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Kirschner H, Heister N, Zouatom M, Zhou T, Hofmann E, Scherkenbeck J, Stoll R. Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase. J Med Chem 2024; 67:6384-6396. [PMID: 38574272 DOI: 10.1021/acs.jmedchem.3c02382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Peptide deformylase (PDF) is involved in bacterial protein maturation processes. Originating from the interest in a new antibiotic, tremendous effort was put into the refinement of PDF inhibitors (PDFIs) and their selectivity. We obtained a full NMR backbone assignment the emergent additional protein backbone resonances of ecPDF 1-147 in complex with 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide (2), a potential new structural scaffold for more selective PDFIs. We also determined the complex crystal structures of E. coli PDF (ecPDF fl) and 2. Our structure suggests an alternative ligand conformation within the protein, a possible starting point for further selectivity optimization. The orientation of the second ligand conformation in the crystal structure points toward a small region of the S1' pocket, which differs between bacterial PDFs and human PDF. Moreover, we analyzed the binding mode of 2 via NMR TITAN line shape analysis, revealing an induced fit mechanism.
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Affiliation(s)
- Hendrik Kirschner
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR, and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany
| | - Nicole Heister
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR, and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany
| | - Manuela Zouatom
- Faculty of Mathematics and Natural Sciences, Bioorganic Chemistry, University of Wuppertal, Gaußstraße 20, Wuppertal 42119, Germany
| | - Tianyi Zhou
- Faculty of Mathematics and Natural Sciences, Bioorganic Chemistry, University of Wuppertal, Gaußstraße 20, Wuppertal 42119, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany
| | - Jürgen Scherkenbeck
- Faculty of Mathematics and Natural Sciences, Bioorganic Chemistry, University of Wuppertal, Gaußstraße 20, Wuppertal 42119, Germany
| | - Raphael Stoll
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR, and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, Bochum 44801, Germany
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2
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Kirschner H, John M, Zhou T, Bachmann N, Schultz A, Hofmann E, Bandow JE, Scherkenbeck J, Metzler-Nolte N, Stoll R. Structural Insights into Antibacterial Payload Release from Gold Nanoparticles Bound to E. coli Peptide Deformylase. ChemMedChem 2024; 19:e202300538. [PMID: 38057137 DOI: 10.1002/cmdc.202300538] [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] [Received: 10/06/2023] [Revised: 11/10/2023] [Indexed: 12/08/2023]
Abstract
The lack of new antibiotics and the rapidly rising number of pathogens resistant to antibiotics pose a serious problem to mankind. In bacteria, the cell membrane provides the first line of defence to antibiotics by preventing them from reaching their molecular target. To overcome this entrance barrier, it has been suggested[1] that small Gold-Nanoparticles (AuNP) could possibly function as drug delivery systems for antibiotic ligands. Using actinonin-based ligands, we provide here proof-of-principle of AuNP functionalisation, the capability to bind and inhibit the target protein of the ligand, and the possibility to selectively release the antimicrobial payload. To this end, we successfully synthesised AuNP coated with thio-functionalised actinonin and a derivative. Interactions between 15N-enriched His-peptide deformylase 1-147 from E. coli (His-ecPDF 1-147) and compound-coated AuNP were investigated via 2D 1H-15N-HSQC NMR spectra proving the direct binding to His-ecPDF 1-147. More importantly by adding dithiothreitol (DTT), we show that the derivative is successfully released from AuNPs while still bound to His-ecPDF 1-147. Our findings indicate that AuNP-conjugated ligands can address and bind intracellular target proteins. The system introduced here presents a new delivery platform for antibiotics and allows for the easy optimisation of ligand coated AuNPs.
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Affiliation(s)
- Hendrik Kirschner
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Milena John
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Tianyi Zhou
- Bioorganic Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Nathalie Bachmann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - André Schultz
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Julia Elisabeth Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Jürgen Scherkenbeck
- Bioorganic Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstraße 20, 42119, Wuppertal, Germany
| | - Nils Metzler-Nolte
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Raphael Stoll
- Biochemistry II, Biomolecular NMR Spectroscopy, RUBiospec|NMR and PhenomeCentre@RUBUAR, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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3
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Alvarez-Garcia D, Schmidtke P, Cubero E, Barril X. Extracting Atomic Contributions to Binding Free Energy Using Molecular Dynamics Simulations with Mixed Solvents (MDmix). Curr Drug Discov Technol 2022; 19:62-68. [PMID: 34951392 PMCID: PMC9906626 DOI: 10.2174/1570163819666211223162829] [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: 08/05/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mixed solvents MD (MDmix) simulations have proved to be a useful and increasingly accepted technique with several applications in structure-based drug discovery. One of the assumptions behind the methodology is the transferability of free energy values from the simulated cosolvent molecules to larger drug-like molecules. However, the binding free energy maps (ΔGbind) calculated for the different moieties of the cosolvent molecules (e.g. a hydroxyl map for the ethanol) are largely influenced by the rest of the solvent molecule and do not reflect the intrinsic affinity of the moiety in question. As such, they are hardly transferable to different molecules. METHOD To achieve transferable energies, we present here a method for decomposing the molecular binding free energy into accurate atomic contributions. RESULT We demonstrate with two qualitative visual examples how the corrected energy maps better match known binding hotspots and how they can reveal hidden hotspots with actual drug design potential. CONCLUSION Atomic decomposition of binding free energies derived from MDmix simulations provides transferable and quantitative binding free energy maps.
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Affiliation(s)
- Daniel Alvarez-Garcia
- Gain Therapeutics, Parc Cientific de Barcelona, Baldiri Reixac 10, 08029 Barcelona, Spain
| | - Peter Schmidtke
- Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain;,Current address: Discngine, 79 Avenue Ledru Rollin, 75012 Paris, France;
| | - Elena Cubero
- Gain Therapeutics, Parc Cientific de Barcelona, Baldiri Reixac 10, 08029 Barcelona, Spain
| | - Xavier Barril
- Gain Therapeutics, Parc Cientific de Barcelona, Baldiri Reixac 10, 08029 Barcelona, Spain;,Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain;,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain,Address correspondence to this author at the Gain Therapeutics, Parc Cientific de Barcelona, Baldiri Reixac 10, 08029 Barcelona, Spain; E-mail:
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4
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Habjanič J, Zerbe O, Freisinger E. A histidine-rich Pseudomonas metallothionein with a disordered tail displays higher binding capacity for cadmium than zinc. Metallomics 2018; 10:1415-1429. [DOI: 10.1039/c8mt00193f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The NMR solution structure of a Pseudomonas metallothionein reveals a different binding capacity for ZnII and CdII ions that results in two novel metal-cluster topologies. Replacement of a non-coordinating residue by histidine decreases the kinetic lability of the cluster. All three structures reported show an identical protein fold.
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Affiliation(s)
- Jelena Habjanič
- Department of Chemistry
- University of Zurich
- Zurich
- Switzerland
| | - Oliver Zerbe
- Department of Chemistry
- University of Zurich
- Zurich
- Switzerland
| | - Eva Freisinger
- Department of Chemistry
- University of Zurich
- Zurich
- Switzerland
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5
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Alontaga AY, Li Y, Chen CH, Ma CT, Malany S, Key DE, Sergienko E, Sun Q, Whipple DA, Matharu DS, Li B, Vega R, Li YJ, Schoenen FJ, Blagg BSJ, Chung TD, Chen Y. Design of high-throughput screening assays and identification of a SUMO1-specific small molecule chemotype targeting the SUMO-interacting motif-binding surface. ACS COMBINATORIAL SCIENCE 2015; 17:239-46. [PMID: 25719760 DOI: 10.1021/co500181b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions are generally challenging to target by small molecules. To address the challenge, we have used a multidisciplinary approach to identify small-molecule disruptors of protein-protein interactions that are mediated by SUMO (small ubiquitin-like modifier) proteins. SUMO modifications have emerged as a target with importance in treating cancer, neurodegenerative disorders, and viral infections. It has been shown that inhibiting SUMO-mediated protein-protein interactions can sensitize cancer cells to chemotherapy and radiation. We have developed highly sensitive assays using time-resolved fluorescence resonance energy transfer (TR-FRET) and fluorescence polarization (FP) that were used for high-throughput screening (HTS) to identify inhibitors for SUMO-dependent protein-protein interactions. Using these assays, we have identified a nonpeptidomimetic small molecule chemotype that binds to SUMO1 but not SUMO2 or 3. NMR chemical shift perturbation studies have shown that the compounds of this chemotype bind to the SUMO1 surface required for protein-protein interaction, despite the high sequence similarity of SUMO1 and SUMO2 and 3 at this surface.
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Affiliation(s)
- Aileen Y. Alontaga
- Department
of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, United States
| | - Yifei Li
- Department
of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, United States
| | - Chih-Hong Chen
- Department
of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, United States
| | - Chen-Ting Ma
- Conrad
Prebys Center for Chemical Genomics, Sanford-Burnham Institute, La Jolla, California 92037, United States
| | - Siobhan Malany
- Conrad
Prebys Center for Chemical Genomics, Sanford-Burnham Institute at Lake Nona, Orlando, Florida 32827, United States
| | - Danielle E. Key
- Conrad
Prebys Center for Chemical Genomics, Sanford-Burnham Institute at Lake Nona, Orlando, Florida 32827, United States
| | - Eduard Sergienko
- Conrad
Prebys Center for Chemical Genomics, Sanford-Burnham Institute, La Jolla, California 92037, United States
| | - Qing Sun
- Conrad
Prebys Center for Chemical Genomics, Sanford-Burnham Institute, La Jolla, California 92037, United States
| | - David A. Whipple
- University of Kansas Specialized Chemistry Center, Lawrence, Kansas 66049, United States
| | - Daljit S. Matharu
- University of Kansas Specialized Chemistry Center, Lawrence, Kansas 66049, United States
| | - Baozong Li
- Department
of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, United States
| | - Ramir Vega
- Department
of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, United States
| | - Yi-Jia Li
- Department
of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, United States
| | - Frank J. Schoenen
- University of Kansas Specialized Chemistry Center, Lawrence, Kansas 66049, United States
| | - Brian S. J. Blagg
- University of Kansas Specialized Chemistry Center, Lawrence, Kansas 66049, United States
| | - Thomas D.Y. Chung
- Conrad
Prebys Center for Chemical Genomics, Sanford-Burnham Institute, La Jolla, California 92037, United States
| | - Yuan Chen
- Department
of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, United States
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6
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Yang Y, Keeler C, Kuo IY, Lolis EJ, Ehrlich BE, Hodsdon ME. Oligomerization of the polycystin-2 C-terminal tail and effects on its Ca2+-binding properties. J Biol Chem 2015; 290:10544-54. [PMID: 25716316 PMCID: PMC4400361 DOI: 10.1074/jbc.m115.641803] [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: 02/02/2015] [Indexed: 02/05/2023] Open
Abstract
Polycystin-2 (PC2) belongs to the transient receptor potential (TRP) family and forms a Ca2+-regulated channel. The C-terminal cytoplasmic tail of human PC2 (HPC2 Cterm) is important for PC2 channel assembly and regulation. In this study, we characterized the oligomeric states and Ca2+-binding profiles in the C-terminal tail using biophysical approaches. Specifically, we determined that HPC2 Cterm forms a trimer in solution with and without Ca2+ bound, although TRP channels are believed to be tetramers. We found that there is only one Ca2+-binding site in the HPC2 Cterm, located within its EF-hand domain. However, the Ca2+ binding affinity of the HPC2 Cterm trimer is greatly enhanced relative to the intrinsic binding affinity of the isolated EF-hand domain. We also employed the sea urchin PC2 (SUPC2) as a model for biophysical and structural characterization. The sea urchin C-terminal construct (SUPC2 Ccore) also forms trimers in solution, independent of Ca2+ binding. In contrast to the human PC2, the SUPC2 Ccore contains two cooperative Ca2+-binding sites within its EF-hand domain. Consequently, trimerization does not further improve the affinity of Ca2+ binding in the SUPC2 Ccore relative to the isolated EF-hand domain. Using NMR, we localized the Ca2+-binding sites in the SUPC2 Ccore and characterized the conformational changes in its EF-hand domain due to trimer formation. Our study provides a structural basis for understanding the Ca2+-dependent regulation of the PC2 channel by its cytosolic C-terminal domain. The improved methodology also serves as a good strategy to characterize other Ca2+-binding proteins.
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Affiliation(s)
- Yifei Yang
- From the Departments of Laboratory Medicine, Pharmacology, and
| | | | | | | | - Barbara E Ehrlich
- Pharmacology, and Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, Connecticut 06520
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7
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Singh RK, Cho K, Padi SKR, Yu J, Haldar M, Mandal T, Yan C, Cook G, Guo B, Mallik S, Srivastava DK. Mechanism of N-Acylthiourea-mediated activation of human histone deacetylase 8 (HDAC8) at molecular and cellular levels. J Biol Chem 2015; 290:6607-19. [PMID: 25605725 DOI: 10.1074/jbc.m114.600627] [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] [Indexed: 11/06/2022] Open
Abstract
We reported previously that an N-acylthiourea derivative (TM-2-51) serves as a potent and isozyme-selective activator for human histone deacetylase 8 (HDAC8). To probe the molecular mechanism of the enzyme activation, we performed a detailed account of the steady-state kinetics, thermodynamics, molecular modeling, and cell biology studies. The steady-state kinetic data revealed that TM-2-51 binds to HDAC8 at two sites in a positive cooperative manner. Isothermal titration calorimetric and molecular modeling data conformed to the two-site binding model of the enzyme-activator complex. We evaluated the efficacy of TM-2-51 on SH-SY5Y and BE(2)-C neuroblastoma cells, wherein the HDAC8 expression has been correlated with cellular malignancy. Whereas TM-2-51 selectively induced cell growth inhibition and apoptosis in SH-SY5Y cells, it showed no such effects in BE(2)-C cells, and this discriminatory feature appears to be encoded in the p53 genotype of the above cells. Our mechanistic and cellular studies on HDAC8 activation have the potential to provide insight into the development of novel anticancer drugs.
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Affiliation(s)
| | | | | | - Junru Yu
- From the Departments of Chemistry and Biochemistry
| | | | | | - Changhui Yan
- Computer Science, North Dakota State University, Fargo, North Dakota 58108
| | - Gregory Cook
- From the Departments of Chemistry and Biochemistry
| | - Bin Guo
- Pharmaceutical Sciences, and
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8
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Nordwald EM, Armstrong GS, Kaar JL. NMR-Guided Rational Engineering of an Ionic-Liquid-Tolerant Lipase. ACS Catal 2014. [DOI: 10.1021/cs500978x] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Erik M. Nordwald
- Department of Chemical and Biological Engineering, ‡Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Geoffrey S. Armstrong
- Department of Chemical and Biological Engineering, ‡Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Joel L. Kaar
- Department of Chemical and Biological Engineering, ‡Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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9
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Singh DV, Bharti SK, Agarwal S, Roy R, Misra K. Study of interaction of human serum albumin with curcumin by NMR and docking. J Mol Model 2014; 20:2365. [DOI: 10.1007/s00894-014-2365-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 06/22/2014] [Indexed: 10/25/2022]
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10
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Probing multimodal ligand binding regions on ubiquitin using nuclear magnetic resonance, chromatography, and molecular dynamics simulations. J Chromatogr A 2012; 1229:113-20. [DOI: 10.1016/j.chroma.2011.12.101] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 11/15/2011] [Accepted: 12/23/2011] [Indexed: 11/23/2022]
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11
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Ziarek JJ, Peterson FC, Lytle BL, Volkman BF. Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Methods Enzymol 2011; 493:241-75. [PMID: 21371594 PMCID: PMC3635485 DOI: 10.1016/b978-0-12-381274-2.00010-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the last 15 years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like compounds because of its ability to identify binding sites, affinities, and ligand poses at the level of individual amino acids without necessarily solving the structure of the protein-ligand complex. However, it can also provide structures of flexible proteins and low-affinity (K(d)>10(-6)M) complexes, which often fail to crystallize. This chapter emphasizes a throughput-focused protocol that aims to identify practical aspects of binding site characterization, automated and semiautomated NMR assignment methods, and structure determination of protein-ligand complexes by NMR.
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Affiliation(s)
- Joshua J. Ziarek
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, 53226 USA
| | - Francis C. Peterson
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, 53226 USA
| | - Betsy L. Lytle
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, 53226 USA
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, 53226 USA
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12
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Neuman RC, Gerig JT. Interaction of Alcohols with [Val5]angiotensin in Alcohol−Water Mixtures. J Phys Chem B 2010; 114:6722-31. [DOI: 10.1021/jp101305u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. C. Neuman
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106
| | - J. T. Gerig
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106
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13
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Amero CD, Byerly DW, McElroy CA, Simmons A, Foster MP. Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase. Biochemistry 2009; 48:7595-607. [PMID: 19627112 DOI: 10.1021/bi900600b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide deformylase (PDF) is an enzyme that is responsible for removing the formyl group from nascently synthesized polypeptides in bacteria, attracting much attention as a potential target for novel antibacterial agents. Efforts to develop potent inhibitors of the enzyme have progressed on the basis of classical medicinal chemistry, combinatorial chemistry, and structural approaches, yet the validity of PDF as an antibacterial target hangs, in part, on the ability of inhibitors to selectively target this enzyme in favor of structurally related metallohydrolases. We have used (15)N NMR spectroscopy and isothermal titration calorimetry to investigate the high-affinity interaction of EcPDF with actinonin, a naturally occurring potent EcPDF inhibitor. Backbone amide chemical shifts, residual dipolar couplings, hydrogen-deuterium exchange, and (15)N relaxation reveal structural and dynamic effects of ligand binding in the immediate vicinity of the ligand-binding site as well as at remote sites. A comparison of the crystal structures of free and actinonin-bound EcPDF with the solution data suggests that most of the consequences of the ligand binding to the protein are lost or obscured during crystallization. The results of these studies improve our understanding of the thermodynamic global minimum and have important implications for structure-based drug design.
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Affiliation(s)
- Carlos D Amero
- Biophysics Program, The Ohio StateUniversity, Columbus, Ohio 43210, USA
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14
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Seco J, Luque FJ, Barril X. Binding site detection and druggability index from first principles. J Med Chem 2009; 52:2363-71. [PMID: 19296650 DOI: 10.1021/jm801385d] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In drug discovery, it is essential to identify binding sites on protein surfaces that drug-like molecules could exploit to exert a biological effect. Both X-ray crystallography and NMR experiments have demonstrated that organic solvents bind precisely at these locations. We show that this effect is reproduced using molecular dynamics with a binary solvent. Furthermore, analysis of the simulations give direct access to interaction free energies between the protein and small organic molecules, which can be used to detect binding sites and to predict the maximal affinity that a drug-like molecule could attain for them. On a set of pharmacologically relevant proteins, we obtain good predictions for druggable sites as well as for protein-protein and low affinity binding sites. This is the first druggability index not based on surface descriptors and, being independent of a training set, is particularly indicated to study unconventional targets such as protein-protein interactions or allosteric binding sites.
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Affiliation(s)
- Jesus Seco
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
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15
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Huang H, Melacini G. High-resolution protein hydration NMR experiments: Probing how protein surfaces interact with water and other non-covalent ligands. Anal Chim Acta 2006; 564:1-9. [PMID: 17723356 DOI: 10.1016/j.aca.2005.10.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 10/13/2005] [Accepted: 10/20/2005] [Indexed: 10/25/2022]
Abstract
High-resolution solution NMR experiments are extremely useful to characterize the location and the dynamics of hydrating water molecules at atomic resolution. However, these methods are severely limited by undesired incoherent transfer pathways such as those arising from exchange-relayed intra-molecular cross-relaxation. Here, we review several complementary exchange network editing methods that can be used in conjunction with other types of NMR hydration experiments such as magnetic relaxation dispersion and 1J(NC') measurements to circumvent these limitations. We also review several recent contributions illustrating how the original solution hydration NMR pulse sequence architecture has inspired new approaches to map other types of non-covalent interactions going well beyond the initial scope of hydration. Specifically, we will show how hydration NMR methods have evolved and have been adapted to binding site mapping, ligand screening, protein-peptide and peptide-lipid interaction profiling.
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Affiliation(s)
- Hao Huang
- Department of Chemistry, McMaster University, 1280 Main Street, W. Hamilton, Ont., Canada L8S 4M1
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16
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Horton DA, Bourne GT, Smythe ML. The combinatorial synthesis of bicyclic privileged structures or privileged substructures. Chem Rev 2003; 103:893-930. [PMID: 12630855 DOI: 10.1021/cr020033s] [Citation(s) in RCA: 2443] [Impact Index Per Article: 116.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Douglas A Horton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, 4072 Queensland, Australia
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