101
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Schnapp G, Klein T, Hoevels Y, Bakker RA, Nar H. Comparative Analysis of Binding Kinetics and Thermodynamics of Dipeptidyl Peptidase-4 Inhibitors and Their Relationship to Structure. J Med Chem 2016; 59:7466-77. [PMID: 27438064 DOI: 10.1021/acs.jmedchem.6b00475] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The binding kinetics and thermodynamics of dipeptidyl peptidase (DPP)-4 inhibitors (gliptins) were investigated using surface plasmon resonance and isothermal titration calorimetry. Binding of gliptins to DPP-4 is a rapid electrostatically driven process. Off-rates were generally slow partly because of reversible covalent bond formation by some gliptins, and partly because of strong and extensive interactions. Binding of all gliptins is enthalpy-dominated due to strong ionic interactions and strong solvent-shielded hydrogen bonds. Using a congeneric series of molecules which represented the intermediates in the lead optimization program of linagliptin, the onset of slow binding kinetics and development of the thermodynamic repertoire were analyzed in the context of incremental changes of the chemical structures. All compounds rapidly associated, and therefore the optimization of affinity and residence time is highly correlated. The major contributor to the increasing free energy of binding was a strong increase of binding enthalpy, whereas entropic contributions remained low and constant despite significant addition of lipophilicity.
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Affiliation(s)
- Gisela Schnapp
- Department of Lead Identification and Optimization Support and ‡Department of CardioMetabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG , Biberach 88397, Germany
| | - Thomas Klein
- Department of Lead Identification and Optimization Support and ‡Department of CardioMetabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG , Biberach 88397, Germany
| | - Yvette Hoevels
- Department of Lead Identification and Optimization Support and ‡Department of CardioMetabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG , Biberach 88397, Germany
| | - Remko A Bakker
- Department of Lead Identification and Optimization Support and ‡Department of CardioMetabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG , Biberach 88397, Germany
| | - Herbert Nar
- Department of Lead Identification and Optimization Support and ‡Department of CardioMetabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG , Biberach 88397, Germany
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102
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Impact, determination and prediction of drug-receptor residence times for GPCRs. Curr Opin Pharmacol 2016; 30:22-26. [PMID: 27428776 DOI: 10.1016/j.coph.2016.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/03/2016] [Accepted: 07/04/2016] [Indexed: 01/02/2023]
Abstract
The residence time of a ligand on a GPCR of interest has become an optimization parameter in many examples in drug design. Long residence times can counterbalance unfavorable pharmacokinetic parameters, contributing to compound safety, and short residence times can be a tool to avoid target related side effects. Unlike the prediction and interpretation of the structure-activity relationship (SAR) of a ligand class on a receptor, the understanding and prediction of the structure-kinetics relationship (SKR) is much more demanding. Experimental and computational approaches are described, which serve to either rationalize SKR or to predict the kinetic parameters such as on-rates and off-rates.
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103
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Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. Biochim Biophys Acta Gen Subj 2016; 1860:1821-35. [PMID: 27241846 DOI: 10.1016/j.bbagen.2016.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics. SCOPE OF REVIEW This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties. MAJOR CONCLUSIONS In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration. GENERAL SIGNIFICANCE An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.
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104
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Ferruz N, De Fabritiis G. Binding Kinetics in Drug Discovery. Mol Inform 2016; 35:216-26. [PMID: 27492236 DOI: 10.1002/minf.201501018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/20/2016] [Indexed: 12/19/2022]
Abstract
Over the last years, researchers have increasingly become interested in measuring and understanding drugs' binding kinetics, namely the time in which drug and its target associate and dissociate. Historically, drug discovery programs focused on the optimization of target affinity as a proxy of in-vivo efficacy. However, often the efficacy of a ligand is not appropriately described by the in-vitro measured drug-receptor affinity, but rather depends on the lifetime of the in-vivo drug-receptor interaction. In this review we review recent works that highlight the importance of binding kinetics, molecular determinants for rational optimization and the recent emergence of computational methods as powerful tools in measuring and understanding binding kinetics.
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Affiliation(s)
- Noelia Ferruz
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra,Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain.,Acellera, Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain
| | - Gianni De Fabritiis
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra,Barcelona Biomedical Research Park (PRBB), C Dr Aiguader 88, 08003, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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105
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Application of the quantum mechanical IEF/PCM-MST hydrophobic descriptors to selectivity in ligand binding. J Mol Model 2016; 22:136. [DOI: 10.1007/s00894-016-2991-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/21/2016] [Indexed: 10/21/2022]
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106
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Hahn-Herrera O, Salcedo G, Barril X, García-Hernández E. Inherent conformational flexibility of F1-ATPase α-subunit. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1392-1402. [PMID: 27137408 DOI: 10.1016/j.bbabio.2016.04.283] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/12/2016] [Accepted: 04/28/2016] [Indexed: 12/30/2022]
Abstract
The core of F1-ATPase consists of three catalytic (β) and three noncatalytic (α) subunits, forming a hexameric ring in alternating positions. A wealth of experimental and theoretical data has provided a detailed picture of the complex role played by catalytic subunits. Although major conformational changes have only been seen in β-subunits, it is clear that α-subunits have to respond to these changes in order to be able to transmit information during the rotary mechanism. However, the conformational behavior of α-subunits has not been explored in detail. Here, we have combined unbiased molecular dynamics (MD) simulations and calorimetrically measured thermodynamic signatures to investigate the conformational flexibility of isolated α-subunits, as a step toward deepening our understanding of its function inside the α3β3 ring. The simulations indicate that the open-to-closed conformational transition of the α-subunit is essentially barrierless, which is ideal to accompany and transmit the movement of the catalytic subunits. Calorimetric measurements of the recombinant α-subunit from Geobacillus kaustophilus indicate that the isolated subunit undergoes no significant conformational changes upon nucleotide binding. Simulations confirm that the nucleotide-free and nucleotide-bound subunits show average conformations similar to that observed in the F1 crystal structure, but they reveal an increased conformational flexibility of the isolated α-subunit upon MgATP binding, which might explain the evolutionary conserved capacity of α-subunits to recognize nucleotides with considerable strength. Furthermore, we elucidate the different dependencies that α- and β-subunits show on Mg(II) for recognizing ATP.
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Affiliation(s)
- Otto Hahn-Herrera
- Instituto de Química Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04630, D.F., Mexico
| | - Guillermo Salcedo
- Instituto de Química Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04630, D.F., Mexico
| | - Xavier Barril
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain; Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Enrique García-Hernández
- Instituto de Química Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México 04630, D.F., Mexico.
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107
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Guo D, Pan AC, Dror RO, Mocking T, Liu R, Heitman LH, Shaw DE, IJzerman AP. Molecular Basis of Ligand Dissociation from the Adenosine A2A Receptor. Mol Pharmacol 2016; 89:485-91. [DOI: 10.1124/mol.115.102657] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/11/2016] [Indexed: 11/22/2022] Open
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108
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Ginex T, Muñoz-Muriedas J, Herrero E, Gibert E, Cozzini P, Luque FJ. Development and validation of hydrophobic molecular fields derived from the quantum mechanical IEF/PCM-MST solvation models in 3D-QSAR. J Comput Chem 2016; 37:1147-62. [DOI: 10.1002/jcc.24305] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/17/2015] [Accepted: 12/17/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Tiziana Ginex
- Dipartimento Di Scienze Degli Alimenti; University of Parma; Parco Area Delle Scienze 59/a Parma 43121 Italy
| | - Jordi Muñoz-Muriedas
- GlaxoSmithKline; Medicines Research Centre; Gunnels Wood Road Stevenage SG1 2NY United Kingdom
| | - Enric Herrero
- Pharmacelera, Jordi Girona 1-3, Campus Nord Universitat Politècnica De Catalunya; Edifici K2M Barcelona 08034 Spain
| | - Enric Gibert
- Pharmacelera, Jordi Girona 1-3, Campus Nord Universitat Politècnica De Catalunya; Edifici K2M Barcelona 08034 Spain
| | - Pietro Cozzini
- Dipartimento Di Scienze Degli Alimenti; University of Parma; Parco Area Delle Scienze 59/a Parma 43121 Italy
| | - F. J. Luque
- Department of Chemical Physics and Institut De Biomedicina (IBUB), Faculty of Pharmacy; University of Barcelona; Av. Prat De La Riba 171 Santa Coloma De Gramenet 08921 Spain
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109
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Jeszenői N, Bálint M, Horváth I, van der Spoel D, Hetényi C. Exploration of Interfacial Hydration Networks of Target–Ligand Complexes. J Chem Inf Model 2016; 56:148-58. [DOI: 10.1021/acs.jcim.5b00638] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Norbert Jeszenői
- Department
of Genetics, Eötvös Loránd University, Pázmány
Péter sétány 1/C, 1117 Budapest, Hungary
- MTA
NAP-B Molecular Neuroendocrinology Group, Institute of Physiology,
Szentágothai Research Center, Center for Neuroscience, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Mónika Bálint
- Department
of Biochemistry, Eötvös Loránd University, Pázmány
Péter sétány 1/C, 1117 Budapest, Hungary
| | - István Horváth
- Chemistry
Doctoral School, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, University of Uppsala, Box 596, SE-75124 Uppsala, Sweden
| | - Csaba Hetényi
- MTA-ELTE
Molecular Biophysics Research Group, Hungarian Academy of Sciences, Pázmány sétány 1/C, 1117 Budapest, Hungary
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110
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Abstract
The drug-target residence time model was first introduced in 2006 and has been broadly adopted across the chemical biology, biotechnology and pharmaceutical communities. While traditional in vitro methods view drug-target interactions exclusively in terms of equilibrium affinity, the residence time model takes into account the conformational dynamics of target macromolecules that affect drug binding and dissociation. The key tenet of this model is that the lifetime (or residence time) of the binary drug-target complex, and not the binding affinity per se, dictates much of the in vivo pharmacological activity. Here, this model is revisited and key applications of it over the past 10 years are highlighted.
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111
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Pathak AK, Bandyopadhyay T. Protein–Drug Interactions with Effective Polarization in Polarizable Water: Oxime Unbinding from AChE Gorge. J Phys Chem B 2015; 119:14460-71. [DOI: 10.1021/acs.jpcb.5b08930] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arup K. Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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112
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Schoop A, Dey F. On-rate based optimization of structure-kinetic relationship--surfing the kinetic map. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 17:9-15. [PMID: 26724331 DOI: 10.1016/j.ddtec.2015.08.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/24/2015] [Indexed: 05/16/2023]
Abstract
In the lead discovery process residence time has become an important parameter for the identification and characterization of the most efficacious compounds in vivo. To enable the success of compound optimization by medicinal chemistry toward a desired residence time the understanding of structure-kinetic relationship (SKR) is essential. This article reviews various approaches to monitor SKR and suggests using the on-rate as the key monitoring parameter. The literature is reviewed and examples of compound series with low variability as well as with significant changes in on-rates are highlighted. Furthermore, findings of kinetic on-rate changes are presented and potential underlying rationales are discussed.
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Affiliation(s)
- Andreas Schoop
- Proteros biostructures GmbH, Bunsenstrasse 7a, 82152 Martinsried, Germany.
| | - Fabian Dey
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland
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113
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Bortolato A, Deflorian F, Weiss DR, Mason JS. Decoding the Role of Water Dynamics in Ligand–Protein Unbinding: CRF1R as a Test Case. J Chem Inf Model 2015; 55:1857-66. [DOI: 10.1021/acs.jcim.5b00440] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Andrea Bortolato
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Francesca Deflorian
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Dahlia R. Weiss
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd., BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, U.K
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114
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Romanowska J, Kokh DB, Fuller JC, Wade RC. Computational Approaches for Studying Drug Binding Kinetics. THERMODYNAMICS AND KINETICS OF DRUG BINDING 2015. [DOI: 10.1002/9783527673025.ch11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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115
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Louvel J, Guo D, Soethoudt M, Mocking TA, Lenselink EB, Mulder-Krieger T, Heitman LH, IJzerman AP. Structure-kinetics relationships of Capadenoson derivatives as adenosine A 1 receptor agonists. Eur J Med Chem 2015. [DOI: 10.1016/j.ejmech.2015.07.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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116
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Mollica L, Decherchi S, Zia SR, Gaspari R, Cavalli A, Rocchia W. Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations. Sci Rep 2015; 5:11539. [PMID: 26103621 PMCID: PMC4477625 DOI: 10.1038/srep11539] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/14/2015] [Indexed: 12/13/2022] Open
Abstract
Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate. Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy. It is indeed becoming increasingly evident that the time a drug spends in contact with its target (aka residence time) can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays. We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold. Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance.
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Affiliation(s)
- Luca Mollica
- CompuNet, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genova, Italy
| | - Sergio Decherchi
- 1] CONCEPT Lab, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genova, Italy [2] BiKi Technologies s.r.l., Via XX Settembre, 33/10, I-16121 Genova, Italy
| | - Syeda Rehana Zia
- CONCEPT Lab, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genova, Italy
| | - Roberto Gaspari
- CONCEPT Lab, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genova, Italy
| | - Andrea Cavalli
- 1] CompuNet, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genova, Italy [2] Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, via Belmeloro 6, I-40126 Bologna, Italy
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia, via Morego, 30, I-16163 Genova, Italy
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117
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Vilums M, Zweemer AJM, Dilanchian A, van Veldhoven JPD, de Vries H, Brussee J, Saunders J, Stamos D, Heitman LH, IJzerman AP. Evaluation of (4-Arylpiperidin-1-yl)cyclopentanecarboxamides As High-Affinity and Long-Residence-Time Antagonists for the CCR2 Receptor. ChemMedChem 2015; 10:1249-58. [DOI: 10.1002/cmdc.201500058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/21/2015] [Indexed: 11/10/2022]
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118
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Design strategies to address kinetics of drug binding and residence time. Bioorg Med Chem Lett 2015; 25:2019-27. [DOI: 10.1016/j.bmcl.2015.02.027] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 02/06/2023]
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119
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Möbitz H. The ABC of protein kinase conformations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1555-66. [PMID: 25839999 DOI: 10.1016/j.bbapap.2015.03.009] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/18/2015] [Accepted: 03/24/2015] [Indexed: 02/06/2023]
Abstract
Due to their involvement in human diseases, protein kinases are an important therapeutic target class. Conformation is a key concept for understanding how functional activity, inhibition and sequence are linked. We assemble and annotate the mammalian structural kinome from the Protein Data Bank on the basis of a universal residue nomenclature. We identify a torsion angle around the Gly of the DFG-motif whose sharp distribution profile corresponds to three eclipsed conformations. This allows the definition a small set of clusters whose distribution shows a bias for the active conformation. A common rationale links the active and inactive state: stabilization of the active conformation, as well as inactivation by displacement of helix-αC or the DFG-motif is governed by the interaction between helix-αC and the DFG motif. In particular, the conformation of the DFG-motif is tightly correlated with the propensity of helix-αC displacement. Our analysis reveals detailed mechanisms for the displacement of helix-αC and the DFG and improves our understanding of the role of individual residues. By pooling conformations from the whole structural kinome, the energetic contributions of sequence and extrinsic factors can be estimated in free energy analyses. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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Affiliation(s)
- Henrik Möbitz
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland.
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120
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Huang YMM, Kang M, Chang CEA. Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics. J Mol Recognit 2015; 27:537-48. [PMID: 25042708 DOI: 10.1002/jmr.2377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 11/05/2022]
Abstract
Revealing the processes of ligand-protein associations deepens our understanding of molecular recognition and binding kinetics. Hydrogen bonds (H-bonds) play a crucial role in optimizing ligand-protein interactions and ligand specificity. In addition to the formation of stable H-bonds in the final bound state, the formation of transient H-bonds during binding processes contributes binding kinetics that define a ligand as a fast or slow binder, which also affects drug action. However, the effect of forming the transient H-bonds on the kinetic properties is little understood. Guided by results from coarse-grained Brownian dynamics simulations, we used classical molecular dynamics simulations in an implicit solvent model and accelerated molecular dynamics simulations in explicit waters to show that the position and distribution of the H-bond donor or acceptor of a drug result in switching intermolecular and intramolecular H-bond pairs during ligand recognition processes. We studied two major types of HIV-1 protease ligands: a fast binder, xk263, and a slow binder, ritonavir. The slow association rate in ritonavir can be attributed to increased flexibility of ritonavir, which yields multistep transitions and stepwise entering patterns and the formation and breaking of complex H-bond pairs during the binding process. This model suggests the importance of conversions of spatiotemporal H-bonds during the association of ligands and proteins, which helps in designing inhibitors with preferred binding kinetics.
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Affiliation(s)
- Yu-ming M Huang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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121
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Preti D, Baraldi PG, Saponaro G, Romagnoli R, Aghazadeh Tabrizi M, Baraldi S, Cosconati S, Bruno A, Novellino E, Vincenzi F, Ravani A, Borea PA, Varani K. Design, synthesis, and biological evaluation of novel 2-((2-(4-(substituted)phenylpiperazin-1-yl)ethyl)amino)-5'-N-ethylcarboxamidoadenosines as potent and selective agonists of the A2A adenosine receptor. J Med Chem 2015; 58:3253-67. [PMID: 25780876 DOI: 10.1021/acs.jmedchem.5b00215] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Stimulation of A2A adenosine receptors (AR) promotes anti-inflammatory responses in animal models of allergic rhinitis, asthma, chronic obstructive pulmonary disease, and rheumatic diseases. Herein we describe the results of a research program aimed at identifying potent and selective agonists of the A2AAR as potential anti-inflammatory agents. The recent crystallographic analysis of A2AAR agonists and antagonists in complex with the receptor provided key information on the structural determinants leading to receptor activation or blocking. In light of this, we designed a new series of 2-((4-aryl(alkyl)piperazin-1-yl)alkylamino)-5'-N-ethylcarboxamidoadenosines with high A2AAR affinity, activation potency and selectivity obtained by merging distinctive structural elements of known agonists and antagonists of the investigated target. Docking-based SAR optimization allowed us to identify compound 42 as one of the most potent and selective A2A agonist discovered so far (Ki hA2AAR = 4.8 nM, EC50 hA2AAR = 4.9 nM, Ki hA1AR > 10 000 nM, Ki hA3AR = 1487 nM, EC50 hA2BAR > 10 000 nM).
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Affiliation(s)
- Delia Preti
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Pier Giovanni Baraldi
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Giulia Saponaro
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Romeo Romagnoli
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Mojgan Aghazadeh Tabrizi
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Stefania Baraldi
- †Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Sandro Cosconati
- §DiSTABiF, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Agostino Bruno
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Ettore Novellino
- ∥Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Fabrizio Vincenzi
- ‡Dipartimento di Scienze Mediche, Sezione di Farmacologia, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Annalisa Ravani
- ‡Dipartimento di Scienze Mediche, Sezione di Farmacologia, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Pier Andrea Borea
- ‡Dipartimento di Scienze Mediche, Sezione di Farmacologia, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Katia Varani
- ‡Dipartimento di Scienze Mediche, Sezione di Farmacologia, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
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GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1-2 September 2014. Naunyn Schmiedebergs Arch Pharmacol 2015; 388:883-903. [PMID: 25772061 PMCID: PMC4495723 DOI: 10.1007/s00210-015-1111-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/24/2015] [Indexed: 01/14/2023]
Abstract
G-protein coupled receptors (GPCRs) are the targets of over half of all prescribed drugs today. The UniProt database has records for about 800 proteins classified as GPCRs, but drugs have only been developed against 50 of these. Thus, there is huge potential in terms of the number of targets for new therapies to be designed. Several breakthroughs in GPCRs biased pharmacology, structural biology, modelling and scoring have resulted in a resurgence of interest in GPCRs as drug targets. Therefore, an international conference, sponsored by the Royal Society, with world-renowned researchers from industry and academia was recently held to discuss recent progress and highlight key areas of future research needed to accelerate GPCR drug discovery. Several key points emerged. Firstly, structures for all three major classes of GPCRs have now been solved and there is increasing coverage across the GPCR phylogenetic tree. This is likely to be substantially enhanced with data from x-ray free electron sources as they move beyond proof of concept. Secondly, the concept of biased signalling or functional selectivity is likely to be prevalent in many GPCRs, and this presents exciting new opportunities for selectivity and the control of side effects, especially when combined with increasing data regarding allosteric modulation. Thirdly, there will almost certainly be some GPCRs that will remain difficult targets because they exhibit complex ligand dependencies and have many metastable states rendering them difficult to resolve by crystallographic methods. Subtle effects within the packing of the transmembrane helices are likely to mask and contribute to this aspect, which may play a role in species dependent behaviour. This is particularly important because it has ramifications for how we interpret pre-clinical data. In summary, collaborative efforts between industry and academia have delivered significant progress in terms of structure and understanding of GPCRs and will be essential for resolving problems associated with the more difficult targets in the future.
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Vilums M, Zweemer AJ, Barmare F, van der Gracht AM, Bleeker DC, Yu Z, de Vries H, Gross R, Clemens J, Krenitsky P, Brussee J, Stamos D, Saunders J, Heitman LH, IJzerman AP. When structure–affinity relationships meet structure–kinetics relationships: 3-((Inden-1-yl)amino)-1-isopropyl-cyclopentane-1-carboxamides as CCR2 antagonists. Eur J Med Chem 2015; 93:121-34. [DOI: 10.1016/j.ejmech.2015.01.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 01/29/2015] [Accepted: 01/31/2015] [Indexed: 02/02/2023]
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124
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Vanderpool D, Grimshaw CE, Lawson JD, Ermolieff J. Residence time and kinetic efficiency analysis of extracellular signal-regulated kinase 2 inhibitors. Anal Biochem 2015; 473:46-52. [DOI: 10.1016/j.ab.2014.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 02/02/2023]
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125
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Sim AYL, Verma C. How does a hydrocarbon staple affect peptide hydrophobicity? J Comput Chem 2015; 36:773-84. [DOI: 10.1002/jcc.23859] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/06/2015] [Accepted: 01/19/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Adelene Y. L. Sim
- Bioinformatics Institute (A*STAR); 30 Biopolis Street #07-01 Matrix 138671 Singapore
| | - Chandra Verma
- Bioinformatics Institute (A*STAR); 30 Biopolis Street #07-01 Matrix 138671 Singapore
- School of Biological Sciences, Nanyang Technological University; 60 Nanyang Drive 637551 Singapore
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543
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126
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Tiwary P, Limongelli V, Salvalaglio M, Parrinello M. Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps. Proc Natl Acad Sci U S A 2015; 112:E386-91. [PMID: 25605901 PMCID: PMC4321287 DOI: 10.1073/pnas.1424461112] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to predict the mechanisms and the associated rate constants of protein-ligand unbinding is of great practical importance in drug design. In this work we demonstrate how a recently introduced metadynamics-based approach allows exploration of the unbinding pathways, estimation of the rates, and determination of the rate-limiting steps in the paradigmatic case of the trypsin-benzamidine system. Protein, ligand, and solvent are described with full atomic resolution. Using metadynamics, multiple unbinding trajectories that start with the ligand in the crystallographic binding pose and end with the ligand in the fully solvated state are generated. The unbinding rate k off is computed from the mean residence time of the ligand. Using our previously computed binding affinity we also obtain the binding rate k on. Both rates are in agreement with reported experimental values. We uncover the complex pathways of unbinding trajectories and describe the critical rate-limiting steps with unprecedented detail. Our findings illuminate the role played by the coupling between subtle protein backbone fluctuations and the solvation by water molecules that enter the binding pocket and assist in the breaking of the shielded hydrogen bonds. We expect our approach to be useful in calculating rates for general protein-ligand systems and a valid support for drug design.
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Affiliation(s)
- Pratyush Tiwary
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, 8006 Zurich, Switzerland; Università della Svizzera Italiana, Faculty of Informatics, Institute of Computational Science, CH-6900 Lugano, Switzerland
| | - Vittorio Limongelli
- Università della Svizzera Italiana, Faculty of Informatics, Institute of Computational Science, CH-6900 Lugano, Switzerland; Department of Pharmacy, University of Naples Federico II, I-80131 Naples, Italy; and
| | - Matteo Salvalaglio
- Università della Svizzera Italiana, Faculty of Informatics, Institute of Computational Science, CH-6900 Lugano, Switzerland; Institute of Process Engineering, Eidgenössische Technische Hochschule Zürich, 8006 Zurich, Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, 8006 Zurich, Switzerland; Università della Svizzera Italiana, Faculty of Informatics, Institute of Computational Science, CH-6900 Lugano, Switzerland;
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127
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Klebe G. The Use of Thermodynamic and Kinetic Data in Drug Discovery: Decisive Insight or Increasing the Puzzlement? ChemMedChem 2014; 10:229-31. [DOI: 10.1002/cmdc.201402521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Indexed: 11/07/2022]
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128
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Tautermann CS, Seeliger D, Kriegl JM. What can we learn from molecular dynamics simulations for GPCR drug design? Comput Struct Biotechnol J 2014; 13:111-21. [PMID: 25709761 PMCID: PMC4334948 DOI: 10.1016/j.csbj.2014.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/28/2014] [Accepted: 12/03/2014] [Indexed: 01/05/2023] Open
Abstract
Recent years have seen a tremendous progress in the elucidation of experimental structural information for G-protein coupled receptors (GPCRs). Although for the vast majority of pharmaceutically relevant GPCRs structural information is still accessible only by homology models the steadily increasing amount of structural information fosters the application of structure-based drug design tools for this important class of drug targets. In this article we focus on the application of molecular dynamics (MD) simulations in GPCR drug discovery programs. Typical application scenarios of MD simulations and their scope and limitations will be described on the basis of two selected case studies, namely the binding of small molecule antagonists to the human CC chemokine receptor 3 (CCR3) and a detailed investigation of the interplay between receptor dynamics and solvation for the binding of small molecules to the human muscarinic acetylcholine receptor 3 (hM3R).
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Affiliation(s)
| | | | - Jan M. Kriegl
- Boehringer Ingelheim Pharma GmbH & Co. KG, Lead Identification and Optimization Support, Birkendorfer Str. 65, D-88397 Biberach a.d. Riss, Germany
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129
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Chaikuad A, Tacconi E, Zimmer J, Liang Y, Gray NS, Tarsounas M, Knapp S. A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics. Nat Chem Biol 2014; 10:853-60. [PMID: 25195011 PMCID: PMC4687050 DOI: 10.1038/nchembio.1629] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 08/05/2014] [Indexed: 01/07/2023]
Abstract
Activation of the ERK pathway is a hallmark of cancer, and targeting of upstream signaling partners led to the development of approved drugs. Recently, SCH772984 has been shown to be a selective and potent ERK1/2 inhibitor. Here we report the structural mechanism for its remarkable selectivity. In ERK1/2, SCH772984 induces a so-far-unknown binding pocket that accommodates the piperazine-phenyl-pyrimidine decoration. This new binding pocket was created by an inactive conformation of the phosphate-binding loop and an outward tilt of helix αC. In contrast, structure determination of SCH772984 with the off-target haspin and JNK1 revealed two canonical but distinct type I binding modes. Notably, the new binding mode with ERK1/2 was associated with slow binding kinetics in vitro as well as in cell-based assay systems. The described binding mode of SCH772984 with ERK1/2 enables the design of a new type of specific kinase inhibitors with prolonged on-target activity.
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Affiliation(s)
- Apirat Chaikuad
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Eliana Tacconi
- Telomere and Genome Stability Group, The CR-UK/MRC Oxford Institute for Radiation Oncology, Old Campus Road Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jutta Zimmer
- Telomere and Genome Stability Group, The CR-UK/MRC Oxford Institute for Radiation Oncology, Old Campus Road Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Yanke Liang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology, Dana Farber Cancer Institute, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Nathanael S. Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Department of Cancer Biology, Dana Farber Cancer Institute, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Madalena Tarsounas
- Telomere and Genome Stability Group, The CR-UK/MRC Oxford Institute for Radiation Oncology, Old Campus Road Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
- Department of Biochemistry & Molecular Medicine, George Washington University, Ross Hall, 2300 Eye Street NW, Washington, DC 20037, USA
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130
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Westermaier Y, Barril X, Scapozza L. Virtual screening: an in silico tool for interlacing the chemical universe with the proteome. Methods 2014; 71:44-57. [PMID: 25193260 DOI: 10.1016/j.ymeth.2014.08.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 07/16/2014] [Accepted: 08/02/2014] [Indexed: 12/28/2022] Open
Abstract
In silico screening both in the forward (traditional virtual screening) and reverse sense (inverse virtual screening (IVS)) are helpful techniques for interlacing the chemical universe of small molecules with the proteome. The former, which is using a protein structure and a large chemical database, is well-known by the scientific community. We have chosen here to provide an overview on the latter, focusing on validation and target prioritization strategies. By comparing it to complementary or alternative wet-lab approaches, we put IVS in the broader context of chemical genomics, target discovery and drug design. By giving examples from the literature and an own example on how to validate the approach, we provide guidance on the issues related to IVS.
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Affiliation(s)
- Yvonne Westermaier
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1211 Geneva 4, Switzerland; Computational Biology & Drug Design Group, Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
| | - Xavier Barril
- Computational Biology & Drug Design Group, Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Leonardo Scapozza
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 1211 Geneva 4, Switzerland.
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131
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Pei J, Yin N, Ma X, Lai L. Systems Biology Brings New Dimensions for Structure-Based Drug Design. J Am Chem Soc 2014; 136:11556-65. [DOI: 10.1021/ja504810z] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jianfeng Pei
- Center
for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Ning Yin
- Center
for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaomin Ma
- Center
for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Luhua Lai
- Center
for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Beijing
National Laboratory for Molecular Science, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
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132
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Abdel-Halim M, Diesel B, Kiemer AK, Abadi AH, Hartmann RW, Engel M. Discovery and optimization of 1,3,5-trisubstituted pyrazolines as potent and highly selective allosteric inhibitors of protein kinase C-ζ. J Med Chem 2014; 57:6513-30. [PMID: 25058929 DOI: 10.1021/jm500521n] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is increasing evidence that the atypical protein kinase C, PKCζ, might be a therapeutic target in pulmonary and hepatic inflammatory diseases. However, targeting the highly conserved ATP-binding pocket in the catalytic domain held little promise to achieve selective inhibition. In the present study, we introduce 1,3,5-trisubstituted pyrazolines as potent and selective allosteric PKCζ inhibitors. The rigid scaffold offered many sites for modification, all acting as hot spots for improving activity, and gave rise to sharp structure-activity relationships. Targeting of PKCζ in cells was confirmed by reporter gene assay, transfection assays, and Western blotting. The strongly reduced cell-free and cellular activities toward a PIF-pocket mutant of PKCζ suggested that the inhibitors most likely bound to the PIF-pocket on the kinase catalytic domain. Thus, using a rigidification strategy and by establishing and optimizing multiple molecular interactions with the binding site, we were able to significantly improve the potency of the previously reported PKCζ inhibitors.
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Affiliation(s)
- Mohammad Abdel-Halim
- Pharmaceutical and Medicinal Chemistry, Saarland University , Campus C2.3, D-66123 Saarbrücken, Germany
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133
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Ernst JT, Neubert T, Liu M, Sperry S, Zuccola H, Turnbull A, Fleck B, Kargo W, Woody L, Chiang P, Tran D, Chen W, Snyder P, Alcacio T, Nezami A, Reynolds J, Alvi K, Goulet L, Stamos D. Identification of novel HSP90α/β isoform selective inhibitors using structure-based drug design. demonstration of potential utility in treating CNS disorders such as Huntington's disease. J Med Chem 2014; 57:3382-400. [PMID: 24673104 DOI: 10.1021/jm500042s] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A structure-based drug design strategy was used to optimize a novel benzolactam series of HSP90α/β inhibitors to achieve >1000-fold selectivity versus the HSP90 endoplasmic reticulum and mitochondrial isoforms (GRP94 and TRAP1, respectively). Selective HSP90α/β inhibitors were found to be equipotent to pan-HSP90 inhibitors in promoting the clearance of mutant huntingtin protein (mHtt) in vitro, however with less cellular toxicity. Improved tolerability profiles may enable the use of HSP90α/β selective inhibitors in treating chronic neurodegenerative indications such as Huntington's disease (HD). A potent, selective, orally available HSP90α/β inhibitor was identified (compound 31) that crosses the blood-brain barrier. Compound 31 demonstrated proof of concept by successfully reducing brain Htt levels following oral dosing in rats.
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Affiliation(s)
- Justin T Ernst
- Vertex Pharmaceuticals , 11010 Torreyana Road, San Diego, California 92121, United States
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135
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Murray JB, Roughley SD, Matassova N, Brough PA. Off-Rate Screening (ORS) By Surface Plasmon Resonance. An Efficient Method to Kinetically Sample Hit to Lead Chemical Space from Unpurified Reaction Products. J Med Chem 2014; 57:2845-50. [DOI: 10.1021/jm401848a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- James B. Murray
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | | | - Natalia Matassova
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
| | - Paul A. Brough
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, U.K
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136
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Abstract
The discovery of novel biologically active small molecules is now a technologically and economically viable proposition for academic and small biotechnology laboratories wishing to build on their biological research into target proteins. Such small molecules may be useful reagents for further biological research or may form the basis for early-stage drug discovery. The availability of specialized virtual screening software to filter large molecular libraries into manageable numbers of compounds for biological assays is the driving force for finding novel ligands. The main focus of this chapter is the basis and use of molecular field methods to assess the interactions that may be made by small molecules. Molecular field based measures of capability and similarity of interaction may be used to discover novel ligands and expand ligand series for potential use as future therapies.
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Affiliation(s)
- Paul J Gane
- Medicinal Chemistry, Wolfson Institute for Biomedical Research, University College London, London, UK
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137
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Computational design of protein–protein interactions. Curr Opin Struct Biol 2013; 23:903-10. [DOI: 10.1016/j.sbi.2013.08.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/06/2013] [Accepted: 08/08/2013] [Indexed: 11/23/2022]
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138
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Tautermann CS, Kiechle T, Seeliger D, Diehl S, Wex E, Banholzer R, Gantner F, Pieper MP, Casarosa P. Molecular Basis for the Long Duration of Action and Kinetic Selectivity of Tiotropium for the Muscarinic M3 Receptor. J Med Chem 2013; 56:8746-56. [DOI: 10.1021/jm401219y] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Christofer S. Tautermann
- Lead Identification and Optimization Support, ‡Respiratory Diseases Research, and §Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach, Germany
| | - Tobias Kiechle
- Lead Identification and Optimization Support, ‡Respiratory Diseases Research, and §Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach, Germany
| | - Daniel Seeliger
- Lead Identification and Optimization Support, ‡Respiratory Diseases Research, and §Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach, Germany
| | - Sonja Diehl
- Lead Identification and Optimization Support, ‡Respiratory Diseases Research, and §Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach, Germany
| | - Eva Wex
- Lead Identification and Optimization Support, ‡Respiratory Diseases Research, and §Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach, Germany
| | - Rolf Banholzer
- Lead Identification and Optimization Support, ‡Respiratory Diseases Research, and §Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach, Germany
| | - Florian Gantner
- Lead Identification and Optimization Support, ‡Respiratory Diseases Research, and §Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach, Germany
| | - Michael P. Pieper
- Lead Identification and Optimization Support, ‡Respiratory Diseases Research, and §Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach, Germany
| | - Paola Casarosa
- Lead Identification and Optimization Support, ‡Respiratory Diseases Research, and §Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach, Germany
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139
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Yin Z, Kelso MJ, Beck JL, Oakley AJ. Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp. J Med Chem 2013; 56:8665-73. [DOI: 10.1021/jm401118f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zhou Yin
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
| | - Michael J. Kelso
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
| | - Jennifer L. Beck
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
| | - Aaron J. Oakley
- School of Chemistry, University of Wollongong, Northfields
Avenue, Wollongong 2522, NSW, Australia
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140
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Mente S, Arnold E, Butler T, Chakrapani S, Chandrasekaran R, Cherry K, DiRico K, Doran A, Fisher K, Galatsis P, Green M, Hayward M, Humphrey J, Knafels J, Li J, Liu S, Marconi M, McDonald S, Ohren J, Paradis V, Sneed B, Walton K, Wager T. Ligand-protein interactions of selective casein kinase 1δ inhibitors. J Med Chem 2013; 56:6819-28. [PMID: 23919824 DOI: 10.1021/jm4006324] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Casein kinase 1δ (CK1δ) and 1ε (CK1ε) are believed to be necessary enzymes for the regulation of circadian rhythms in all mammals. On the basis of our previously published work demonstrating a CK1ε-preferring compound to be an ineffective circadian clock modulator, we have synthesized a series of pyrazole-substitued pyridine inhibitors, selective for the CK1δ isoform. Additionally, using structure-based drug design, we have been able to exploit differences in the hinge region between CK1δ and p38 to find selective inhibitors that have minimal p38 activity. The SAR, brain exposure, and the effect of these inhibitors on mouse circadian rhythms are described. The in vivo evaluation of these inhibitors demonstrates that selective inhibition of CK1δ at sufficient central exposure levels is capable of modulating circadian rhythms.
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Affiliation(s)
- Scot Mente
- Pfizer Worldwide Research and Development , 700 Main Street, Cambridge, Massachusetts 02139, United States
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141
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Capelli AM, Bruno A, Entrena Guadix A, Costantino G. Unbinding Pathways from the Glucocorticoid Receptor Shed Light on the Reduced Sensitivity of Glucocorticoid Ligands to a Naturally Occurring, Clinically Relevant Mutant Receptor. J Med Chem 2013; 56:7003-14. [DOI: 10.1021/jm400802b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Anna Maria Capelli
- Chemistry Research and Drug
Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli, Parma, Italy
- Dipartimento di Farmacia, Universita’ degli Studi di Parma, viale Area
delle Scienze 27/A, Parma, Italy
| | - Agostino Bruno
- Dipartimento di Farmacia, Universita’ degli Studi di Parma, viale Area
delle Scienze 27/A, Parma, Italy
| | - Antonio Entrena Guadix
- Departamento de Quımica
Farmaceutica y Organica, Facultad de Farmacia, Universidad de Granada, Campus de Cartuja s/n, 18071 Granada, Spain
| | - Gabriele Costantino
- Dipartimento di Farmacia, Universita’ degli Studi di Parma, viale Area
delle Scienze 27/A, Parma, Italy
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142
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Pearlstein RA, Sherman W, Abel R. Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors. Proteins 2013; 81:1509-26. [PMID: 23468227 DOI: 10.1002/prot.24276] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 01/29/2013] [Accepted: 02/08/2013] [Indexed: 11/11/2022]
Abstract
In our previous work, we proposed that desolvation and resolvation of the binding sites of proteins can serve as the slowest steps during ligand association and dissociation, respectively, and tested this hypothesis on two protein-ligand systems with known binding kinetics behavior. In the present work, we test this hypothesis on another kinetically-determined protein-ligand system-that of p38α and eight Type II BIRB 796 inhibitor analogs. The kon values among the inhibitor analogs are narrowly distributed (10⁴ ≤ kon ≤ 10⁵ M⁻¹ s⁻¹), suggesting a common rate-determining step, whereas the koff values are widely distributed (10⁻¹ ≤ koff ≤ 10⁻⁶ s⁻¹), suggesting a spectrum of rate-determining steps. We calculated the solvation properties of the DFG-out protein conformation using an explicit solvent molecular dynamics simulation and thermodynamic analysis method implemented in WaterMap to predict the enthalpic and entropic costs of water transfer to and from bulk solvent incurred upon association and dissociation of each inhibitor. The results suggest that the rate-determining step for association consists of the transfer of a common set of enthalpically favorable solvating water molecules from the binding site to bulk solvent. The rate-determining step for inhibitor dissociation consists of the transfer of water from bulk solvent to specific binding site positions that are unfavorably solvated in the apo protein, and evacuated during ligand association. Different sets of unfavorable solvation are evacuated by each ligand, and the observed dissociation barriers are qualitatively consistent with the calculated solvation free energies of those sets.
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Affiliation(s)
- Robert A Pearlstein
- Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, Massachusetts 02139
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143
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Pan AC, Borhani DW, Dror RO, Shaw DE. Molecular determinants of drug–receptor binding kinetics. Drug Discov Today 2013; 18:667-73. [DOI: 10.1016/j.drudis.2013.02.007] [Citation(s) in RCA: 265] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/01/2013] [Accepted: 02/15/2013] [Indexed: 12/01/2022]
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144
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Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS. Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study. J Chem Inf Model 2013; 53:1700-13. [DOI: 10.1021/ci4001458] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Bortolato
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Ben G. Tehan
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Michael S. Bodnarchuk
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan W. Essex
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
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145
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Song G, Bai FY, Xing N, Chen C, Shan H, Xing YH. Crystal engineering of multiple-component organic compound: Organic co-crystals of the functional groups of carboxyl and amino with persistent hydrogen bonding motifs. Chem Res Chin Univ 2013. [DOI: 10.1007/s40242-013-2327-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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146
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Abstract
In contrast with the very well explored concept of structure-activity relationship, similar studies are missing for the dependency between binding kinetics and compound structure of a protein ligand complex, the structure-kinetic relationship. Here, we present a structure-kinetic relationship study of the cyclin-dependent kinase 8 (CDK8)/cyclin C (CycC) complex. The scaffold moiety of the compounds is anchored in the kinase deep pocket and extended with diverse functional groups toward the hinge region and the front pocket. These variations can cause the compounds to change from fast to slow binding kinetics, resulting in an improved residence time. The flip of the DFG motif ("DMG" in CDK8) to the inactive DFG-out conformation appears to have relatively little influence on the velocity of binding. Hydrogen bonding with the kinase hinge region contributes to the residence time but has less impact than hydrophobic complementarities within the kinase front pocket.
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147
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Emileh A, Tuzer F, Yeh H, Umashankara M, Moreira DRM, Lalonde JM, Bewley CA, Abrams CF, Chaiken IM. A model of peptide triazole entry inhibitor binding to HIV-1 gp120 and the mechanism of bridging sheet disruption. Biochemistry 2013; 52:2245-61. [PMID: 23470147 DOI: 10.1021/bi400166b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Peptide triazole (PT) entry inhibitors prevent HIV-1 infection by blocking the binding of viral gp120 to both the HIV-1 receptor and the coreceptor on target cells. Here, we used all-atom explicit solvent molecular dynamics (MD) to propose a model for the encounter complex of the peptide triazoles with gp120. Saturation transfer difference nuclear magnetic resonance (STD NMR) and single-site mutagenesis experiments were performed to test the simulation results. We found that docking of the peptide to a conserved patch of residues lining the "F43 pocket" of gp120 in a bridging sheet naïve gp120 conformation of the glycoprotein led to a stable complex. This pose prevents formation of the bridging sheet minidomain, which is required for receptor-coreceptor binding, providing a mechanistic basis for dual-site antagonism of this class of inhibitors. Burial of the peptide triazole at the gp120 inner domain-outer domain interface significantly contributed to complex stability and rationalizes the significant contribution of hydrophobic triazole groups to peptide potency. Both the simulation model and STD NMR experiments suggest that the I-X-W [where X is (2S,4S)-4-(4-phenyl-1H-1,2,3-triazol-1-yl)pyrrolidine] tripartite hydrophobic motif in the peptide is the major contributor of contacts at the gp120-PT interface. Because the model predicts that the peptide Trp side chain hydrogen bonding with gp120 S375 contributes to the stability of the PT-gp120 complex, we tested this prediction through analysis of peptide binding to gp120 mutant S375A. The results showed that a peptide triazole KR21 inhibits S375A with 20-fold less potency than WT, consistent with predictions of the model. Overall, the PT-gp120 model provides a starting point for both the rational design of higher-affinity peptide triazoles and the development of structure-minimized entry inhibitors that can trap gp120 into an inactive conformation and prevent infection.
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Affiliation(s)
- Ali Emileh
- Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
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148
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Yin Z, Song Y, Rehse PH. Thymoquinone blocks pSer/pThr recognition by Plk1 Polo-box domain as a phosphate mimic. ACS Chem Biol 2013; 8:303-8. [PMID: 23135290 DOI: 10.1021/cb3004379] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phosphorylation-dependent protein-protein interaction has rarely been targeted in medicinal chemistry. Thymoquinone, a naturally occurring antitumor agent, disrupts prephosphorylated substrate recognition by the polo-box domain of polo-like kinase 1, a key mitotic regulator responsible for various carcinogenesis when overexpressed. Here, crystallographic studies reveal that the phosphoserine/phosphothreonine recognition site of the polo-box domain is the binding pocket for thymoquinone and its analogue poloxime. Both small molecules displace phosphopeptides bound with the polo-box domain in a slow but noncovalent binding mode. A conserved water bridge and a cation-π interaction were found as their competition strategy against the phosphate group. This mechanism sheds light on small-molecule intervention of phospho-recognition by the polo-box domain of polo-like kinase 1 and other phospho-binding proteins in general.
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Affiliation(s)
- Zhou Yin
- School of Life Science and Technology, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, Jiangsu 210009, China
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149
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Yin N, Pei J, Lai L. A comprehensive analysis of the influence of drug binding kinetics on drug action at molecular and systems levels. MOLECULAR BIOSYSTEMS 2013; 9:1381-9. [DOI: 10.1039/c3mb25471b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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150
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Druggability predictions: methods, limitations, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1134] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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