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Pinto MF, Sirina J, Holliday ND, McWhirter CL. High-throughput kinetics in drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100170. [PMID: 38964171 DOI: 10.1016/j.slasd.2024.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/21/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
The importance of a drug's kinetic profile and interplay of structure-kinetic activity with PK/PD has long been appreciated in drug discovery. However, technical challenges have often limited detailed kinetic characterization of compounds to the latter stages of projects. This review highlights the advances that have been made in recent years in techniques, instrumentation, and data analysis to increase the throughput of detailed kinetic and mechanistic characterization, enabling its application earlier in the drug discovery process.
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Affiliation(s)
- Maria Filipa Pinto
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom
| | - Julija Sirina
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom
| | - Nicholas D Holliday
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom; School of Life Sciences, The Medical School, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
| | - Claire L McWhirter
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom.
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2
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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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3
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Wang G, Moitessier N, Mittermaier AK. Computational and biophysical methods for the discovery and optimization of covalent drugs. Chem Commun (Camb) 2023; 59:10866-10882. [PMID: 37609777 DOI: 10.1039/d3cc03285j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Drugs that act by covalently attaching to their targets have been used to treat human diseases for over a hundred years. However, the deliberate design of covalent drugs was discouraged due to concerns of toxicity and off-target effects. Recent successes in covalent drug discovery have sparked fresh interest in this field. New screening and testing methods aimed at covalent inhibitors can play pivotal roles in facilitating the discovery process. This feature article focuses on computational and biophysical advances originating from our labs over the past decade and how these approaches have contributed to the design of prolyl oligopeptidase (POP) and SARS-CoV-2 3CLpro covalent inhibitors.
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Affiliation(s)
- Guanyu Wang
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
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4
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Allosteric binding cooperativity in a kinetic context. Drug Discov Today 2023; 28:103441. [PMID: 36372329 DOI: 10.1016/j.drudis.2022.103441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Allosteric modulators are of prime interest in drug discovery. These drugs regulate the binding and function of endogenous ligands, with some advantages over orthosteric ligands. A typical pharmacological parameter in allosteric modulation is binding cooperativity. This property can yield unexpected but illuminating results when decomposed into its kinetic parameters. Using two reference models (the allosteric ternary complex receptor model and a heterodimer receptor model), a relationship has been derived for the cooperativity rate constant parameters. This relationship allows many combinations of the cooperativity kinetic parameters for a single binding cooperativity value obtained under equilibrium conditions. This assessment may help understand striking experimental results involving allosteric modulation and suggest further investigations in the field.
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5
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Srivastava M, Mittal L, Kumari A, Agrahari AK, Singh M, Mathur R, Asthana S. Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint. Protein Sci 2022; 31:e4398. [PMID: 36629250 PMCID: PMC9835771 DOI: 10.1002/pro.4398] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 01/21/2023]
Abstract
The ability to predict the intricate mechanistic behavior of ligands and associated structural determinants during protein-ligand (un)binding is of great practical importance in drug discovery. Ubiquitin specific protease-7 (USP7) is a newly emerging attractive cancer therapeutic target with bound allosteric inhibitors. However, none of the inhibitors have reached clinical trials, allowing opportunities to examine every aspect of allosteric modulation. The crystallographic insights reveal that these inhibitors have common properties such as chemical scaffolds, binding site and interaction fingerprinting. However, they still possess a broader range of binding potencies, ranging from 22 nM to 1,300 nM. Hence, it becomes more critical to decipher the structural determinants guiding the enhanced binding potency of the inhibitors. In this regard, we elucidated the atomic-level insights from both interacting partners, that is, protein-ligand perspective, and established the structure-activity link between USP7 inhibitors by using classical and advanced molecular dynamics simulations combined with linear interaction energy and molecular mechanics-Poisson Boltzmann surface area. We revealed the inhibitor potency differences by examining the contributions of chemical moieties and USP7 residues, the involvement of water-mediated interactions, and the thermodynamic landscape alterations. Additionally, the dissociation profiles aided in the establishment of a correlation between experimental potencies and structural determinants. Our study demonstrates the critical role of blocking loop 1 in allosteric inhibition and enhanced binding affinity. Comprehensively, our findings provide a constructive expansion of experimental outcomes and show the basis for varying binding potency using in-silico approaches. We expect this atomistic approach to be useful for effective drug design.
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Affiliation(s)
- Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
- Delhi Pharmaceutical Sciences and Research University (DPSRU)New DelhiIndia
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
| | - Anita Kumari
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
| | | | - Mrityunjay Singh
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
| | - Rajani Mathur
- Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR)New DelhiIndia
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI)FaridabadIndia
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6
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A Scintillation Proximity Assay for Real-Time Kinetic Analysis of Chemokine–Chemokine Receptor Interactions. Cells 2022; 11:cells11081317. [PMID: 35455996 PMCID: PMC9024993 DOI: 10.3390/cells11081317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/05/2022] [Accepted: 04/11/2022] [Indexed: 11/23/2022] Open
Abstract
Chemokine receptors are extensively involved in a broad range of physiological and pathological processes, making them attractive drug targets. However, despite considerable efforts, there are very few approved drugs targeting this class of seven transmembrane domain receptors to date. In recent years, the importance of including binding kinetics in drug discovery campaigns was emphasized. Therefore, kinetic insight into chemokine–chemokine receptor interactions could help to address this issue. Moreover, it could additionally deepen our understanding of the selectivity and promiscuity of the chemokine–chemokine receptor network. Here, we describe the application, optimization and validation of a homogenous Scintillation Proximity Assay (SPA) for real-time kinetic profiling of chemokine–chemokine receptor interactions on the example of ACKR3 and CXCL12. The principle of the SPA is the detection of radioligand binding to receptors reconstituted into nanodiscs by scintillation light. No receptor modifications are required. The nanodiscs provide a native-like environment for receptors and allow for full control over bilayer composition and size. The continuous assay format enables the monitoring of binding reactions in real-time, and directly accounts for non-specific binding and potential artefacts. Minor adaptations additionally facilitate the determination of equilibrium binding metrics, making the assay a versatile tool for the study of receptor–ligand interactions.
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7
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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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8
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Höfurthner T, Mateos B, Konrat R. On-Cell NMR Contributions to Membrane Receptor Binding Characterization. Chempluschem 2021; 86:938-945. [PMID: 34160899 DOI: 10.1002/cplu.202100134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/28/2021] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy has matured into a powerful tool to characterize interactions between biological molecules at atomic resolution, most importantly even under near to native (physiological) conditions. The field of in-cell NMR aims to study proteins and nucleic acids inside living cells. However, cells interrogate their environment and are continuously modulated by external stimuli. Cell signaling processes are often initialized by membrane receptors on the cell surface; therefore, characterizing their interactions at atomic resolution by NMR, hereafter referred as on-cell NMR, can provide valuable mechanistic information. This review aims to summarize recent on-cell NMR tools that give information about the binding site and the affinity of membrane receptors to their ligands together with potential applications to in vivo drug screening systems.
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Affiliation(s)
- Theresa Höfurthner
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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9
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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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10
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Structural Basis and Binding Kinetics of Vaborbactam in Class A β-Lactamase Inhibition. Antimicrob Agents Chemother 2020; 64:AAC.00398-20. [PMID: 32778546 DOI: 10.1128/aac.00398-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022] Open
Abstract
Class A β-lactamases are a major cause of β-lactam resistance in Gram-negative bacteria. The recently FDA-approved cyclic boronate vaborbactam is a reversible covalent inhibitor of class A β-lactamases, including CTX-M extended-spectrum β-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity for these two enzymes, despite their similarity. A 1.0-Å crystal structure of CTX-M-14 demonstrated that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25-Å crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, as well as alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the β3 strand on the inactivation rate, as well as the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved β-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.
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11
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van der Velden WJC, Heitman LH, Rosenkilde MM. Perspective: Implications of Ligand-Receptor Binding Kinetics for Therapeutic Targeting of G Protein-Coupled Receptors. ACS Pharmacol Transl Sci 2020; 3:179-189. [PMID: 32296761 DOI: 10.1021/acsptsci.0c00012] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 12/16/2022]
Abstract
The concept of ligand-receptor binding kinetics has been broadly applied in drug development pipelines focusing on G protein-coupled receptors (GPCRs). The ligand residence time (RT) for a receptor describes how long a ligand-receptor complex exists, and is defined as the reciprocal of the dissociation rate constant (k off). RT has turned out to be a valuable parameter for GPCR researchers focusing on drug development as a good predictor of in vivo efficacy. The positive correlation between RT and in vivo efficacy has been established for several drugs targeting class A GPCRs (e.g., the neurokinin-1 receptor (NK1R), the β2 adrenergic receptor (β2AR), and the muscarinic 3 receptor (M3R)) and for drugs targeting class B1 (e.g., the glucagon-like peptide 1 receptor (GLP-1R)). Recently, the association rate constant (k on) has gained similar attention as another parameter affecting in vivo efficacy. In the current perspective, we address the importance of studying ligand-receptor binding kinetics for therapeutic targeting of GPCRs, with an emphasis on how binding kinetics can be altered by subtle molecular changes in the ligands and/or the receptors and how such changes affect treatment outcome. Moreover, we speculate on the impact of binding kinetic parameters for functional selectivity and sustained receptor signaling from endosomal compartments; phenomena that have gained increasing interest in attempts to improve therapeutic targeting of GPCRs.
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Affiliation(s)
- Wijnand J C van der Velden
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK 2200, Denmark
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK 2200, Denmark
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12
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Borisov DV, Veselovsky AV. [Ligand-receptor binding kinetics in drug design]. BIOMEDITSINSKAIA KHIMIIA 2020; 66:42-53. [PMID: 32116225 DOI: 10.18097/pbmc20206601042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditionally, the thermodynamic values of affinity are considered as the main criterion for the development of new drugs. Usually, these values for drugs are measured <i>in vitro</i> at steady concentrations of the receptor and ligand, which are differed from <i>in vivo</i> environment. Recent studies have shown that the kinetics of the process of drug binding to its receptor make significant contribution in the drug effectiveness. This has increased attention in characterizing and predicting the rate constants of association and dissociation of the receptor ligand at the stage of preclinical studies of drug candidates. A drug with a long residence time can determine ligand-receptor selectivity (kinetic selectivity), maintain pharmacological activity of the drug at its low concentration in vivo. The paper discusses the theoretical basis of protein-ligand binding, molecular determinants that control the kinetics of the drug-receptor binding. Understanding the molecular features underlying the kinetics of receptor-ligand binding will contribute to the rational design of drugs with desired properties.
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Affiliation(s)
- D V Borisov
- Institute of Biomedical Chemistry, Moscow, Russia
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13
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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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14
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Long residence time adenosine A1 receptor agonists produce sustained wash-resistant antilipolytic effect in rat adipocytes. Biochem Pharmacol 2019; 164:45-52. [DOI: 10.1016/j.bcp.2019.03.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/20/2019] [Indexed: 02/06/2023]
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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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Roberts RS, Sevilla S, Ferrer M, Taltavull J, Hernández B, Segarra V, Gràcia J, Lehner MD, Gavaldà A, Andrés M, Cabedo J, Vilella D, Eichhorn P, Calama E, Carcasona C, Miralpeix M. 4-Amino-7,8-dihydro-1,6-naphthyridin-5(6 H)-ones as Inhaled Phosphodiesterase Type 4 (PDE4) Inhibitors: Structural Biology and Structure-Activity Relationships. J Med Chem 2018; 61:2472-2489. [PMID: 29502405 DOI: 10.1021/acs.jmedchem.7b01751] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rational design of a novel template of naphthyridinones rapidly led to PDE4 inhibitors with subnanomolar enzymatic potencies. X-ray crystallography confirmed the binding mode of this novel template. We achieved compounds with double-digit picomolar enzymatic potencies through further structure-based design by targeting both the PDE4 enzyme metal-binding pocket and occupying the solvent-filled pocket. A strategy for lung retention and long duration of action based on low aqueous solubility was followed. In vivo efficacies were measured in a rat lung neutrophilia model by suspension microspray and dry powder administration. Suspension microspray of potent compounds showed in vivo efficacy with a clear dose-response. Despite sustained lung levels, dry powder administration performed much less well and without proper dose-response, highlighting clear differences between the two formulations. This indicates a deficiency in the low aqueous solubility strategy for long duration lung efficacy.
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Affiliation(s)
- Richard S Roberts
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | - Sara Sevilla
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | - Manel Ferrer
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | - Joan Taltavull
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | - Begoña Hernández
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | - Victor Segarra
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | - Jordi Gràcia
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | - Martin D Lehner
- Bionorica SE , Kerschensteinerstraße 11-15 , 92318 Neumarkt , Germany
| | | | - Miriam Andrés
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | - Judit Cabedo
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | - Dolors Vilella
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
| | | | | | | | - Montserrat Miralpeix
- Medicinal Chemistry & Screening , ‡Pharmacokinetics & Metabolism , and §Experimental Dermatology , Almirall S.A., Centro de Investigación y Desarrollo , Crta. Laureà Miró 408-410 , Sant Feliu de Llobregat, 08980 Barcelona , Spain
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17
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Guo D, IJzerman AP. Molecular Basis of Ligand Dissociation from G Protein-Coupled Receptors and Predicting Residence Time. Methods Mol Biol 2018; 1705:197-206. [PMID: 29188564 DOI: 10.1007/978-1-4939-7465-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
G protein-coupled receptors (GPCRs) are integral membrane proteins and represent the largest class of drug targets. During the past decades progress in structural biology has enabled the crystallographic elucidation of the architecture of these important macromolecules. It also provided atomic-level visualization of ligand-receptor interactions, dramatically boosting the impact of structure-based approaches in drug discovery. However, knowledge obtained through crystallography is limited to static structural information. Less information is available showing how a ligand associates with or dissociates from a given receptor, whose importance is in fact increasingly recognized by the drug research community. Owing to recent advances in computer power and algorithms, molecular dynamics stimulations have become feasible that help in analyzing the kinetics of the ligand binding process. Here, we review what is currently known about the dynamics of GPCRs in the context of ligand association and dissociation, as determined through both crystallography and computer simulations. We particularly focus on the molecular basis of ligand dissociation from GPCRs and provide case studies that predict ligand dissociation pathways and residence time.
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Affiliation(s)
- Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands.
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18
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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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19
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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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20
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Tian H, Sakmar TP, Huber T. The Energetics of Chromophore Binding in the Visual Photoreceptor Rhodopsin. Biophys J 2017; 113:60-72. [PMID: 28700926 DOI: 10.1016/j.bpj.2017.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 01/06/2023] Open
Abstract
The visual photoreceptor rhodopsin is a prototypical G-protein-coupled receptor (GPCR) that stabilizes its inverse agonist ligand, 11-cis-retinal (11CR), by a covalent, protonated Schiff base linkage. In the visual dark adaptation, the fundamental molecular event after photobleaching of rhodopsin is the recombination reaction between its apoprotein opsin and 11CR. Here we present a detailed analysis of the kinetics and thermodynamics of this reaction, also known as the "regeneration reaction". We compared the regeneration of purified rhodopsin reconstituted into phospholipid/detergent bicelles with rhodopsin reconstituted into detergent micelles. We found that the lipid bilayer of bicelles stabilized the chromophore-free opsin over the long timescale required for the regeneration experiments, and also facilitated the ligand reuptake binding reaction. We utilized genetic code expansion and site-specific bioorthogonal labeling of rhodopsin with Alexa488 to enable, to our knowledge, a novel fluorescence resonance energy transfer-based measurement of the binding kinetics between opsin and 11CR. Based on these results, we report a complete energy diagram for the regeneration reaction of rhodopsin. We show that the dissociation reaction of rhodopsin to 11CR and opsin has a 25-pM equilibrium dissociation constant, which corresponds to only 0.3 kcal/mol stabilization compared to the noncovalent, tightly bound antagonist-GPCR complex of iodopindolol and β-adrenergic receptor. However, 11CR dissociates four orders-of-magnitude slower than iodopindolol, which corresponds to a 6-kcal/mol higher dissociation free energy barrier. We further used isothermal titration calorimetry to show that ligand binding in rhodopsin is enthalpy driven with -22 kcal/mol, which is 12 kcal/mol more stable than the antagonist-GPCR complex. Our data provide insights into the ligand-receptor binding reaction for rhodopsin in particular, and for GPCRs more broadly.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden.
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York.
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21
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Doornbos MLJ, Cid JM, Haubrich J, Nunes A, van de Sande JW, Vermond SC, Mulder-Krieger T, Trabanco AA, Ahnaou A, Drinkenburg WH, Lavreysen H, Heitman LH, IJzerman AP, Tresadern G. Discovery and Kinetic Profiling of 7-Aryl-1,2,4-triazolo[4,3-a]pyridines: Positive Allosteric Modulators of the Metabotropic Glutamate Receptor 2. J Med Chem 2017; 60:6704-6720. [DOI: 10.1021/acs.jmedchem.7b00669] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Maarten L. J. Doornbos
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - José María Cid
- Janssen Research and Development, Calle Jarama 75A, 45007, Toledo, Spain
| | - Jordi Haubrich
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Alexandro Nunes
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Jasper W. van de Sande
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Sophie C. Vermond
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Thea Mulder-Krieger
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Andrés A. Trabanco
- Janssen Research and Development, Calle Jarama 75A, 45007, Toledo, Spain
| | - Abdellah Ahnaou
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Hilde Lavreysen
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Laura H. Heitman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300RA Leiden, The Netherlands
| | - Gary Tresadern
- Janssen Research and Development, Calle Jarama 75A, 45007, Toledo, Spain
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22
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Ivan T, Enkvist E, Sinijarv H, Uri A. Competitive ligands facilitate dissociation of the complex of bifunctional inhibitor and protein kinase. Biophys Chem 2017. [PMID: 28651101 DOI: 10.1016/j.bpc.2017.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Dissociation of the complex of a ligand and a protein usually follows the kinetic profile of the first order process and the rate of dissociation is not affected by the presence of competitive ligands. We discovered that dissociation of the complex between a bifunctional ligand and a protein kinase (the catalytic subunit of cAMP-dependent protein kinase), an enzyme possessing 2 different substrate binding sites, was accelerated (facilitated) over 50-fold in the presence of competitive ligands at higher concentrations. Structurally diverse compounds revealed >10-fold different efficiency for acceleration of dissociation of the complex. These results show that the kinetic behavior of flexible biomolecular complexes possessing two spatially separated contact areas is highly dynamic. This property of biomolecular complexes should be carefully considered for effective application of bifunctional ligands for regulation of activity of target proteins in cells.
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Affiliation(s)
- Taavi Ivan
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Hedi Sinijarv
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Asko Uri
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia.
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23
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Bonnat L, Bar L, Génnaro B, Bonnet H, Jarjayes O, Thomas F, Dejeu J, Defrancq E, Lavergne T. Template-Mediated Stabilization of a DNA G-Quadruplex formed in the HIV-1 Promoter and Comparative Binding Studies. Chemistry 2017; 23:5602-5613. [PMID: 28264144 DOI: 10.1002/chem.201700417] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Indexed: 02/06/2023]
Abstract
G-rich DNA oligonucleotides derived from the promoter region of the HIV-1 long terminal repeat (LTR) were assembled onto an addressable cyclopeptide platform through sequential oxime ligation, a thiol-iodoacetamide SN2 reaction, and copper-catalyzed azide-alkyne cycloaddition reactions. The resulting conjugate was shown to fold into a highly stable antiparallel G4 architecture as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. The binding affinities of six state-of-the-art G4-binding ligands toward the HIV-G4 structure were compared to those obtained with a telomeric G4 structure and a hairpin structure. Surface plasmon resonance binding analysis provides new insights into the binding mode of broadly exploited G4 chemical probes and further suggests that potent and selective recognition of viral G4 structures of functional significance might be achieved.
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Affiliation(s)
- Laureen Bonnat
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France.,Univ. Grenoble Alpes, CNRS, DPM UMR-5063, 38000, Grenoble, France
| | - Laure Bar
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Béatrice Génnaro
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Hugues Bonnet
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Olivier Jarjayes
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Fabrice Thomas
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Jérôme Dejeu
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Eric Defrancq
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
| | - Thomas Lavergne
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, 38000, Grenoble, France
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24
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Johnstone S, Albert JS. Pharmacological property optimization for allosteric ligands: A medicinal chemistry perspective. Bioorg Med Chem Lett 2017; 27:2239-2258. [PMID: 28408223 DOI: 10.1016/j.bmcl.2017.03.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 12/11/2022]
Abstract
New strategies to potentially improve drug safety and efficacy emerge with allosteric programs. Biased allosteric modulators can be designed with high subtype selectivity and defined receptor signaling endpoints, however, selecting the most meaningful parameters for optimization can be perplexing. Historically, "potency hunting" at the expense of physicochemical and pharmacokinetic optimization has led to numerous tool compounds with excellent pharmacological properties but no path to drug development. Conversely, extensive physicochemical and pharmacokinetic screening with only post hoc bias and allosteric characterization has led to inefficacious compounds or compounds with on-target toxicities. This field is rapidly evolving with new mechanistic understanding, changes in terminology, and novel opportunities. The intent of this digest is to summarize current understanding and debates within the field. We aim to discuss, from a medicinal chemistry perspective, the parameter choices available to drive SAR.
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Affiliation(s)
- Shawn Johnstone
- Department of Chemistry, IntelliSyn Pharma, 7171 Frederick-Banting, Montreal, Quebec H4S 1Z9, Canada.
| | - Jeffrey S Albert
- Department of Chemistry, IntelliSyn Pharma, 7171 Frederick-Banting, Montreal, Quebec H4S 1Z9, Canada; Department of Chemistry, AviSyn Pharma, 4275 Executive Square, Suite 200, La Jolla, CA 92037, United States.
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25
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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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26
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Cramer J, Krimmer SG, Fridh V, Wulsdorf T, Karlsson R, Heine A, Klebe G. Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin. ACS Chem Biol 2017; 12:225-233. [PMID: 27959500 DOI: 10.1021/acschembio.6b00979] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Kinetic parameters of protein-ligand interactions are progressively acknowledged as valuable information for rational drug discovery. However, a targeted optimization of binding kinetics is not easy to achieve, and further systematic studies are necessary to increase the understanding about molecular mechanisms involved. We determined association and dissociation rate constants for 17 inhibitors of the metalloprotease thermolysin by surface plasmon resonance spectroscopy and correlated kinetic data with high-resolution crystal structures in complex with the protein. From the structure-kinetics relationship, we conclude that the strength of interaction with Asn112 correlates with the rate-limiting step of dissociation. This residue is located at the beginning of a β-strand motif that lines the binding cleft and is commonly believed to align a substrate for catalysis. A reduced mobility of the Asn112 side chain owing to an enhanced engagement in charge-assisted hydrogen bonds prevents the conformational adjustment associated with ligand release and transformation of the enzyme to its open state. This hypothesis is supported by kinetic data of ZFPLA, a known pseudopeptidic inhibitor of thermolysin, which blocks the conformational transition of Asn112. Interference with this retrograde induced-fit mechanism results in variation of the residence time of thermolysin inhibitors by a factor of 74 000. The high conservation of this structural motif within the M4 and M13 metalloprotease families underpins the importance of this feature and has significant implications for drug discovery.
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Affiliation(s)
- Jonathan Cramer
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Stefan G. Krimmer
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Veronica Fridh
- GE Healthcare Bio-Sciences AB, SE-751 84 Uppsala, Sweden
| | - Tobias Wulsdorf
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | | | - Andreas Heine
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
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27
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Nederpelt I, Bunnik J, IJzerman AP, Heitman LH. Kinetic Profile of Neuropeptide–Receptor Interactions. Trends Neurosci 2016; 39:830-839. [DOI: 10.1016/j.tins.2016.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 01/18/2023]
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28
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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
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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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29
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Hamedani NS, Rühl H, Zimmermann JJ, Heiseler T, Oldenburg J, Mayer G, Pötzsch B, Müller J. In Vitro Evaluation of Aptamer-Based Reversible Inhibition of Anticoagulant Activated Protein C as a Novel Supportive Hemostatic Approach. Nucleic Acid Ther 2016; 26:355-362. [PMID: 27736370 DOI: 10.1089/nat.2016.0645] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Activated protein C (APC) is a critical regulator of thrombin formation and thereby protects against thrombosis. On the other hand, overwhelming formation of APC increases the risk of bleeding such as in trauma-induced coagulopathy. Thus, pharmacological inhibition of APC activity may improve blood clottability in certain clinical situations. In this study, we demonstrate that the DNA aptamer HS02-52G binds with fast onset (1.118 ± 0.013 × 105 M-1 s-1) to APC and possesses a long residence time of 13.5 min within the aptamer-APC complex. Functional analysis revealed HS02-52G as a highly potent and specific inhibitor of APC in plasma and whole blood with IC50 values ≤30 nM, whose activity can be readily neutralized by the short complementary DNA molecule AD22. These features qualify the novel aptamer-antidote pair as a candidate treatment option for acute APC-related bleedings.
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Affiliation(s)
- Nasim Shahidi Hamedani
- 1 Institute of Experimental Hematology and Transfusion Medicine, University of Bonn Medical Center , Bonn, Germany
| | - Heiko Rühl
- 1 Institute of Experimental Hematology and Transfusion Medicine, University of Bonn Medical Center , Bonn, Germany
| | - Julia Janina Zimmermann
- 1 Institute of Experimental Hematology and Transfusion Medicine, University of Bonn Medical Center , Bonn, Germany
| | | | - Johannes Oldenburg
- 1 Institute of Experimental Hematology and Transfusion Medicine, University of Bonn Medical Center , Bonn, Germany
| | - Günter Mayer
- 3 Life and Medical Sciences Institute, University of Bonn , Bonn, Germany
| | - Bernd Pötzsch
- 1 Institute of Experimental Hematology and Transfusion Medicine, University of Bonn Medical Center , Bonn, Germany
| | - Jens Müller
- 1 Institute of Experimental Hematology and Transfusion Medicine, University of Bonn Medical Center , Bonn, Germany
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30
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Guo D, Heitman LH, IJzerman AP. The Added Value of Assessing Ligand-Receptor Binding Kinetics in Drug Discovery. ACS Med Chem Lett 2016; 7:819-21. [PMID: 27660682 DOI: 10.1021/acsmedchemlett.6b00273] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the past decade drug research community has started to appreciate the indispensable role of ligand-receptor binding kinetics (BK) in drug discovery. Next to the classical equilibrium-based drug evaluation process with affinity and potency values as outcomes, kinetic investigation of the ligand-receptor interaction can aid compound triage in the hit-to-lead campaign and provide additional information to understand the molecular mechanism of drug action. Translational models incorporating BK are emerging as well, which represent powerful tools for the prediction of in vivo effects. In this viewpoint we will summarize some recent findings and discuss and emphasize the added value of ligand-receptor binding kinetics in drug research.
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Affiliation(s)
- Dong Guo
- Jiangsu
Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221004, Jiangsu, China
| | - Laura H. Heitman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300 RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O.
Box 9502, 2300 RA Leiden, The Netherlands
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31
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Zhu Y, Li R, Lin Y, Shui M, Liu X, Chen H, Wang Y. Engineering Factor Xa Inhibitor with Multiple Platelet-Binding Sites Facilitates its Platelet Targeting. Sci Rep 2016; 6:29895. [PMID: 27432161 PMCID: PMC4949463 DOI: 10.1038/srep29895] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/22/2016] [Indexed: 11/09/2022] Open
Abstract
Targeted delivery of antithrombotic drugs centralizes the effects in the thrombosis site and reduces the hemorrhage side effects in uninjured vessels. We have recently reported that the platelet-targeting factor Xa (FXa) inhibitors, constructed by engineering one Arg-Gly-Asp (RGD) motif into Ancylostoma caninum anticoagulant peptide 5 (AcAP5), can reduce the risk of systemic bleeding than non-targeted AcAP5 in mouse arterial injury model. Increasing the number of platelet-binding sites of FXa inhibitors may facilitate their adhesion to activated platelets, and further lower the bleeding risks. For this purpose, we introduced three RGD motifs into AcAP5 to generate a variant NR4 containing three platelet-binding sites. NR4 reserved its inherent anti-FXa activity. Protein-protein docking showed that all three RGD motifs were capable of binding to platelet receptor αIIbβ3. Molecular dynamics simulation demonstrated that NR4 has more opportunities to interact with αIIbβ3 than single-RGD-containing NR3. Flow cytometry analysis and rat arterial thrombosis model further confirmed that NR4 possesses enhanced platelet targeting activity. Moreover, NR4-treated mice showed a trend toward less tail bleeding time than NR3-treated mice in carotid artery endothelium injury model. Therefore, our data suggest that engineering multiple binding sites in one recombinant protein is a useful tool to improve its platelet-targeting efficiency.
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Affiliation(s)
- Yuanjun Zhu
- Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, China
| | - Ruyi Li
- Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengyang Shui
- Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, China
| | - Xiaoyan Liu
- Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, China
| | - Huan Chen
- Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, China
| | - Yinye Wang
- Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, China
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32
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Impact, determination and prediction of drug-receptor residence times for GPCRs. Curr Opin Pharmacol 2016; 30:22-26. [PMID: 27428776 DOI: 10.1016/j.coph.2016.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/03/2016] [Accepted: 07/04/2016] [Indexed: 01/02/2023]
Abstract
The residence time of a ligand on a GPCR of interest has become an optimization parameter in many examples in drug design. Long residence times can counterbalance unfavorable pharmacokinetic parameters, contributing to compound safety, and short residence times can be a tool to avoid target related side effects. Unlike the prediction and interpretation of the structure-activity relationship (SAR) of a ligand class on a receptor, the understanding and prediction of the structure-kinetics relationship (SKR) is much more demanding. Experimental and computational approaches are described, which serve to either rationalize SKR or to predict the kinetic parameters such as on-rates and off-rates.
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33
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Dickson CJ, Hornak V, Velez-Vega C, McKay DJJ, Reilly J, Sandham DA, Shaw D, Fairhurst RA, Charlton SJ, Sykes DA, Pearlstein RA, Duca JS. Uncoupling the Structure-Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding. J Med Chem 2016; 59:5780-9. [PMID: 27239696 DOI: 10.1021/acs.jmedchem.6b00358] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Ligand binding to membrane proteins may be significantly influenced by the interaction of ligands with the membrane. In particular, the microscopic ligand concentration within the membrane surface solvation layer may exceed that in bulk solvent, resulting in overestimation of the intrinsic protein-ligand binding contribution to the apparent/measured affinity. Using published binding data for a set of small molecules with the β2 adrenergic receptor, we demonstrate that deconvolution of membrane and protein binding contributions allows for improved structure-activity relationship analysis and structure-based drug design. Molecular dynamics simulations of ligand bound membrane protein complexes were used to validate binding poses, allowing analysis of key interactions and binding site solvation to develop structure-activity relationships of β2 ligand binding. The resulting relationships are consistent with intrinsic binding affinity (corrected for membrane interaction). The successful structure-based design of ligands targeting membrane proteins may require an assessment of membrane affinity to uncouple protein binding from membrane interactions.
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Affiliation(s)
- Callum J Dickson
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Daniel J J McKay
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - John Reilly
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - David A Sandham
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Duncan Shaw
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Robin A Fairhurst
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG , Werk Klybeck, Postfach, CH-4002 Basel, Switzerland
| | - Steven J Charlton
- Cell Signalling Research Group, School of Life Sciences, University of Nottingham, Queen's Medical Centre , Nottingham NG7 2UH, U.K
| | - David A Sykes
- Cell Signalling Research Group, School of Life Sciences, University of Nottingham, Queen's Medical Centre , Nottingham NG7 2UH, U.K
| | - Robert A Pearlstein
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Jose S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
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34
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Guo D, Heitman LH, IJzerman AP. Kinetic Aspects of the Interaction between Ligand and G Protein-Coupled Receptor: The Case of the Adenosine Receptors. Chem Rev 2016; 117:38-66. [DOI: 10.1021/acs.chemrev.6b00025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dong Guo
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Laura H. Heitman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division of Medicinal Chemistry,
Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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35
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Equilibrium and kinetic selectivity profiling on the human adenosine receptors. Biochem Pharmacol 2016; 105:34-41. [DOI: 10.1016/j.bcp.2016.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/26/2016] [Indexed: 11/23/2022]
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