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Wienen-Schmidt B, Schmidt D, Gerber HD, Heine A, Gohlke H, Klebe G. Surprising Non-Additivity of Methyl Groups in Drug-Kinase Interaction. ACS Chem Biol 2019; 14:2585-2594. [PMID: 31638770 DOI: 10.1021/acschembio.9b00476] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drug optimization is guided by biophysical methods with increasing popularity. In the context of lead structure modifications, the introduction of methyl groups is a simple but potentially powerful approach. Hence, it is crucial to systematically investigate the influence of ligand methylation on biophysical characteristics such as thermodynamics. Here, we investigate the influence of ligand methylation in different positions and combinations on the drug-kinase interaction. Binding modes and complex structures were analyzed using protein crystallography. Thermodynamic signatures were measured via isothermal titration calorimetry (ITC). An extensive computational analysis supported the understanding of the underlying mechanisms. We found that not only position but also stereochemistry of the methyl group has an influence on binding potency as well as the thermodynamic signature of ligand binding to the protein. Strikingly, the combination of single methyl groups does not lead to additive effects. In our case, the merger of two methyl groups in one ligand leads to an entirely new alternative ligand binding mode in the protein ligand complex. Moreover, the combination of the two methyl groups also resulted in a nonadditive thermodynamic profile of ligand binding. Molecular dynamics (MD) simulations revealed distinguished characteristic motions of the ligands in solution explaining the pronounced thermodynamic changes. The unexpected drastic change in protein ligand interaction highlights the importance of crystallographic control even for minor modifications such as the introduction of a methyl group. For an in-depth understanding of ligand binding behavior, MD simulations have shown to be a powerful tool.
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Affiliation(s)
- Barbara Wienen-Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Denis Schmidt
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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53
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Zender M, Witzgall F, Kiefer A, Kirsch B, Maurer CK, Kany AM, Xu N, Schmelz S, Börger C, Blankenfeldt W, Empting M. Flexible Fragment Growing Boosts Potency of Quorum-Sensing Inhibitors against Pseudomonas aeruginosa Virulence. ChemMedChem 2019; 15:188-194. [PMID: 31709767 PMCID: PMC7004148 DOI: 10.1002/cmdc.201900621] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Indexed: 12/24/2022]
Abstract
Hit-to-lead optimization is a critical phase in drug discovery. Herein, we report on the fragment-based discovery and optimization of 2-aminopyridine derivatives as a novel lead-like structure for the treatment of the dangerous opportunistic pathogen Pseudomonas aeruginosa. We pursue an innovative treatment strategy by interfering with the Pseudomonas quinolone signal (PQS) quorum sensing (QS) system leading to an abolishment of bacterial pathogenicity. Our compounds act on the PQS receptor (PqsR), a key transcription factor controlling the expression of various pathogenicity determinants. In this target-driven approach, we made use of biophysical screening via surface plasmon resonance (SPR) followed by isothermal titration calorimetry (ITC)-enabled enthalpic efficiency (EE) evaluation. Hit optimization then involved growth vector identification and exploitation. Astonishingly, the latter was successfully achieved by introducing flexible linkers rather than rigid motifs leading to a boost in activity on the target receptor and anti-virulence potency.
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Affiliation(s)
- Michael Zender
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Florian Witzgall
- Structure and Function of Proteins (SFPR), Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Alexander Kiefer
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Benjamin Kirsch
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Christine K Maurer
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Andreas M Kany
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Ningna Xu
- Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Stefan Schmelz
- Structure and Function of Proteins (SFPR), Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Carsten Börger
- PharmBioTec GmbH, Science Park 1, 66123, Saarbrücken, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins (SFPR), Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany.,Biotechnology and Bioinformatics, Institute for Biochemistry, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Martin Empting
- Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
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54
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Ferenczy GG, Keserű GM. Thermodynamic profiling for fragment-based lead discovery and optimization. Expert Opin Drug Discov 2019; 15:117-129. [PMID: 31741402 DOI: 10.1080/17460441.2020.1691166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The enthalpic and entropic components of the ligand-protein binding free energy reflect the type and quality of the interactions and relate to the physicochemical properties of the ligands. These findings have significance in medicinal chemistry optimizations since they suggest that the thermodynamic profiling of the binding may help monitor and control the unfavorable size and hydrophobicity increase typically accompanying affinity improvements and leading to suboptimal pharmacokinetic properties.Areas covered: This review describes the ligand-protein binding event in terms of elementary steps, their associated interactions, and their enthalpic and entropic consequences. The relationships among the breaking and forming interactions, the binding thermodynamic profile, and the physicochemical properties of the ligands are also discussed.Expert opinion: Analysis of the size dependence of available affinity and favorable enthalpy highlights the limitation of the simultaneous optimization of these quantities. Indeed, moderate, rather than very high affinities can be conciliated with favorable physicochemical and pharmacokinetic profiles as it is supported by the affinity range of historical oral drugs. Although thermodynamic quantities are not suitable endpoints for medicinal chemistry optimizations owing to the complexity of the binding thermodynamics, thermodynamic profiling together with structural studies can be advantageously used to understand the details of the binding process and to optimize it.
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Affiliation(s)
- György G Ferenczy
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest, Hungary
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55
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Binding site plasticity in viral PPxY Late domain recognition by the third WW domain of human NEDD4. Sci Rep 2019; 9:15076. [PMID: 31636332 PMCID: PMC6803667 DOI: 10.1038/s41598-019-50701-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/13/2019] [Indexed: 11/26/2022] Open
Abstract
The recognition of PPxY viral Late domains by the third WW domain of the HECT-E3 ubiquitin ligase NEDD4 (hNEDD4-WW3) is essential for the completion of the budding process of numerous enveloped viruses, including Ebola, Marburg, HTLV1 or Rabies. hNEDD4-WW3 has been validated as a promising target for the development of novel host-oriented broad spectrum antivirals. Nonetheless, finding inhibitors with good properties as therapeutic agents remains a challenge since the key determinants of binding affinity and specificity are still poorly understood. We present here a detailed structural and thermodynamic study of the interactions of hNEDD4-WW3 with viral Late domains combining isothermal titration calorimetry, NMR structural determination and molecular dynamics simulations. Structural and energetic differences in Late domain recognition reveal a highly plastic hNEDD4-WW3 binding site that can accommodate PPxY-containing ligands with varying orientations. These orientations are mostly determined by specific conformations adopted by residues I859 and T866. Our results suggest a conformational selection mechanism, extensive to other WW domains, and highlight the functional relevance of hNEDD4-WW3 domain conformational flexibility at the binding interface, which emerges as a key element to consider in the search for potent and selective inhibitors of therapeutic interest.
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Varese M, Guardiola S, García J, Giralt E. Enthalpy‐ versus Entropy‐Driven Molecular Recognition in the Era of Biologics. Chembiochem 2019; 20:2981-2986. [DOI: 10.1002/cbic.201900270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Monica Varese
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac, 10 08028 Barcelona Spain
| | - Salvador Guardiola
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac, 10 08028 Barcelona Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac, 10 08028 Barcelona Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac, 10 08028 Barcelona Spain
- Department of Inorganic and Organic ChemistryUniversity of Barcelona Martí i Franquès 1–11 08028 Barcelona Spain
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57
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Bauer CA, Schneider G, Göller AH. Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies. J Cheminform 2019; 11:59. [PMID: 33430967 PMCID: PMC6737620 DOI: 10.1186/s13321-019-0381-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/10/2019] [Indexed: 02/06/2023] Open
Abstract
We present machine learning (ML) models for hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD) strengths. Quantum chemical (QC) free energies in solution for 1:1 hydrogen-bonded complex formation to the reference molecules 4-fluorophenol and acetone serve as our target values. Our acceptor and donor databases are the largest on record with 4426 and 1036 data points, respectively. After scanning over radial atomic descriptors and ML methods, our final trained HBA and HBD ML models achieve RMSEs of 3.8 kJ mol-1 (acceptors), and 2.3 kJ mol-1 (donors) on experimental test sets, respectively. This performance is comparable with previous models that are trained on experimental hydrogen bonding free energies, indicating that molecular QC data can serve as substitute for experiment. The potential ramifications thereof could lead to a full replacement of wetlab chemistry for HBA/HBD strength determination by QC. As a possible chemical application of our ML models, we highlight our predicted HBA and HBD strengths as possible descriptors in two case studies on trends in intramolecular hydrogen bonding.
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Affiliation(s)
- Christoph A Bauer
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), 8093, Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), 8093, Zurich, Switzerland.
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58
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Geschwindner S, Ulander J. The current impact of water thermodynamics for small-molecule drug discovery. Expert Opin Drug Discov 2019; 14:1221-1225. [DOI: 10.1080/17460441.2019.1664468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Stefan Geschwindner
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Johan Ulander
- Data Science and Modelling, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
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59
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Tsopelas F, Tsantili-Kakoulidou A. Advances with weak affinity chromatography for fragment screening. Expert Opin Drug Discov 2019; 14:1125-1135. [DOI: 10.1080/17460441.2019.1648425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fotios Tsopelas
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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60
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Meyer-Almes FJ. Determination of the binding mechanism of histone deacetylase inhibitors. Chem Biol Drug Des 2019; 93:1214-1250. [PMID: 30480375 DOI: 10.1111/cbdd.13449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/14/2018] [Accepted: 11/11/2018] [Indexed: 12/20/2022]
Abstract
This article places its focus on methods and tools enabling the elucidation of the mechanism by which ligands, small-molecule inhibitors, or substrates interact with zinc-containing bacterial or human members of the histone deacetylase family (HDACs). These methods include biochemical and biophysical approaches and can be subdivided into equilibrium and kinetic methods. More information about the exact mode of action can be obtained by combining these methods with specific mutant variants of the enzymes and/or series of structural similar ligands. All available equilibrium and kinetic data including additional information from 3D structures of HDAC-ligand complexes can be beneficially combined in a data analysis procedure called Integrated Global-Fit analysis eventually providing the most likely binding mechanism.
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Affiliation(s)
- Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Darmstadt, Germany
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61
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Umuhire Juru A, Patwardhan NN, Hargrove AE. Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions. ACS Chem Biol 2019; 14:824-838. [PMID: 31042354 DOI: 10.1021/acschembio.8b00945] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The implication of RNA in multiple cellular processes beyond protein coding has revitalized interest in the development of small molecules for therapeutically targeting RNA and for further probing its cellular biology. However, the process of rationally designing such small molecule probes is hampered by the paucity of information about fundamental molecular recognition principles of RNA. In this Review, we summarize two important and often underappreciated aspects of RNA-small molecule recognition: RNA conformational dynamics and the biophysical properties of interactions of small molecules with RNA, specifically thermodynamics and kinetics. While conformational flexibility is often said to impede RNA ligand development, the ability of small molecules to influence the RNA conformational landscape can have a significant effect on the cellular functions of RNA. An analysis of the conformational landscape of RNA and the interactions of individual conformations with ligands can thus guide the development of new small molecule probes, which needs to be investigated further. Additionally, while it is common practice to quantify the binding affinities ( Ka or Kd) of small molecules for biomacromolecules as a measure of their activity, further biophysical characterization of their interaction can provide a deeper understanding. Studies that focus on the thermodynamic and kinetic parameters for interaction between RNA and ligands are next discussed. Finally, this Review provides the reader with a perspective on how such in-depth analysis of biophysical characteristics of the interaction of RNA and small molecules can impact our understanding of these interactions and how they will benefit the future design of small molecule probes.
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Affiliation(s)
- Aline Umuhire Juru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Neeraj N. Patwardhan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Amanda E. Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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62
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Discovery of a new class of MTH1 inhibitor by X-ray crystallographic screening. Eur J Med Chem 2019; 167:153-160. [DOI: 10.1016/j.ejmech.2019.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 11/19/2022]
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63
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Yasmeen S, Riyazuddeen, Khatun S, Abul Qais F. Characterization of interactions between cromolyn sodium and bovine serum albumin by spectroscopic, calorimetric and computational methods. J Biomol Struct Dyn 2019; 38:722-732. [DOI: 10.1080/07391102.2019.1586588] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Shama Yasmeen
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Riyazuddeen
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Samima Khatun
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
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64
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Minari K, de Azevedo ÉC, Kiraly VTR, Batista FAH, de Moraes FR, de Melo FA, Nascimento AS, Gava LM, Ramos CHI, Borges JC. Thermodynamic analysis of interactions of the Hsp90 with adenosine nucleotides: A comparative perspective. Int J Biol Macromol 2019; 130:125-138. [PMID: 30797004 DOI: 10.1016/j.ijbiomac.2019.02.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
Abstract
Hsp90s are key proteins in cellular homeostasis since they interact with many client proteins. Several studies indicated that Hsp90s are potential targets for treating diseases, such as cancer or malaria. It has been shown that Hsp90s from different organisms have peculiarities despite their high sequence identity. Therefore, a detailed comparative analysis of several Hsp90 proteins is relevant to the overall understanding of their activity. Accordingly, the goal of this work was to evaluate the interaction of either ADP or ATP with recombinant Hsp90s from different organisms (human α and β isoforms, Plasmodium falciparum, Leishmania braziliensis, yeast and sugarcane) by isothermal titration calorimetry. The measured thermodynamic signatures of those interactions indicated that despite the high identity among all Hsp90s, they have specific thermodynamic characteristics. Specifically, the interactions with ADP are driven by enthalpy but are opposed by entropy, whereas the interaction with ATP is driven by both enthalpy and entropy. Complimentary structural and molecular dynamics studies suggested that specific interactions with ADP that differ from those with ATP may contribute to the observed enthalpies and entropies. Altogether, the data suggest that selective inhibition may be more easily achieved using analogues of the Hsp90-ADP bound state than those of Hsp90-ATP bound state.
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Affiliation(s)
- Karine Minari
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP 13566-590, Brazil; Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, SP 13560-970, Brazil
| | - Érika Chang de Azevedo
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP 13560-970, Brazil
| | | | | | - Fábio Rogério de Moraes
- Biosciences, Languages, and Exact Sciences Institute, Multiuser Center for Biological Innovation (CMIB), São Paulo State University, São José do Rio Preto, SP 15054-000, Brazil
| | - Fernando Alves de Melo
- Biosciences, Languages, and Exact Sciences Institute, Multiuser Center for Biological Innovation (CMIB), São Paulo State University, São José do Rio Preto, SP 15054-000, Brazil
| | | | - Lisandra Marques Gava
- Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, SP 13560-970, Brazil
| | | | - Júlio César Borges
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP 13566-590, Brazil.
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65
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Bestgen B, Kufareva I, Seetoh W, Abell C, Hartmann RW, Abagyan R, Le Borgne M, Filhol O, Cochet C, Lomberget T, Engel M. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 2. Structure-Based Optimization and Investigation of Effects Specific to the Allosteric Mode of Action. J Med Chem 2019; 62:1817-1836. [PMID: 30689946 DOI: 10.1021/acs.jmedchem.8b01765] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein CK2 has gained much interest as an anticancer drug target in the past decade. We had previously described the identification of a new allosteric site on the catalytic α-subunit, along with first small molecule ligands based on the 4-(4-phenylthiazol-2-ylamino)benzoic acid scaffold. In the present work, structure optimizations guided by a binding model led to the identification of the lead compound 2-hydroxy-4-((4-(naphthalen-2-yl)thiazol-2-yl)amino)benzoic acid (27), showing a submicromolar potency against purified CK2α (IC50 = 0.6 μM). Furthermore, 27 induced apoptosis and cell death in 786-O renal cell carcinoma cells (EC50 = 5 μM) and inhibited STAT3 activation even more potently than the ATP-competitive drug candidate CX-4945 (EC50 of 1.6 μM vs 5.3 μM). Notably, the potencies of our allosteric ligands to inhibit CK2 varied depending on the individual substrate. Altogether, the novel allosteric pocket was proved a druggable site, offering an excellent perspective to develop efficient and selective allosteric CK2 inhibitors.
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Affiliation(s)
- Benoît Bestgen
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, 69373 Lyon Cedex 8, France.,Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2.3, 66123 Saarbrücken , Germany.,Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Commissariat à l'Energie Atomique, Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Weiguang Seetoh
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Chris Abell
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Rolf W Hartmann
- Department of Drug Design and Optimization , Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus C2.3, 66123 Saarbrücken , Germany
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Marc Le Borgne
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, 69373 Lyon Cedex 8, France
| | - Odile Filhol
- Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Commissariat à l'Energie Atomique, Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - Claude Cochet
- Institut National de la Santé et de la Recherche Médicale , U1036, 38000 Grenoble , France.,Commissariat à l'Energie Atomique, Institute of Life Sciences Research and Technologies, Biology of Cancer and Infection, 38000 Grenoble , France.,Unité Mixte de Recherche-S1036 , University of Grenoble Alpes , 38000 Grenoble , France
| | - Thierry Lomberget
- Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, 69373 Lyon Cedex 8, France
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry , Saarland University , Campus C2.3, 66123 Saarbrücken , Germany
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66
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Klebe G. Broad-scale analysis of thermodynamic signatures in medicinal chemistry: are enthalpy-favored binders the better development option? Drug Discov Today 2019; 24:943-948. [PMID: 30708050 DOI: 10.1016/j.drudis.2019.01.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/30/2022]
Abstract
Thermodynamic profiles of ligand binding, particularly enthalpically favored binding signatures, have been suggested as a criterion to support the decision-making process around which compounds to select for further optimization in drug development. The concept was enthusiastically taken up, but turned out to be too superficial, either because many aspects determining thermodynamic profiles are insufficiently appreciated or because it is difficult to compare such data on a global scale. The impact of water, changes in protonation states, along with buffer dependencies and incompatible measurement conditions that are far from standard conditions hamper such broad-scale comparisons. However, thermodynamic signatures can make us aware of the impact of these aspects and provide important hints for improving our understanding of the binding process and defining criteria for drug optimization.
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Affiliation(s)
- Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
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67
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Structures, Activities and Drug-Likeness of Anti-Infective Xanthone Derivatives Isolated from the Marine Environment: A Review. Molecules 2019; 24:molecules24020243. [PMID: 30634698 PMCID: PMC6359551 DOI: 10.3390/molecules24020243] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 12/24/2022] Open
Abstract
Marine organisms represent almost half of total biodiversity and are a very important source of new bioactive substances. Within the varied biological activities found in marine products, their antimicrobial activity is one of the most relevant. Infectious diseases are responsible for high levels of morbidity and mortality and many antimicrobials lose their effectiveness with time due to the development of resistance. These facts justify the high importance of finding new, effective and safe anti-infective agents. Among the variety of biological activities of marine xanthone derivatives, one that must be highlighted is their anti-infective properties. In this work, a literature review of marine xanthones with anti-infective activity, namely antibacterial, antifungal, antiparasitic and antiviral, is presented. Their structures, biological activity, sources and the methods used for bioactivity evaluation are described. The xanthone derivatives are grouped in three sets: xanthones, hydroxanthones and glycosylated derivatives. Moreover, molecular descriptors, biophysico-chemical properties, and pharmacokinetic parameters were calculated, and the chemical space occupied by marine xanthone derivatives is recognized. The chemical space was compared with marketed drugs and framed accordingly to the drug-likeness concept in order to profile the pharmacokinetic of anti-infective marine xanthone derivatives.
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Polshakov VI, Batuev EA, Mantsyzov AB. NMR screening and studies of target–ligand interactions. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Intrinsic Thermodynamics of Protein-Ligand Binding by Isothermal Titration Calorimetry as Aid to Drug Design. Methods Mol Biol 2019; 1964:61-74. [PMID: 30929235 DOI: 10.1007/978-1-4939-9179-2_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Isothermal titration calorimetry (ITC) is one of the main techniques to determine specific interactions between molecules dissolved in aqueous solution. This technique is commonly used in drug development programs when low-molecular-weight molecules are sought that bind tightly and specifically to a protein (disease target) molecule. The method allows a complete thermodynamic characterization of an interaction, i.e., ITC enables direct determination of the model-independent observed interaction change in enthalpy (ΔH) and a model-dependent observed interaction affinity (change in Gibbs free energy, ΔG) in a single experiment. The product of temperature and change in entropy (TΔS) can be obtained by the subtraction of ΔG from ΔH, and the change in heat capacity (ΔCp) can be determined as a slope of the temperature dependence of the binding ΔH.Despite the apparent value of ITC in characterization of interactions, it is often forgotten that many protein-ligand binding reactions are linked to protonation-deprotonation reactions or various conformational changes. In such cases, it is important to determine the linked-reaction contributions and obtain the intrinsic values of the changes in Gibbs energy (affinity), enthalpy, and entropy. These energy values can then be used in various SAR-type structure-thermodynamics and combined with structure-kinetics correlations in drug design, when searching for small molecules that would bind the protein target molecule. This manuscript provides a detailed protocol on how to determine the intrinsic values of protein-ligand binding thermodynamics by ITC.
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Bauer CA, Schneider G, Göller AH. Gaussian Process Regression Models for the Prediction of Hydrogen Bond Acceptor Strengths. Mol Inform 2018; 38:e1800115. [DOI: 10.1002/minf.201800115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Christoph A. Bauer
- Swiss Federal Institute of Technology (ETH)Department of Chemistry and Applied Biosciences 8093 Zurich Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH)Department of Chemistry and Applied Biosciences 8093 Zurich Switzerland
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Naylor MR, Ly AM, Handford MJ, Ramos DP, Pye CR, Furukawa A, Klein VG, Noland RP, Edmondson Q, Turmon AC, Hewitt WM, Schwochert J, Townsend CE, Kelly CN, Blanco MJ, Lokey RS. Lipophilic Permeability Efficiency Reconciles the Opposing Roles of Lipophilicity in Membrane Permeability and Aqueous Solubility. J Med Chem 2018; 61:11169-11182. [DOI: 10.1021/acs.jmedchem.8b01259] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Matthew R. Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Andrew M. Ly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Mason J. Handford
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Daniel P. Ramos
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R. Pye
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Akihiro Furukawa
- Modality Research Laboratories, Daiichi Sankyo Company, Ltd., 1-2-58 Hiromachi, Shingawa-ku, Tokyo 140-8710, Japan
| | - Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Ryan P. Noland
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Quinn Edmondson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Alexandra C. Turmon
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - William M. Hewitt
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E. Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Colin N. Kelly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria-Jesus Blanco
- Sage Therapeutics, 215 First Street, Suite 220, Cambridge, Massachusetts 02142, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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Su H, Xu Y. Application of ITC-Based Characterization of Thermodynamic and Kinetic Association of Ligands With Proteins in Drug Design. Front Pharmacol 2018; 9:1133. [PMID: 30364164 PMCID: PMC6193069 DOI: 10.3389/fphar.2018.01133] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/18/2018] [Indexed: 01/20/2023] Open
Abstract
A comprehensive characterization of the thermodynamic and kinetic profiling of ligands binding to a given target protein is crucial for the hit selection as well as the hit-to-lead-to-drug evolution. Isothermal titration calorimetry (ITC), widely known as an invaluable tool to measure the thermodynamic data, has recently found its way to determine the binding kinetics too. The extensive application of ITC in measurement of both thermodynamic and kinetic data manifests unique roles of ITC in drug discovery and development. This mini-review concentrates on elaborating how to gain the thermodynamic and kinetic data using ITC, highlighting the importance of these data in lead discovery and optimization, and intends to provide an overview of the technical and conceptual advances that offer unprecedented access to protein–ligand recognition by ITC measurement.
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Affiliation(s)
- Haixia Su
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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73
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Sharma A, Kumar V, Pratap S, Kumar P. The inhibitory and binding studies of methyl-sulfone hydroxamate based inhibitors against LpxC from drug resistant Moraxella catarrhalis using biophysical, biochemical and in silico approaches. Int J Biol Macromol 2018; 118:1747-1762. [DOI: 10.1016/j.ijbiomac.2018.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 01/17/2023]
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Sepuru KM, Nagarajan B, Desai UR, Rajarathnam K. Structural basis, stoichiometry, and thermodynamics of binding of the chemokines KC and MIP2 to the glycosaminoglycan heparin. J Biol Chem 2018; 293:17817-17828. [PMID: 30257866 DOI: 10.1074/jbc.ra118.004866] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/10/2018] [Indexed: 01/21/2023] Open
Abstract
Keratinocyte-derived chemokine (KC or mCXCL1) and macrophage inflammatory protein 2 (MIP2 or mCXCL2) play nonredundant roles in trafficking blood neutrophils to sites of infection and injury. The functional responses of KC and MIP2 are intimately coupled to their interactions with glycosaminoglycans (GAGs). GAG interactions orchestrate chemokine concentration gradients and modulate receptor activity, which together regulate neutrophil trafficking. Here, using NMR, molecular dynamics (MD) simulations, and isothermal titration calorimetry (ITC), we characterized the molecular basis of KC and MIP2 binding to the GAG heparin. Both chemokines reversibly exist as monomers and dimers, and the NMR analysis indicates that the dimer binds heparin with higher affinity. The ITC experiments indicate a stoichiometry of two GAGs per KC or MIP2 dimer and that the enthalpic and entropic contributions vary significantly between the two chemokine-heparin complexes. NMR-based structural models of heparin-KC and heparin-MIP2 complexes reveal that different combinations of residues from the N-loop, 40s turn, β3-strand, and C-terminal helix form a binding surface within a monomer and that both conserved residues and residues unique to a particular chemokine mediate the binding interactions. MD simulations indicate significant residue-specific differences in their contribution to binding and affinity for a given chemokine and between chemokines. On the basis of our observations that KC and MIP2 bind to GAG via distinct molecular interactions, we propose that the differences in these GAG interactions lead to differences in neutrophil recruitment and play nonoverlapping roles in resolution of inflammation.
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Affiliation(s)
- Krishna Mohan Sepuru
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555
| | - Balaji Nagarajan
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Krishna Rajarathnam
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555; Microbiology and Immunology.
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Tashiro S, Caaveiro JMM, Nakakido M, Tanabe A, Nagatoishi S, Tamura Y, Matsuda N, Liu D, Hoang QQ, Tsumoto K. Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1. ACS Chem Biol 2018; 13:2783-2793. [PMID: 30063823 DOI: 10.1021/acschembio.8b00701] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DJ-1 is a Parkinson's disease associated protein endowed with enzymatic, redox sensing, regulatory, chaperoning, and neuroprotective activities. Although DJ-1 has been vigorously studied for the past decade and a half, its exact role in the progression of the disease remains uncertain. In addition, little is known about the spatiotemporal regulation of DJ-1, or the biochemical basis explaining its numerous biological functions. Progress has been hampered by the lack of inhibitors with precisely known mechanisms of action. Herein, we have employed biophysical methodologies and X-ray crystallography to identify and to optimize a family of compounds inactivating the critical Cys106 residue of human DJ-1. We demonstrate these compounds are potent inhibitors of various activities of DJ-1 in vitro and in cell-based assays. This study reports a new family of DJ-1 inhibitors with a defined mechanism of action, and contributes toward the understanding of the biological function of DJ-1.
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Affiliation(s)
- Shinya Tashiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jose M. M. Caaveiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Makoto Nakakido
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Aki Tanabe
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasushi Tamura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | | | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 108-8639, Japan
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76
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Nguyen TH, Rustenburg AS, Krimmer SG, Zhang H, Clark JD, Novick PA, Branson K, Pande VS, Chodera JD, Minh DDL. Bayesian analysis of isothermal titration calorimetry for binding thermodynamics. PLoS One 2018; 13:e0203224. [PMID: 30212471 PMCID: PMC6136728 DOI: 10.1371/journal.pone.0203224] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/16/2018] [Indexed: 12/04/2022] Open
Abstract
Isothermal titration calorimetry (ITC) is the only technique able to determine both the enthalpy and entropy of noncovalent association in a single experiment. The standard data analysis method based on nonlinear regression, however, provides unrealistically small uncertainty estimates due to its neglect of dominant sources of error. Here, we present a Bayesian framework for sampling from the posterior distribution of all thermodynamic parameters and other quantities of interest from one or more ITC experiments, allowing uncertainties and correlations to be quantitatively assessed. For a series of ITC measurements on metal:chelator and protein:ligand systems, the Bayesian approach yields uncertainties which represent the variability from experiment to experiment more accurately than the standard data analysis. In some datasets, the median enthalpy of binding is shifted by as much as 1.5 kcal/mol. A Python implementation suitable for analysis of data generated by MicroCal instruments (and adaptable to other calorimeters) is freely available online.
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Affiliation(s)
- Trung Hai Nguyen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Ariën S. Rustenburg
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY, United States of America
| | - Stefan G. Krimmer
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, Marburg, Germany
| | - Hexi Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
| | - John D. Clark
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Paul A. Novick
- Department of Chemistry, Stanford University, Stanford, CA, United States of America
| | - Kim Branson
- Department of Chemistry, Stanford University, Stanford, CA, United States of America
| | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, CA, United States of America
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- * E-mail: (JDC); (DDLM)
| | - David D. L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, United States of America
- * E-mail: (JDC); (DDLM)
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77
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Li A, Gilson MK. Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox. J Chem Phys 2018; 149:072311. [PMID: 30134726 DOI: 10.1063/1.5027439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Calorimetric studies of protein-ligand binding sometimes yield thermodynamic data that are difficult to understand. Today, molecular simulations can be used to seek insight into such calorimetric puzzles, and, when simulations and experiments diverge, the results can usefully motivate further improvements in computational methods. Here, we apply near-millisecond duration simulations to estimate the relative binding enthalpies of four peptidic ligands with the Grb2 SH2 domain. The ligands fall into matched pairs, where one member of each pair has an added bond that preorganizes the ligand for binding and thus may be expected to favor binding entropically, due to a smaller loss in configurational entropy. Calorimetric studies have shown that the constrained ligands do in fact bind the SH2 domain more tightly than the flexible ones, but, paradoxically, the improvement in affinity for the constrained ligands is enthalpic, rather than entropic. The present enthalpy calculations yield the opposite trend, as they suggest that the flexible ligands bind more exothermically. Additionally, the small relative binding enthalpies are found to be balances of large differences in the energies of structural components such as ligand and the binding site residues. As a consequence, the deviations from experiment in the relative binding enthalpies represent small differences between these large numbers and hence may be particularly susceptible to error, due, for example, to approximations in the force field. We also computed first-order estimates of changes in configurational entropy on binding. These too are, arguably, paradoxical, as they tend to favor binding of the flexible ligands. The paradox is explained in part by the fact that the more rigid constrained ligands reduce the entropy of binding site residues more than their flexible analogs do, at least in the simulations. This result offers a rather general counterargument to the expectation that preorganized ligands should be associated with more favorable binding entropies, other things being equal.
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Affiliation(s)
- Amanda Li
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0419, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0736, USA
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78
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Xiao CQ, Lai L, Zhang L, Wang SY, Yuan S, Xu ZQ, Liu Y. Spectroscopic and Isothermal Titration Calorimetry Studies of Binding Interactions Between Carbon Nanodots and Serum Albumins. J SOLUTION CHEM 2018. [DOI: 10.1007/s10953-018-0792-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Affiliation(s)
- Hasan Y. Alniss
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
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80
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Wienen-Schmidt B, Jonker HRA, Wulsdorf T, Gerber HD, Saxena K, Kudlinzki D, Sreeramulu S, Parigi G, Luchinat C, Heine A, Schwalbe H, Klebe G. Paradoxically, Most Flexible Ligand Binds Most Entropy-Favored: Intriguing Impact of Ligand Flexibility and Solvation on Drug–Kinase Binding. J Med Chem 2018; 61:5922-5933. [DOI: 10.1021/acs.jmedchem.8b00105] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Barbara Wienen-Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Hendrik R. A. Jonker
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Krishna Saxena
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Denis Kudlinzki
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM/CIRMMP) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM/CIRMMP) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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81
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Meira LHR, Soares GAB, Bonomini HIM, Lopes JF, De Sousa FB. Thermodynamic compatibility between cyclodextrin supramolecular complexes and surfactant. Int J Pharm 2018; 544:203-212. [PMID: 29679752 DOI: 10.1016/j.ijpharm.2018.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 11/16/2022]
Abstract
Supramolecular structures based on cyclodextrins have been extensively used for drug delivery systems over decades. However, combining host and guest molecules in a pharmaceutical formulation is not a trivial process, being one of the majors concern the inclusion complex compatibility with other excipients presented in the final formulation. Herein, experimental and theoretical calculations were used to investigate the competition of sodium dodecyl sulfate (SDS) with atenolol (ATE) or losartan (LOS), antihypertensive drugs widely used in the treatment of hypertension. Our findings, using nuclear magnetic resonance and isothermal titrations calorimetry experiments and molecular dynamic simulations demonstrated that LOS remain included into CD cavity after excipient (SDS) addition, which was not verified for ATE ternary system, being the drug displaced by SDS molecule.
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Affiliation(s)
- Larissa H R Meira
- Laboratório de Sistemas Poliméricos e Supramoleculares (LSPS), Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 MG, Brazil
| | - Guilherme A B Soares
- Laboratório de Química Computacional (LaQC), Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 MG, Brazil
| | - Homero I M Bonomini
- Laboratório de Química Computacional (LaQC), Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 MG, Brazil
| | - Juliana Fedoce Lopes
- Laboratório de Química Computacional (LaQC), Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 MG, Brazil
| | - Frederico B De Sousa
- Laboratório de Sistemas Poliméricos e Supramoleculares (LSPS), Instituto de Física e Química, Universidade Federal de Itajubá (UNIFEI), Itajubá, 37500-903 MG, Brazil.
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82
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Hamilton PD, Andley UP. In vitro interactions of histones and α-crystallin. Biochem Biophys Rep 2018; 15:7-12. [PMID: 30023439 PMCID: PMC6047474 DOI: 10.1016/j.bbrep.2018.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 11/15/2022] Open
Abstract
The aggregation of crystallins in lenses is associated with cataract formation. We previously reported that mutant crystallins are associated with an increased abundance of histones in knock-in and knockout mouse models. However, very little is known about the specific interactions between lens crystallins and histones. Here, we performed in vitro analyses to determine whether α-crystallin interacts with histones directly. Isothermal titration calorimetry revealed a strong histone–α-crystallin binding with a Kd of 4 × 10−7 M, and the thermodynamic parameters suggested that the interaction was both entropy and enthalpy driven. Size-exclusion chromatography further showed that histone–α-crystallin complexes are water soluble but become water insoluble as the concentration of histones is increased. Right-angle light scattering measurements of the water-soluble fractions of histone–α-crystallin mixtures showed a decrease in the oligomeric molecular weight of α-crystallin, indicating that histones alter the oligomerization of α-crystallin. Taken together, these findings reveal for the first time that histones interact with and affect the solubility and aggregation of α-crystallin, indicating that the interaction between α-crystallin and histones in the lens is functionally important. Histones are upregulated in α-crystallin mutant mice with hereditary cataracts. Isothermal titration calorimetry reveals histones and α-crystallin interact. These interactions are enthalpy and entropy driven. Histones affect the solubility and aggregation behavior of α-crystallin in vitro.
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Affiliation(s)
- Paul D Hamilton
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Usha P Andley
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
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83
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Sepasi Tehrani H, Moosavi-Movahedi AA. Catalase and its mysteries. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018. [PMID: 29530789 DOI: 10.1016/j.pbiomolbio.2018.03.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalase is one of the firsts in every realm of biological sciences. At the same time it also has a number of unusual features. It has one of the highest turnover numbers of all enzymes. It is essential for neutralizing the noxious hydrogen peroxide both in the nature and the various industries such as dairy, textile and pharmaceutics. It also has the merit of being one of the first protein crystals to be isolated. Ironically its three-dimensional structure was discerned some forty years later. However through the times this senile enzyme has continued to intrigue the scientists by surprising facts and phenomena, such as peculiar interweaving of subunits and remarkable thermal stability. It is also known for suicide inactivation by its own substrate. Catalase is known to be implicated in various medical scenarios and its levels have served as a marker in that capacity. It has even been incorporated into several pharmaceuticals. This review strives to clarify these perspectives. It also draws attention to the biophysical contributions offered by thermodynamics and kinetics in these discoveries. The ultimate aim of this review, however, is to state that the venerable catalase will continue to bewilder us with its mysteries well into the twenty-first century.
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Affiliation(s)
- Hessam Sepasi Tehrani
- Department of Biology, Islamic Azad University, Science and Research Branch, Tehran, Iran.
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84
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Büttner D, Kramer JS, Klingler FM, Wittmann SK, Hartmann MR, Kurz CG, Kohnhäuser D, Weizel L, Brüggerhoff A, Frank D, Steinhilber D, Wichelhaus TA, Pogoryelov D, Proschak E. Challenges in the Development of a Thiol-Based Broad-Spectrum Inhibitor for Metallo-β-Lactamases. ACS Infect Dis 2018; 4:360-372. [PMID: 29172434 DOI: 10.1021/acsinfecdis.7b00129] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Pathogens, expressing metallo-β-lactamases (MBLs), become resistant against most β-lactam antibiotics. Besides the dragging search for new antibiotics, development of MBL inhibitors would be an alternative weapon against resistant bacterial pathogens. Inhibition of resistance enzymes could restore the antibacterial activity of β-lactams. Various approaches to MBL inhibitors are described; among others, the promising motif of a zinc coordinating thiol moiety is very popular. Nevertheless, since the first report of a thiol-based MBL inhibitor (thiomandelic acid) in 2001, no steps in development of thiol based MBL inhibitors were reported that go beyond clinical isolate testing. In this study, we report on the synthesis and biochemical characterization of thiol-based MBL inhibitors and highlight the challenges behind the development of thiol-based compounds, which exhibit good in vitro activity toward a broad spectrum of MBLs, selectivity against human off-targets, and reasonable activity against clinical isolates.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Denia Frank
- Institute of Medical Microbiology and Infection Control, Goethe University Hospital, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany
| | | | - Thomas A. Wichelhaus
- Institute of Medical Microbiology and Infection Control, Goethe University Hospital, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany
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85
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Smirnov A, Zubrienė A, Manakova E, Gražulis S, Matulis D. Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding. PeerJ 2018; 6:e4412. [PMID: 29503769 PMCID: PMC5831161 DOI: 10.7717/peerj.4412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/04/2018] [Indexed: 11/28/2022] Open
Abstract
The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure.
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Affiliation(s)
- Alexey Smirnov
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Elena Manakova
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Saulius Gražulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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86
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NMR-Fragment Based Virtual Screening: A Brief Overview. Molecules 2018; 23:molecules23020233. [PMID: 29370102 PMCID: PMC6017141 DOI: 10.3390/molecules23020233] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 01/23/2023] Open
Abstract
Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.
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87
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Sebastián M, Anoz-Carbonell E, Gracia B, Cossio P, Aínsa JA, Lans I, Medina M. Discovery of antimicrobial compounds targeting bacterial type FAD synthetases. J Enzyme Inhib Med Chem 2017; 33:241-254. [PMID: 29258359 PMCID: PMC7012052 DOI: 10.1080/14756366.2017.1411910] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The increase of bacterial strains resistant to most of the available antibiotics shows a need to explore novel antibacterial targets to discover antimicrobial drugs. Bifunctional bacterial FAD synthetases (FADSs) synthesise the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). These cofactors act in vital processes as part of flavoproteins, making FADS an essential enzyme. Bacterial FADSs are potential antibacterial targets because of differences to mammalian enzymes, particularly at the FAD producing site. We have optimised an activity-based high throughput screening assay targeting Corynebacterium ammoniagenes FADS (CaFADS) that identifies inhibitors of its different activities. We selected the three best high-performing inhibitors of the FMN:adenylyltransferase activity (FMNAT) and studied their inhibition mechanisms and binding properties. The specificity of the CaFADS hits was evaluated by studying also their effect on the Streptococcus pneumoniae FADS activities, envisaging differences that can be used to discover species-specific antibacterial drugs. The antimicrobial effect of these compounds was also evaluated on C. ammoniagenes, S. pneumoniae, and Mycobacterium tuberculosis cultures, finding hits with favourable antimicrobial properties.
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Affiliation(s)
- María Sebastián
- a Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias , Universidad de Zaragoza , Zaragoza , Spain.,b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain
| | - Ernesto Anoz-Carbonell
- a Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias , Universidad de Zaragoza , Zaragoza , Spain.,b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain.,c Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública. Facultad de Medicina , Universidad de Zaragoza , Zaragoza , Spain
| | - Begoña Gracia
- c Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública. Facultad de Medicina , Universidad de Zaragoza , Zaragoza , Spain.,d CIBER Enfermedades Respiratorias (CIBERES) , Instituto de Salud Carlos III , Madrid , Spain
| | - Pilar Cossio
- e Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Frankfurt , Germany.,f Biophysics of Tropical Diseases, Max Planck Tandem Group , University of Antioquia , Medellín , Colombia
| | - José Antonio Aínsa
- b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain.,c Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública. Facultad de Medicina , Universidad de Zaragoza , Zaragoza , Spain.,d CIBER Enfermedades Respiratorias (CIBERES) , Instituto de Salud Carlos III , Madrid , Spain
| | - Isaías Lans
- f Biophysics of Tropical Diseases, Max Planck Tandem Group , University of Antioquia , Medellín , Colombia
| | - Milagros Medina
- a Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias , Universidad de Zaragoza , Zaragoza , Spain.,b Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and CBsC-CSIC Joint Units) , Universidad de Zaragoza , Zaragoza , Spain
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88
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Baggio C, Udompholkul P, Barile E, Pellecchia M. Enthalpy-Based Screening of Focused Combinatorial Libraries for the Identification of Potent and Selective Ligands. ACS Chem Biol 2017; 12:2981-2989. [PMID: 29094589 DOI: 10.1021/acschembio.7b00717] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In modern drug discovery, the ability of biophysical methods, including nuclear magnetic resonance spectroscopy or surface plasmon resonance, to detect and characterize ligand-protein interactions accurately and unambiguously makes these approaches preferred versus conventional biochemical high-throughput screening of large collections of compounds. Nonetheless, ligand screening strategies that address simultaneously potency and selectivity have not yet been fully developed. In this work, we propose a novel method for screening large collections of combinatorial libraries using enthalpy measurements as a primary screening technique. We demonstrate that selecting binders that are driven by enthalpy (ΔH) results in agents that are not only potent but also more selective for a given target. This general and novel approach, we termed ΔH screening of fPOS (enthalpy screening of focused positional scanning library), combines the principles of focused combinatorial chemistry with rapid calorimetry measurements to efficiently identify potent and selective inhibitors.
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Affiliation(s)
- Carlo Baggio
- Division of Biomedical Sciences,
School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Parima Udompholkul
- Division of Biomedical Sciences,
School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Elisa Barile
- Division of Biomedical Sciences,
School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Maurizio Pellecchia
- Division of Biomedical Sciences,
School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
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89
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Reynolds CH, Reynolds RC. Group Additivity in Ligand Binding Affinity: An Alternative Approach to Ligand Efficiency. J Chem Inf Model 2017; 57:3086-3093. [PMID: 29111708 DOI: 10.1021/acs.jcim.7b00381] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Group additivity is a concept that has been successfully applied to a variety of thermochemical and kinetic properties. This includes drug discovery, where functional group additivity is often assumed in ligand binding. Ligand efficiency can be recast as a special case of group additivity where ΔG/HA is the group equivalent (HA is the number of non-hydrogen atoms in a ligand). Analysis of a large data set of protein-ligand binding affinities (Ki) for diverse targets shows that in general ligand binding is distinctly nonlinear. It is possible to create a group equivalent scheme for ligand binding, but only in the context of closely related proteins, at least with regard to size. This finding has broad implications for drug design from both experimental and computational points of view. It also offers a path forward for a more general scheme to assess the efficiency of ligand binding.
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Affiliation(s)
- Charles H Reynolds
- Gfree Bio, LLC , 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Ryan C Reynolds
- Gfree Bio, LLC , 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
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90
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Kumar PKR. Systematic screening of viral entry inhibitors using surface plasmon resonance. Rev Med Virol 2017; 27. [PMID: 29047180 DOI: 10.1002/rmv.1952] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 08/02/2017] [Accepted: 09/07/2017] [Indexed: 12/12/2022]
Abstract
Viral binding and entry into host cells for various viruses have been studied extensively, yielding a detailed understanding of the overall viral entry process. As cell entry is an essential and requisite process by which a virus initiates infection, it is an attractive target for therapeutic intervention. The advantages of targeting viral entry are an extracellular target site, relatively easy access for biological interventions, and lower toxicity. Several cell-based strategies and biophysical techniques have been used to screen compounds that block viral entry. These studies led to the discovery of inhibitors against HIV, HCV, influenza, Ebola, and RSV. In recent years, several compounds screened by fragment-based drug discovery have been approved as drugs or are in the final stages of clinical trials. Among fragment screening technologies, surface plasmon resonance has been widely used because it provides accurate information on binding kinetics, allows real-time monitoring of ligand-drug interactions, requires very small sample amounts to perform analyses, and requires no modifications to or labeling of ligands. This review focuses on surface plasmon resonance-based schemes for screening viral entry inhibitors.
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Affiliation(s)
- Penmetcha K R Kumar
- National Institute of Advanced Industrial Science and Technology, Tsukuba City, Ibaraki, Japan
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91
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Wang Y, Edalji RP, Panchal SC, Sun C, Djuric SW, Vasudevan A. Are We There Yet? Applying Thermodynamic and Kinetic Profiling on Embryonic Ectoderm Development (EED) Hit-to-Lead Program. J Med Chem 2017; 60:8321-8335. [DOI: 10.1021/acs.jmedchem.7b00576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ying Wang
- AbbVie Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Rohinton P. Edalji
- AbbVie Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Sanjay C. Panchal
- AbbVie Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Chaohong Sun
- AbbVie Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Stevan W. Djuric
- AbbVie Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
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92
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Han SG, Ko S, Lee WK, Jung ST, Yu YG. Determination of the endothelin-1 recognition sites of endothelin receptor type A by the directed-degeneration method. Sci Rep 2017; 7:7577. [PMID: 28790412 PMCID: PMC5548930 DOI: 10.1038/s41598-017-08096-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/04/2017] [Indexed: 12/20/2022] Open
Abstract
G-protein coupled receptors (GPCRs) play indispensable physiological roles in cell proliferation, differentiation, and migration; therefore, identifying the mechanisms by which ligands bind to GPCRs is crucial for developing GPCR-targeting pharmaceutics and for understanding critical biological functions. Although some structural information is available regarding the interactions between GPCRs and their small molecule ligands, knowledge of how GPCRs interact with their corresponding macromolecule ligands, such as peptides and proteins, remains elusive. In this study, we have developed a novel strategy to investigate the precise ligand recognition mechanisms involved in the interaction of endothelin receptor type A (ETA) with its ligand, endothelin-1 (ET-1); we call this method “directed degeneration” method. Through flow cytometric screening of a randomized ETA library, statistical analysis of the identified sequences, and biochemical studies, the ligand interaction map was successfully obtained.
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Affiliation(s)
- Seong-Gu Han
- Department of Chemistry, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul, 136-702, Republic of Korea
| | - Sanghwan Ko
- Department of Chemistry, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul, 136-702, Republic of Korea
| | - Won-Kyu Lee
- Department of Chemistry, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul, 136-702, Republic of Korea.,New Drug Development Center, Osong Medical Innovation Foundation, Osong Sengmyung-Ro 123, Osong-eup, Heungdeok-gu, Cheongju-si, Chungbuk, Republic of Korea
| | - Sang Taek Jung
- Department of Chemistry, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul, 136-702, Republic of Korea.
| | - Yeon Gyu Yu
- Department of Chemistry, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul, 136-702, Republic of Korea.
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93
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Meyners C, Meyer-Almes FJ. Impact of binding mechanism on selective inhibition of histone deacetylase isoforms. Chem Biol Drug Des 2017; 90:1215-1225. [PMID: 28730718 DOI: 10.1111/cbdd.13041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/05/2017] [Indexed: 12/15/2022]
Abstract
Industrialized drug screening campaigns usually deliver hundreds of compounds that are active on a particular pharmaceutical target. In light of high failure rates of drug candidates due to unforeseeable off-target toxicity, the early identification of the most promising compounds with high potential for target selectivity is an urgent need to improve the quality of lead compounds and lower attrition rates in the drug development process. The reliable prediction of the selectivity of active substances for a target protein is a challenging task. A comprehensive study of the binding kinetics, thermodynamics, and selectivity of chemically related ligands of histone deacetylase (HDAC) like amidohydrolase from Pseudomonas aeruginosa (HDAHpa ) reveals one general binding mechanism for all analyzed compounds consisting of a preceding conformational selection step followed by an optional subsequent induced fit. Depending on the chemical structure, the ligands bind to one or two of at least three protein conformations with different rate constants. Although these kinetic and mechanistic differences hamper the predictability of selectivity for the HDAC inhibitors, we demonstrate that the enthalpy-weighted binding constant KdΔH is a useful metric to predict isoform selectivity of inhibitors against HDAC enzymes and relatively robust toward different but related binding mechanisms.
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Affiliation(s)
- Christian Meyners
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Darmstadt, Germany
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Darmstadt, Germany
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94
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The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket. Biochim Biophys Acta Gen Subj 2017; 1861:1855-1863. [DOI: 10.1016/j.bbagen.2017.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/08/2017] [Accepted: 04/02/2017] [Indexed: 12/11/2022]
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95
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Bata Z, Qian R, Roller A, Horak J, Bencze LC, Paizs C, Hammerschmidt F, Vértessy BG, Poppe L. A Methylidene Group in the Phosphonic Acid Analogue of Phenylalanine Reverses the Enantiopreference of Binding to Phenylalanine Ammonia-Lyases. Adv Synth Catal 2017; 359:2109-2120. [PMID: 28919846 PMCID: PMC5573973 DOI: 10.1002/adsc.201700428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/02/2017] [Indexed: 12/19/2022]
Abstract
Aromatic amino acid ammonia‐lyases and aromatic amino acid 2,3‐aminomutases contain the post‐translationally formed prosthetic 3,5‐dihydro‐4‐methylidene‐5H‐imidazol‐5‐one (MIO) group. MIO enzymes catalyze the stereoselective synthesis of α‐ or β‐amino acid enantiomers, making these chemical processes environmentally friendly and affordable. Characterization of novel inhibitors enables structural understanding of enzyme mechanism and recognizes promising herbicide candidates as well. The present study found that both enantiomers of the aminophosphonic acid analogue of the natural substrate phenylalanine and a novel derivative bearing a methylidene at the β‐position inhibited phenylalanine ammonia‐lyases (PAL), representing MIO enzymes. X‐ray methods unambiguously determined the absolute configuration of all tested enantiomers during their synthesis. Enzyme kinetic measurements revealed the enantiomer of the methylidene‐substituted substrate analogue as being a mirror image relation to the natural l‐phenylalanine as the strongest inhibitor. Isothermal titration calorimetry (ITC) confirmed the binding constants and provided a detailed analysis of the thermodynamic driving forces of ligand binding. Molecular docking suggested that binding of the (R)‐ and (S)‐enantiomers is possible by a mirror image packing. ![]()
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Affiliation(s)
- Zsófia Bata
- Department of Organic Chemistry and Technology Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary.,Institute of Enzymology HAS-Research Center of Natural Sciences, Budapest, H-1117 Magyar tudósok krt. 2. Budapest Hungary
| | - Renzhe Qian
- Institute of Organic Chemistry University of Vienna Währinger Str. 38 1090 Vienna Austria
| | - Alexander Roller
- Institute of Inorganic Chemistry University of Vienna Währinger Str. 42. A-1090 Vienna Austria
| | - Jeannie Horak
- Institute of Pharmaceutical Sciences Pharmaceutical (Bio-)Analysis Eberhard-Karls-University Tübingen Auf der Morgensstelle 872076 Tübingen Germany
| | - László Csaba Bencze
- Biocatalysis and Biotransformation Research Centre Faculty of Chemistry and Chemical Engineering Babeş-Bolyai University of Cluj-Napoca Arany János Str. 11400028 Cluj-Napoca Romania
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre Faculty of Chemistry and Chemical Engineering Babeş-Bolyai University of Cluj-Napoca Arany János Str. 11400028 Cluj-Napoca Romania
| | | | - Beáta G Vértessy
- Institute of Enzymology HAS-Research Center of Natural Sciences, Budapest, H-1117 Magyar tudósok krt. 2. Budapest Hungary.,Department of Applied Biotechnology and Food Science Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary.,Biocatalysis and Biotransformation Research Centre Faculty of Chemistry and Chemical Engineering Babeş-Bolyai University of Cluj-Napoca Arany János Str. 11400028 Cluj-Napoca Romania
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96
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Martinelli LKB, Rotta M, Villela AD, Rodrigues-Junior VS, Abbadi BL, Trindade RV, Petersen GO, Danesi GM, Nery LR, Pauli I, Campos MM, Bonan CD, de Souza ON, Basso LA, Santos DS. Functional, thermodynamics, structural and biological studies of in silico-identified inhibitors of Mycobacterium tuberculosis enoyl-ACP(CoA) reductase enzyme. Sci Rep 2017; 7:46696. [PMID: 28436453 PMCID: PMC5402281 DOI: 10.1038/srep46696] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/28/2017] [Indexed: 11/25/2022] Open
Abstract
Novel chemotherapeutics agents are needed to kill Mycobacterium tuberculosis, the main causative agent of tuberculosis (TB). The M. tuberculosis 2-trans-enoyl-ACP(CoA) reductase enzyme (MtInhA) is the druggable bona fide target of isoniazid. New chemotypes were previously identified by two in silico approaches as potential ligands to MtInhA. The inhibition mode was determined by steady-state kinetics for seven compounds that inhibited MtInhA activity. Dissociation constant values at different temperatures were determined by protein fluorescence spectroscopy. van't Hoff analyses of ligand binding to MtInhA:NADH provided the thermodynamic signatures of non-covalent interactions (ΔH°, ΔS°, ΔG°). Phenotypic screening showed that five compounds inhibited in vitro growth of M. tuberculosis H37Rv strain. Labio_16 and Labio_17 compounds also inhibited the in vitro growth of PE-003 multidrug-resistant strain. Cytotoxic effects on Hacat, Vero and RAW 264.7 cell lines were assessed for the latter two compounds. The Labio_16 was bacteriostatic and Labio_17 bactericidal in an M. tuberculosis-infected macrophage model. In Zebrafish model, Labio_16 showed no cardiotoxicity whereas Labio_17 showed dose-dependent cardiotoxicity. Accordingly, a model was built for the MtInhA:NADH:Labio_16 ternary complex. The results show that the Labio_16 compound is a direct inhibitor of MtInhA, and it may represent a hit for the development of chemotherapeutic agents to treat TB.
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Affiliation(s)
- Leonardo K. B. Martinelli
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Mariane Rotta
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Anne D. Villela
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Valnês S. Rodrigues-Junior
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Bruno L. Abbadi
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Rogério V. Trindade
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Guilherme O. Petersen
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Giuliano M. Danesi
- Instituto de Toxicologia e Farmacologia, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
- Faculdade de Medicina, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Laura R. Nery
- Laboratório de Neuroquímica e Psicofarmacologia, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Ivani Pauli
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas – LABIO, Faculdade de Informática, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Maria M. Campos
- Instituto de Toxicologia e Farmacologia, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
- Faculdade de Odontologia, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Carla D. Bonan
- Laboratório de Neuroquímica e Psicofarmacologia, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Osmar Norberto de Souza
- Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas – LABIO, Faculdade de Informática, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
- Laboratório de FarmInformática - FarmInf, Faculdade de Farmácia, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Luiz A. Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
| | - Diogenes S. Santos
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900, Porto Alegre, RS, Brazil
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97
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The low binding affinity of D-serine at the ionotropic glutamate receptor GluD2 can be attributed to the hinge region. Sci Rep 2017; 7:46145. [PMID: 28387240 PMCID: PMC5384001 DOI: 10.1038/srep46145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/13/2017] [Indexed: 01/24/2023] Open
Abstract
Ionotropic glutamate receptors (iGluRs) are responsible for most of the fast excitatory communication between neurons in our brain. The GluD2 receptor is a puzzling member of the iGluR family: It is involved in synaptic plasticity, plays a role in human diseases, e.g. ataxia, binds glycine and D-serine with low affinity, yet no ligand has been discovered so far that can activate its ion channel. In this study, we show that the hinge region connecting the two subdomains of the GluD2 ligand-binding domain is responsible for the low affinity of D-serine, by analysing GluD2 mutants with electrophysiology, isothermal titration calorimetry and molecular dynamics calculations. The hinge region is highly variable among iGluRs and fine-tunes gating activity, suggesting that in GluD2 this region has evolved to only respond to micromolar concentrations of D-serine.
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98
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Bartus É, Hegedüs Z, Wéber E, Csipak B, Szakonyi G, Martinek TA. De Novo Modular Development of a Foldameric Protein-Protein Interaction Inhibitor for Separate Hot Spots: A Dynamic Covalent Assembly Approach. ChemistryOpen 2017; 6:236-241. [PMID: 28413758 PMCID: PMC5390796 DOI: 10.1002/open.201700012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions stabilized by multiple separate hot spots are highly challenging targets for synthetic scaffolds. Surface-mimetic foldamers bearing multiple recognition segments are promising candidate inhibitors. In this work, a modular bottom-up approach is implemented by identifying short foldameric recognition segments that interact with the independent hot spots, and connecting them through dynamic covalent library (DCL) optimization. The independent hot spots of a model target (calmodulin) are mapped with hexameric β-peptide helices using a pull-down assay. Recognition segment hits are subjected to a target-templated DCL ligation through thiol-disulfide exchange. The most potent derivative displays low nanomolar affinity towards calmodulin and effectively inhibits the calmodulin-TRPV1 interaction. The DCL assembly of the folded segments offers an efficient approach towards the de novo development of a high-affinity inhibitor of protein-protein interactions.
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Affiliation(s)
- Éva Bartus
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Zsófia Hegedüs
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Edit Wéber
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Brigitta Csipak
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Tamás A. Martinek
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
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99
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Proschak E, Heitel P, Kalinowsky L, Merk D. Opportunities and Challenges for Fatty Acid Mimetics in Drug Discovery. J Med Chem 2017; 60:5235-5266. [PMID: 28252961 DOI: 10.1021/acs.jmedchem.6b01287] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fatty acids beyond their role as an endogenous energy source and storage are increasingly considered as signaling molecules regulating various physiological effects in metabolism and inflammation. Accordingly, the molecular targets involved in formation and physiological activities of fatty acids hold significant therapeutic potential. A number of these fatty acid targets are addressed by some of the oldest and most widely used drugs such as cyclooxygenase inhibiting NSAIDs, whereas others remain unexploited. Compounds orthosterically binding to proteins that endogenously bind fatty acids are considered as fatty acid mimetics. On the basis of their structural resemblance, fatty acid mimetics constitute a family of bioactive compounds showing specific binding thermodynamics and following similar pharmacokinetic mechanisms. This perspective systematically evaluates targets for fatty acid mimetics, investigates their common structural characteristics, and highlights demands in their discovery and design. In summary, fatty acid mimetics share particularly favorable characteristics justifying the conclusion that their therapeutic potential vastly outweighs the challenges in their design.
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Affiliation(s)
- Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Pascal Heitel
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Lena Kalinowsky
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
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100
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Fox JM, Kang K, Sastry M, Sherman W, Sankaran B, Zwart PH, Whitesides GM. Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase. Angew Chem Int Ed Engl 2017; 56:3833-3837. [PMID: 28252841 DOI: 10.1002/anie.201609409] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/21/2016] [Indexed: 01/09/2023]
Abstract
This study uses mutants of human carbonic anhydrase (HCAII) to examine how changes in the organization of water within a binding pocket can alter the thermodynamics of protein-ligand association. Results from calorimetric, crystallographic, and theoretical analyses suggest that most mutations strengthen networks of water-mediated hydrogen bonds and reduce binding affinity by increasing the enthalpic cost and, to a lesser extent, the entropic benefit of rearranging those networks during binding. The organization of water within a binding pocket can thus determine whether the hydrophobic interactions in which it engages are enthalpy-driven or entropy-driven. Our findings highlight a possible asymmetry in protein-ligand association by suggesting that, within the confines of the binding pocket of HCAII, binding events associated with enthalpically favorable rearrangements of water are stronger than those associated with entropically favorable ones.
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Affiliation(s)
- Jerome M Fox
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Kyungtae Kang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Madhavi Sastry
- Schrödinger, Sanali Infopark, 8-2-120/113 Banjara Hills, Hyderabad, 11937, Andhra Pradesh, India
| | - Woody Sherman
- Schrödinger, Inc., 120 West 45thStreet, New York, NY, 10036, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter H Zwart
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - George M Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
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