1
|
Martin MP, Endicott JA, Noble MEM, Tatum NJ. Crystallographic fragment screening in academic cancer drug discovery. Methods Enzymol 2023; 690:211-234. [PMID: 37858530 DOI: 10.1016/bs.mie.2023.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Fragment-based drug discovery (FBDD) has brought several drugs to the clinic, notably to target proteins once considered to be challenging, or even undruggable. Screening in FBDD relies upon observing and/or measuring weak (millimolar-scale) binding events using biophysical techniques or crystallographic fragment screening. This latter structural approach provides no information about binding affinity but can reveal binding mode and atomic detail on protein-fragment interactions to accelerate hit-to-lead development. In recent years, high-throughput platforms have been developed at synchrotron facilities to screen thousands of fragment-soaked crystals. However, using accessible manual techniques it is possible to run informative, smaller-scale screens within an academic lab setting. This chapter describes general protocols for home laboratory-scale fragment screening, from fragment soaking through to structure solution and, where appropriate, signposts to background, protocols or alternatives elsewhere.
Collapse
Affiliation(s)
- Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Jane A Endicott
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Natalie J Tatum
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom.
| |
Collapse
|
2
|
Piserchio A, Isiorho EA, Dalby KN, Ghose R. Structure of the complex between calmodulin and a functional construct of eukaryotic elongation factor 2 kinase bound to an ATP-competitive inhibitor. J Biol Chem 2023:104813. [PMID: 37172726 DOI: 10.1016/j.jbc.2023.104813] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023] Open
Abstract
The calmodulin-activated α-kinase, eukaryotic elongation factor 2 kinase (eEF-2K) serves as a master regulator of translational elongation by specifically phosphorylating and reducing the ribosome-affinity of the guanosine triphosphatase, eukaryotic elongation factor 2 (eEF-2). Given its critical role in a fundamental cellular process, dysregulation of eEF-2K has been implicated in several human diseases, including those of the cardiovascular system, chronic neuropathies, and many cancers, making it a critical pharmacological target. In the absence of high-resolution structural information, high-throughput screening efforts have yielded small-molecule candidates that show promise as eEF-2K antagonists. Principal among these is the ATP-competitive pyrimido-pyrimidinedione inhibitor, A-484954, which shows high specificity towards eEF-2K relative to a panel of "typical" protein kinases. A-484954 has been shown to have some degree of efficacy in animal models of several disease states. It has also been widely deployed as a reagent in eEF-2K-specific biochemical and cell-biological studies. However, given the absence of structural information, the precise mechanism of the A-484954-mediated inhibition of eEF-2K has remained obscure. Leveraging our identification of the calmodulin-activatable catalytic core of eEF-2K and our recent determination of its long-elusive structure, here we present the structural basis for its specific inhibition by A-484954. This structure, which represents the first for an inhibitor-bound catalytic domain of a member of the α-kinase family, enables rationalization of the existing structure-activity relationship data for A-484954 variants and lays the groundwork for further optimization of this scaffold to attain enhanced specificity/potency against eEF-2K.
Collapse
Affiliation(s)
- Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031
| | - Eta A Isiorho
- Macromolecular Crystallization Facility, CUNY ASRC, New York, NY 10031
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, the University of Texas, Austin, TX 78712; Interdisciplinary Life Sciences Graduate Program, the University of Texas, Austin, TX 78712.
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031; PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016; PhD Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016; PhD Program in Physics, The Graduate Center of CUNY, New York, NY 10016.
| |
Collapse
|
3
|
Lin W, Huber AD, Poudel S, Li Y, Seetharaman J, Miller DJ, Chen T. Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein. Proc Natl Acad Sci U S A 2023; 120:e2217804120. [PMID: 36848571 PMCID: PMC10013835 DOI: 10.1073/pnas.2217804120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/30/2023] [Indexed: 03/01/2023] Open
Abstract
Ligand-binding promiscuity in detoxification systems protects the body from toxicological harm but is a roadblock to drug development due to the difficulty in optimizing small molecules to both retain target potency and avoid metabolic events. Immense effort is invested in evaluating metabolism of molecules to develop safer, more effective treatments, but engineering specificity into or out of promiscuous proteins and their ligands is a challenging task. To better understand the promiscuous nature of detoxification networks, we have used X-ray crystallography to characterize a structural feature of pregnane X receptor (PXR), a nuclear receptor that is activated by diverse molecules (with different structures and sizes) to up-regulate transcription of drug metabolism genes. We found that large ligands expand PXR's ligand-binding pocket, and the ligand-induced expansion occurs through a specific unfavorable compound-protein clash that likely contributes to reduced binding affinity. Removing the clash by compound modification resulted in more favorable binding modes with significantly enhanced binding affinity. We then engineered the unfavorable ligand-protein clash into a potent, small PXR ligand, resulting in marked reduction in PXR binding and activation. Structural analysis showed that PXR is remodeled, and the modified ligands reposition in the binding pocket to avoid clashes, but the conformational changes result in less favorable binding modes. Thus, ligand-induced binding pocket expansion increases ligand-binding potential of PXR but is an unfavorable event; therefore, drug candidates can be engineered to expand PXR's ligand-binding pocket and reduce their safety liability due to PXR binding.
Collapse
Affiliation(s)
- Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Andrew D. Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Yongtao Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Darcie J. Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| |
Collapse
|
4
|
Celastrol suppresses colorectal cancer via covalent targeting peroxiredoxin 1. Signal Transduct Target Ther 2023; 8:51. [PMID: 36732502 PMCID: PMC9895061 DOI: 10.1038/s41392-022-01231-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/19/2022] [Accepted: 10/11/2022] [Indexed: 02/04/2023] Open
Abstract
As a terpenoids natural product isolated from the plant Thunder God Vine, Celastrol is widely studied for its pharmacological activities, including anti-tumor activities. The clinical application of Celastrol is strictly limited due to its severe side effects, whereas previously revealed targets and mechanism of Celastrol seldom reduce its in vivo toxicity via structural optimization. Target identification has a far-reaching influence on the development of innovative drugs, and omics data has been widely used for unbiased target prediction. However, it is difficult to enrich target of specific phenotype from thousands of genes or proteins, especially for natural products with broad promising activities. Here, we developed a text-mining-based web-server tool to enrich targets from omics data of inquired compounds. Then peroxiredoxin 1 (PRDX1) was identified as the ROS-manipulating target protein of Celastrol in colorectal cancer. Our solved high-resolution crystal structure revealed the unique covalent binding mode of Celastrol with PRDX1. New derivative compound 19-048 with improved potency against PRDX1 and selectivity towards PRDX2~PRDX6 were synthesized based on crystal structure analysis. Both Celastrol and 19-048 effectively suppressed the proliferation of colorectal cancer cells. The anti-tumor efficacy of Celastrol and 19-048 was significantly diminished on xenograft nude mice bearing PRDX1 knock-down colorectal cancer cells. Several downstream genes of p53 signaling pathway were dramatically up-regulated with Celastrol or 19-048 treatment. Our findings reveal that the side effects of Celastrol could be reduced via structural modification, and PRDX1 inhibition is promising for the treatment of colorectal cancer.
Collapse
|
5
|
Tong Y, Ma X, Hu T, Chen K, Cui G, Su P, Xu H, Gao W, Jiang T, Huang L. Structural and mechanistic insights into the precise product synthesis by a bifunctional miltiradiene synthase. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:165-175. [PMID: 36161753 PMCID: PMC9829396 DOI: 10.1111/pbi.13933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 07/22/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Selaginella moellendorffii miltiradiene synthase (SmMDS) is a unique bifunctional diterpene synthase (diTPS) that catalyses the successive cyclization of (E,E,E)-geranylgeranyl diphosphate (GGPP) via (+)-copalyl diphosphate (CPP) to miltiradiene, which is a crucial precursor of important medicinal compounds, such as triptolide, ecabet sodium and carnosol. Miltiradiene synthetic processes have been studied in monofunctional diTPSs, while the precise mechanism by which active site amino acids determine product simplicity and the experimental evidence for reaction intermediates remain elusive. In addition, how bifunctional diTPSs work compared to monofunctional enzymes is attractive for detailed research. Here, by mutagenesis studies of SmMDS, we confirmed that pimar-15-en-8-yl+ is an intermediate in miltiradiene synthesis. Moreover, we determined the apo-state and the GGPP-bound state crystal structures of SmMDS. By structure analysis and mutagenesis experiments, possible contributions of key residues both in class I and II active sites were suggested. Based on the structural and functional analyses, we confirmed the copal-15-yl+ intermediate and unveiled more details of the catalysis process in the SmMDS class I active site. Moreover, the structural and experimental results suggest an internal channel for (+)-CPP produced in the class II active site moving towards the class I active site. Our research is a good example for intermediate identification of diTPSs and provides new insights into the product specificity determinants and intermediate transport, which should greatly facilitate the precise controlled synthesis of various diterpenes.
Collapse
Affiliation(s)
- Yuru Tong
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
- School of Pharmaceutical SciencesCapital Medical UniversityBeijingChina
| | - Xiaoli Ma
- National Laboratory of BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Tianyuan Hu
- School of Pharmaceutical SciencesCapital Medical UniversityBeijingChina
| | - Kang Chen
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Guanghong Cui
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Ping Su
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - Haifeng Xu
- National Laboratory of BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Wei Gao
- Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Tao Jiang
- National Laboratory of BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Luqi Huang
- National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| |
Collapse
|
6
|
Structural Analysis of the Complex of Human Transthyretin with 3′,5′-Dichlorophenylanthranilic Acid at 1.5 Å Resolution. Molecules 2022; 27:molecules27217206. [DOI: 10.3390/molecules27217206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/01/2022] [Accepted: 10/09/2022] [Indexed: 11/16/2022] Open
Abstract
Human transthyretin (hTTR) can form amyloid deposits that accumulate in nerves and organs, disrupting cellular function. Molecules such as tafamidis that bind to and stabilize the TTR tetramer can reduce such amyloid formation. Here, we studied the interaction of VCP-6 (2-((3,5-dichlorophenyl)amino)benzoic acid) with hTTR. VCP-6 binds to hTTR with 5 times the affinity of the cognate ligand, thyroxine (T4). The structure of the hTTR:VCP-6 complex was determined by X-ray crystallography at 1.52 Å resolution. VCP-6 binds deeper in the binding channel than T4 with the 3′,5′-dichlorophenyl ring binding in the ‘forward’ mode towards the channel centre. The dichlorophenyl ring lies along the 2-fold axis coincident with the channel centre, while the 2-carboxylatephenylamine ring of VCP-6 is symmetrically displaced from the 2-fold axis, allowing the 2-carboxylate group to form a tight intermolecular hydrogen bond with Nζ of Lys15 and an intramolecular hydrogen bond with the amine of VCP-6, stabilizing its conformation and explaining the greater affinity of VCP-6 compared to T4. This arrangement maintains optimal halogen bonding interactions in the binding sites, via chlorine atoms rather than iodine of the thyroid hormone, thereby explaining why the dichloro substitution pattern is a stronger binder than either the diiodo or dibromo analogues.
Collapse
|
7
|
Mandal PK, Collie GW, Kauffmann B, Huc I. Racemic crystal structures of A-DNA duplexes. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:709-715. [PMID: 35647918 PMCID: PMC9159285 DOI: 10.1107/s2059798322003928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/10/2022] [Indexed: 11/20/2022]
Abstract
Racemic crystallography benefits the identification of a structural form of a DNA sequence that was not previously observed for the enantiopure equivalent. The ease with which racemic mixtures crystallize compared with the equivalent chiral systems is routinely taken advantage of to produce crystals of small molecules. However, biological macromolecules such as DNA and proteins are naturally chiral, and thus the limited range of chiral space groups available hampers the crystallization of such molecules. Inspiring work over the past 15 years has shown that racemic mixtures of proteins, which were made possible by impressive advances in protein chemical synthesis, can indeed improve the success rate of protein crystallization experiments. More recently, the racemic crystallization approach was extended to include nucleic acids as a possible aid in the determination of enantiopure DNA crystal structures. Here, findings are reported that suggest that the benefits may extend beyond this. Two racemic crystal structures of the DNA sequence d(CCCGGG) are described which were found to fold into A-form DNA. This form differs from the Z-form DNA conformation adopted by the chiral equivalent in the solid state, suggesting that the use of racemates may also favour the emergence of new conformations. Importantly, the racemic mixture forms interactions in the solid state that differ from the chiral equivalent (including the formation of racemic pseudo-helices), suggesting that the use of racemic DNA mixtures could provide new possibilities for the design of precise self-assembled nanomaterials and nanostructures.
Collapse
|
8
|
Shelton CL, Meneely KM, Ronnebaum TA, Chilton AS, Riley AP, Prisinzano TE, Lamb AL. Rational inhibitor design for Pseudomonas aeruginosa salicylate adenylation enzyme PchD. J Biol Inorg Chem 2022; 27:541-551. [PMID: 35513576 PMCID: PMC9470617 DOI: 10.1007/s00775-022-01941-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/21/2022] [Indexed: 12/04/2022]
Abstract
Pseudomonas aeruginosa is an increasingly antibiotic-resistant pathogen that causes severe lung infections, burn wound infections, and diabetic foot infections. P. aeruginosa produces the siderophore pyochelin through the use of a non-ribosomal peptide synthetase (NRPS) biosynthetic pathway. Targeting members of siderophore NRPS proteins is one avenue currently under investigation for the development of new antibiotics against antibiotic-resistant organisms. Here, the crystal structure of the pyochelin adenylation domain PchD is reported. The structure was solved to 2.11 Å when co-crystallized with the adenylation inhibitor 5'-O-(N-salicylsulfamoyl)adenosine (salicyl-AMS) and to 1.69 Å with a modified version of salicyl-AMS designed to target an active site cysteine (4-cyano-salicyl-AMS). In the structures, PchD adopts the adenylation conformation, similar to that reported for AB3403 from Acinetobacter baumannii.
Collapse
Affiliation(s)
- Catherine L. Shelton
- grid.266515.30000 0001 2106 0692Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA ,grid.261132.50000 0001 2180 142XPresent Address: Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky 41099 USA
| | - Kathleen M. Meneely
- grid.266515.30000 0001 2106 0692Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA ,grid.215352.20000000121845633Present Address: Department of Chemistry, University of Texas San Antonio, San Antonio, TX 78249 USA
| | - Trey A. Ronnebaum
- grid.266515.30000 0001 2106 0692Department of Chemistry, University of Kansas, Lawrence, KS 66045 USA ,grid.25879.310000 0004 1936 8972Present Address: Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323 USA
| | - Annemarie S. Chilton
- grid.266515.30000 0001 2106 0692Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA
| | - Andrew P. Riley
- grid.185648.60000 0001 2175 0319Present Address: Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612 USA ,grid.266515.30000 0001 2106 0692Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66045 USA
| | - Thomas E. Prisinzano
- grid.266515.30000 0001 2106 0692Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66045 USA ,grid.266539.d0000 0004 1936 8438Present Address: Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596 USA
| | - Audrey L. Lamb
- grid.266515.30000 0001 2106 0692Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA ,grid.215352.20000000121845633Present Address: Department of Chemistry, University of Texas San Antonio, San Antonio, TX 78249 USA
| |
Collapse
|
9
|
Brzezinski D, Porebski PJ, Kowiel M, Macnar JM, Minor W. Recognizing and validating ligands with CheckMyBlob. Nucleic Acids Res 2021; 49:W86-W92. [PMID: 33905501 PMCID: PMC8262754 DOI: 10.1093/nar/gkab296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/04/2021] [Accepted: 04/11/2021] [Indexed: 11/15/2022] Open
Abstract
Structure-guided drug design depends on the correct identification of ligands in crystal structures of protein complexes. However, the interpretation of the electron density maps is challenging and often burdened with confirmation bias. Ligand identification can be aided by automatic methods such as CheckMyBlob, a machine learning algorithm that learns to generalize ligand descriptions from sets of moieties deposited in the Protein Data Bank. Here, we present the CheckMyBlob web server, a platform that can identify ligands in unmodeled fragments of electron density maps or validate ligands in existing models. The server processes PDB/mmCIF and MTZ files and returns a ranking of 10 most likely ligands for each detected electron density blob along with interactive 3D visualizations. Additionally, for each prediction/validation, a plugin script is generated that enables users to conduct a detailed analysis of the server results in Coot. The CheckMyBlob web server is available at https://checkmyblob.bioreproducibility.org.
Collapse
Affiliation(s)
- Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.,Institute of Computing Science, Poznan University of Technology, Poznan, 60-965, Poland.,Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Joanna M Macnar
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, 02-097, Poland.,Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, 02-089, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|
10
|
Lima GMA, Jagudin E, Talibov VO, Benz LS, Marullo C, Barthel T, Wollenhaupt J, Weiss MS, Mueller U. FragMAXapp: crystallographic fragment-screening data-analysis and project-management system. Acta Crystallogr D Struct Biol 2021; 77:799-808. [PMID: 34076593 PMCID: PMC8171072 DOI: 10.1107/s2059798321003818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/08/2021] [Indexed: 01/13/2023] Open
Abstract
Crystallographic fragment screening (CFS) has become one of the major techniques for screening compounds in the early stages of drug-discovery projects. Following the advances in automation and throughput at modern macromolecular crystallography beamlines, the bottleneck for CFS has shifted from collecting data to organizing and handling the analysis of such projects. The complexity that emerges from the use of multiple methods for processing and refinement and to search for ligands requires an equally sophisticated solution to summarize the output, allowing researchers to focus on the scientific questions instead of on software technicalities. FragMAXapp is the fragment-screening project-management tool designed to handle CFS projects at MAX IV Laboratory. It benefits from the powerful computing infrastructure of large-scale facilities and, as a web application, it is accessible from everywhere.
Collapse
Affiliation(s)
| | - Elmir Jagudin
- BioMAX, MAX IV Laboratory, Fotongatan 2, 224 84 Lund, Sweden
| | | | - Laila S. Benz
- Institut für Chemie und Biochemie, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | | | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| |
Collapse
|
11
|
Whitfield H, Hemmings AM, Mills SJ, Baker K, White G, Rushworth S, Riley AM, Potter BVL, Brearley CA. Allosteric Site on SHIP2 Identified Through Fluorescent Ligand Screening and Crystallography: A Potential New Target for Intervention. J Med Chem 2021; 64:3813-3826. [PMID: 33724834 PMCID: PMC7610569 DOI: 10.1021/acs.jmedchem.0c01944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Src homology 2 domain-containing inositol phosphate phosphatase 2 (SHIP2) is one of the 10 human inositol phosphate 5-phosphatases. One of its physiological functions is dephosphorylation of phosphatidylinositol 3,4,5-trisphosphate, PtdIns(3,4,5)P3. It is therefore a therapeutic target for pathophysiologies dependent on PtdIns(3,4,5)P3 and PtdIns(3,4)P2. Therapeutic interventions are limited by the dearth of crystallographic data describing ligand/inhibitor binding. An active site-directed fluorescent probe facilitated screening of compound libraries for SHIP2 ligands. With two additional orthogonal assays, several ligands including galloflavin were identified as low micromolar Ki inhibitors. One ligand, an oxo-linked ethylene-bridged dimer of benzene 1,2,4-trisphosphate, was shown to be an uncompetitive inhibitor that binds to a regulatory site on the catalytic domain. We posit that binding of ligands to this site restrains L4 loop motions that are key to interdomain communications that accompany high catalytic activity with phosphoinositide substrate. This site may, therefore, be a future druggable target for medicinal chemistry.
Collapse
Affiliation(s)
- Hayley Whitfield
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Andrew M Hemmings
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Stephen J Mills
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Kendall Baker
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Gaye White
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Stuart Rushworth
- Department of Molecular Haematology; Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Andrew M Riley
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Barry V L Potter
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| |
Collapse
|
12
|
Drakou CE, Gardeli C, Tsialtas I, Alexopoulos S, Mallouchos A, Koulas SM, Tsagkarakou AS, Asimakopoulos D, Leonidas DD, Psarra AMG, Skamnaki VT. Affinity Crystallography Reveals Binding of Pomegranate Juice Anthocyanins at the Inhibitor Site of Glycogen Phosphorylase: The Contribution of a Sugar Moiety to Potency and Its Implications to the Binding Mode. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10191-10199. [PMID: 32840370 DOI: 10.1021/acs.jafc.0c04205] [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] [Indexed: 06/11/2023]
Abstract
Anthocyanins (ACNs) are dietary phytochemicals with an acknowledged therapeutic significance. Pomegranate juice (PJ) is a rich source of ACNs with potential applications in nutraceutical development. Glycogen phosphorylase (GP) catalyzes the first step of glycogenolysis and is a molecular target for the development of antihyperglycemics. The inhibitory potential of the ACN fraction of PJ is assessed through a combination of in vitro assays, ex vivo investigation in hepatic cells, and X-ray crystallography studies. The ACN extract potently inhibits muscle and liver isoforms of GP. Affinity crystallography reveals the structural basis of inhibition through the binding of pelargonidin-3-O-glucoside at the GP inhibitor site. The glucopyranose moiety is revealed as a major determinant of potency as it promotes a structural binding mode different from that observed for other flavonoids. This inhibitory effect of the ACN scaffold and its binding mode at the GP inhibitor binding site may have significant implications for future structure-based drug design endeavors.
Collapse
Affiliation(s)
- Christina E Drakou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| | - Chrysavgi Gardeli
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens 118 55, Greece
| | - Ioannis Tsialtas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| | - Serafeim Alexopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| | - Athanasios Mallouchos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| | - Symeon M Koulas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| | - Anastasia S Tsagkarakou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| | - Demetres Asimakopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| | - Anna-Maria G Psarra
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| | - Vasiliki T Skamnaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500, Larisa, Greece
| |
Collapse
|
13
|
Krypotou E, Scortti M, Grundström C, Oelker M, Luisi BF, Sauer-Eriksson AE, Vázquez-Boland J. Control of Bacterial Virulence through the Peptide Signature of the Habitat. Cell Rep 2020; 26:1815-1827.e5. [PMID: 30759392 PMCID: PMC6389498 DOI: 10.1016/j.celrep.2019.01.073] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/09/2018] [Accepted: 01/17/2019] [Indexed: 12/20/2022] Open
Abstract
To optimize fitness, pathogens selectively activate their virulence program upon host entry. Here, we report that the facultative intracellular bacterium Listeria monocytogenes exploits exogenous oligopeptides, a ubiquitous organic N source, to sense the environment and control the activity of its virulence transcriptional activator, PrfA. Using a genetic screen in adsorbent-treated (PrfA-inducing) medium, we found that PrfA is functionally regulated by the balance between activating and inhibitory nutritional peptides scavenged via the Opp transport system. Activating peptides provide essential cysteine precursor for the PrfA-inducing cofactor glutathione (GSH). Non-cysteine-containing peptides cause promiscuous PrfA inhibition. Biophysical and co-crystallization studies reveal that peptides inhibit PrfA through steric blockade of the GSH binding site, a regulation mechanism directly linking bacterial virulence and metabolism. L. monocytogenes mutant analysis in macrophages and our functional data support a model in which changes in the balance of antagonistic Opp-imported oligopeptides promote PrfA induction intracellularly and PrfA repression outside the host. Listeria PrfA virulence regulation is controlled by antagonistic nutritional peptides Opp-imported peptides regulate PrfA upstream of the activating cofactor GSH PrfA is activated by peptides that provide essential cysteine for GSH biosynthesis Blockade of PrfA’s GSH binding site by peptides inhibits virulence gene activation
Collapse
Affiliation(s)
- Emilia Krypotou
- Microbial Pathogenesis Group, Infection Medicine, Edinburgh Medical School (Biomedical Sciences) and The Roslin Institute, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Mariela Scortti
- Microbial Pathogenesis Group, Infection Medicine, Edinburgh Medical School (Biomedical Sciences) and The Roslin Institute, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Christin Grundström
- Department of Chemistry and Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Melanie Oelker
- Department of Chemistry and Umeå Centre for Microbial Research, Umeå University, 901 87 Umeå, Sweden
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - José Vázquez-Boland
- Microbial Pathogenesis Group, Infection Medicine, Edinburgh Medical School (Biomedical Sciences) and The Roslin Institute, University of Edinburgh, Edinburgh EH16 4SB, UK.
| |
Collapse
|
14
|
Kowiel M, Brzezinski D, Porebski PJ, Shabalin IG, Jaskolski M, Minor W. Automatic recognition of ligands in electron density by machine learning. Bioinformatics 2019; 35:452-461. [PMID: 30016407 DOI: 10.1093/bioinformatics/bty626] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 07/12/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without solid support from the electron density maps. Ligand identification can be aided by automatic methods, but existing approaches are based on time-consuming iterative fitting. Results Here we report a new machine learning algorithm called CheckMyBlob that identifies ligands from experimental electron density maps. In benchmark tests on portfolios of up to 219 931 ligand binding sites containing the 200 most popular ligands found in the Protein Data Bank, CheckMyBlob markedly outperforms the existing automatic methods for ligand identification, in some cases doubling the recognition rates, while requiring significantly less time. Our work shows that machine learning can improve the automation of structure modeling and significantly accelerate the drug screening process of macromolecule-ligand complexes. Availability and implementation Code and data are available on GitHub at https://github.com/dabrze/CheckMyBlob. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, VA, USA
| |
Collapse
|
15
|
Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol 2019; 75:861-877. [PMID: 31588918 PMCID: PMC6778852 DOI: 10.1107/s2059798319011471] [Citation(s) in RCA: 3405] [Impact Index Per Article: 681.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/15/2019] [Indexed: 12/16/2022] Open
Abstract
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
Collapse
Affiliation(s)
- Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew L. Baker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gábor Bunkóczi
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Vincent B. Chen
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Tristan I. Croll
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Bradley Hintze
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Li-Wei Hung
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Swati Jain
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert D. Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | | | | | - Massimo D. Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Duncan H. Stockwell
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England
| | - Thomas C. Terwilliger
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Alexandre G. Urzhumtsev
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 67404 Illkirch, France
- Faculté des Sciences et Technologies, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | | | | | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
16
|
1-Phenyl-dihydrobenzoindazoles as novel colchicine site inhibitors: Structural basis and antitumor efficacy. Eur J Med Chem 2019; 177:448-456. [DOI: 10.1016/j.ejmech.2019.04.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/13/2019] [Accepted: 04/14/2019] [Indexed: 12/11/2022]
|
17
|
Kenjić N, Hoag MR, Moraski GC, Caperelli CA, Moran GR, Lamb AL. PvdF of pyoverdin biosynthesis is a structurally unique N 10-formyltetrahydrofolate-dependent formyltransferase. Arch Biochem Biophys 2019; 664:40-50. [PMID: 30689984 DOI: 10.1016/j.abb.2019.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 11/17/2022]
Abstract
The hydroxyornithine transformylase from Pseudomonas aeruginosa is known by the gene name pvdF, and has been hypothesized to use N10-formyltetrahydrofolate (N10-fTHF) as a co-substrate formyl donor to convert N5-hydroxyornithine (OHOrn) to N5-formyl- N5-hydroxyornithine (fOHOrn). PvdF is in the biosynthetic pathway for pyoverdin biosynthesis, a siderophore generated under iron-limiting conditions that has been linked to virulence, quorum sensing and biofilm formation. The structure of PvdF was determined by X-ray crystallography to 2.3 Å, revealing a formyltransferase fold consistent with N10-formyltetrahydrofolate dependent enzymes, such as the glycinamide ribonucleotide transformylases, N-sugar transformylases and methionyl-tRNA transformylases. Whereas the core structure, including the catalytic triad, is conserved, PvdF has three insertions of 18 or more amino acids, which we hypothesize are key to binding the OHOrn substrate. Steady state kinetics revealed a non-hyperbolic rate curve, promoting the hypothesis that PvdF uses a random-sequential mechanism, and favors folate binding over OHOrn.
Collapse
Affiliation(s)
- Nikola Kenjić
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA
| | - Matthew R Hoag
- Department of Chemistry and Biochemistry, 3210 N Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Garrett C Moraski
- Department of Chemistry and Biochemistry, 103 Chemistry and Biochemistry Building, Montana State University, Bozeman, MT, 59717, USA
| | - Carol A Caperelli
- Winkle College of Pharmacy, University of Cincinnati, ML 0514, 231 Albert Sabin Way, MSB 3109B, Cincinnati, OH, 45267, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Audrey L Lamb
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA.
| |
Collapse
|
18
|
Chen W, Zhang H, Chen Z, Jiang H, Liao L, Fan S, Xing J, Xie Y, Chen S, Ding H, Chen K, Jiang H, Luo C, Zheng M, Yao Z, Huang Y, Zhang Y. Development and evaluation of a novel series of Nitroxoline-derived BET inhibitors with antitumor activity in renal cell carcinoma. Oncogenesis 2018; 7:83. [PMID: 30385738 PMCID: PMC6212493 DOI: 10.1038/s41389-018-0093-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/10/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
Small molecular inhibitors targeting BRD4 family proteins are emerging as promising therapies in many types of human malignancies. However, whether BRD4, as well as other BET family members, may serve as therapeutic targets in renal cell carcinoma (RCC) remains unknown. In this study, we found that both BRD2 and BRD4 were over-expressed in RCC tissues, knock-down both of which achieved potent anti-proliferative effects in RCC cells. A novel category of BET inhibitors, originated from an approved drug Nitroxoline, were synthesized and evaluated with biochemical and cellular assays, as well as the method of crystallography. The complex crystal structures of several compounds in this category with the first bromodomain of BRD4 (BRD4-BD1) were solved, revealing the binding mechanism and facilitating further structural optimizations. Among them, compound BDF-1253 showed an approximately four-fold improvement in BRD4 inhibition compared with the prototype Nitroxoline and had good selectivity for BET proteins against other bromodomain proteins or epi-enzymes in biochemical assays. Compound BDF-1253 efficiently suppressed the expression of BET downstream genes, impaired RCC cells viability via inducing cell cycle arrest and apoptosis, and decreased tumor growth in RCC xenografts. In summary, these results suggest that inhibition of BET family members has great therapeutic potentials in the treatment of RCC, and the novel series of BET inhibitors reported here are promising to become RCC drug candidates.
Collapse
Affiliation(s)
- Wei Chen
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China
| | - Hao Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhifeng Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Hao Jiang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liping Liao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shijie Fan
- School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jing Xing
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiqian Xie
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Shijie Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Hong Ding
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Kaixian Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hualiang Jiang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Luo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingyue Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhiyi Yao
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 210032, China
| | - Yiran Huang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, China.
| | - Yuanyuan Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
19
|
Bongarzone S, Nadal M, Kaczmarska Z, Machón C, Álvarez M, Albericio F, Coll M. Structure-Driven Discovery of α,γ-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase. ACS OMEGA 2018; 3:8497-8505. [PMID: 31458978 PMCID: PMC6645139 DOI: 10.1021/acsomega.8b01472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 07/19/2018] [Indexed: 05/27/2023]
Abstract
Human cytomegalovirus (HCMV) is an opportunistic pathogen causing a variety of severe viral infections, including irreversible congenital disabilities. Nowadays, HCMV infection is treated by inhibiting the viral DNA polymerase. However, DNA polymerase inhibitors have several drawbacks. An alternative strategy is to use compounds against the packaging machinery or terminase complex, which is essential for viral replication. Our discovery that raltegravir (1), a human immunodeficiency virus drug, inhibits the nuclease function of UL89, one of the protein subunits of the complex, prompted us to further develop terminase inhibitors. On the basis of the structure of 1, a library of diketoacid (α,γ-DKA and β,δ-DKA) derivatives were synthesized and tested for UL89-C nuclease activity. The mode of action of α,γ-DKA derivatives on the UL89 active site was elucidated by using X-ray crystallography, molecular docking, and in vitro experiments. Our studies identified α,γ-DKA derivative 14 able to inhibit UL89 in vitro in the low micromolar range, making 14 an optimal candidate for further development and virus-infected cell assay.
Collapse
Affiliation(s)
- Salvatore Bongarzone
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Marta Nadal
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Zuzanna Kaczmarska
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Cristina Machón
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Mercedes Álvarez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
- Laboratory
of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
- Department
of Organic Chemistry, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Miquel Coll
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| |
Collapse
|
20
|
Tararina MA, Xue S, Smith LC, Muellers SN, Miranda PO, Janda KD, Allen KN. Crystallography Coupled with Kinetic Analysis Provides Mechanistic Underpinnings of a Nicotine-Degrading Enzyme. Biochemistry 2018; 57:3741-3751. [PMID: 29812904 PMCID: PMC6295333 DOI: 10.1021/acs.biochem.8b00384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nicotine oxidoreductase (NicA2) is a bacterial flavoenzyme, which catalyzes the first step of nicotine catabolism by oxidizing S-nicotine into N-methyl-myosmine. It has been proposed as a biotherapeutic for nicotine addiction because of its nanomolar substrate binding affinity. The first crystal structure of NicA2 has been reported, establishing NicA2 as a member of the monoamine oxidase (MAO) family. However, substrate specificity and structural determinants of substrate binding and/or catalysis have not been explored. Herein, analysis of the pH-rate profile, single-turnover kinetics, and binding data establish that pH does not significantly affect the catalytic rate and product release is not rate-limiting. The X-ray crystal structure of NicA2 with S-nicotine refined to 2.65 Å resolution reveals a hydrophobic binding site with a solvent exclusive cavity. Hydrophobic interactions predominantly orient the substrate, promoting the binding of a deprotonated species and supporting a hydride-transfer mechanism. Notably, NicA2 showed no activity against neurotransmitters oxidized by the two isoforms of human MAO. To further probe the substrate range of NicA2, enzyme activity was evaluated using a series of substrate analogues, indicating that S-nicotine is the optimal substrate and substitutions within the pyridyl ring abolish NicA2 activity. Moreover, mutagenesis and kinetic analysis of active-site residues reveal that removal of a hydrogen bond between the pyridyl ring of S-nicotine and the hydroxyl group of T381 has a 10-fold effect on KM, supporting the role of this bond in positioning the catalytically competent form of the substrate. Together, crystallography combined with kinetic analysis provides a deeper understanding of this enzyme's remarkable specificity.
Collapse
Affiliation(s)
- Margarita A. Tararina
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, Massachusetts 02118, United States
| | - Song Xue
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
| | - Lauren C. Smith
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
| | - Samantha N. Muellers
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Pedro O. Miranda
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
| | - Kim D. Janda
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology
- Worm Institute for Medical Research (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, BCC-582, La Jolla, California 92037, United States
| | - Karen N. Allen
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| |
Collapse
|
21
|
Jacques B, Coinçon M, Sygusch J. Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases. J Biol Chem 2018; 293:7737-7753. [PMID: 29593097 PMCID: PMC5961046 DOI: 10.1074/jbc.ra117.001098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/21/2018] [Indexed: 01/07/2023] Open
Abstract
Crystal structures of two bacterial metal (Zn2+)-dependent d-fructose-1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 Å resolution. The ligand complexes cryotrapped in native or mutant Helicobacter pylori aldolase crystals enabled a novel mechanistic description of FBP C3-C4 bond cleavage. The reaction mechanism uses active site remodeling during the catalytic cycle, implicating relocation of the Zn2+ cofactor that is mediated by conformational changes of active site loops. Substrate binding initiates conformational changes triggered upon P1 phosphate binding, which liberates the Zn2+-chelating His-180, allowing it to act as a general base for the proton abstraction at the FBP C4 hydroxyl group. A second zinc-chelating His-83 hydrogen bonds the substrate C4 hydroxyl group and assists cleavage by stabilizing the developing negative charge during proton abstraction. Cleavage is concerted with relocation of the metal cofactor from an interior to a surface-exposed site, thereby stabilizing the nascent enediolate form. Conserved residue Glu-142 is essential for protonation of the enediolate form prior to product release. A d-tagatose 1,6-bisphosphate enzymatic complex reveals how His-180-mediated proton abstraction controls stereospecificity of the cleavage reaction. Recognition and discrimination of the reaction products, dihydroxyacetone-P and d-glyceraldehyde 3-P, occurs via charged hydrogen bonds between hydroxyl groups of the triose-Ps and conserved residues, Asp-82 and Asp-255, respectively, and are crucial aspects of the enzyme's role in gluconeogenesis. Conformational changes in mobile loops β5-α7 and β6-α8 (containing catalytic residues Glu-142 and His-180, respectively) drive active site remodeling, enabling the relocation of the metal cofactor.
Collapse
Affiliation(s)
- Benoit Jacques
- From the Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Mathieu Coinçon
- From the Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Jurgen Sygusch
- From the Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada, To whom correspondence should be addressed:
Biochimie et Médecine moléculaire, Université de Montréal, CP 6128, Station Centre Ville, Montréal, Quebec H3C 3J7, Canada. Tel.:
514-343-2389; Fax:
514-343-6463; E-mail:
| |
Collapse
|
22
|
Beyerlein KR, Dierksmeyer D, Mariani V, Kuhn M, Sarrou I, Ottaviano A, Awel S, Knoska J, Fuglerud S, Jönsson O, Stern S, Wiedorn MO, Yefanov O, Adriano L, Bean R, Burkhardt A, Fischer P, Heymann M, Horke DA, Jungnickel KEJ, Kovaleva E, Lorbeer O, Metz M, Meyer J, Morgan A, Pande K, Panneerselvam S, Seuring C, Tolstikova A, Lieske J, Aplin S, Roessle M, White TA, Chapman HN, Meents A, Oberthuer D. Mix-and-diffuse serial synchrotron crystallography. IUCRJ 2017; 4:769-777. [PMID: 29123679 PMCID: PMC5668862 DOI: 10.1107/s2052252517013124] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/13/2017] [Indexed: 05/21/2023]
Abstract
Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.
Collapse
Affiliation(s)
- Kenneth R. Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Manuela Kuhn
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Angelica Ottaviano
- Department of Physics, California State University, Northridge, California, USA
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Silje Fuglerud
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olof Jönsson
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Stephan Stern
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- European X-ray Free-Electron Laser Facility GmbH (XFEL), Schenefeld, Germany
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Luigi Adriano
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anja Burkhardt
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Michael Heymann
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Daniel A. Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | | | - Elena Kovaleva
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Olga Lorbeer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Markus Metz
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Meyer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Andrew Morgan
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kanupriya Pande
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
| | - Aleksandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Julia Lieske
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Steve Aplin
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| |
Collapse
|
23
|
Beshnova DA, Pereira J, Lamzin VS. Estimation of the protein-ligand interaction energy for model building and validation. Acta Crystallogr D Struct Biol 2017; 73:195-202. [PMID: 28291754 PMCID: PMC5349431 DOI: 10.1107/s2059798317003400] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 03/01/2017] [Indexed: 12/03/2022] Open
Abstract
Macromolecular X-ray crystallography is one of the main experimental techniques to visualize protein-ligand interactions. The high complexity of the ligand universe, however, has delayed the development of efficient methods for the automated identification, fitting and validation of ligands in their electron-density clusters. The identification and fitting are primarily based on the density itself and do not take into account the protein environment, which is a step that is only taken during the validation of the proposed binding mode. Here, a new approach, based on the estimation of the major energetic terms of protein-ligand interaction, is introduced for the automated identification of crystallographic ligands in the indicated binding site with ARP/wARP. The applicability of the method to the validation of protein-ligand models from the Protein Data Bank is demonstrated by the detection of models that are `questionable' and the pinpointing of unfavourable interatomic contacts.
Collapse
Affiliation(s)
- Daria A. Beshnova
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Joana Pereira
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| |
Collapse
|
24
|
Das A, Bhattacharya S. Different Types of Molecular Docking Based on Variations of Interacting Molecules. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Molecular docking plays an important role in drug discovery research by facilitating target identification, target validation, virtual screening for lead identification and lead optimization. Depending upon the nature of the disease of interest, targets can be either protein or DNA while drugs are mostly organic small molecules. Different types of molecular docking techniques like protein-protein or protein-DNA or protein-small molecule or DNA-small molecule are employed for achieving the above mentioned objectives. This chapter provides a clear idea of the position of molecular docking in drug discovery with detailed discussion on different types of molecular docking based on the varieties of interacting partners. Subsequently the authors provide a detailed list of tools that can be used for docking in drug discovery and discus some examples of molecular docking in drug discovery before concluding with a remark on future areas of improvement in molecular docking related to drug discovery.
Collapse
|
25
|
Costa KC, Glasser NR, Conway SJ, Newman DK. Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms. Science 2016; 355:170-173. [PMID: 27940577 DOI: 10.1126/science.aag3180] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/14/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa produces colorful redox-active metabolites called phenazines, which underpin biofilm development, virulence, and clinical outcomes. Although phenazines exist in many forms, the best studied is pyocyanin. Here, we describe pyocyanin demethylase (PodA), a hitherto uncharacterized protein that oxidizes the pyocyanin methyl group to formaldehyde and reduces the pyrazine ring via an unusual tautomerizing demethylation reaction. Treatment with PodA disrupts P. aeruginosa biofilm formation similarly to DNase, suggesting interference with the pyocyanin-dependent release of extracellular DNA into the matrix. PodA-dependent pyocyanin demethylation also restricts established biofilm aggregate populations experiencing anoxic conditions. Together, these results show that modulating extracellular redox-active metabolites can influence the fitness of a biofilm-forming microorganism.
Collapse
Affiliation(s)
- Kyle C Costa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nathaniel R Glasser
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. .,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
26
|
Battles MB, Langedijk JP, Furmanova-Hollenstein P, Chaiwatpongsakorn S, Costello HM, Kwanten L, Vranckx L, Vink P, Jaensch S, Jonckers THM, Koul A, Arnoult E, Peeples ME, Roymans D, McLellan JS. Molecular mechanism of respiratory syncytial virus fusion inhibitors. Nat Chem Biol 2016; 12:87-93. [PMID: 26641933 PMCID: PMC4731865 DOI: 10.1038/nchembio.1982] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/29/2015] [Indexed: 12/21/2022]
Abstract
Respiratory syncytial virus (RSV) is a leading cause of pneumonia and bronchiolitis in young children and the elderly. Therapeutic small molecules have been developed that bind the RSV F glycoprotein and inhibit membrane fusion, yet their binding sites and molecular mechanisms of action remain largely unknown. Here we show that these inhibitors bind to a three-fold-symmetric pocket within the central cavity of the metastable prefusion conformation of RSV F. Inhibitor binding stabilizes this conformation by tethering two regions that must undergo a structural rearrangement to facilitate membrane fusion. Inhibitor-escape mutations occur in residues that directly contact the inhibitors or are involved in the conformational rearrangements required to accommodate inhibitor binding. Resistant viruses do not propagate as well as wild-type RSV in vitro, indicating a fitness cost for inhibitor escape. Collectively, these findings provide new insight into class I viral fusion proteins and should facilitate development of optimal RSV fusion inhibitors.
Collapse
Affiliation(s)
- Michael B Battles
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | | | | | - Supranee Chaiwatpongsakorn
- Center for Vaccines & Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Heather M Costello
- Center for Vaccines & Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Leen Kwanten
- Respiratory Infections Research, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Luc Vranckx
- Respiratory Infections Research, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Paul Vink
- Discovery Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Steffen Jaensch
- Discovery Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Tim H M Jonckers
- Medicinal Chemistry Department, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Anil Koul
- Respiratory Infections Research, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Eric Arnoult
- Computational Chemistry, Janssen R&DLLC, Spring House, Pennsylvania, USA
| | - Mark E Peeples
- Center for Vaccines & Immunity, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Dirk Roymans
- Respiratory Infections Research, Janssen Infectious Diseases & Vaccines BVBA, Beerse, Belgium
| | - Jason S McLellan
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| |
Collapse
|
27
|
Das A, Bhattacharya S. Different Types of Molecular Docking Based on Variations of Interacting Molecules. METHODS AND ALGORITHMS FOR MOLECULAR DOCKING-BASED DRUG DESIGN AND DISCOVERY 2016. [DOI: 10.4018/978-1-5225-0115-2.ch006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Molecular docking plays an important role in drug discovery research by facilitating target identification, target validation, virtual screening for lead identification and lead optimization. Depending upon the nature of the disease of interest, targets can be either protein or DNA while drugs are mostly organic small molecules. Different types of molecular docking techniques like protein-protein or protein-DNA or protein-small molecule or DNA-small molecule are employed for achieving the above mentioned objectives. This chapter provides a clear idea of the position of molecular docking in drug discovery with detailed discussion on different types of molecular docking based on the varieties of interacting partners. Subsequently the authors provide a detailed list of tools that can be used for docking in drug discovery and discus some examples of molecular docking in drug discovery before concluding with a remark on future areas of improvement in molecular docking related to drug discovery.
Collapse
|
28
|
Deller MC, Rupp B. Models of protein-ligand crystal structures: trust, but verify. J Comput Aided Mol Des 2015; 29:817-36. [PMID: 25665575 PMCID: PMC4531100 DOI: 10.1007/s10822-015-9833-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/29/2015] [Indexed: 11/26/2022]
Abstract
X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.
Collapse
Affiliation(s)
- Marc C Deller
- The Joint Center for Structural Genomics, San Diego, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Bernhard Rupp
- , k.-k. Hofkristallamt 991 Audrey Place, Vista, CA, 92084, USA.
- Department of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstr. 41, 6020, Innsbruck, Austria.
| |
Collapse
|
29
|
Hattne J, Reyes FE, Nannenga BL, Shi D, de la Cruz MJ, Leslie AGW, Gonen T. MicroED data collection and processing. Acta Crystallogr A Found Adv 2015; 71:353-60. [PMID: 26131894 PMCID: PMC4487423 DOI: 10.1107/s2053273315010669] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 06/02/2015] [Indexed: 11/30/2022] Open
Abstract
MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.
Collapse
Affiliation(s)
- Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Francis E. Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Brent L. Nannenga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - M. Jason de la Cruz
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew G. W. Leslie
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| |
Collapse
|
30
|
McNamara DE, Senese S, Yeates TO, Torres JZ. Structures of potent anticancer compounds bound to tubulin. Protein Sci 2015; 24:1164-72. [PMID: 25970265 DOI: 10.1002/pro.2704] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 12/12/2022]
Abstract
Small molecules that bind to tubulin exert powerful effects on cell division and apoptosis (programmed cell death). Cell-based high-throughput screening combined with chemo/bioinformatic and biochemical analyses recently revealed a novel compound MI-181 as a potent mitotic inhibitor with heightened activity towards melanomas. MI-181 causes tubulin depolymerization, activates the spindle assembly checkpoint arresting cells in mitosis, and induces apoptotic cell death. C2 is an unrelated compound previously shown to have lethal effects on microtubules in tumorigenic cell lines. We report 2.60 Å and 3.75 Å resolution structures of MI-181 and C2, respectively, bound to a ternary complex of αβ-tubulin, the tubulin-binding protein stathmin, and tubulin tyrosine ligase. In the first of these structures, our crystallographic results reveal a unique binding mode for MI-181 extending unusually deep into the well-studied colchicine-binding site on β-tubulin. In the second structure the C2 compound occupies the colchicine-binding site on β-tubulin with two chemical moieties recapitulating contacts made by colchicine, in combination with another system of atomic contacts. These insights reveal the source of the observed effects of MI-181 and C2 on microtubules, mitosis, and cultured cancer cell lines. The structural details of the interaction between tubulin and the described compounds may guide the development of improved derivative compounds as therapeutic candidates or molecular probes to study cancer cell division.
Collapse
Affiliation(s)
- Dan E McNamara
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, 90095
| | - Silvia Senese
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, 90095
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, 90095.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, 90095.,Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, 90095
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, 90095.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, 90095.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, 90095
| |
Collapse
|
31
|
Weichenberger CX, Afonine PV, Kantardjieff K, Rupp B. The solvent component of macromolecular crystals. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1023-38. [PMID: 25945568 PMCID: PMC4427195 DOI: 10.1107/s1399004715006045] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/25/2015] [Indexed: 11/10/2022]
Abstract
The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.
Collapse
Affiliation(s)
- Christian X. Weichenberger
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, Bozen/Bolzano, I-39100 Südtirol/Alto Adige, Italy
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mail Stop 64R0121, Berkeley, CA 94720, USA
| | - Katherine Kantardjieff
- College of Science and Mathematics, California State University, San Marcos, CA 92078, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
| |
Collapse
|
32
|
Brandmann T, Jinek M. Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group A rotavirus protein VP3. Proteins 2015; 83:997-1002. [PMID: 25758703 PMCID: PMC5068548 DOI: 10.1002/prot.24794] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/24/2015] [Indexed: 11/20/2022]
Abstract
In response to viral infections, the mammalian innate immune system induces the production of the second messenger 2′–5′ oligoadenylate (2–5A) to activate latent ribonuclease L (RNase L) that restricts viral replication and promotes apoptosis. A subset of rotaviruses and coronaviruses encode 2′,5′‐phosphodiesterase enzymes that hydrolyze 2–5A, thereby inhibiting RNase L activation. We report the crystal structure of the 2′,5′‐phosphodiesterase domain of group A rotavirus protein VP3 at 1.39 Å resolution. The structure exhibits a 2H phosphoesterase fold and reveals conserved active site residues, providing insights into the mechanism of 2–5A degradation in viral evasion of host innate immunity. Proteins 2015; 83:997–1002. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Tobias Brandmann
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | |
Collapse
|
33
|
Lord DM, Uzgoren Baran A, Soo VWC, Wood TK, Peti W, Page R. McbR/YncC: implications for the mechanism of ligand and DNA binding by a bacterial GntR transcriptional regulator involved in biofilm formation. Biochemistry 2014; 53:7223-31. [PMID: 25376905 PMCID: PMC4245980 DOI: 10.1021/bi500871a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
MqsR-controlled
colanic acid and biofilm regulator (McbR, also
known as YncC) is the protein product of a highly induced gene in
early Escherichia coli biofilm development
and has been regarded as an attractive target for blocking biofilm
formation. This protein acts as a repressor for genes involved in
exopolysaccharide production and an activator for genes involved in
stress response. To better understand the role of McbR in governing
the switch from exponential growth to the biofilm state, we determined
the crystal structure of McbR to 2.1 Å. The structure reveals
McbR to be a member of the FadR C-terminal domain (FCD) family of
the GntR superfamily of transcriptional regulators (this family was
named after the first identified member, GntR, a transcriptional repressor
of the gluconate operon of Bacillus subtilis). Previous to this study, only six of the predicted 2800 members
of this family had been structurally characterized. Here, we identify
the residues that constitute the McbR effector and DNA binding sites.
In addition, comparison of McbR with other members of the FCD domain
family shows that this family of proteins adopts highly distinct oligomerization
interfaces, which has implications for DNA binding and regulation.
Collapse
Affiliation(s)
- Dana M Lord
- Department of Molecular Biology, Cell Biology and Biochemistry, ‡Graduate Program in Molecular Pharmacology and Physiology, and §Department of Molecular Pharmacology, Physiology and Biotechnology & Chemistry, Brown University , Providence, Rhode Island 02903, United States
| | | | | | | | | | | |
Collapse
|
34
|
Nannenga BL, Shi D, Hattne J, Reyes FE, Gonen T. Structure of catalase determined by MicroED. eLife 2014; 3:e03600. [PMID: 25303172 PMCID: PMC4359365 DOI: 10.7554/elife.03600] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/28/2014] [Indexed: 11/13/2022] Open
Abstract
MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI:http://dx.doi.org/10.7554/eLife.03600.001
Collapse
Affiliation(s)
- Brent L Nannenga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| |
Collapse
|
35
|
Lee SJ, Park YS, Kim SJ, Lee BJ, Suh SW. Crystal structure of PhoU from Pseudomonas aeruginosa, a negative regulator of the Pho regulon. J Struct Biol 2014; 188:22-9. [PMID: 25220976 DOI: 10.1016/j.jsb.2014.08.010] [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: 04/08/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 11/27/2022]
Abstract
In Escherichia coli, seven genes (pstS, pstC, pstA, pstB, phoU, phoR, and phoB) are involved in sensing environmental phosphate (Pi) and controlling the expression of the Pho regulon. PhoU is a negative regulator of the Pi-signaling pathway and modulates Pi transport through Pi transporter proteins (PstS, PstC, PstA, and PstB) through the two-component system PhoR and PhoB. Inactivation of PhoY2, one of the two PhoU homologs in Mycobacterium tuberculosis, causes defects in persistence phenotypes and increased susceptibility to antibiotics and stresses. Despite the important biological role, the mechanism of PhoU function is still unknown. Here we have determined the crystal structure of PhoU from Pseudomonas aeruginosa. It exists as a dimer in the crystal, with each monomer consisting of two structurally similar three-helix bundles. Our equilibrium sedimentation measurements support the reversible monomer-dimer equilibrium model in which P. aeruginosa PhoU exists in solution predominantly as dimers, with monomers in a minor fraction, at low protein concentrations. The dissociation constant for PhoU dimerization is 3.2×10(-6)M. The overall structure of P. aeruginosa PhoU dimer resembles those of Aquifex aeolicus PhoU and Thermotoga maritima PhoU2. However, it shows distinct structural features in some loops and the dimerization pattern.
Collapse
Affiliation(s)
- Sang Jae Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea; Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ye Seol Park
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Chonnam 534-729, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea; Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
| |
Collapse
|
36
|
Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA. A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore. Nat Chem Biol 2014; 10:686-91. [PMID: 24952597 PMCID: PMC4104137 DOI: 10.1038/nchembio.1561] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 05/21/2014] [Indexed: 01/30/2023]
Abstract
Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.
Collapse
Affiliation(s)
- Hao Huang
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Nikolai B. Suslov
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Sandip A. Shelke
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Molly E. Evans
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | | | - Phoebe A. Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Joseph A. Piccirilli
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| |
Collapse
|
37
|
Carolan CG, Lamzin VS. Automated identification of crystallographic ligands using sparse-density representations. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1844-53. [PMID: 25004962 PMCID: PMC4089483 DOI: 10.1107/s1399004714008578] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 04/15/2014] [Indexed: 12/05/2022]
Abstract
A novel procedure for the automatic identification of ligands in macromolecular crystallographic electron-density maps is introduced. It is based on the sparse parameterization of density clusters and the matching of the pseudo-atomic grids thus created to conformationally variant ligands using mathematical descriptors of molecular shape, size and topology. In large-scale tests on experimental data derived from the Protein Data Bank, the procedure could quickly identify the deposited ligand within the top-ranked compounds from a database of candidates. This indicates the suitability of the method for the identification of binding entities in fragment-based drug screening and in model completion in macromolecular structure determination.
Collapse
Affiliation(s)
- C. G. Carolan
- European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - V. S. Lamzin
- European Molecular Biology Laboratory (EMBL), c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| |
Collapse
|
38
|
Munshi P, Snell EH, van der Woerd MJ, Judge RA, Myles DAA, Ren Z, Meilleur F. Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant. ACTA ACUST UNITED AC 2014; 70:414-20. [DOI: 10.1107/s1399004713029684] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/28/2013] [Indexed: 11/10/2022]
Abstract
Ketol-isomerases catalyze the reversible isomerization between aldoses and ketoses. D-Xylose isomerase carries out the first reaction in the catabolism of D-xylose, but is also able to convert D-glucose to D-fructose. The first step of the reaction is an enzyme-catalyzed ring opening of the cyclic substrate. The active-site amino-acid acid/base pair involved in ring opening has long been investigated and several models have been proposed. Here, the structure of the xylose isomerase E186Q mutant with cyclic glucose bound at the active site, refined against joint X-ray and neutron diffraction data, is reported. Detailed analysis of the hydrogen-bond networks at the active site of the enzyme suggests that His54, which is doubly protonated, is poised to protonate the glucose O5 position, while Lys289, which is neutral, promotes deprotonation of the glucose O1H hydroxyl groupviaan activated water molecule. The structure also reveals an extended hydrogen-bonding network that connects the conserved residues Lys289 and Lys183 through three structurally conserved water molecules and residue 186, which is a glutamic acid to glutamine mutation.
Collapse
|
39
|
Schacherl M, Waltersperger S, Baumann U. Structural characterization of the ribonuclease H-like type ASKHA superfamily kinase MK0840 from Methanopyrus kandleri. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2440-50. [PMID: 24311585 DOI: 10.1107/s0907444913022683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/12/2013] [Indexed: 11/10/2022]
Abstract
Murein recycling is a process in which microorganisms recover peptidoglycan-degradation products in order to utilize them in cell wall biosynthesis or basic metabolic pathways. Methanogens such as Methanopyrus kandleri contain pseudomurein, which differs from bacterial murein in its composition and branching. Here, four crystal structures of the putative sugar kinase MK0840 from M. kandleri in apo and nucleotide-bound states are reported. MK0840 shows high similarity to bacterial anhydro-N-acetylmuramic acid kinase, which is involved in murein recycling. The structure shares a common fold with panthothenate kinase and the 2-hydroxyglutaryl-CoA dehydratase component A, both of which are members of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases. Local conformational changes in the nucleotide-binding site between the apo and holo forms are observed upon nucleotide binding. Further insight is given into domain movements and putative active-site residues are identified.
Collapse
Affiliation(s)
- Magdalena Schacherl
- Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, 50674 Cologne, Germany
| | | | | |
Collapse
|
40
|
Tsai Y, McPhillips SE, González A, McPhillips TM, Zinn D, Cohen AE, Feese MD, Bushnell D, Tiefenbrunn T, Stout CD, Ludaescher B, Hedman B, Hodgson KO, Soltis SM. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:796-803. [PMID: 23633588 PMCID: PMC3640469 DOI: 10.1107/s0907444913001984] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/20/2013] [Indexed: 11/10/2022]
Abstract
AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.
Collapse
Affiliation(s)
- Yingssu Tsai
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080, USA
| | - Scott E. McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ana González
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Timothy M. McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Zinn
- LogicBlox Inc., 1349 West Peachtree Street NW, Atlanta, GA 30309, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael D. Feese
- Cocrystal Discovery Inc., 19805 North Creek Parkway, Bothell, WA 98011, USA
| | - David Bushnell
- Cocrystal Discovery Inc., 19805 North Creek Parkway, Bothell, WA 98011, USA
| | - Theresa Tiefenbrunn
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - C. David Stout
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Bertram Ludaescher
- Department of Computer Science and Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080, USA
| | - Keith O. Hodgson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080, USA
| | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| |
Collapse
|
41
|
Abstract
Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality.
Collapse
Affiliation(s)
- Zorik Chilingaryan
- School of Chemistry, University of Wollongong, Northfields Ave, Wollongong 2522, NSW, Australia.
| | | | | |
Collapse
|
42
|
Lang BS, Gorren ACF, Oberdorfer G, Wenzl MV, Furdui CM, Poole LB, Mayer B, Gruber K. Vascular bioactivation of nitroglycerin by aldehyde dehydrogenase-2: reaction intermediates revealed by crystallography and mass spectrometry. J Biol Chem 2012; 287:38124-34. [PMID: 22988236 PMCID: PMC3488082 DOI: 10.1074/jbc.m112.371716] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Aldehyde dehydrogenase-2 (ALDH2) catalyzes the bioactivation of nitroglycerin (glyceryl trinitrate, GTN) in blood vessels, resulting in vasodilation by nitric oxide (NO) or a related species. Because the mechanism of this reaction is still unclear we determined the three-dimensional structures of wild-type (WT) ALDH2 and of a triple mutant of the protein that exhibits low denitration activity (E268Q/C301S/C303S) in complex with GTN. The structure of the triple mutant showed that GTN binds to the active site via polar contacts to the oxyanion hole and to residues 268 and 301 as well as by van der Waals interactions to hydrophobic residues of the catalytic pocket. The structure of the GTN-soaked wild-type protein revealed a thionitrate adduct to Cys-302 as the first reaction intermediate, which was also found by mass spectrometry (MS) experiments. In addition, the MS data identified sulfinic acid as the irreversibly inactivated enzyme species. Assuming that the structures of the triple mutant and wild-type ALDH2 reflect binding of GTN to the catalytic site and the first reaction step, respectively, superposition of the two structures indicates that denitration of GTN is initiated by nucleophilic attack of Cys-302 at one of the terminal nitrate groups, resulting in formation of the observed thionitrate intermediate and release of 1,2-glyceryl dinitrate. Our results shed light on the molecular mechanism of the GTN denitration reaction and provide useful information on the structural requirements for high affinity binding of organic nitrates to the catalytic site of ALDH2.
Collapse
Affiliation(s)
- Barbara S Lang
- Department of Pharmacology and Toxicology, University of Graz, 8010 Graz, Austria
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Debreczeni JÉ, Emsley P. Handling ligands with Coot. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:425-30. [PMID: 22505262 PMCID: PMC3322601 DOI: 10.1107/s0907444912000200] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 01/03/2012] [Indexed: 11/21/2022]
Abstract
Coot is a molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Recently, tools have been added to work with small molecules. The newly incorporated tools for the manipulation and validation of ligands include interaction with PRODRG, subgraph isomorphism-based tools, representation of ligand chemistry, ligand fitting and analysis, and are described here.
Collapse
Affiliation(s)
- Judit É Debreczeni
- Structure and Biophysics, DS, AstraZeneca, Alderley Park SK10 4TG, England.
| | | |
Collapse
|
44
|
Martić M, Pernot L, Westermaier Y, Perozzo R, Kraljević TG, Krištafor S, Raić-Malić S, Scapozza L, Ametamey S. Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:293-315. [PMID: 21623543 DOI: 10.1080/15257770.2011.581258] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Novel C-6 substituted pyrimidine derivatives are good substrates of herpes simplex virus type 1 thymidine kinase (HSV1-TK). Enzyme kinetic experiments showed that our lead compound, N-methyl DHBT (N-methyl-6-(1,3-dihydroxyisobutyl) thymine; N-Me DHBT), is phosphorylated at a similar rate compared to "gold standard" 9-[4-fluoro-3-(hydroxymethyl)butyl]guanine, FHBG, (K(m) = 10 ± 0.3 μM; k(cat) = 0.036 ± 0.015 sec(-1)). Additionally, it does not show cytotoxic properties on B16F1 cells up to a concentration of 10 mM. The x-ray analysis of the crystal structures of HSV1-TK with N-Me DHBT and of HSV1-TK with the fluorinated derivative N-Me FHBT confirmed the binding mode predicted by docking studies and their substrate characteristics. Moreover, the crystal structure of HSV1-TK with N-Me DHBT revealed an additional water-mediated H-bond interesting for the design of further analogues.
Collapse
Affiliation(s)
- Miljen Martić
- Center for Pharmaceutical Science of ETH, PSI and USZ, ETH Zurich, Zurich, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
le Maire A, Gelin M, Pochet S, Hoh F, Pirocchi M, Guichou JF, Ferrer JL, Labesse G. In-plate protein crystallization, in situ ligand soaking and X-ray diffraction. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:747-55. [PMID: 21904027 DOI: 10.1107/s0907444911023249] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/14/2011] [Indexed: 11/10/2022]
Abstract
X-ray crystallography is now a recognized technique for ligand screening, especially for fragment-based drug design. However, protein crystal handling is still tedious and limits further automation. An alternative method for the solution of crystal structures of proteins in complex with small ligands is proposed. Crystallization drops are directly exposed to an X-ray beam after cocrystallization or soaking with the desired ligands. The use of dedicated plates in connection with an optimal parametrization of the G-rob robot allows efficient data collection. Three proteins currently under study in our laboratory for ligand screening by X-ray crystallography were used as validation test cases. The protein crystals belonged to different space groups, including a challenging monoclinic case. The resulting diffraction data can lead to clear ligand recognition, including indication of alternating conformations. These results demonstrate a possible method for automation of ligand screening by X-ray crystallography.
Collapse
Affiliation(s)
- Albane le Maire
- Université Montpellier 1 et 2, Centre de Biochimie Structurale, France
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. The Phenix software for automated determination of macromolecular structures. Methods 2011; 55:94-106. [PMID: 21821126 DOI: 10.1016/j.ymeth.2011.07.005] [Citation(s) in RCA: 660] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 07/14/2011] [Accepted: 07/15/2011] [Indexed: 11/26/2022] Open
Abstract
X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface.
Collapse
Affiliation(s)
- Paul D Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Abstract
The fragment-based approach is now well established as an important component of modern drug discovery. A key part in establishing its position as a viable technique has been the development of a range of biophysical methodologies with sufficient sensitivity to detect the binding of very weakly binding molecules. X-ray crystallography was one of the first techniques demonstrated to be capable of detecting such weak binding, but historically its potential for screening was under-appreciated and impractical due to its relatively low throughput. In this chapter we discuss the various benefits associated with fragment-screening by X-ray crystallography, and describe the technical developments we have implemented to allow its routine use in drug discovery. We emphasize how this approach has allowed a much greater exploitation of crystallography than has traditionally been the case within the pharmaceutical industry, with the rapid and timely provision of structural information having maximum impact on project direction.
Collapse
|
48
|
To automate or not to automate: this is the question. ACTA ACUST UNITED AC 2010; 11:211-21. [PMID: 20526815 PMCID: PMC2921494 DOI: 10.1007/s10969-010-9092-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 05/14/2010] [Indexed: 11/26/2022]
Abstract
New protocols and instrumentation significantly boost the outcome of structural biology, which has resulted in significant growth in the number of deposited Protein Data Bank structures. However, even an enormous increase of the productivity of a single step of the structure determination process may not significantly shorten the time between clone and deposition or publication. For example, in a medium size laboratory equipped with the LabDB and HKL-3000 systems, we show that automation of some (and integration of all) steps of the X-ray structure determination pathway is critical for laboratory productivity. Moreover, we show that the lag period after which the impact of a technology change is observed is longer than expected.
Collapse
|
49
|
Langendorf CG, Key TLG, Fenalti G, Kan WT, Buckle AM, Caradoc-Davies T, Tuck KL, Law RHP, Whisstock JC. The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+/enzyme interactions. PLoS One 2010; 5:e9280. [PMID: 20174634 PMCID: PMC2823781 DOI: 10.1371/journal.pone.0009280] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 01/23/2010] [Indexed: 01/14/2023] Open
Abstract
Background In mammals succinic semialdehyde dehydrogenase (SSADH) plays an essential role in the metabolism of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) to succinic acid (SA). Deficiency of SSADH in humans results in elevated levels of GABA and γ-Hydroxybutyric acid (GHB), which leads to psychomotor retardation, muscular hypotonia, non-progressive ataxia and seizures. In Escherichia coli, two genetically distinct forms of SSADHs had been described that are essential for preventing accumulation of toxic levels of succinic semialdehyde (SSA) in cells. Methodology/Principal Findings Here we structurally characterise SSADH encoded by the E coli gabD gene by X-ray crystallographic studies and compare these data with the structure of human SSADH. In the E. coli SSADH structure, electron density for the complete NADP+ cofactor in the binding sites is clearly evident; these data in particular revealing how the nicotinamide ring of the cofactor is positioned in each active site. Conclusions/Significance Our structural data suggest that a deletion of three amino acids in E. coli SSADH permits this enzyme to use NADP+, whereas in contrast the human enzyme utilises NAD+. Furthermore, the structure of E. coli SSADH gives additional insight into human mutations that result in disease.
Collapse
Affiliation(s)
- Christopher G. Langendorf
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Trevor L. G. Key
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- School of Chemistry, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Gustavo Fenalti
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Wan-Ting Kan
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Melbourne, Victoria, Australia
| | - Ashley M. Buckle
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | | | - Kellie L. Tuck
- School of Chemistry, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Ruby H. P. Law
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Melbourne, Victoria, Australia
- * E-mail: (RHPL); (JCW)
| | - James C. Whisstock
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Melbourne, Victoria, Australia
- * E-mail: (RHPL); (JCW)
| |
Collapse
|
50
|
Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. PHENIX: a comprehensive Python-based system for macromolecular structure solution. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:213-21. [PMID: 20124702 PMCID: PMC2815670 DOI: 10.1107/s0907444909052925] [Citation(s) in RCA: 18641] [Impact Index Per Article: 1331.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 12/09/2009] [Indexed: 12/02/2022]
Abstract
The PHENIX software for macromolecular structure determination is described. Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
Collapse
Affiliation(s)
- Paul D Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|