1
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Dawson JRD, Wadman GM, Zhang P, Tebben A, Carter PH, Gu S, Shroka T, Borrega-Roman L, Salanga CL, Handel TM, Kufareva I. Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.567150. [PMID: 38014122 PMCID: PMC10680698 DOI: 10.1101/2023.11.15.567150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
By driving monocyte chemotaxis, the chemokine receptor CCR2 shapes inflammatory responses and the formation of tumor microenvironments. This makes it a promising target in inflammation and immuno-oncology; however, despite extensive efforts, there are no FDA-approved CCR2-targeting therapeutics. Cited challenges include the redundancy of the chemokine system, suboptimal properties of compound candidates, and species differences that confound the translation of results from animals to humans. Structure-based drug design can rationalize and accelerate the discovery and optimization of CCR2 antagonists to address these challenges. The prerequisites for such efforts include an atomic-level understanding of the molecular determinants of action of existing antagonists. In this study, using molecular docking and artificial-intelligence-powered compound library screening, we uncover the structural principles of small molecule antagonism and selectivity towards CCR2 and its sister receptor CCR5. CCR2 orthosteric inhibitors are shown to universally occupy an inactive-state-specific tunnel between receptor helices 1 and 7; we also discover an unexpected role for an extra-helical groove accessible through this tunnel, suggesting its potential as a new targetable interface for CCR2 and CCR5 modulation. By contrast, only shape complementarity and limited helix 8 hydrogen bonding govern the binding of various chemotypes of allosteric antagonists. CCR2 residues S1012.63 and V2446.36 are implicated as determinants of CCR2/CCR5 and human/mouse orthosteric and allosteric antagonist selectivity, respectively, and the role of S1012.63 is corroborated through experimental gain-of-function mutagenesis. We establish a critical role of induced fit in antagonist recognition, reveal strong chemotype selectivity of existing structures, and demonstrate the high predictive potential of a new deep-learning-based compound scoring function. Finally, this study expands the available CCR2 structural landscape with computationally generated chemotype-specific models well-suited for structure-based antagonist design.
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Affiliation(s)
- John R D Dawson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Grant M Wadman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Percy H Carter
- Bristol Myers Squibb Company, Princeton, NJ, USA
- (current affiliation) Blueprint Medicines, Cambridge, MA, USA
| | - Siyi Gu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Lycia Therapeutics, South San Francisco, CA
| | - Thomas Shroka
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Avidity Biosciences Inc., San Diego, CA
| | - Leire Borrega-Roman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Catherina L Salanga
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
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2
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Wolf S. Predicting Protein-Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges. J Chem Inf Model 2023; 63:2902-2910. [PMID: 37133392 DOI: 10.1021/acs.jcim.3c00151] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The prediction of drug-target binding and unbinding kinetics that occur on time scales between milliseconds and several hours is a prime challenge for biased molecular dynamics simulation approaches. This Perspective gives a concise summary of the theory and the current state-of-the-art of such predictions via biased simulations, of insights into the molecular mechanisms defining binding and unbinding kinetics as well as of the extraordinary challenges predictions of ligand kinetics pose in comparison to binding free energy predictions.
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Affiliation(s)
- Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
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3
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Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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4
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Srinivasan B. A guide to enzyme kinetics in early drug discovery. FEBS J 2022; 290:2292-2305. [PMID: 35175693 DOI: 10.1111/febs.16404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 12/28/2022]
Abstract
Drugs interact with their target of interest to bring about the desired phenotypic outcome that results in disease alleviation. Traditionally, most lead optimization exercises were driven by affinity measures (like IC50 ) to inform structure-activity relationship (SAR)-guided medicinal chemistry. However, an IC50 value is a thermodynamic estimate measured under equilibrium conditions that can vary as a function of substrate concentration and/or time (the latter especially for nonequilibrium modalities). Further, like other thermodynamic estimates, it is a state-function that is indifferent to the path traversed from the initial state to the final state. This can be a cause for concern in drug discovery given the predominance of nonequilibrium interactions and the open thermodynamic nature of the human system. Under such situations, employing rates along with equilibrium constants (or IC50 values) would be far more relevant to capture the time evolution of the small molecule's interaction with the target of interest. These rates are generally typified by the rate of association, rate of dissociation and the residence time of the small molecule on the target (target occupancy). These parameters, when combined with the concept of target vulnerability, therapeutic window, pharmacokinetic profile of the small molecule, estimates of endogenous ligand and target turnover, will shed critical insights into the kinetics and dynamics of a small molecule's interaction with the protein, and allow realistic modelling of the system to enable optimizations and dosing decisions. With that aim, this guide will attempt to introduce the traditional role of mechanistic enzymology within drug discovery and emphasize the importance of kinetics in guiding SAR-based optimizations. It will also present initial ideas on how kinetic investigation should be positioned relative to the temporal span of a drug-discovery pipeline to leverage maximal utility from the investment in time and effort.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic and Structural Biology Discovery Sciences R&D AstraZeneca Cambridge UK
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5
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Lay CS, Thomas DA, Evans JP, Campbell M, McCombe K, Phillipou AN, Gordon LJ, Jones EJ, Riching K, Mahmood M, Messenger C, Carver CE, Gatfield KM, Craggs PD. Development of an intracellular quantitative assay to measure compound binding kinetics. Cell Chem Biol 2022; 29:287-299.e8. [PMID: 34520747 DOI: 10.1016/j.chembiol.2021.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/09/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023]
Abstract
Contemporary drug discovery typically quantifies the effect of a molecule on a biological target using the equilibrium-derived measurements of IC50, EC50, or KD. Kinetic descriptors of drug binding are frequently linked with the effectiveness of a molecule in modulating a disease phenotype; however, these parameters are yet to be fully adopted in early drug discovery. Nanoluciferase bioluminescence resonance energy transfer (NanoBRET) can be used to measure interactions between fluorophore-conjugated probes and luciferase fused target proteins. Here, we describe an intracellular NanoBRET competition assay that can be used to quantify cellular kinetic rates of compound binding to nanoluciferase-fused bromodomain and extra-terminal (BET) proteins. Comparative rates are generated using a cell-free NanoBRET assay and by utilizing orthogonal recombinant protein-based methodologies. A screen of known pan-BET inhibitors is used to demonstrate the value of this approach in the investigation of kinetic selectivity between closely related proteins.
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Affiliation(s)
- Charles S Lay
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Daniel A Thomas
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; Arctoris, Oxford OX14 4SA, UK
| | - John P Evans
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Matthew Campbell
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Kristopher McCombe
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Alexander N Phillipou
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Laurie J Gordon
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Emma J Jones
- Protein and Cellular Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | | | - Mahnoor Mahmood
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Cassie Messenger
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Charlotte E Carver
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Kelly M Gatfield
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Peter D Craggs
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; GSK-Francis Crick Institute Linklabs, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
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6
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Ortiz Zacarías NV, Bemelmans MP, Handel TM, de Visser KE, Heitman LH. Anticancer opportunities at every stage of chemokine function. Trends Pharmacol Sci 2021; 42:912-928. [PMID: 34521537 DOI: 10.1016/j.tips.2021.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 02/01/2023]
Abstract
The chemokine system, comprising 48 chemokines and 23 receptors, is critically involved in several hallmarks of cancer. Yet, despite extensive efforts from the pharmaceutical sector, only two drugs aimed at this system are currently approved for clinical use against cancer. To date, numerous pharmacological approaches have been developed to successfully intervene at different stages of chemokine function: (i) chemokine availability; (ii) chemokine-glycosaminoglycan binding; and (iii) chemokine receptor binding. Many of these strategies have been tested in preclinical cancer models, and some have advanced to clinical trials as potential anticancer therapies. Here we will review the strategies and growing pharmacological toolbox for manipulating the chemokine system in cancer, and address novel methods poised for future (pre)clinical testing.
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Affiliation(s)
- Natalia V Ortiz Zacarías
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands; Oncode Institute, Leiden University, Leiden, The Netherlands
| | - Martijn P Bemelmans
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Tracy M Handel
- University of California San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, USA
| | - Karin E de Visser
- Oncode Institute, Leiden University, Leiden, The Netherlands; Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Immunology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands; Oncode Institute, Leiden University, Leiden, The Netherlands.
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7
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Khurana P, McWilliams L, Wingfield J, Barratt D, Srinivasan B. A Novel High-Throughput FLIPR Tetra-Based Method for Capturing Highly Confluent Kinetic Data for Structure-Kinetic Relationship Guided Early Drug Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:684-697. [PMID: 33783249 DOI: 10.1177/24725552211000676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Target engagement by small molecules is necessary for producing a physiological outcome. In the past, a lot of emphasis was placed on understanding the thermodynamics of such interactions to guide structure-activity relationships. It is becoming clearer, however, that understanding the kinetics of the interaction between a small-molecule inhibitor and the biological target [structure-kinetic relationship (SKR)] is critical for selection of the optimum candidate drug molecule for clinical trial. However, the acquisition of kinetic data in a high-throughput manner using traditional methods can be labor intensive, limiting the number of molecules that can be tested. As a result, in-depth kinetic studies are often carried out on only a small number of compounds, and usually at a later stage in the drug discovery process. Fundamentally, kinetic data should be used to drive key decisions much earlier in the drug discovery process, but the throughput limitations of traditional methods preclude this. A major limitation that hampers acquisition of high-throughput kinetic data is the technical challenge in collecting substantially confluent data points for accurate parameter estimation from time course analysis. Here, we describe the use of the fluorescent imaging plate reader (FLIPR), a charge-coupled device (CCD) camera technology, as a potential high-throughput tool for generating biochemical kinetic data with smaller time intervals. Subsequent to the design and optimization of the assay, we demonstrate the collection of highly confluent time-course data for various kinase protein targets with reasonable throughput to enable SKR-guided medicinal chemistry. We select kinase target 1 as a special case study with covalent inhibition, and demonstrate methods for rapid and detailed analysis of the resultant kinetic data for parameter estimation. In conclusion, this approach has the potential to enable rapid kinetic studies to be carried out on hundreds of compounds per week and drive project decisions with kinetic data at an early stage in drug discovery.
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Affiliation(s)
- Puneet Khurana
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Lisa McWilliams
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Jonathan Wingfield
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Derek Barratt
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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8
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Falconer RJ, Schuur B, Mittermaier AK. Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020. J Mol Recognit 2021; 34:e2901. [PMID: 33975380 DOI: 10.1002/jmr.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.
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Affiliation(s)
- Robert J Falconer
- School of Chemical Engineering & Advanced Materials, University of Adelaide, Adelaide, South Australia, Australia
| | - Boelo Schuur
- Faculty of Science and Technology, University of Twente, Enschede, Netherlands
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9
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Amangeldiuly N, Karlov D, Fedorov MV. Baseline Model for Predicting Protein–Ligand Unbinding Kinetics through Machine Learning. J Chem Inf Model 2020; 60:5946-5956. [DOI: 10.1021/acs.jcim.0c00450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nurlybek Amangeldiuly
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Dmitry Karlov
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Maxim V. Fedorov
- Center for Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, Glasgow G4 0NG, U.K
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10
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Torrens-Fontanals M, Stepniewski TM, Aranda-García D, Morales-Pastor A, Medel-Lacruz B, Selent J. How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs. Int J Mol Sci 2020; 21:E5933. [PMID: 32824756 PMCID: PMC7460635 DOI: 10.3390/ijms21165933] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 01/08/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are implicated in nearly every physiological process in the human body and therefore represent an important drug targeting class. Advances in X-ray crystallography and cryo-electron microscopy (cryo-EM) have provided multiple static structures of GPCRs in complex with various signaling partners. However, GPCR functionality is largely determined by their flexibility and ability to transition between distinct structural conformations. Due to this dynamic nature, a static snapshot does not fully explain the complexity of GPCR signal transduction. Molecular dynamics (MD) simulations offer the opportunity to simulate the structural motions of biological processes at atomic resolution. Thus, this technique can incorporate the missing information on protein flexibility into experimentally solved structures. Here, we review the contribution of MD simulations to complement static structural data and to improve our understanding of GPCR physiology and pharmacology, as well as the challenges that still need to be overcome to reach the full potential of this technique.
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Affiliation(s)
- Mariona Torrens-Fontanals
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
- InterAx Biotech AG, PARK innovAARE, 5234 Villigen, Switzerland
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland
| | - David Aranda-García
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Adrián Morales-Pastor
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Brian Medel-Lacruz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
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11
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Fyfe TJ, Kellam B, Sykes DA, Capuano B, Scammells PJ, Lane JR, Charlton SJ, Mistry SN. Structure-Kinetic Profiling of Haloperidol Analogues at the Human Dopamine D 2 Receptor. J Med Chem 2019; 62:9488-9520. [PMID: 31580666 DOI: 10.1021/acs.jmedchem.9b00864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Haloperidol is a typical antipsychotic drug (APD) associated with an increased risk of extrapyramidal side effects (EPSs) and hyperprolactinemia relative to atypical APDs such as clozapine. Both drugs are dopamine D2 receptor (D2R) antagonists, with contrasting kinetic profiles. Haloperidol displays fast association/slow dissociation at the D2R, whereas clozapine exhibits relatively slow association/fast dissociation. Recently, we have provided evidence that slow dissociation from the D2R predicts hyperprolactinemia, whereas fast association predicts EPS. Unfortunately, clozapine can cause severe side effects independent of its D2R action. Our results suggest an optimal kinetic profile for D2R antagonist APDs that avoids EPS. To begin exploring this hypothesis, we conducted a structure-kinetic relationship study of haloperidol and revealed that subtle structural modifications dramatically change binding kinetic rate constants, affording compounds with a clozapine-like kinetic profile. Thus, optimization of these kinetic parameters may allow development of novel APDs based on the haloperidol scaffold with improved side-effect profiles.
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Affiliation(s)
- Tim J Fyfe
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Barrie Kellam
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - David A Sykes
- School of Life Sciences, Queen's Medical Centre , University of Nottingham , Nottingham NG7 2UH , U.K.,Centre of Membrane Protein and Receptors , University of Nottingham , Nottingham NG7 2UH , U.K
| | | | | | - J Robert Lane
- School of Life Sciences, Queen's Medical Centre , University of Nottingham , Nottingham NG7 2UH , U.K.,Centre of Membrane Protein and Receptors , University of Nottingham , Nottingham NG7 2UH , U.K
| | - Steven J Charlton
- School of Life Sciences, Queen's Medical Centre , University of Nottingham , Nottingham NG7 2UH , U.K.,Centre of Membrane Protein and Receptors , University of Nottingham , Nottingham NG7 2UH , U.K.,Excellerate Bioscience Ltd., BioCity , Nottingham NG1 1GF , U.K
| | - Shailesh N Mistry
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
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12
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Cheng R, Huang C, Hennig M, Nar H, Schnapp G. In situ
crystallography as an emerging method for structure solution of membrane proteins: the case of CCR2A. FEBS J 2019; 287:866-873. [DOI: 10.1111/febs.15098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/10/2019] [Accepted: 10/15/2019] [Indexed: 12/27/2022]
Affiliation(s)
| | - Chia‐Ying Huang
- Swiss Light Source Paul Scherrer Institute Villigen Switzerland
| | | | - Herbert Nar
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
| | - Gisela Schnapp
- Boehringer Ingelheim Pharma GmbH & Co. KG Biberach Germany
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13
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Wu G, Zhao T, Kang D, Zhang J, Song Y, Namasivayam V, Kongsted J, Pannecouque C, De Clercq E, Poongavanam V, Liu X, Zhan P. Overview of Recent Strategic Advances in Medicinal Chemistry. J Med Chem 2019; 62:9375-9414. [PMID: 31050421 DOI: 10.1021/acs.jmedchem.9b00359] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.
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Affiliation(s)
- Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Yuning Song
- Department of Clinical Pharmacy , Qilu Hospital of Shandong University , 250012 Ji'nan , China
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
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14
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IJzerman AP, Guo D. Drug-Target Association Kinetics in Drug Discovery. Trends Biochem Sci 2019; 44:861-871. [PMID: 31101454 DOI: 10.1016/j.tibs.2019.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
The important role of ligand-receptor binding kinetics in drug design and discovery is increasingly recognized by the drug research community. Over the past decade, accumulating evidence has shown that optimizing the ligand's dissociation rate constant can lead to desirable duration of in vivo target occupancy and, hence, improved pharmacodynamic properties. However, the association rate constant as a pharmacological principle remains less investigated, whereas it can play an equally important role in the selection of drug candidates. This review provides a compilation and discussion of otherwise scarce and dispersed information on this topic, bringing to light the importance of drug-target association in kinetics-directed drug design and discovery.
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Affiliation(s)
- Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
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15
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Magarkar A, Schnapp G, Apel AK, Seeliger D, Tautermann CS. Enhancing Drug Residence Time by Shielding of Intra-Protein Hydrogen Bonds: A Case Study on CCR2 Antagonists. ACS Med Chem Lett 2019; 10:324-328. [PMID: 30891134 DOI: 10.1021/acsmedchemlett.8b00590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022] Open
Abstract
The target residence time (RT) for a given ligand is one of the important parameters that have to be optimized during drug design. It is well established that shielding the receptor-ligand hydrogen bond (H-bond) interactions from water has been one of the factors in increasing ligand RT. Building on this foundation, here we report that shielding an intra-protein H-bond, which confers rigidity to the binding pocket and which is not directly involved in drug-receptor interactions, can strongly influence RT for CCR2 antagonists. Based on our recently solved CCR2 structure with MK-0812 and molecular dynamics (MD) simulations, we show that the RT for this and structurally related ligands is directly dependent on the shielding of the Tyr120-Glu291 H-bond from the water. If solvated this H-bond is often broken, making the binding pocket flexible and leading to shorter RT.
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Affiliation(s)
- Aniket Magarkar
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Gisela Schnapp
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Anna-Katharina Apel
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Daniel Seeliger
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Christofer S. Tautermann
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
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16
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Apel AK, Cheng RK, Tautermann CS, Brauchle M, Huang CY, Pautsch A, Hennig M, Nar H, Schnapp G. Crystal Structure of CC Chemokine Receptor 2A in Complex with an Orthosteric Antagonist Provides Insights for the Design of Selective Antagonists. Structure 2019; 27:427-438.e5. [DOI: 10.1016/j.str.2018.10.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/08/2018] [Accepted: 10/25/2018] [Indexed: 12/23/2022]
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17
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Georgi V, Schiele F, Berger BT, Steffen A, Marin Zapata PA, Briem H, Menz S, Preusse C, Vasta JD, Robers MB, Brands M, Knapp S, Fernández-Montalván A. Binding Kinetics Survey of the Drugged Kinome. J Am Chem Soc 2018; 140:15774-15782. [PMID: 30362749 DOI: 10.1021/jacs.8b08048] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Target residence time is emerging as an important optimization parameter in drug discovery, yet target and off-target engagement dynamics have not been clearly linked to the clinical performance of drugs. Here we developed high-throughput binding kinetics assays to characterize the interactions of 270 protein kinase inhibitors with 40 clinically relevant targets. Analysis of the results revealed that on-rates are better correlated with affinity than off-rates and that the fraction of slowly dissociating drug-target complexes increases from early/preclinical to late stage and FDA-approved compounds, suggesting distinct contributions by each parameter to clinical success. Combining binding parameters with PK/ADME properties, we illustrate in silico and in cells how kinetic selectivity could be exploited as an optimization strategy. Furthermore, using bio- and chemoinformatics we uncovered structural features influencing rate constants. Our results underscore the value of binding kinetics information in rational drug design and provide a resource for future studies on this subject.
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Affiliation(s)
- Victoria Georgi
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany.,Structural Genomics Consortium, Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 9 , 60438 Frankfurt am Main , Germany
| | - Felix Schiele
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Benedict-Tilman Berger
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany.,Structural Genomics Consortium, Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 9 , 60438 Frankfurt am Main , Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 15 , 60438 Frankfurt am Main , Germany
| | - Andreas Steffen
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Paula A Marin Zapata
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Hans Briem
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Stephan Menz
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Cornelia Preusse
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - James D Vasta
- Promega Corporation , 2800 Woods Hollow Road , Fitchburg , Wisconsin 53711 , United States
| | - Matthew B Robers
- Promega Corporation , 2800 Woods Hollow Road , Fitchburg , Wisconsin 53711 , United States
| | - Michael Brands
- Bayer AG, Drug Discovery, Pharmaceuticals , Müllerstraße 178 , 13353 Berlin , Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 9 , 60438 Frankfurt am Main , Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences , Johann Wolfgang Goethe-University , Max-von-Laue-Straße 15 , 60438 Frankfurt am Main , Germany
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18
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Quinn JG, Pitts KE, Steffek M, Mulvihill MM. Determination of Affinity and Residence Time of Potent Drug-Target Complexes by Label-free Biosensing. J Med Chem 2018; 61:5154-5161. [PMID: 29772180 DOI: 10.1021/acs.jmedchem.7b01829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prolonged drug-target occupancy has become increasingly important in lead optimization, and biophysical assays that measure residence time are in high demand. Here we report a practical label-free assay methodology that provides kinetic and affinity measurements suitable for most target classes without long preincubations and over comparatively short sample contact times. The method, referred to as a "chaser" assay, has been applied to three sets of unrelated kinase/inhibitor panels in order to measure the residence times, where correlation with observed efficacy was suspected. A lower throughput chaser assay measured a residence time of 3.6 days ±3.4% (95% CI) and provided single digit pM sensitivity. A higher throughput chaser methodology enabled a maximum capacity of 108 compounds in duplicate/day with an upper residence time limit of 9 h given an assay dissociation time of 34 min.
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Affiliation(s)
- John G Quinn
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Keith E Pitts
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Micah Steffek
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Melinda M Mulvihill
- Biophysical group, Biochemical and Cellular Pharmacology , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
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19
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Qin LH, Wang ZL, Xie X, Long YQ. Discovery and synthesis of 6,7,8,9-tetrahydro-5H-pyrido[4,3-c]azepin-5-one-based novel chemotype CCR2 antagonists via scaffold hopping strategy. Bioorg Med Chem 2018; 26:3559-3572. [PMID: 29805075 DOI: 10.1016/j.bmc.2018.05.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/18/2018] [Accepted: 05/19/2018] [Indexed: 12/16/2022]
Abstract
The chemokine CC receptor subtype 2 (CCR2) has attracted intensive interest for drug development in diverse therapeutic areas, including chronic inflammatory diseases, diabetes, neuropathic pain, atherogenesis and cancer. By employing a cut-and-sew scaffold hopping strategy, we identified an active scaffold of 3,4-dihydro-2,6-naphthyridin-1(2H)-one as the central pharmacophore to derive novel CCR2 antagonists. Systematic structure-activity relationship study with respect to the ring size and the substitution on the naphthyridinone ring gave birth to 1-arylamino-6-alkylheterocycle-6,7,8,9-tetrahydro-5H-pyrido[4,3-c]azepin-5-ones as a brand new chemotype of CCR2 antagonists with nanomolar inhibitory activity. The best antagonism activity in this series was exemplified by compound 13a, which combined the optimal substitutions of 3,4-dichlorophenylamino at C-1 and 3-(4-(N-methylmethylsulfonamido)piperidin-1-yl)propyl at N-6 position, leading to an IC50 value of 61 nM and 10-fold selectivity for CCR2 over CCR5. Efficient and general synthesis was established to construct the innovative core structure and derive the compound collections. This is the first report on our designed 6,7,8,9-tetrahydro-5H-pyrido[4,3-c]azepin-5-one as novel CCR2 antagonist scaffold and its synthesis.
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Affiliation(s)
- Li-Huai Qin
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; College of Pharmaceutic Sciences, Soochow University, 199 Renai Road, Suzhou 215123, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhi-Long Wang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xin Xie
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ya-Qiu Long
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; College of Pharmaceutic Sciences, Soochow University, 199 Renai Road, Suzhou 215123, China.
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20
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Guo D, Peletier LA, Bridge L, Keur W, de Vries H, Zweemer A, Heitman LH, IJzerman AP. A two-state model for the kinetics of competitive radioligand binding. Br J Pharmacol 2018; 175:1719-1730. [PMID: 29486053 PMCID: PMC5913406 DOI: 10.1111/bph.14184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 12/11/2017] [Accepted: 02/19/2018] [Indexed: 01/09/2023] Open
Abstract
Background and Purpose Ligand–receptor binding kinetics is receiving increasing attention in the drug research community. The Motulsky and Mahan model, a one‐state model, offers a method for measuring the binding kinetics of an unlabelled ligand, with the assumption that the labelled ligand has no preference while binding to distinct states or conformations of a drug target. As such, the one‐state model is not applicable if the radioligand displays biphasic binding kinetics to the receptor. Experimental Approach We extended the Motulsky and Mahan model to a two‐state model, in which the kinetics of the unlabelled competitor binding to different receptor states (R1 and R2) can be measured. With this extended model, we determined the binding kinetics of unlabelled N‐5′‐ethylcarboxamidoadenosine (NECA), a representative agonist for the adenosine A1 receptor. Subsequently, an application of the model was exemplified by measuring the binding kinetics of other A1 receptor ligands. In addition, limitations of the model were investigated as well. Key Results The kinetic rate constants of unlabelled NECA were comparable with the results of kinetic radioligand binding assays in which [3H]‐NECA was used. The model was further validated by good correlation between simulated results and the experimental data. Conclusion The two‐state model is sufficient to analyse the binding kinetics of an unlabelled ligand, when a radioligand shows biphasic association characteristics. We expect this two‐state model to have general applicability for other targets as well.
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Affiliation(s)
- Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | | | - Lloyd Bridge
- Department of Mathematics, Swansea University, Swansea, UK.,Department of Engineering Design and Mathematics, University of the West of England, Bristol, UK
| | - Wesley Keur
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Annelien Zweemer
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
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21
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Di Trani JM, De Cesco S, O'Leary R, Plescia J, do Nascimento CJ, Moitessier N, Mittermaier AK. Rapid measurement of inhibitor binding kinetics by isothermal titration calorimetry. Nat Commun 2018; 9:893. [PMID: 29497037 PMCID: PMC5832847 DOI: 10.1038/s41467-018-03263-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/31/2018] [Indexed: 11/23/2022] Open
Abstract
Although drug development typically focuses on binding thermodynamics, recent studies suggest that kinetic properties can strongly impact a drug candidate’s efficacy. Robust techniques for measuring inhibitor association and dissociation rates are therefore essential. To address this need, we have developed a pair of complementary isothermal titration calorimetry (ITC) techniques for measuring the kinetics of enzyme inhibition. The advantages of ITC over standard techniques include speed, generality, and versatility; ITC also measures the rate of catalysis directly, making it ideal for quantifying rapid, inhibitor-dependent changes in enzyme activity. We used our methods to study the reversible covalent and non-covalent inhibitors of prolyl oligopeptidase (POP). We extracted kinetics spanning three orders of magnitude, including those too rapid for standard methods, and measured sub-nM binding affinities below the typical ITC limit. These results shed light on the inhibition of POP and demonstrate the general utility of ITC-based enzyme inhibition kinetic measurements. There is growing evidence that the kinetics of interactions between inhibitors and their targets can strongly impact therapeutic efficacy. Here the authors describe an isothermal titration calorimetry-based method that can rapidly quantify inhibition kinetics and measure sub-nM binding affinities.
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Affiliation(s)
- Justin M Di Trani
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Stephane De Cesco
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Rebecca O'Leary
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Jessica Plescia
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Claudia Jorge do Nascimento
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada.,Institute of Biosciences, Federal University of the State of Rio de Janeiro, Urca, 22290-240, Rio de Janeiro, Brazil
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
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22
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Knowe MT, Danneman MW, Sun S, Pink M, Johnston JN. Biomimetic Desymmetrization of a Carboxylic Acid. J Am Chem Soc 2018; 140:1998-2001. [PMID: 29400455 DOI: 10.1021/jacs.7b12185] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The enantioselective desymmetrization of carboxylic acids by chiral Brønsted base catalysis is reported, leading to bridged bicyclic lactones with up to 94% ee. Crystallographic analysis of a substrate-catalyst complex suggests an origin of stereocontrol, reminiscent of functional Brønsted bases in biological settings, and enabled reaction optimization. The products contain an all-carbon quaternary stereocenter and can be derivatized to functionalized cyclopentanes.
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Affiliation(s)
- Matthew T Knowe
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37235-1822, United States
| | - Michael W Danneman
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37235-1822, United States
| | - Sarah Sun
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37235-1822, United States
| | - Maren Pink
- Indiana University Molecular Structure Center , Bloomington, Indiana 47405, United States
| | - Jeffrey N Johnston
- Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37235-1822, United States
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23
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Trigo-Mouriño P, Griesinger C, Lee D. Label-free NMR-based dissociation kinetics determination. JOURNAL OF BIOMOLECULAR NMR 2017; 69:229-235. [PMID: 29143948 DOI: 10.1007/s10858-017-0150-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Understanding the dissociation of molecules is the basis to modulate interactions of biomedical interest. Optimizing drugs for dissociation rates is found to be important for their efficacy, selectivity, and safety. Here, we show an application of the high-power relaxation dispersion (RD) method to the determination of the dissociation rates of weak binding ligands from receptors. The experiment probes proton RD on the ligand and, therefore, avoids the need for any isotopic labeling. The large ligand excess eases the detection significantly. Importantly, the use of large spin-lock fields allows the detection of faster dissociation rates than other relaxation approaches. Moreover, this experimental approach allows to access directly the off-rate of the binding process without the need for analyzing a series of samples with increasing ligand saturation. The validity of the method is shown with small molecule interactions using two macromolecules, bovine serum albumin and tubulin heterodimers.
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Affiliation(s)
- Pablo Trigo-Mouriño
- Department of NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Donghan Lee
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA.
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24
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Xia L, de Vries H, Lenselink EB, Louvel J, Waring MJ, Cheng L, Pahlén S, Petersson MJ, Schell P, Olsson RI, Heitman LH, Sheppard RJ, IJzerman AP. Structure-Affinity Relationships and Structure-Kinetic Relationships of 1,2-Diarylimidazol-4-carboxamide Derivatives as Human Cannabinoid 1 Receptor Antagonists. J Med Chem 2017; 60:9545-9564. [PMID: 29111736 PMCID: PMC5734604 DOI: 10.1021/acs.jmedchem.7b00861] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
We
report on the synthesis and biological evaluation of a series of 1,2-diarylimidazol-4-carboxamide
derivatives developed as CB1 receptor antagonists. These
were evaluated in a radioligand displacement binding assay, a [35S]GTPγS binding assay, and in a competition association
assay that enables the relatively fast kinetic screening of multiple
compounds. The compounds show high affinities and a diverse range
of kinetic profiles at the CB1 receptor and their structure–kinetic
relationships (SKRs) were established. Using the recently resolved
hCB1 receptor crystal structures, we also performed a modeling
study that sheds light on the crucial interactions for both the affinity
and dissociation kinetics of this family of ligands. We provide evidence
that, next to affinity, additional knowledge of binding kinetics is
useful for selecting new hCB1 receptor antagonists in the
early phases of drug discovery.
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Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | - Julien Louvel
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | | | | | - Sara Pahlén
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit, AstraZeneca , Gothenburg SE-431 83, Sweden
| | - Maria J Petersson
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit, AstraZeneca , Gothenburg SE-431 83, Sweden
| | | | | | - Laura H Heitman
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
| | - Robert J Sheppard
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca , Cambridge SK10 2NA, United Kingdom
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, LACDR, Leiden University , 2300RA Leiden, The Netherlands
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25
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Xia L, de Vries H, Yang X, Lenselink EB, Kyrizaki A, Barth F, Louvel J, Dreyer MK, van der Es D, IJzerman AP, Heitman LH. Kinetics of human cannabinoid 1 (CB1) receptor antagonists: Structure-kinetics relationships (SKR) and implications for insurmountable antagonism. Biochem Pharmacol 2017; 151:166-179. [PMID: 29102677 DOI: 10.1016/j.bcp.2017.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
While equilibrium binding affinities and in vitro functional antagonism of CB1 receptor antagonists have been studied in detail, little is known on the kinetics of their receptor interaction. In this study, we therefore conducted kinetic assays for nine 1-(4,5-diarylthiophene-2-carbonyl)-4-phenylpiperidine-4-carboxamide derivatives and included the CB1 antagonist rimonabant as a comparison. For this we newly developed a dual-point competition association assay with [3H]CP55940 as the radioligand. This assay yielded Kinetic Rate Index (KRI) values from which structure-kinetics relationships (SKR) of hCB1 receptor antagonists could be established. The fast dissociating antagonist 6 had a similar receptor residence time (RT) as rimonabant, i.e. 19 and 14 min, respectively, while the slowest dissociating antagonist (9) had a very long RT of 2222 min, i.e. pseudo-irreversible dissociation kinetics. In functional assays, 9 displayed insurmountable antagonism, while the effects of the shortest RT antagonist 6 and rimonabant were surmountable. Taken together, this study shows that hCB1 receptor antagonists can have very divergent RTs, which are not correlated to their equilibrium affinities. Furthermore, their RTs appear to define their mode of functional antagonism, i.e. surmountable vs. insurmountable. Finally, based on the recently resolved hCB1 receptor crystal structure, we propose that the differences in RT can be explained by a different binding mode of antagonist 9 from short RT antagonists that is able to displace unfavorable water molecules. Taken together, these findings are of importance for future design and evaluation of potent and safe hCB1 receptor antagonists.
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Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Xue Yang
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Athina Kyrizaki
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Francis Barth
- Sanofi-Aventis Research and Development, 371, Rue du Professeur Blayac, 34184 Montpellier Cedex 04, France
| | - Julien Louvel
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Matthias K Dreyer
- Sanofi-Aventis Deutschland GmbH R&D, Integrated Drug Discovery, Industriepark Hoechst, 65926 Frankfurt, Germany
| | - Daan van der Es
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands.
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26
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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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27
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Kufareva I, Gustavsson M, Zheng Y, Stephens BS, Handel TM. What Do Structures Tell Us About Chemokine Receptor Function and Antagonism? Annu Rev Biophys 2017; 46:175-198. [PMID: 28532213 PMCID: PMC5764094 DOI: 10.1146/annurev-biophys-051013-022942] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chemokines and their cell surface G protein-coupled receptors are critical for cell migration, not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provided unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs. In parallel, chemokine receptor structures with small molecules reveal the complicated and diverse structural foundations of small molecule antagonism and allostery, highlight the inherent physicochemical challenges of receptor:chemokine interfaces, and suggest novel epitopes that can be exploited to overcome these challenges. The structures and models promote unique understanding of chemokine receptor biology, including the interpretation of two decades of experimental studies, and will undoubtedly assist future drug discovery endeavors.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Yi Zheng
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Bryan S Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
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28
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Schuetz DA, de Witte WEA, Wong YC, Knasmueller B, Richter L, Kokh DB, Sadiq SK, Bosma R, Nederpelt I, Heitman LH, Segala E, Amaral M, Guo D, Andres D, Georgi V, Stoddart LA, Hill S, Cooke RM, De Graaf C, Leurs R, Frech M, Wade RC, de Lange ECM, IJzerman AP, Müller-Fahrnow A, Ecker GF. Kinetics for Drug Discovery: an industry-driven effort to target drug residence time. Drug Discov Today 2017; 22:896-911. [PMID: 28412474 DOI: 10.1016/j.drudis.2017.02.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/24/2017] [Accepted: 02/17/2017] [Indexed: 01/05/2023]
Abstract
A considerable number of approved drugs show non-equilibrium binding characteristics, emphasizing the potential role of drug residence times for in vivo efficacy. Therefore, a detailed understanding of the kinetics of association and dissociation of a target-ligand complex might provide crucial insight into the molecular mechanism-of-action of a compound. This deeper understanding will help to improve decision making in drug discovery, thus leading to a better selection of interesting compounds to be profiled further. In this review, we highlight the contributions of the Kinetics for Drug Discovery (K4DD) Consortium, which targets major open questions related to binding kinetics in an industry-driven public-private partnership.
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Affiliation(s)
- Doris A Schuetz
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | | | - Yin Cheong Wong
- Division of Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bernhard Knasmueller
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Lars Richter
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Daria B Kokh
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - S Kashif Sadiq
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
| | - Reggie Bosma
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, P.O. Box 7161, 1007 MC Amsterdam, The Netherlands
| | - Indira Nederpelt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Elena Segala
- Heptares Therapeutics,Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Marta Amaral
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany; Instituto de Biologia Experimental e Tecnológica, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Dong Guo
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Dorothee Andres
- Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, Müllerstr. 178, 13353 Berlin, Germany
| | - Victoria Georgi
- Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, Müllerstr. 178, 13353 Berlin, Germany
| | - Leigh A Stoddart
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Steve Hill
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Robert M Cooke
- Heptares Therapeutics,Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Chris De Graaf
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, P.O. Box 7161, 1007 MC Amsterdam, The Netherlands
| | - Rob Leurs
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, P.O. Box 7161, 1007 MC Amsterdam, The Netherlands
| | - Matthias Frech
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Elizabeth Cunera Maria de Lange
- Division of Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, Leiden, Einsteinweg 55, Leiden, 2300RA, The Netherlands
| | - Anke Müller-Fahrnow
- Bayer AG, Drug Discovery, Pharmaceuticals, Lead Discovery Berlin, Müllerstr. 178, 13353 Berlin, Germany
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria.
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29
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White DR, Wolfe JP. Stereocontrolled Synthesis of Amino-Substituted Carbocycles by Pd-Catalyzed Alkene Carboamination Reactions. Chemistry 2017; 23:5419-5423. [PMID: 28295688 DOI: 10.1002/chem.201700466] [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: 01/31/2017] [Indexed: 12/30/2022]
Abstract
Amino-substituted alkylidenecyclopentanes were synthesized through a stereoselective intermolecular Pd-catalyzed alkene carboamination reaction between alkenyl triflates bearing a pendant alkene and exogenous amine nucleophiles. The reactions are effective with a range of different substrate combinations, and proceed with generally high diastereoselectivity. Use of (S)-tBuPhox as the ligand in reactions of achiral substrates provides enantioenriched products with up to 98.5:1.5 e.r.
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Affiliation(s)
- Derick R White
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109-1055, USA
| | - John P Wolfe
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109-1055, USA
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30
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Bot I, Ortiz Zacarías NV, de Witte WEA, de Vries H, van Santbrink PJ, van der Velden D, Kröner MJ, van der Berg DJ, Stamos D, de Lange ECM, Kuiper J, IJzerman AP, Heitman LH. A novel CCR2 antagonist inhibits atherogenesis in apoE deficient mice by achieving high receptor occupancy. Sci Rep 2017; 7:52. [PMID: 28246398 PMCID: PMC5427923 DOI: 10.1038/s41598-017-00104-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 02/06/2017] [Indexed: 12/21/2022] Open
Abstract
CC Chemokine Receptor 2 (CCR2) and its endogenous ligand CCL2 are involved in a number of diseases, including atherosclerosis. Several CCR2 antagonists have been developed as potential therapeutic agents, however their in vivo clinical efficacy was limited. In this report, we aimed to determine whether 15a, an antagonist with a long residence time on the human CCR2, is effective in inhibiting the development of atherosclerosis in a mouse disease model. First, radioligand binding assays were performed to determine affinity and binding kinetics of 15a on murine CCR2. To assess the in vivo efficacy, western-type diet fed apoE-/- mice were treated daily with 15a or vehicle as control. Treatment with 15a reduced the amount of circulating CCR2+ monocytes and the size of the atherosclerotic plaques in both the carotid artery and the aortic root. We then showed that the long pharmacokinetic half-life of 15a combined with the high drug concentrations ensured prolonged CCR2 occupancy. These data render 15a a promising compound for drug development and confirms high receptor occupancy as a key parameter when targeting chemokine receptors.
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Affiliation(s)
- Ilze Bot
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Natalia V Ortiz Zacarías
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Wilhelmus E A de Witte
- Division of Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Peter J van Santbrink
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Daniël van der Velden
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Mara J Kröner
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Dirk-Jan van der Berg
- Division of Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | | | - Elizabeth C M de Lange
- Division of Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Johan Kuiper
- Division of Biopharmaceutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands.
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31
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Kaminski T, Gunnarsson A, Geschwindner S. Harnessing the Versatility of Optical Biosensors for Target-Based Small-Molecule Drug Discovery. ACS Sens 2017; 2:10-15. [PMID: 28722441 DOI: 10.1021/acssensors.6b00735] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Optical biosensors entered target-based small-molecule drug discovery more than two decades ago and have since transformed into a value-adding component in the decision-making process. Here, we briefly highlight the major application areas of optical biosensors and focus on desirable profiles of such platforms in order to ensure their effective use in small molecule drug discovery. Furthermore, we will emphasize current technology-based constraints and discuss experimental strategies to address these limitations as well as provide a view of necessary technology improvements for next generation platforms.
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Affiliation(s)
- Tim Kaminski
- Discovery Sciences, Innovative
Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, S-43183 Mölndal, Sweden
| | - Anders Gunnarsson
- Discovery Sciences, Innovative
Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, S-43183 Mölndal, Sweden
| | - Stefan Geschwindner
- Discovery Sciences, Innovative
Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, S-43183 Mölndal, Sweden
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32
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Moschen T, Grutsch S, Juen MA, Wunderlich CH, Kreutz C, Tollinger M. Measurement of Ligand-Target Residence Times by 1H Relaxation Dispersion NMR Spectroscopy. J Med Chem 2016; 59:10788-10793. [PMID: 27933946 PMCID: PMC5150660 DOI: 10.1021/acs.jmedchem.6b01110] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
A ligand-observed 1H NMR
relaxation experiment is introduced
for measuring the binding kinetics of low-molecular-weight compounds
to their biomolecular targets. We show that this approach, which does
not require any isotope labeling, is applicable to ligand–target
systems involving proteins and nucleic acids of variable molecular
size. The experiment is particularly useful for the systematic investigation
of low affinity molecules with residence times in the micro- to millisecond
time regime.
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Affiliation(s)
- Thomas Moschen
- Institute of Organic Chemistry and Centre for Molecular Biosciences (CMBI), University of Innsbruck , Innsbruck 6020, Austria
| | - Sarina Grutsch
- Institute of Organic Chemistry and Centre for Molecular Biosciences (CMBI), University of Innsbruck , Innsbruck 6020, Austria
| | - Michael A Juen
- Institute of Organic Chemistry and Centre for Molecular Biosciences (CMBI), University of Innsbruck , Innsbruck 6020, Austria
| | - Christoph H Wunderlich
- Institute of Organic Chemistry and Centre for Molecular Biosciences (CMBI), University of Innsbruck , Innsbruck 6020, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Centre for Molecular Biosciences (CMBI), University of Innsbruck , Innsbruck 6020, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Centre for Molecular Biosciences (CMBI), University of Innsbruck , Innsbruck 6020, Austria
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33
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Kinetic and structural insights into the binding of histone deacetylase 1 and 2 (HDAC1, 2) inhibitors. Bioorg Med Chem 2016; 24:4008-4015. [DOI: 10.1016/j.bmc.2016.06.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/17/2016] [Accepted: 06/18/2016] [Indexed: 12/22/2022]
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34
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Shimizu Y, Ogawa K, Nakayama M. Characterization of Kinetic Binding Properties of Unlabeled Ligands via a Preincubation Endpoint Binding Approach. ACTA ACUST UNITED AC 2016; 21:729-37. [PMID: 27270099 DOI: 10.1177/1087057116652065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022]
Abstract
The dissociation rates of unlabeled drugs have been well studied by kinetic binding analyses. Since kinetic assays are laborious, we developed a simple method to determine the kinetic binding parameters of unlabeled competitors by a preincubation endpoint assay. The probe binding after preincubation of a competitor can be described by a single equation as a function of time. Simulations using the equation revealed the degree of IC50 change induced by preincubation of a competitor depended on the dissociation rate koff of the competitor but not on the association rate kon To validate the model, an in vitro binding assay was performed using a smoothened receptor (SMO) and [(3)H]TAK-441, a SMO antagonist. The equilibrium dissociation constants (KI) and koff of SMO antagonists determined by globally fitting the model to the concentration-response curves obtained with and without 24 h preincubation correlated well with those determined by other methods. This approach could be useful for early-stage optimization of drug candidates by enabling determination of binding kinetics in a high-throughput manner because it does not require kinetic measurements, an intermediate washout step during the reaction, or prior determination of competitors' KI values.
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Affiliation(s)
- Yuji Shimizu
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Kazumasa Ogawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Masaharu Nakayama
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
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35
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Frank AT, Andricioaei I. Reaction Coordinate-Free Approach to Recovering Kinetics from Potential-Scaled Simulations: Application of Kramers’ Rate Theory. J Phys Chem B 2016; 120:8600-5. [DOI: 10.1021/acs.jpcb.6b02654] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aaron T. Frank
- Department
of Chemistry, The University of California, Irvine, 4212 Natural
Sciences 1, Irvine, California 92697, United States
| | - Ioan Andricioaei
- Department
of Chemistry, The University of California, Irvine, 4212 Natural
Sciences 1, Irvine, California 92697, United States
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36
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The role of kinetic context in apparent biased agonism at GPCRs. Nat Commun 2016; 7:10842. [PMID: 26905976 PMCID: PMC4770093 DOI: 10.1038/ncomms10842] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/27/2016] [Indexed: 12/27/2022] Open
Abstract
Biased agonism describes the ability of ligands to stabilize different conformations of a GPCR linked to distinct functional outcomes and offers the prospect of designing pathway-specific drugs that avoid on-target side effects. This mechanism is usually inferred from pharmacological data with the assumption that the confounding influences of observational (that is, assay dependent) and system (that is, cell background dependent) bias are excluded by experimental design and analysis. Here we reveal that ‘kinetic context', as determined by ligand-binding kinetics and the temporal pattern of receptor-signalling processes, can have a profound influence on the apparent bias of a series of agonists for the dopamine D2 receptor and can even lead to reversals in the direction of bias. We propose that kinetic context must be acknowledged in the design and interpretation of studies of biased agonism. Biased agonists act at a receptor to preferentially induce distinct intracellular signalling responses over others. Here the authors show how kinetics of ligand binding and signaling responses greatly influence observed bias profiles, and hence must be considered when studying biased agonists.
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37
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Zech SG, Kohlmann A, Zhou T, Li F, Squillace RM, Parillon LE, Greenfield MT, Miller DP, Qi J, Thomas RM, Wang Y, Xu Y, Miret JJ, Shakespeare WC, Zhu X, Dalgarno DC. Novel Small Molecule Inhibitors of Choline Kinase Identified by Fragment-Based Drug Discovery. J Med Chem 2016; 59:671-86. [PMID: 26700752 DOI: 10.1021/acs.jmedchem.5b01552] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Choline kinase α (ChoKα) is an enzyme involved in the synthesis of phospholipids and thereby plays key roles in regulation of cell proliferation, oncogenic transformation, and human carcinogenesis. Since several inhibitors of ChoKα display antiproliferative activity in both cellular and animal models, this novel oncogene has recently gained interest as a promising small molecule target for cancer therapy. Here we summarize our efforts to further validate ChoKα as an oncogenic target and explore the activity of novel small molecule inhibitors of ChoKα. Starting from weakly binding fragments, we describe a structure based lead discovery approach, which resulted in novel highly potent inhibitors of ChoKα. In cancer cell lines, our lead compounds exhibit a dose-dependent decrease of phosphocholine, inhibition of cell growth, and induction of apoptosis at low micromolar concentrations. The druglike lead series presented here is optimizable for improvements in cellular potency, drug target residence time, and pharmacokinetic parameters. These inhibitors may be utilized not only to further validate ChoKα as antioncogenic target but also as novel chemical matter that may lead to antitumor agents that specifically interfere with cancer cell metabolism.
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Affiliation(s)
- Stephan G Zech
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Anna Kohlmann
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Tianjun Zhou
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Feng Li
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Rachel M Squillace
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Lois E Parillon
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Matthew T Greenfield
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - David P Miller
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Jiwei Qi
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - R Mathew Thomas
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Yihan Wang
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Yongjin Xu
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Juan J Miret
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - William C Shakespeare
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Xiaotian Zhu
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - David C Dalgarno
- ARIAD Pharmaceuticals, Inc. , 26 Landsdowne Street, Cambridge, Massachusetts 02139, United States
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38
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Xia L, de Vries H, IJzerman AP, Heitman LH. Scintillation proximity assay (SPA) as a new approach to determine a ligand's kinetic profile. A case in point for the adenosine A1 receptor. Purinergic Signal 2015; 12:115-26. [PMID: 26647040 PMCID: PMC4749533 DOI: 10.1007/s11302-015-9485-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/19/2015] [Indexed: 01/11/2023] Open
Abstract
Scintillation proximity assay (SPA) is a radio-isotopic technology format used to measure a wide range of biological interactions, including drug-target binding affinity studies. The assay is homogeneous in nature, as it relies on a “mix and measure” format. It does not involve a filtration step to separate bound from free ligand as is the case in a traditional receptor-binding assay. For G protein-coupled receptors (GPCRs), it has been shown that optimal binding kinetics, next to a high affinity of a ligand, can result in more desirable pharmacological profiles. However, traditional techniques to assess kinetic parameters tend to be cumbersome and laborious. We thus aimed to evaluate whether SPA can be an alternative platform for real-time receptor-binding kinetic measurements on GPCRs. To do so, we first validated the SPA technology for equilibrium binding studies on a prototypic class A GPCR, the human adenosine A1 receptor (hA1R). Differently to classic kinetic studies, the SPA technology allowed us to study binding kinetic processes almost real time, which is impossible in the filtration assay. To demonstrate the reliability of this technology for kinetic purposes, we performed the so-called competition association experiments. The association and dissociation rate constants (kon and koff) of unlabeled hA1R ligands were reliably and quickly determined and agreed very well with the same parameters from a traditional filtration assay performed simultaneously. In conclusion, SPA is a very promising technique to determine the kinetic profile of the drug-target interaction. Its robustness and potential for high-throughput may render this technology a preferred choice for further kinetic studies.
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Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Ad P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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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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40
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Guo D, Heitman LH, IJzerman AP. The Role of Target Binding Kinetics in Drug Discovery. ChemMedChem 2015; 10:1793-6. [DOI: 10.1002/cmdc.201500310] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Dong Guo
- Division of Medicinal Chemistry; Leiden Academic Centre for Drug Research (LACDR); P.O. Box 9502 2300 RA Leiden the Netherlands
| | - Laura H. Heitman
- Division of Medicinal Chemistry; Leiden Academic Centre for Drug Research (LACDR); P.O. Box 9502 2300 RA Leiden the Netherlands
| | - Adriaan P. IJzerman
- Division of Medicinal Chemistry; Leiden Academic Centre for Drug Research (LACDR); P.O. Box 9502 2300 RA Leiden the Netherlands
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41
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Lai CT, Li HJ, Yu W, Shah S, Bommineni GR, Perrone V, Garcia-Diaz M, Tonge PJ, Simmerling C. Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA. Biochemistry 2015; 54:4683-91. [PMID: 26147157 DOI: 10.1021/acs.biochem.5b00284] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Slow-onset enzyme inhibitors are the subject of considerable interest as an approach to increasing the potency of pharmaceutical compounds by extending the residence time of the inhibitor on the target (the lifetime of the drug-receptor complex). However, rational modulation of residence time presents significant challenges because it requires additional mechanistic insight, such as the nature of the transition state for postbinding isomerization. Our previous work, based on X-ray crystallography, enzyme kinetics, and molecular dynamics simulation, suggested that the slow step in inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA involves a change in the conformation of the substrate binding loop from an open state in the initial enzyme-inhibitor complex to a closed state in the final enzyme-inhibitor complex. Here, we use multidimensional free energy landscapes for loop isomerization to obtain a computational model for the transition state. The results suggest that slow-onset inhibitors crowd key side chains on helices that slide past each other during isomerization, resulting in a steric clash. The landscapes become significantly flatter when residues involved in the steric clash are replaced with alanine. Importantly, this lower barrier can be increased by rational inhibitor redesign to restore the steric clash. Crystallographic studies and enzyme kinetics confirm the predicted effects on loop structure and flexibility, as well as inhibitor residence time. These loss and regain of function studies validate our mechanistic hypothesis for interactions controlling substrate binding loop isomerization, providing a platform for the future design of inhibitors with longer residence times and better in vivo potency. Similar opportunities for slow-onset inhibition via the same mechanism are identified in other pathogens.
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42
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Yu Z, van Veldhoven JPD, Louvel J, ’t Hart IME, Rook MB, van der Heyden MAG, Heitman LH, IJzerman AP. Structure–Affinity Relationships (SARs) and Structure–Kinetics Relationships (SKRs) of Kv11.1 Blockers. J Med Chem 2015; 58:5916-29. [DOI: 10.1021/acs.jmedchem.5b00518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Zhiyi Yu
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jacobus P. D. van Veldhoven
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Julien Louvel
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Ingrid M. E. ’t Hart
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Martin B. Rook
- Department of Medical Physiology, Division Heart & Lungs, University Medical Centre Utrecht, 3584 CM Utrecht, The Netherlands
| | - Marcel A. G. van der Heyden
- Department of Medical Physiology, Division Heart & Lungs, University Medical Centre Utrecht, 3584 CM Utrecht, The Netherlands
| | - Laura H. Heitman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
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43
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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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Vilums M, Heuberger J, Heitman LH, IJzerman AP. Indanes--Properties, Preparation, and Presence in Ligands for G Protein Coupled Receptors. Med Res Rev 2015; 35:1097-126. [PMID: 26018667 DOI: 10.1002/med.21352] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The indane (2,3-dihydro-1H-indene) ring system is an attractive scaffold for biologically active compounds due to the combination of aromatic and aliphatic properties fused together in one rigid system. This bicyclic structure provides a wide range of possibilities to incorporate specific substituents in different directionalities, thus being an attractive scaffold for medicinal chemists. Notably, many indane-based compounds are being used in the clinic to treat various diseases, such as indinavir, an HIV-1 protease inhibitor; indantadol, a potent Monoamine Oxidase (MAO)-inhibitor; the amine uptake inhibitor indatraline; and the ultra-long-acting β-adrenoceptor agonist indacaterol. Given the diversity of targets these drugs act on, one could argue that the indane ring system is a privileged substructure. In the present review, the synthetic and medicinal chemistry of the indane ring system is described. In more detail, it contains a comprehensive overview of compounds bearing the indane substructure with G protein coupled receptor (GPCR) activity, with particular emphasis on their structure-activity relationships (SAR).
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Affiliation(s)
- Maris Vilums
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Jules Heuberger
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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45
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Bradshaw JM, McFarland JM, Paavilainen VO, Bisconte A, Tam D, Phan VT, Romanov S, Finkle D, Shu J, Patel V, Ton T, Li X, Loughhead DG, Nunn PA, Karr DE, Gerritsen ME, Funk JO, Owens TD, Verner E, Brameld KA, Hill RJ, Goldstein DM, Taunton J. Prolonged and tunable residence time using reversible covalent kinase inhibitors. Nat Chem Biol 2015; 11:525-31. [PMID: 26006010 PMCID: PMC4472506 DOI: 10.1038/nchembio.1817] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/13/2015] [Indexed: 12/11/2022]
Abstract
Drugs with prolonged, on-target residence time often show superior efficacy, yet general strategies for optimizing drug-target residence time are lacking. Here, we demonstrate progress toward this elusive goal by targeting a noncatalytic cysteine in Bruton's tyrosine kinase (BTK) with reversible covalent inhibitors. Utilizing an inverted orientation of the cysteine-reactive cyanoacrylamide electrophile, we identified potent and selective BTK inhibitors that demonstrate biochemical residence times spanning from minutes to 7 days. An inverted cyanoacrylamide with prolonged residence time in vivo remained bound to BTK more than 18 hours after clearance from the circulation. The inverted cyanoacrylamide strategy was further utilized to discover fibroblast growth factor receptor (FGFR) kinase inhibitors with residence times of several days, demonstrating generalizability of the approach. Targeting noncatalytic cysteines with inverted cyanoacrylamides may serve as a broadly applicable platform that facilitates “residence time by design”, the ability to modulate and improve the duration of target engagement in vivo.
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Affiliation(s)
| | - Jesse M McFarland
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | - Ville O Paavilainen
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | | | - Danny Tam
- Principia Biopharma, South San Francisco, California, USA
| | - Vernon T Phan
- Principia Biopharma, South San Francisco, California, USA
| | | | - David Finkle
- Principia Biopharma, South San Francisco, California, USA
| | - Jin Shu
- Principia Biopharma, South San Francisco, California, USA
| | - Vaishali Patel
- Principia Biopharma, South San Francisco, California, USA
| | - Tony Ton
- Principia Biopharma, South San Francisco, California, USA
| | - Xiaoyan Li
- Principia Biopharma, South San Francisco, California, USA
| | | | - Philip A Nunn
- Principia Biopharma, South San Francisco, California, USA
| | - Dane E Karr
- Principia Biopharma, South San Francisco, California, USA
| | | | | | | | - Erik Verner
- Principia Biopharma, South San Francisco, California, USA
| | - Ken A Brameld
- Principia Biopharma, South San Francisco, California, USA
| | - Ronald J Hill
- Principia Biopharma, South San Francisco, California, USA
| | | | - Jack Taunton
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California, USA
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46
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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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47
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Van Steenwinckel J, Auvynet C, Sapienza A, Reaux-Le Goazigo A, Combadière C, Melik Parsadaniantz S. Stromal cell-derived CCL2 drives neuropathic pain states through myeloid cell infiltration in injured nerve. Brain Behav Immun 2015; 45:198-210. [PMID: 25449579 DOI: 10.1016/j.bbi.2014.10.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 10/18/2014] [Accepted: 10/18/2014] [Indexed: 12/24/2022] Open
Abstract
Neuropathic pain resulting from peripheral nerve injury involves many persistent neuroinflammatory processes including inflammatory chemokines that control leukocyte trafficking and activate resident cells. Several studies have shown that CCL2 chemokine, a potent attractant of monocytes, and its cognate receptor, CCR2, play a critical role in regulating nociceptive processes during neuropathic pain. However, the role of CCL2 in peripheral leukocyte infiltration-associated neuropathic pain remains poorly understood. In particular, the contribution of individual CCL2-expressing cell populations (i.e. stromal and leukocytes) to immune cell recruitment into the injured nerve has not been established. Here, in preclinical model of peripheral neuropathic pain (i.e. chronic constriction injury of the sciatic nerve), we have demonstrated that, CCL2 content was increased specifically in nerve fibers. This upregulation of CCL2 correlated with local monocyte/macrophage infiltration and pain processing. Furthermore, sciatic intraneural microinjection of CCL2 in naïve animals triggered long-lasting pain behavior associated with local monocyte/macrophage recruitment. Using a specific CCR2 antagonist and mice with a CCL2 genetic deletion, we have also established that the CCL2/CCR2 axis drives monocyte/macrophage infiltration and pain hypersensitivity in the CCI model. Finally, specific deletion of CCL2 in stromal or immune cells respectively using irradiated bone marrow-chimeric CCI mice demonstrated that stromal cell-derived CCL2 (in contrast to CCL2 immune cell-derived) tightly controls monocyte/macrophage recruitment into the lesion and plays a major role in the development of neuropathic pain. These findings demonstrate that in chronic pain states, CCL2 expressed by sciatic nerve cells predominantly drove local neuro-immune interactions and pain-related behavior through CCR2 signaling.
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Affiliation(s)
- Juliette Van Steenwinckel
- UMR 1141 INSERM, Hôpital Robert Debré, F-75019, Paris, France; Université Paris Diderot, Faculté de Médecine, F-75019, Paris, France; PremUP, 75014 Paris, France
| | - Constance Auvynet
- Sorbonne Universités, UPMC Université Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris). 91 Bd de l'hôpital, F-75013, Paris, France; Inserm, U1135, CIMI-Paris, 91 Bd de l'hôpital, F-75013, Paris, France; CNRS, ERL 8255, CIMI-Paris, 91 Bd de l'hôpital, F-75013, Paris, France
| | - Anaïs Sapienza
- Sorbonne Universités, UPMC Université Paris 06, Institut de la vision, équipe S12, 17 rue Moreau, F-75012, Paris, France; UMR_S 968 INSERM, 17 rue Moreau, F-75012, Paris, France; UMR 7210 CNRS, 17 rue Moreau, F-75012, Paris, France
| | - Annabelle Reaux-Le Goazigo
- Sorbonne Universités, UPMC Université Paris 06, Institut de la vision, équipe S12, 17 rue Moreau, F-75012, Paris, France; UMR_S 968 INSERM, 17 rue Moreau, F-75012, Paris, France; UMR 7210 CNRS, 17 rue Moreau, F-75012, Paris, France
| | - Christophe Combadière
- Sorbonne Universités, UPMC Université Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris). 91 Bd de l'hôpital, F-75013, Paris, France; Inserm, U1135, CIMI-Paris, 91 Bd de l'hôpital, F-75013, Paris, France; CNRS, ERL 8255, CIMI-Paris, 91 Bd de l'hôpital, F-75013, Paris, France
| | - Stéphane Melik Parsadaniantz
- Sorbonne Universités, UPMC Université Paris 06, Institut de la vision, équipe S12, 17 rue Moreau, F-75012, Paris, France; UMR_S 968 INSERM, 17 rue Moreau, F-75012, Paris, France; UMR 7210 CNRS, 17 rue Moreau, F-75012, Paris, France.
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48
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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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49
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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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50
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Design and synthesis of novel small molecule CCR2 antagonists: Evaluation of 4-aminopiperidine derivatives. Bioorg Med Chem Lett 2014; 24:5377-80. [DOI: 10.1016/j.bmcl.2014.10.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/14/2014] [Accepted: 10/17/2014] [Indexed: 11/18/2022]
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