarkierung durch enzymatische Phosphocholinierung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502618] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
9
|
Heller K, Ochtrop P, Albers MF, Zauner FB, Itzen A, Hedberg C. Covalent Protein Labeling by Enzymatic Phosphocholination. Angew Chem Int Ed Engl 2015; 54:10327-30. [PMID: 26147231 DOI: 10.1002/anie.201502618] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Indexed: 11/07/2022]
Abstract
We present a new protein labeling method based on the covalent enzymatic phosphocholination of a specific octapeptide amino acid sequence in intact proteins. The bacterial enzyme AnkX from Legionella pneumophila has been established to transfer functional phosphocholine moieties from synthetically produced CDP-choline derivatives to N-termini, C-termini, and internal loop regions in proteins of interest. Furthermore, the covalent modification can be hydrolytically removed by the action of the Legionella enzyme Lem3. Only a short peptide sequence (eight amino acids) is required for efficient protein labeling and a small linker group (PEG-phosphocholine) is introduced to attach the conjugated cargo.
Collapse
Affiliation(s)
- Katharina Heller
- Center for Integrated Protein Science Munich, Technische Universität München, Department Chemistry, Lichtenbergstrasse 4, 85748 Garching (Germany)
| | - Philipp Ochtrop
- Chemical Biology Center (KBC), Institute of Chemistry, Umeå University, 90187 Umeå (Sweden)
| | - Michael F Albers
- Chemical Biology Center (KBC), Institute of Chemistry, Umeå University, 90187 Umeå (Sweden)
| | - Florian B Zauner
- Center for Integrated Protein Science Munich, Technische Universität München, Department Chemistry, Lichtenbergstrasse 4, 85748 Garching (Germany)
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich, Technische Universität München, Department Chemistry, Lichtenbergstrasse 4, 85748 Garching (Germany).
| | - Christian Hedberg
- Chemical Biology Center (KBC), Institute of Chemistry, Umeå University, 90187 Umeå (Sweden). .,Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund (Germany).
| |
Collapse
|
10
|
Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
11
|
Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
Collapse
Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
| | | | | |
Collapse
|
12
|
Webster WAJ, McFadden GI. From the genome to the phenome: tools to understand the basic biology of Plasmodium falciparum. J Eukaryot Microbiol 2014; 61:655-71. [PMID: 25227912 DOI: 10.1111/jeu.12176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 11/30/2022]
Abstract
Malaria plagues one out of every 30 humans and contributes to almost a million deaths, and the problem could worsen. Our current therapeutic options are compromised by emerging resistance by the parasite to our front line drugs. It is thus imperative to better understand the basic biology of the parasite and develop novel drugs to stem this disease. The most facile approach to analyse a gene's function is to remove it from the genome or inhibit its activity. Although genetic manipulation of the human malaria parasite Plasmodium falciparum is a relatively standard procedure, there is no optimal method to perturb genes essential to the intraerythrocytic development cycle--the part of the life cycle that produces the clinical manifestation of malaria. This is a severe impediment to progress because the phenotype we wish to study is exactly the one that is so elusive. In the absence of any utilitarian way to conditionally delete essential genes, we are prevented from investigating the parasite's most vulnerable points. This review aims to focus on the development of tools identifying essential genes of P. falciparum and our ability to elicit phenotypic mutation.
Collapse
Affiliation(s)
- Wesley A J Webster
- Centre for Regional and Rural Futures, School of Life and Environmental Sciences, Deakin University, Burwood, 3125, Victoria, Australia; Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Melbourne, 3010, Victoria, Australia
| | | |
Collapse
|
13
|
Crystal structures of IspF from Plasmodium falciparum and Burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment. BMC STRUCTURAL BIOLOGY 2014; 14:1. [PMID: 24410837 PMCID: PMC3927217 DOI: 10.1186/1472-6807-14-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/20/2013] [Indexed: 11/17/2022]
Abstract
Background 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF) catalyzes the conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate to 2C-methyl-D-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. IspF is found in the protozoan Plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many Gram-negative bacteria such as Burkholderia cenocepacia. IspF represents a potential target for development of broad-spectrum antimicrobial drugs since it is proven or inferred as essential in these pathogens and absent from mammals. Structural studies of IspF from these two important yet distinct pathogens, and comparisons with orthologues have been carried out to generate reagents, to support and inform a structure-based approach to early stage drug discovery. Results Efficient recombinant protein production and crystallization protocols were developed, and high-resolution crystal structures of IspF from P. falciparum (Emphasis/Emphasis>IspF) and B. cenocepacia (BcIspF) in complex with cytidine nucleotides determined. Comparisons with orthologues, indicate a high degree of order and conservation in parts of the active site where Zn2+ is bound and where recognition of the cytidine moiety of substrate occurs. However, conformational flexibility is noted in that area of the active site responsible for binding the methylerythritol component of substrate. Unexpectedly, one structure of BcIspF revealed two molecules of cytidine monophosphate in the active site, and another identified citrate coordinating to the catalytic Zn2+. In both cases interactions with ligands appear to help order a flexible loop at one side of the active site. Difficulties were encountered when attempting to derive complex structures with other ligands. Conclusions High-resolution crystal structures of IspF from two important human pathogens have been obtained and compared to orthologues. The studies reveal new data on ligand binding, with citrate coordinating to the active site Zn2+ and when present in high concentrations cytidine monophosphate displays two binding modes in the active site. Ligand binding appears to order a part of the active site involved in substrate recognition. The high degree of structural conservation in and around the IspF active site suggests that any structural model might be suitable to support a program of structure-based drug discovery.
Collapse
|
14
|
Witschel M, Röhl F, Niggeweg R, Newton T. In search of new herbicidal inhibitors of the non-mevalonate pathway. PEST MANAGEMENT SCIENCE 2013; 69:559-563. [PMID: 23471898 DOI: 10.1002/ps.3479] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 12/04/2012] [Accepted: 01/03/2013] [Indexed: 06/01/2023]
Abstract
The first five steps of the non-mevalonate pathway have been tested in high-throughput screening (HTS) campaigns, using enzymes of plant origin. Hit rates were in general relatively low, which could be attributed to the high polarity and charged nature of substrates and active sites of these enzymes. Still, for all the enzymes, apart from IspF (2-methylerythritol 2,4-cyclodiphosphate synthase), inhibitors could be identified with activities below 100 μM, and these were followed up to identify structure-activity relationships (SARs). For the enzyme IspD (2C-methyl-D-erythritol 4-phosphate cytidyltransferase), inhibitors with IC50 down to 35 nM were identified that also showed herbicidal activity.
Collapse
Affiliation(s)
- Matthias Witschel
- BASF-SE, GVA/HC-B009, Global Research Herbicides, Ludwigshafen, Germany.
| | | | | | | |
Collapse
|
15
|
Bitok JK, Meyers CF. Synthesis and evaluation of stable substrate analogs as potential modulators of cyclodiphosphate synthase IspF. MEDCHEMCOMM 2013; 4:130-134. [PMID: 23509611 DOI: 10.1039/c2md20175e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Stable IspF substrate analogs were synthesized. In the presence of substrate analogs, the E. coli IspF-MEP complex shows activities distinct from IspF, and bisphosphonates (BP) behave differently than their diphosphate (DP) counterparts. Bisphosphonate analogs activate and/or stabilize IspF, and only the closest structural substrate analog weakly inhibits the IspF-MEP complex.
Collapse
Affiliation(s)
- J Kipchirchir Bitok
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | | |
Collapse
|
16
|
Bitok JK, Meyers CF. 2C-Methyl-d-erythritol 4-phosphate enhances and sustains cyclodiphosphate synthase IspF activity. ACS Chem Biol 2012; 7:1702-10. [PMID: 22839733 DOI: 10.1021/cb300243w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
There is significant progress toward understanding catalysis throughout the essential MEP pathway to isoprenoids in human pathogens; however, little is known about pathway regulation. The present study begins by testing the hypothesis that isoprenoid biosynthesis is regulated via feedback inhibition of the fifth enzyme cyclodiphosphate synthase IspF by downstream isoprenoid diphosphates. Here, we demonstrate recombinant E. coli IspF is not inhibited by downstream metabolites isopentenyl diphosphate (IDP), dimethylallyl diphosphate (DMADP), geranyl diphosphate (GDP), and farnesyl diphosphate (FDP) under standard assay conditions. However, 2C-methyl-d-erythritol 4-phosphate (MEP), the product of reductoisomerase IspC and first committed MEP pathway intermediate, activates and sustains this enhanced IspF activity, and the IspF-MEP complex is inhibited by FDP. We further show that the methylerythritol scaffold itself, which is unique to this pathway, drives the activation and stabilization of active IspF. Our results suggest a novel feed-forward regulatory mechanism for 2C-methyl-d-erythritol 2,4-cyclodiphosphate (MEcDP) production and support an isoprenoid biosynthesis regulatory mechanism via feedback inhibition of the IspF-MEP complex by FDP. The results have important implications for development of inhibitors against the IspF-MEP complex, which may be the physiologically relevant form of the enzyme.
Collapse
Affiliation(s)
- J. Kipchirchir Bitok
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore,
Maryland 21205, United States
| | - Caren Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore,
Maryland 21205, United States
| |
Collapse
|
17
|
Hale I, O'Neill PM, Berry NG, Odom A, Sharma R. The MEP pathway and the development of inhibitors as potential anti-infective agents. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md00298a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
18
|
Gräwert T, Groll M, Rohdich F, Bacher A, Eisenreich W. Biochemistry of the non-mevalonate isoprenoid pathway. Cell Mol Life Sci 2011; 68:3797-814. [PMID: 21744068 PMCID: PMC11114746 DOI: 10.1007/s00018-011-0753-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/26/2011] [Accepted: 06/14/2011] [Indexed: 02/08/2023]
Abstract
The non-mevalonate pathway of isoprenoid (terpenoid) biosynthesis is essential in many eubacteria including the major human pathogen, Mycobacterium tuberculosis, in apicomplexan protozoa including the Plasmodium spp. causing malaria, and in the plastids of plants. The metabolic route is absent in humans and is therefore qualified as a promising target for new anti-infective drugs and herbicides. Biochemical and structural knowledge about all enzymes involved in the pathway established the basis for discovery and development of inhibitors by high-throughput screening of compound libraries and/or structure-based rational design.
Collapse
Affiliation(s)
- Tobias Gräwert
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Michael Groll
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | | | - Adelbert Bacher
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| |
Collapse
|
19
|
Witschel MC, Höffken HW, Seet M, Parra L, Mietzner T, Thater F, Niggeweg R, Röhl F, Illarionov B, Rohdich F, Kaiser J, Fischer M, Bacher A, Diederich F. Inhibitoren des Herbizid-Targets IspD: Bindung in einer allosterischen Tasche. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
20
|
Witschel MC, Höffken HW, Seet M, Parra L, Mietzner T, Thater F, Niggeweg R, Röhl F, Illarionov B, Rohdich F, Kaiser J, Fischer M, Bacher A, Diederich F. Inhibitors of the Herbicidal Target IspD: Allosteric Site Binding. Angew Chem Int Ed Engl 2011; 50:7931-5. [DOI: 10.1002/anie.201102281] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Indexed: 11/07/2022]
|
21
|
Huthmacher C, Hoppe A, Bulik S, Holzhütter HG. Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC SYSTEMS BIOLOGY 2010; 4:120. [PMID: 20807400 PMCID: PMC2941759 DOI: 10.1186/1752-0509-4-120] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 08/31/2010] [Indexed: 12/20/2022]
Abstract
BACKGROUND Despite enormous efforts to combat malaria the disease still afflicts up to half a billion people each year of which more than one million die. Currently no approved vaccine is available and resistances to antimalarials are widely spread. Hence, new antimalarial drugs are urgently needed. RESULTS Here, we present a computational analysis of the metabolism of Plasmodium falciparum, the deadliest malaria pathogen. We assembled a compartmentalized metabolic model and predicted life cycle stage specific metabolism with the help of a flux balance approach that integrates gene expression data. Predicted metabolite exchanges between parasite and host were found to be in good accordance with experimental findings when the parasite's metabolic network was embedded into that of its host (erythrocyte). Knock-out simulations identified 307 indispensable metabolic reactions within the parasite. 35 out of 57 experimentally demonstrated essential enzymes were recovered and another 16 enzymes, if additionally the assumption was made that nutrient uptake from the host cell is limited and all reactions catalyzed by the inhibited enzyme are blocked. This predicted set of putative drug targets, shown to be enriched with true targets by a factor of at least 2.75, was further analyzed with respect to homology to human enzymes, functional similarity to therapeutic targets in other organisms and their predicted potency for prophylaxis and disease treatment. CONCLUSIONS The results suggest that the set of essential enzymes predicted by our flux balance approach represents a promising starting point for further drug development.
Collapse
Affiliation(s)
- Carola Huthmacher
- Institute of Biochemistry, Charité, Monbijoustraße 2, 10117 Berlin, Germany
| | - Andreas Hoppe
- Institute of Biochemistry, Charité, Monbijoustraße 2, 10117 Berlin, Germany
| | - Sascha Bulik
- Institute of Biochemistry, Charité, Monbijoustraße 2, 10117 Berlin, Germany
| | | |
Collapse
|
22
|
Thiazolopyrimidine Inhibitors of 2-Methylerythritol 2,4-Cyclodiphosphate Synthase (IspF) from Mycobacterium tuberculosis and Plasmodium falciparum. ChemMedChem 2010; 5:1092-101. [DOI: 10.1002/cmdc.201000083] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
23
|
Ramsden NL, Buetow L, Dawson A, Kemp LA, Ulaganathan V, Brenk R, Klebe G, Hunter WN. A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy. J Med Chem 2009; 52:2531-42. [PMID: 19320487 PMCID: PMC2669732 DOI: 10.1021/jm801475n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The nonmevalonate route to isoprenoid biosynthesis is essential in Gram-negative bacteria and apicomplexan parasites. The enzymes of this pathway are absent from mammals, contributing to their appeal as chemotherapeutic targets. One enzyme, 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), has been validated as a target by genetic approaches in bacteria. Virtual screening against Escherichia coli IspF (EcIspF) was performed by combining a hierarchical filtering methodology with molecular docking. Docked compounds were inspected and 10 selected for experimental validation. A surface plasmon resonance assay was developed and two weak ligands identified. Crystal structures of EcIspF complexes were determined to support rational ligand development. Cytosine analogues and Zn2+-binding moieties were characterized. One of the putative Zn2+-binding compounds gave the lowest measured KD to date (1.92 ± 0.18 μM). These data provide a framework for the development of IspF inhibitors to generate lead compounds of therapeutic potential against microbial pathogens.
Collapse
Affiliation(s)
- Nicola L Ramsden
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Eoh H, Brennan PJ, Crick DC. The Mycobacterium tuberculosis MEP (2C-methyl-d-erythritol 4-phosphate) pathway as a new drug target. Tuberculosis (Edinb) 2008; 89:1-11. [PMID: 18793870 DOI: 10.1016/j.tube.2008.07.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 07/15/2008] [Accepted: 07/23/2008] [Indexed: 10/21/2022]
Abstract
Tuberculosis (TB) is still a major public health problem, compounded by the human immunodeficiency virus (HIV)-TB co-infection and recent emergence of multidrug-resistant (MDR) and extensively drug resistant (XDR)-TB. Novel anti-TB drugs are urgently required. In this context, the 2C-methyl-d-erythritol 4-phosphate (MEP) pathway of Mycobacterium tuberculosis has drawn attention; it is one of several pathways vital for M. tuberculosis viability and the human host lacks homologous enzymes. Thus, the MEP pathway promises bacterium-specific drug targets and the potential for identification of lead compounds unencumbered by target-based toxicity. Indeed, fosmidomycin is now known to inhibit the second step in the MEP pathway. This review describes the cardinal features of the main enzymes of the MEP pathway in M. tuberculosis and how these can be manipulated in high throughput screening campaigns in the search for new anti-infectives against TB.
Collapse
Affiliation(s)
- Hyungjin Eoh
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
| | | | | |
Collapse
|
25
|
Hirsch AKH, Lauw S, Gersbach P, Schweizer WB, Rohdich F, Eisenreich W, Bacher A, Diederich F. Nonphosphate inhibitors of IspE protein, a kinase in the non-mevalonate pathway for isoprenoid biosynthesis and a potential target for antimalarial therapy. ChemMedChem 2008; 2:806-10. [PMID: 17361977 DOI: 10.1002/cmdc.200700014] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Anna K H Hirsch
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Zürcher M, Diederich F. Structure-Based Drug Design: Exploring the Proper Filling of Apolar Pockets at Enzyme Active Sites. J Org Chem 2008; 73:4345-61. [DOI: 10.1021/jo800527n] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina Zürcher
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
| | - François Diederich
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
| |
Collapse
|
27
|
Synthesis and Characterization of Cytidine Derivatives that Inhibit the Kinase IspE of the Non-Mevalonate Pathway for Isoprenoid Biosynthesis. ChemMedChem 2008; 3:91-101. [DOI: 10.1002/cmdc.200700208] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
28
|
Hirsch AKH, Alphey MS, Lauw S, Seet M, Barandun L, Eisenreich W, Rohdich F, Hunter WN, Bacher A, Diederich F. Inhibitors of the kinase IspE: structure–activity relationships and co-crystal structure analysis. Org Biomol Chem 2008; 6:2719-30. [DOI: 10.1039/b804375b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
29
|
Abstract
The inhibition of essential enzymes in microbial pathogens offers a route to treatment of infectious diseases. However, although the biology of the organism dictates a need for a particular enzyme activity, this does not necessarily mean that the enzyme is a good drug target. The chemistry of the active site (size, shape and properties) determines the likelihood of finding a molecule with the right properties to influence drug discovery. Discriminating between good and less-good targets is important. Studies on enzymes involved in the regulation of oxidative stress and pterin/folate metabolism of trypanosomatid parasites and isoprenoid precursor biosynthesis in bacteria and apicomplexan parasites illustrates a range of active sites representing those that are challenging with respect to the discovery of potent inhibitors, to others that provide more promising opportunities in drug discovery.
Collapse
|
30
|
Buetow L, Brown AC, Parish T, Hunter WN. The structure of Mycobacteria 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery. BMC STRUCTURAL BIOLOGY 2007; 7:68. [PMID: 17956607 PMCID: PMC2151065 DOI: 10.1186/1472-6807-7-68] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 10/23/2007] [Indexed: 11/17/2022]
Abstract
Background The prevalence of tuberculosis, the prolonged and expensive treatment that this disease requires and an increase in drug resistance indicate an urgent need for new treatments. The 1-deoxy-D-xylulose 5-phosphate pathway of isoprenoid precursor biosynthesis is an attractive chemotherapeutic target because it occurs in many pathogens, including Mycobacterium tuberculosis, and is absent from humans. To underpin future drug development it is important to assess which enzymes in this biosynthetic pathway are essential in the actual pathogens and to characterize them. Results The fifth enzyme of this pathway, encoded by ispF, is 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF). A two-step recombination strategy was used to construct ispF deletion mutants in M. tuberculosis but only wild-type double crossover strains were isolated. The chromosomal copy could be deleted when a second functional copy was provided on an integrating plasmid, demonstrating that ispF is an essential gene under the conditions tested thereby confirming its potential as a drug target. We attempted structure determination of the M. tuberculosis enzyme (MtIspF), but failed to obtain crystals. We instead analyzed the orthologue M. smegmatis IspF (MsIspF), sharing 73% amino acid sequence identity, at 2.2 Å resolution. The high level of sequence conservation is particularly pronounced in and around the active site. MsIspF is a trimer with a hydrophobic cavity at its center that contains density consistent with diphosphate-containing isoprenoids. The active site, created by two subunits, comprises a rigid CDP-Zn2+ binding pocket with a flexible loop to position the 2C-methyl-D-erythritol moiety of substrate. Sequence-structure comparisons indicate that the active site and interactions with ligands are highly conserved. Conclusion Our study genetically validates MtIspF as a therapeutic target and provides a model system for structure-based ligand design.
Collapse
Affiliation(s)
- Lori Buetow
- Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | | | | | | |
Collapse
|
31
|
Schlitzer M. Malaria Chemotherapeutics Part I: History of Antimalarial Drug Development, Currently Used Therapeutics, and Drugs in Clinical Development. ChemMedChem 2007; 2:944-86. [PMID: 17530725 DOI: 10.1002/cmdc.200600240] [Citation(s) in RCA: 179] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Since ancient times, humankind has had to struggle against the persistent onslaught of pathogenic microorganisms. Nowadays, malaria is still the most important infectious disease worldwide. Considerable success in gaining control over malaria was achieved in the 1950s and 60s through landscaping measures, vector control with the insecticide DDT, and the widespread administration of chloroquine, the most important antimalarial agent ever. In the late 1960s, the final victory over malaria was believed to be within reach. However, the parasites could not be eradicated because they developed resistance against the most widely used and affordable drugs of that time. Today, cases of malaria infections are on the rise and have reached record numbers. This review gives a short description of the malaria disease, briefly addresses the history of antimalarial drug development, and focuses on drugs currently available for malaria therapy. The present knowledge regarding their mode of action and the mechanisms of resistance are explained, as are the attempts made by numerous research groups to overcome the resistance problem within classes of existing drugs and in some novel classes. Finally, this review covers all classes of antimalarials for which at least one drug candidate is in clinical development. Antimalarial agents that are solely in early development stages will be addressed in a separate review.
Collapse
Affiliation(s)
- Martin Schlitzer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
| |
Collapse
|
32
|
Structure-Based Design and Synthesis of the First Weak Non-Phosphate Inhibitors for IspF, an Enzyme in the Non-Mevalonate Pathway of Isoprenoid Biosynthesis. Helv Chim Acta 2007. [DOI: 10.1002/hlca.200790105] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
33
|
Hirsch A, Fischer F, Diederich F. Molekulare Erkennung von Phosphaten in der Strukturbiologie. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603420] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
34
|
Abstract
Drug-discovery research in the past decade has seen an increased selection of targets with phosphate recognition sites, such as protein kinases and phosphatases, in the past decade. This review attempts, with the help of database-mining tools, to give an overview of the most important principles in molecular recognition of phosphate groups by enzymes. A total of 3003 X-ray crystal structures from the RCSB Protein Data Bank with bound organophosphates has been analyzed individually, in particular for H-bonding interactions between proteins and ligands. The various known binding motifs for phosphate binding are reviewed, and similarities to phosphate complexation by synthetic receptors are highlighted. An analysis of the propensities of amino acids in various classes of phosphate-binding enzymes showed characteristic distributions of amino acids used for phosphate binding. This review demonstrates that structure-based lead development and optimization should carefully address the phosphate-binding-site environment and also proposes new alternatives for filling such sites.
Collapse
Affiliation(s)
- Anna K H Hirsch
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
| | | | | |
Collapse
|
35
|
Bioorganic Chemistry: K. Sandhoff, H. Kessler, F. Diederich, and K. C. Nicolaou awarded. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/anie.200600226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|