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Mansouri N, Benslama O, Arhab R. Homology modeling, docking and molecular dynamics studies of some secondary metabolites of actinomycetes as biocontrol agents against the 3HNR enzyme of the phytopathogenic fungus Alternaria alternata. J Biomol Struct Dyn 2023; 41:871-883. [PMID: 34895071 DOI: 10.1080/07391102.2021.2014970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Early blight of tomatoes is a common disease caused by the phytopathogenic fungi Alternaria, in particular the species A. alternata. This disease causes significant losses in the tomato harvest. The enzyme 1,3,8-trihydroxynaphthalene reductase (3HNR) is a key enzyme involved in the production of melanin, that plays a crucial role in the process of fungi invasion. This enzyme is the target of some chemical fungicides, but the problem of resistance against these molecules requires the search for new molecules that are both effective and environment-friendly. Actinomycetes represent an important source of secondary metabolites with antimicrobial activity. Thus, in this study 110 secondary metabolites of actinomycetes were subjected to an in silico screening of their antifungal activity as possible inhibitors of the 3HNR of A. alternata. For this reason, the 3D structure of this enzyme was modeled. Then, a molecular docking study of the secondary actinomycetal metabolites was carried out within the catalytic site of the enzyme. Indole-3-carboxylic acid, Streptokordin, 3-Phenylpropionic acid, Phenylacetate, and 8-Hydroxyquinoline have shown the most promising results with binding energies of -6.1 kcal/mol, -6.1 kcal/mol, -5.4 kcal/mol, -5.3 kcal/mol, and -5.0 kcal/mol, respectively. These metabolites have also shown satisfactory results for drug-likeness and ADMET analysis. The interaction stability of the Streptokordin, Indole-3-carboxylic acid, Phenylacetate, and 8-Hydroxyquinoline within the catalytic site of 3HNR was confirmed by the results of the MD simulation and MM-PBSA analyzes. With their favorable interactive and pharmacokinetic characteristics, these metabolites may be potential antifungal molecules against A. alternata, and good candidates for further studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nedjwa Mansouri
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, Department of Natural and Life Sciences, Larbi Ben M'Hidi University, Oum El Bouaghi, Algeria
| | - Ouided Benslama
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, Department of Natural and Life Sciences, Larbi Ben M'Hidi University, Oum El Bouaghi, Algeria
| | - Rabah Arhab
- Laboratory of Natural Substances, Biomolecules and Biotechnological Applications, Department of Natural and Life Sciences, Larbi Ben M'Hidi University, Oum El Bouaghi, Algeria
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Abbod M, Safaie N, Gholivand K, Mehrabadi M, Bonsaii M. Mode of action of 3-butylidene phthalide as a competent natural pesticide. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 164:228-236. [PMID: 32284131 DOI: 10.1016/j.pestbp.2020.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/29/2020] [Accepted: 02/01/2020] [Indexed: 06/11/2023]
Abstract
In this study, the biological activities and mode of action of 3-butylidene phthalide (3-BPH) were studied. 3-BPH had a superior efficiency against microsclerotia of Macrophomina phaseolina compared to the commercial fungicide tricyclazole. The microsclerotia formation and pigmentation were inhibited at 100 μg/mL. Moreover, the fungicide exhibited in silico affinity toward trihydroxy naphthalene reductase (3HNR). Both 3-BPH and tricyclazole showed congruence in the orientation and interaction within the 3HNR active site. 3-BPH displayed a strong interaction with SER-164, TYR-178, and TYR-223, with estimated binding energy and inhibition constant of -6.78 kcal mol-1, and Ki = 12.6 μM, respectively. Furthermore, it showed in vitro and in silico inhibitory activity against Drosophila melanogaster acetylcholinesterase in a concentration-dependent manner with IC50 = 730 μg/mL. It also impaired Galleria mellonella phenol oxidase enzyme, which corresponds with the insect's immune system. Phytotoxicity of 3-BPH was evident against Lemna minor at 1000 μg /mL; nevertheless, it was nontoxic at the concentrations inhibiting M. phaseolina microsclerotia and dark pigments suggest that it may be safe for use on other plants at low doses. Further assays are wanted to develop 3-BPH as a novel crop protection compound.
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Affiliation(s)
- Mohsen Abbod
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, P.O.B. 14115-336, Tehran, Iran
| | - Naser Safaie
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, P.O.B. 14115-336, Tehran, Iran.
| | - Khodayar Gholivand
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Mohammad Mehrabadi
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115-336, Tehran, Iran
| | - Mahyar Bonsaii
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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Aamir M, Singh VK, Dubey MK, Meena M, Kashyap SP, Katari SK, Upadhyay RS, Umamaheswari A, Singh S. In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against Fusarium Wilt in Tomato. Front Pharmacol 2018; 9:1038. [PMID: 30405403 PMCID: PMC6204350 DOI: 10.3389/fphar.2018.01038] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 08/27/2018] [Indexed: 12/31/2022] Open
Abstract
Vascular wilt of tomato caused by Fusarium oxysporum f.sp. lycopersici (FOL) is one of the most devastating diseases, that delimits the tomato production worldwide. Fungal short-chain dehydrogenases/reductases (SDRs) are NADP(H) dependent oxidoreductases, having shared motifs and common functional mechanism, have been demonstrated as biochemical targets for commercial fungicides. The 1,3,6,8 tetra hydroxynaphthalene reductase (T4HNR) protein, a member of SDRs family, catalyzes the naphthol reduction reaction in fungal melanin biosynthesis. We retrieved an orthologous member of T4HNR, (complexed with NADP(H) and pyroquilon from Magnaporthe grisea) in the FOL (namely; FOXG_04696) based on homology search, percent identity and sequence similarity (93% query cover; 49% identity). The hypothetical protein FOXG_04696 (T4HNR like) had conserved T-G-X-X-X-G-X-G motif (cofactor binding site) at N-terminus, similar to M. grisea (1JA9) and Y-X-X-X-K motif, as a part of the active site, bearing homologies with two fungal keto reductases T4HNR (M. grisea) and 17-β-hydroxysteroid dehydrogenase from Curvularia lunata (teleomorph: Cochliobolus lunatus PDB ID: 3IS3). The catalytic tetrad of T4HNR was replaced with ASN115, SER141, TYR154, and LYS158 in the FOXG_04696. The structural alignment and superposition of FOXG_04696 over the template proteins (3IS3 and 1JA9) revealed minimum RMSD deviations of the C alpha atomic coordinates, and therefore, had structural conservation. The best protein model (FOXG_04696) was docked with 37 fungicides, to evaluate their binding affinities. The Glide XP and YASARA docked complexes showed discrepancies in results, for scoring and ranking the binding affinities of fungicides. The docked complexes were further refined and rescored from their docked poses through 50 ns long MD simulations, and binding free energies (ΔGbind) calculations, using MM/GBSA analysis, revealed Oxathiapiprolin and Famoxadone as better fungicides among the selected one. However, Famoxadone had better interaction of the docked residues, with best protein ligand contacts, minimum RMSD (high accuracy of the docking pose) and RMSF (structural integrity and conformational flexibility of docking) at the specified docking site. The Famoxadone was found to be acceptable based on in silico toxicity and in vitro growth inhibition assessment. We conclude that the FOXG_04696, could be employed as a novel candidate protein, for structure-based design, and screening of target fungicides against the FOL pathogen.
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Affiliation(s)
- Mohd Aamir
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Manish Kumar Dubey
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Mukesh Meena
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India.,Department of Botany, University College of Science, Mohanlal Sukhadia University, Udaipur, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement and Biotechnology, Indian Institute of Vegetable Research, Indian Council of Agricultural Research (ICAR), Varanasi, India
| | - Sudheer Kumar Katari
- Bioinformatics Centre, Department of Bioinformatics, Sri Venkateswara Institute of Medical Sciences University, Tirupati, India
| | - Ram Sanmukh Upadhyay
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Amineni Umamaheswari
- Bioinformatics Centre, Department of Bioinformatics, Sri Venkateswara Institute of Medical Sciences University, Tirupati, India
| | - Surendra Singh
- Laboratory of Mycopathology and Microbial Technology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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Lǚ Z, Kang X, Xiang Z, He N. Laccase Gene Sh-lac Is Involved in the Growth and Melanin Biosynthesis of Scleromitrula shiraiana. PHYTOPATHOLOGY 2017; 107:353-361. [PMID: 27870600 DOI: 10.1094/phyto-04-16-0180-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Scleromitrula shiraiana causes the popcorn disease in mulberry trees resulting in severe economic losses. Previous studies have shown that melanin may play a vital role in establishing the pathogenicity of fungi. In the present study, we identified the melanin produced in S. shiraiana belongs to DHN melanin by gas chromatography-mass spectrometry, and cloned the laccase Sh-lac, a potential DHN melanin biosynthesis gene from S. shiraiana. We obtained two stable Sh-lac silenced transformants using RNAi, ilac-4 and 8 to elucidate the DHN melanin biosynthetic pathway in S. shiraiana. The melanin production of ilac-4 and ilac-8 was significantly reduced, and their vegetative growth was also suppressed. Results such as these led to a proposal that Sh-lac played a key role in DHN melanin formation in S. shiraiana and may function differentially with other melanin biosynthetic genes. The inhibition of melanin was accompanied by the decrease of oxalic acid and the adhesion of hyphae was impaired. Our results indicated that laccase was an important enzyme in the synthesis of melanin and might play a critical role in the pathogenicity of S. shiraiana.
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Affiliation(s)
- Zhiyuan Lǚ
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Xin Kang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
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Hydroxyl regioisomerization of anthracycline catalyzed by a four-enzyme cascade. Proc Natl Acad Sci U S A 2017; 114:1554-1559. [PMID: 28137838 DOI: 10.1073/pnas.1610097114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ranking among the most effective anticancer drugs, anthracyclines represent an important family of aromatic polyketides generated by type II polyketide synthases (PKSs). After formation of polyketide cores, the post-PKS tailoring modifications endow the scaffold with various structural diversities and biological activities. Here we demonstrate an unprecedented four-enzyme-participated hydroxyl regioisomerization process involved in the biosynthesis of kosinostatin. First, KstA15 and KstA16 function together to catalyze a cryptic hydroxylation of the 4-hydroxyl-anthraquinone core, yielding a 1,4-dihydroxyl product, which undergoes a chemically challenging asymmetric reduction-dearomatization subsequently acted by KstA11; then, KstA10 catalyzes a region-specific reduction concomitant with dehydration to afford the 1-hydroxyl anthraquinone. Remarkably, the shunt product identifications of both hydroxylation and reduction-dehydration reactions, the crystal structure of KstA11 with bound substrate and cofactor, and isotope incorporation experiments reveal mechanistic insights into the redox dearomatization and rearomatization steps. These findings provide a distinguished tailoring paradigm for type II PKS engineering.
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The three-dimensional structure of Clostridium absonum 7α-hydroxysteroid dehydrogenase: new insights into the conserved arginines for NADP(H) recognition. Sci Rep 2016; 6:22885. [PMID: 26961171 PMCID: PMC4785404 DOI: 10.1038/srep22885] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/23/2016] [Indexed: 11/09/2022] Open
Abstract
7α-hydroxysteroid dehydrogenase (7α-HSDH) can catalyse the oxidation of C7 α-OH of the steroid nucleus in the bile acid metabolism. In the paper we determined the crystal structure of 7α-HSDH from Clostridium absonum (CA 7α-HSDH) complexed with taurochenodeoxycholic acid (TCDCA) and NADP(+) by X-ray diffraction, which, as a tetramer, possesses the typical α/β folding pattern. The four subunits of an asymmetric unit lie in the fact that there are the stable hydrophobic interactions between Q-axis-related subunits. Significantly, we captured an active state of the NADP(+), confirming that nicotinamide moiety of NADP(+) act as electron carrier in the dehydrogenation. On the basis of crystal structure analysis, site-directed mutagenesis and MD simulation, furthermore, we find that the guanidinium of Arg38 can form the stable cation-π interaction with the adenine ring of NADP(+), and the cation-π interaction and hydrogen bonds between Arg38 and NADP(+) have a significant anchor effect on the cofactor binding to CA 7α-HSDH.
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Chen H, Han X, Qin N, Wei L, Yang Y, Rao L, Chi B, Feng L, Ren Y, Wan J. Synthesis and biological evaluation of novel inhibitors against 1,3,8-trihydroxynaphthalene reductase from Magnaporthe grisea. Bioorg Med Chem 2016; 24:1225-30. [DOI: 10.1016/j.bmc.2016.01.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
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Conradt D, Schätzle MA, Husain SM, Müller M. Diversity in Reduction with Short-Chain Dehydrogenases: Tetrahydroxynaphthalene Reductase, Trihydroxynaphthalene Reductase, and Glucose Dehydrogenase. ChemCatChem 2015. [DOI: 10.1002/cctc.201500605] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- David Conradt
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
| | - Michael A. Schätzle
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
- Roche Pharma AG; Emil-Barell-Str. 1 79639 Grenzach-Wyhlen (Germany
| | - Syed Masood Husain
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
- Centre of Biomedical Research; Raebareli Road, Lucknow 226 014 Uttar Pradesh India
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg Germany
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Takeshita D, Kataoka M, Miyakawa T, Miyazono KI, Kumashiro S, Nagai T, Urano N, Uzura A, Nagata K, Shimizu S, Tanokura M. Structural basis of stereospecific reduction by quinuclidinone reductase. AMB Express 2014; 4:6. [PMID: 24507746 PMCID: PMC3922912 DOI: 10.1186/2191-0855-4-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 12/28/2013] [Indexed: 11/10/2022] Open
Abstract
Chiral molecule (R)-3-quinuclidinol, a valuable compound for the production of various pharmaceuticals, is efficiently synthesized from 3-quinuclidinone by using NADPH-dependent 3-quinuclidinone reductase (RrQR) from Rhodotorula rubra. Here, we report the crystal structure of RrQR and the structure-based mutational analysis. The enzyme forms a tetramer, in which the core of each protomer exhibits the α/β Rossmann fold and contains one molecule of NADPH, whereas the characteristic substructures of a small lobe and a variable loop are localized around the substrate-binding site. Modeling and mutation analyses of the catalytic site indicated that the hydrophobicity of two residues, I167 and F212, determines the substrate-binding orientation as well as the substrate-binding affinity. Our results revealed that the characteristic substrate-binding pocket composed of hydrophobic amino acid residues ensures substrate docking for the stereospecific reaction of RrQR in spite of its loose interaction with the substrate.
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The phytoalexin camalexin induces fundamental changes in the proteome of Alternaria brassicicola different from those caused by brassinin. Fungal Biol 2014; 118:83-93. [DOI: 10.1016/j.funbio.2013.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 10/22/2013] [Accepted: 11/19/2013] [Indexed: 02/07/2023]
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Hou J, Wojciechowska K, Zheng H, Chruszcz M, Cooper DR, Cymborowski M, Skarina T, Gordon E, Luo H, Savchenko A, Minor W. Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:632-7. [PMID: 22684058 PMCID: PMC3370898 DOI: 10.1107/s1744309112017939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 04/22/2012] [Indexed: 11/10/2022]
Abstract
The crystal structure of a short-chain dehydrogenase/reductase from Bacillus anthracis strain `Ames Ancestor' complexed with NADP has been determined and refined to 1.87 Å resolution. The structure of the enzyme consists of a Rossmann fold composed of seven parallel β-strands sandwiched by three α-helices on each side. An NADP molecule from an endogenous source is bound in the conserved binding pocket in the syn conformation. The loop region responsible for binding another substrate forms two perpendicular short helices connected by a sharp turn.
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Affiliation(s)
- Jing Hou
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Kamila Wojciechowska
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
| | - Heping Zheng
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Maksymilian Chruszcz
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - David R. Cooper
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Marcin Cymborowski
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Tatiana Skarina
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada
| | - Elena Gordon
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada
| | - Haibin Luo
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada
| | - Wladek Minor
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
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Insights into subtle conformational differences in the substrate-binding loop of fungal 17β-hydroxysteroid dehydrogenase: a combined structural and kinetic approach. Biochem J 2011; 441:151-60. [DOI: 10.1042/bj20110567] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The 17β-HSD (17β-hydroxysteroid dehydrogenase) from the filamentous fungus Cochliobolus lunatus (17β-HSDcl) is a NADP(H)-dependent enzyme that preferentially catalyses the interconversion of inactive 17-oxo-steroids and their active 17β-hydroxy counterparts. 17β-HSDcl belongs to the SDR (short-chain dehydrogenase/reductase) superfamily. It is currently the only fungal 17β-HSD member that has been described and represents one of the model enzymes of the cP1 classical subfamily of NADPH-dependent SDR enzymes. A thorough crystallographic analysis has been performed to better understand the structural aspects of this subfamily and provide insights into the evolution of the HSD enzymes. The crystal structures of the 17β-HSDcl apo, holo and coumestrol-inhibited ternary complex, and the active-site Y167F mutant reveal subtle conformational differences in the substrate-binding loop that probably modulate the catalytic activity of 17β-HSDcl. Coumestrol, a plant-derived non-steroidal compound with oestrogenic activity, inhibits 17β-HSDcl [IC50 2.8 μM; at 100 μM substrate (4-oestrene-3,17-dione)] by occupying the putative steroid-binding site. In addition to an extensive hydrogen-bonding network, coumestrol binding is stabilized further by π–π stacking interactions with Tyr212. A stopped-flow kinetic experiment clearly showed the coenzyme dissociation as the slowest step of the reaction and, in addition to the low steroid solubility, it prevents the accumulation of enzyme–coenzyme–steroid ternary complexes.
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Ueshima S, Muramatsu H, Nakajima T, Yamamoto H, Kato SI, Misono H, Nagata S. Identification, Cloning, and Characterization of l-Phenylserine Dehydrogenase from Pseudomonas syringae NK-15. Enzyme Res 2010; 2010:597010. [PMID: 21048868 PMCID: PMC2963168 DOI: 10.4061/2010/597010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 10/28/2009] [Accepted: 11/29/2009] [Indexed: 11/20/2022] Open
Abstract
The gene encoding d-phenylserine dehydrogenase from Pseudomonas syringae NK-15 was identified, and a 9,246-bp nucleotide sequence containing the gene was sequenced. Six ORFs were confirmed in the sequenced region, four of which were predicted to form an operon. A homology search of each ORF predicted that orf3 encoded l-phenylserine dehydrogenase. Hence, orf3 was cloned and overexpressed in Escherichia coli cells and recombinant ORF3 was purified to homogeneity and characterized. The purified ORF3 enzyme showed l-phenylserine dehydrogenase activity. The enzymological properties and primary structure of l-phenylserine dehydrogenase (ORF3) were quite different from those of d-phenylserine dehydrogenase previously reported. l-Phenylserine dehydrogenase catalyzed the NAD+-dependent oxidation of the β-hydroxyl group of l-β-phenylserine. l-Phenylserine and l-threo-(2-thienyl)serine were good substrates for l-phenylserine dehydrogenase. The genes encoding l-phenylserine dehydrogenase and d-phenylserine dehydrogenase, which is induced by phenylserine, are located in a single operon. The reaction products of both enzymatic reactions were 2-aminoacetophenone and CO2.
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Affiliation(s)
- Sakuko Ueshima
- The United Graduate School of Agricultural Science, Ehime University, 3-5-7 Tarumi, Matsuyama 790-8566, Japan
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Pacios LF, Campos VM, Merino I, Gómez L. Structures and thermodynamics of biphenyl dihydrodiol stereoisomers and their metabolites in the enzymatic degradation of arene xenobiotics. J Comput Chem 2009; 30:2420-32. [PMID: 19360792 DOI: 10.1002/jcc.21248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A key step in the metabolic degradation of biphenyl xenobiotics is catechol formation upon dehydrogenation of cis- and trans-dihydrodiols in prokaryotic and eukaryotic pathways, respectively. Structure and thermodynamics of stereoisomers of cis-, trans-2,3-biphenyl-dihydrodiols (I) and their dehydrogenation products (hydroxyketones, II), as well as final catechol (2,3-biphenyldiol, III) are studied by means of ab initio MP2/6-311++G(2df,2p)//MP2/6-311G(d,p) calculations. Formation of stereoisomers I and II is exothermic and endergonic, whereas III is enthalpically and entropically driven. Dehydrogenations are endothermic (DeltaHR0 approximately 1.5-4 kcal mol(-1)) and exergonic (DeltaGR0 approximately -5 to -7.5 kcal mol(-1)) without noticeable differences between cis and trans pathways, although the same keto stereoisomer II-(2S) is found to be the more favored product from both cis- and trans-I. The final II --> III tautomerization is thermodynamically enhanced (DeltaHR0 approximately -27, DeltaGR0 approximately -28 kcal mol(-1)) but the process is shown to have a large activation energy if it had to occur via unimolecular path. Although this tautomerization is generally assumed to be a nonenzymatic process as it involves rearomatization of an oxygenated ring, proton transfer with an anionic intermediate might be a more probable process.
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Affiliation(s)
- Luis F Pacios
- Unidad de Química y Bioquímica, Departamento de Biotecnología, E. T. S. Ingenieros de Montes, Universidad Politécnica de Madrid, 28040 Madrid, Spain.
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Brunskole M, Štefane B, Zorko K, Anderluh M, Stojan J, Lanišnik Rižner T, Gobec S. Towards the first inhibitors of trihydroxynaphthalene reductase from Curvularia lunata: Synthesis of artificial substrate, homology modelling and initial screening. Bioorg Med Chem 2008; 16:5881-9. [DOI: 10.1016/j.bmc.2008.04.066] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 04/19/2008] [Accepted: 04/25/2008] [Indexed: 11/26/2022]
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17
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Dybala-Defratyka A, Rostkowski M, Paneth P. Enzyme mechanisms from molecular modeling and isotope effects. Arch Biochem Biophys 2008; 474:274-82. [DOI: 10.1016/j.abb.2008.01.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 01/11/2008] [Accepted: 01/12/2008] [Indexed: 11/28/2022]
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18
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Kristan K, Adamski J, Rizner TL, Stojan J. His164 regulates accessibility to the active site in fungal 17β-hydroxysteroid dehydrogenase. Biochimie 2007; 89:63-71. [PMID: 17034927 DOI: 10.1016/j.biochi.2006.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 09/04/2006] [Indexed: 11/20/2022]
Abstract
17beta-Hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus (17beta-HSDcl) is an NADPH-dependent member of the short-chain dehydrogenase/ reductase superfamily. To study the catalytic properties of this enzyme, we prepared several specific mutations of 17beta-HSDcl (Tyr167Phe, His164Trp/Gly, Tyr212Ala). Wild-type 17beta-HSDcl and the 17beta-HSDcl mutants were evaluated by chromatographic, kinetic and thermodynamic means. The Tyr167Phe mutation resulted in a complete loss of enzyme activity, while substitution of His164 with Trp and Gly both resulted in higher specificity number (V/K) for the steroid substrates, which are mainly a consequence of easier accessibility of steroid substrates to the active-site hollow under optimized conditions. The Tyr212Ala mutant showed increased activity in the oxidative direction, which appears to be a consequence of increased NADPH dissociation. The kinetic characterizations and thermodynamic analyses also suggest that His164 and Tyr212 in 17beta-HSDcl have a role in the opening and closing of the active site of this enzyme and in the discrimination between oxidized and reduced coenzyme.
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Affiliation(s)
- Katja Kristan
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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19
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Cassetta A, Büdefeld T, Rizner TL, Kristan K, Stojan J, Lamba D. Crystallization, X-ray diffraction analysis and phasing of 17beta-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1032-4. [PMID: 16511227 PMCID: PMC1978160 DOI: 10.1107/s1744309105034949] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Accepted: 10/26/2005] [Indexed: 11/11/2022]
Abstract
17beta-Hydroxysteroid dehydrogenase from the filamentous fungus Cochliobolus lunatus (17beta-HSDcl) is an NADP(H)-dependent enzyme that preferentially catalyses the oxidoreduction of oestrogens and androgens. The enzyme belongs to the short-chain dehydrogenase/reductase superfamily and is the only fungal hydroxysteroid dehydrogenase known to date. 17beta-HSDcl has recently been characterized and cloned and has been the subject of several functional studies. Although several hypotheses on the physiological role of 17beta-HSDcl in fungal metabolism have been formulated, its function is still unclear. An X-ray crystallographic study has been undertaken and the optimal conditions for crystallization of 17beta-HSDcl (apo form) were established, resulting in well shaped crystals that diffracted to 1.7 A resolution. The space group was identified as I4(1)22, with unit-cell parameters a = b = 67.14, c = 266.77 A. Phasing was successfully performed by Patterson search techniques. A catalytic inactive mutant Tyr167Phe was also engineered, expressed, purified and crystallized for functional and structural studies.
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Affiliation(s)
- Alberto Cassetta
- Institute of Crystallography, CNR, Trieste Outstation, Area Science Park-Basovizza, S.S.14, I-34012 Trieste, Italy.
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20
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Korman TP, Hill JA, Vu TN, Tsai SC. Structural analysis of actinorhodin polyketide ketoreductase: cofactor binding and substrate specificity. Biochemistry 2005; 43:14529-38. [PMID: 15544323 PMCID: PMC2263080 DOI: 10.1021/bi048133a] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aromatic polyketides are a class of natural products that include many pharmaceutically important aromatic compounds. Understanding the structure and function of PKS will provide clues to the molecular basis of polyketide biosynthesis specificity. Polyketide chain reduction by ketoreductase (KR) provides regio- and stereochemical diversity. Two cocrystal structures of actinorhodin polyketide ketoreductase (act KR) were solved to 2.3 A with either the cofactor NADP(+) or NADPH bound. The monomer fold is a highly conserved Rossmann fold. Subtle differences between structures of act KR and fatty acid KRs fine-tune the tetramer interface and substrate binding pocket. Comparisons of the NADP(+)- and NADPH-bound structures indicate that the alpha6-alpha7 loop region is highly flexible. The intricate proton-relay network in the active site leads to the proposed catalytic mechanism involving four waters, NADPH, and the active site tetrad Asn114-Ser144-Tyr157-Lys161. Acyl carrier protein and substrate docking models shed light on the molecular basis of KR regio- and stereoselectivity, as well as the differences between aromatic polyketide and fatty acid biosyntheses. Sequence comparison indicates that the above features are highly conserved among aromatic polyketide KRs. The structures of act KR provide an important step toward understanding aromatic PKS and will enhance our ability to design novel aromatic polyketide natural products with different reduction patterns.
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Affiliation(s)
| | | | | | - Shiou-Chuan Tsai
- * Address correspondence to this author. E-mail: . Phone: 949-824-4486. Fax: 949-824-8552
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21
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Taguchi T, Kunieda K, Takeda-Shitaka M, Takaya D, Kawano N, Kimberley MR, Booker-Milburn KI, Stephenson GR, Umeyama H, Ebizuka Y, Ichinose K. Remarkably different structures and reaction mechanisms of ketoreductases for the opposite stereochemical control in the biosynthesis of BIQ antibiotics. Bioorg Med Chem 2004; 12:5917-27. [PMID: 15498668 DOI: 10.1016/j.bmc.2004.08.026] [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] [Received: 07/21/2004] [Revised: 08/16/2004] [Accepted: 08/17/2004] [Indexed: 10/26/2022]
Abstract
Two ketoreductases, RED1 and RED2, are involved in the biosynthesis of actinorhodin in Streptomyces coelicolor A3(2) and dihydrogranaticin in S. violaceoruber Tu22, respectively. They are responsible for the stereospecific reductions of the bicyclic intermediate to give (S)- or (R)-DNPA, although there is no similarity between their amino acid sequences. Biotransformation using synthetic analogous substrates revealed that the substrate specificities are quite different. Homology modelling studies and site directed mutagenesis showed remarkable differences in three-dimensional structures and catalytic mechanisms between RED1 and RED2.
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Affiliation(s)
- Takaaki Taguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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22
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Duax WL, Pletnev V, Addlagatta A, Bruenn J, Weeks CM. Rational proteomics I. Fingerprint identification and cofactor specificity in the short-chain oxidoreductase (SCOR) enzyme family. Proteins 2004; 53:931-43. [PMID: 14635134 DOI: 10.1002/prot.10512] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The short-chain oxidoreductase (SCOR) family of enzymes includes over 2000 members identified in sequenced genomes. Of these enzymes, approximately 200 have been characterized functionally, and the three-dimensional crystal structures of approximately 40 have been reported. Since some SCOR enzymes are involved in hypertension, diabetes, breast cancer, and polycystic kidney disease, it is important to characterize the other members of the family for which the biological functions are currently unknown. Although the SCOR family appears to have only a single fully conserved residue, it was possible, using bioinformatics methods, to determine characteristic fingerprints composed of 30-40 residues that are conserved at the 70% or greater level in SCOR subgroups. These fingerprints permit reliable prediction of several important structure-function features including NAD/NADP cofactor preference. For example, the correlation of aspartate or arginine residues with NAD or NADP binding, respectively, predicts the cofactor preference of more than 70% of the SCOR proteins with unknown function. The analysis of conserved residues surrounding the cofactor has revealed the presence of previously undetected CH em leader O hydrogen bonds in the majority of the SCOR crystal structures, predicts the presence of similar hydrogen bonds in 90% of the SCOR proteins of unknown function, and suggests that these hydrogen bonds may play a critical role in the catalytic functions of these enzymes.
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Affiliation(s)
- William L Duax
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, SUNY at Buffalo, Buffalo, New York, USA.
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23
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Sogabe S, Yoshizumi A, Fukami TA, Shiratori Y, Shimizu S, Takagi H, Nakamori S, Wada M. The crystal structure and stereospecificity of levodione reductase from Corynebacterium aquaticum M-13. J Biol Chem 2003; 278:19387-95. [PMID: 12621044 DOI: 10.1074/jbc.m208146200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The (6R)-2,2,6-trimethyl-1,4-cyclohexanedione (levodione) reductase (LVR) of the soil isolate bacterium Corynebacterium aquaticum M-13 is a NAD(H)-linked enzyme that catalyzes reversible oxidoreduction between (4R)-hydroxy-(6R)-2,2,6-trimethylcyclohexanone (actinol) and levodione. Here the crystal structure of a ternary complex of LVR with NADH and its inhibitor 2-methyl-2,4-pentanediol has been determined by molecular replacement and refined at 1.6-A resolution with a crystallographic R factor of 0.199. The overall structure is similar to those of other short-chain alcohol dehydrogenase/reductase enzymes. The positions of NADH and 2-methyl-2,4-pentanediol indicate the binding site of the substrate and identify residues that are likely to be important in the catalytic reaction. Modeling of the substrate binding in the active site suggests that the specificity of LVR is determined by electrostatic interactions between the negatively charged surface of Glu-103 of LVR and the positively charged surface on the re side of levodione. Mutant LVR enzymes in which Glu-103 is substituted with alanine (E103A), glutamine (E103Q), asparagines (E103N), or aspartic acid (E103D) show a 2-6-fold increase in Km values as compared with wild-type LVR and a much lower enantiomeric excess of the reaction products (60%) than the wild-type enzyme (95%). Together, these data indicate that Glu-103 has an important role in determining the stereospecificity of LVR.
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Affiliation(s)
- Satoshi Sogabe
- Nippon Roche Research Center, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan
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24
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Oppermann U, Filling C, Hult M, Shafqat N, Wu X, Lindh M, Shafqat J, Nordling E, Kallberg Y, Persson B, Jörnvall H. Short-chain dehydrogenases/reductases (SDR): the 2002 update. Chem Biol Interact 2003; 143-144:247-53. [PMID: 12604210 DOI: 10.1016/s0009-2797(02)00164-3] [Citation(s) in RCA: 478] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Short-chain dehydrogenases/reductases (SDR) form a large, functionally heterogeneous protein family presently with about 3000 primary and about 30 3D structures deposited in databases. Despite low sequence identities between different forms (about 15-30%), the 3D structures display highly similar alpha/beta folding patterns with a central beta-sheet, typical of the Rossmann-fold. Based on distinct sequence motifs functional assignments and classifications are possible, making it possible to build a general nomenclature system. Recent mutagenetic and structural studies considerably extend the knowledge on the general reaction mechanism, thereby establishing a catalytic tetrad of Asn-Ser-Tyr-Lys residues, which presumably form the framework for a proton relay system including the 2'-OH of the nicotinamide ribose, similar to the mechanism found in horse liver ADH. Based on their cellular functions, several SDR enzymes appear as possible and promising pharmacological targets with application areas spanning hormone-dependent cancer forms or metabolic diseases such as obesity and diabetes, and infectious diseases.
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Affiliation(s)
- Udo Oppermann
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177, Stockholm, Sweden.
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25
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Kuhn P, Wilson K, Patch MG, Stevens RC. The genesis of high-throughput structure-based drug discovery using protein crystallography. Curr Opin Chem Biol 2002; 6:704-10. [PMID: 12413557 DOI: 10.1016/s1367-5931(02)00361-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Over the past 12 years, drugs have been developed using structure-based drug design relying upon traditional crystallographic methods. Established successes, such as the drugs designed against HIV-1 protease and neuraminidase, demonstrate the utility of a structure-based approach in the drug-discovery process. However, the approach has historically lacked throughput and reliability capabilities; these bottlenecks are being overcome by breakthroughs in high-throughput structural biology. Recent technological innovations such as submicroliter high-throughput crystallization, high-performance synchrotron beamlines and rapid binding-site analysis of de novo targets using virtual ligand screening and small molecule co-crystallization have resulted in a significant advance in structure-based drug discovery.
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Affiliation(s)
- Peter Kuhn
- Stanford Synchrotron Radiation Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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