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Patel D, Huma ZE, Duncan D. Reversible Covalent Inhibition─Desired Covalent Adduct Formation by Mass Action. ACS Chem Biol 2024; 19:824-838. [PMID: 38567529 PMCID: PMC11040609 DOI: 10.1021/acschembio.3c00805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
Covalent inhibition has seen a resurgence in the last several years. Although long-plagued by concerns of off-target effects due to nonspecific reactions leading to covalent adducts, there has been success in developing covalent inhibitors, especially within the field of anticancer therapy. Covalent inhibitors can have an advantage over noncovalent inhibitors since the formation of a covalent adduct may serve as an additional mode of selectivity due to the intrinsic reactivity of the target protein that is absent in many other proteins. Unfortunately, many covalent inhibitors form irreversible adducts with off-target proteins, which can lead to considerable side-effects. By designing the inhibitor to form reversible covalent adducts, one can leverage competing on/off kinetics in complex formation by taking advantage of the law of mass action. Although covalent adducts do form with off-target proteins, the reversible nature of inhibition prevents accumulation of the off-target adduct, thus limiting side-effects. In this perspective, we outline important characteristics of reversible covalent inhibitors, including examples and a guide for inhibitor development.
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Affiliation(s)
| | | | - Dustin Duncan
- Department of Chemistry, Brock
University, St. Catharines, Ontario L2S 3A1, Canada
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McNaught-Flores DA, Kooistra AJ, Chen YC, Arias-Montano JA, Panula P, Leurs R. Pharmacological Characterization of the Zebrafish (Danio Rerio) Histamine H 1 Receptor Reveals the Involvement of the Second Extracellular Loop in the Binding of Histamine. Mol Pharmacol 2024; 105:84-96. [PMID: 37977823 DOI: 10.1124/molpharm.123.000741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
The zebrafish (Danio rerio) histamine H1 receptor gene (zfH1R) was cloned in 2007 and reported to be involved in fish locomotion. Yet, no detailed characterization of its pharmacology and signaling properties have so far been reported. In this study, we pharmacologically characterized the zfH1R expressed in HEK-293T cells by means of [3H]-mepyramine binding and G protein-signaling assays. The zfH1R [dissociation constant (KD), 0.7 nM] displayed similar affinity for the antagonist [3H]-mepyramine as the human histamine H1 receptor (hH1R) (KD, 1.5 nM), whereas the affinity for histamine is 100-fold higher than for the human H1R. The zfH1R couples to Gαq/11 proteins and activates several reporter genes, i.e., NFAT, NFϰB, CRE, VEGF, COX-2, SRE, and AP-1, and zfH1R-mediated signaling is prevented by the Gαq/11 inhibitor YM-254890 and the antagonist mepyramine. Molecular modeling of the zfH1R and human H1R shows that the binding pockets are identical, implying that variations along the ligand binding pathway could underly the differences in histamine affinity instead. Targeting differentially charged residues in extracellular loop 2 (ECL2) using site-directed mutagenesis revealed that Arg21045x55 is most likely involved in the binding process of histamine in zfH1R. This study aids the understanding of the pharmacological differences between H1R orthologs and the role of ECL2 in histamine binding and provides fundamental information for the understanding of the histaminergic system in the zebrafish. SIGNIFICANCE STATEMENT: The use of the zebrafish as in vivo models in neuroscience is growing exponentially, which asks for detailed characterization of the aminergic neurotransmitter systems in this model. This study is the first to pharmacologically characterize the zebrafish histamine H1 receptor after expression in HEK-293T cells. The results show a high pharmacological and functional resemblance with the human ortholog but also reveal interesting structural differences and unveils an important role of the second extracellular loop in histamine binding.
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Affiliation(s)
- Daniel A McNaught-Flores
- Amsterdam Institute for Molecules, Medicines, and Systems (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands (D.A.M.-F., A.J.K., R.L.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); Department of Anatomy, University of Helsinki, Helsinki, Finland (Y.-C.C., P.P.); and Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, México (J.-A.A.-M.)
| | - Albert J Kooistra
- Amsterdam Institute for Molecules, Medicines, and Systems (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands (D.A.M.-F., A.J.K., R.L.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); Department of Anatomy, University of Helsinki, Helsinki, Finland (Y.-C.C., P.P.); and Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, México (J.-A.A.-M.)
| | - Yu-Chia Chen
- Amsterdam Institute for Molecules, Medicines, and Systems (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands (D.A.M.-F., A.J.K., R.L.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); Department of Anatomy, University of Helsinki, Helsinki, Finland (Y.-C.C., P.P.); and Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, México (J.-A.A.-M.)
| | - Jose-Antonio Arias-Montano
- Amsterdam Institute for Molecules, Medicines, and Systems (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands (D.A.M.-F., A.J.K., R.L.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); Department of Anatomy, University of Helsinki, Helsinki, Finland (Y.-C.C., P.P.); and Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, México (J.-A.A.-M.)
| | - Pertti Panula
- Amsterdam Institute for Molecules, Medicines, and Systems (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands (D.A.M.-F., A.J.K., R.L.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); Department of Anatomy, University of Helsinki, Helsinki, Finland (Y.-C.C., P.P.); and Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, México (J.-A.A.-M.)
| | - Rob Leurs
- Amsterdam Institute for Molecules, Medicines, and Systems (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands (D.A.M.-F., A.J.K., R.L.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); Department of Anatomy, University of Helsinki, Helsinki, Finland (Y.-C.C., P.P.); and Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, México (J.-A.A.-M.)
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Wang AF, Ayyar VS. Pharmacodynamic Models of Indirect Effects and Irreversible Inactivation with Turnover: Applicability to Mechanism-Based Modeling of Gene Silencing and Targeted Protein Degradation. J Pharm Sci 2024; 113:191-201. [PMID: 37884193 DOI: 10.1016/j.xphs.2023.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
Indirect response (IDR) and turnover with inactivation (TI) comprise two arrays of mechanism-based pharmacodynamic (PD) models widely used to describe delayed drug effects. IDR Model-IV (stimulation of response loss) and TI (irreversible loss) have been described with discerning "signature" profiles; classical IDR-IV response-time profiles display slow declines where peak response shifts later with increasing dose, whereas TI profiles feature steep response declines with earlier-shifting nadirs. Herein, we demonstrate mathematical convergence of IDR-IV and TI models upon implementation with identical linear versus nonlinear pharmacologic effect terms. Time of peak response in IDR-IV can in fact shift earlier or later depending on PK or PD parameters (e.g., kel, Smax) and effect type. A generalized dynamic model linking mRNA and protein turnover is proposed. Applicability of IDR-IV and TI, with either linear or nonlinear terms acting on degradation/catabolism/loss of response, is demonstrated through model-fitting PK-PD effects of three proteolysis-targeting chimeras (PROTACs) and two ligand-conjugated small interfering RNAs (siRNA). This work clarifies mathematical properties, convergence, and expected responses of IDR-IV and TI, demonstrates their applicability for targeted gene-silencing and protein-degrading agents, and illustrates how well-designed in vivo studies covering broad dose ranges with richly sampled time-points can influence PK-PD model structure and parameter resolution.
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Affiliation(s)
- Angelia F Wang
- Clinical Pharmacology & Pharmacometrics, Janssen Research and Development, Spring House, PA, USA
| | - Vivaswath S Ayyar
- Clinical Pharmacology & Pharmacometrics, Janssen Research and Development, Spring House, PA, USA.
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Sadee W. Ligand-Free Signaling of G-Protein-Coupled Receptors: Physiology, Pharmacology, and Genetics. Molecules 2023; 28:6375. [PMID: 37687205 PMCID: PMC10489045 DOI: 10.3390/molecules28176375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are ubiquitous sensors and regulators of cellular functions. Each GPCR exists in complex aggregates with multiple resting and active conformations. Designed to detect weak stimuli, GPCRs can also activate spontaneously, resulting in basal ligand-free signaling. Agonists trigger a cascade of events leading to an activated agonist-receptor G-protein complex with high agonist affinity. However, the ensuing signaling process can further remodel the receptor complex to reduce agonist affinity, causing rapid ligand dissociation. The acutely activated ligand-free receptor can continue signaling, as proposed for rhodopsin and μ opioid receptors, resulting in robust receptor activation at low agonist occupancy with enhanced agonist potency. Continued receptor stimulation can further modify the receptor complex, regulating sustained ligand-free signaling-proposed to play a role in opioid dependence. Basal, acutely agonist-triggered, and sustained elevated ligand-free signaling could each have distinct functions, reflecting multi-state conformations of GPCRs. This review addresses basal and stimulus-activated ligand-free signaling, its regulation, genetic factors, and pharmacological implications, focusing on opioid and serotonin receptors, and the growth hormone secretagogue receptor (GHSR). The hypothesis is proposed that ligand-free signaling of 5-HT2A receptors mediate therapeutic effects of psychedelic drugs. Research avenues are suggested to close the gaps in our knowledge of ligand-free GPCR signaling.
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Affiliation(s)
- Wolfgang Sadee
- Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- Aether Therapeutics Inc., Austin, TX 78756, USA
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