1
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Semeano A, Garland R, Bonifazi A, Lee KH, Famiglietti J, Zhang W, Jo YJ, Battiti FO, Shi L, Newman AH, Yano H. Linkers in Bitopic Agonists Shape Bias Profile among Transducers for the Dopamine D2 and D3 Receptors. ACS Pharmacol Transl Sci 2024; 7:2333-2349. [PMID: 39144557 PMCID: PMC11320723 DOI: 10.1021/acsptsci.4c00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/10/2024] [Accepted: 06/13/2024] [Indexed: 08/16/2024]
Abstract
Bitopic ligands bind both orthosteric and allosteric or secondary binding sites within the same receptor, often resulting in an improvement of receptor selectivity, potency, and efficacy. In particular, for both agonists and antagonists of the dopamine D2 and D3 receptors (D2R and D3R), the primary therapeutic targets for several neurological and neuropsychiatric disorders, bitopic ligand design has proved advantageous in achieving better pharmacological profiles in vitro. Although the two pharmacophores within a bitopic ligand are typically considered the main drivers of conformational change for a receptor, the role of the linker that connects the two has not yet been systematically studied for its relevance in receptor activity profiles. Here, we present a comprehensive analysis of sumanirole and PF592,379-based indole-containing bitopic compounds in agonist activity at D2R and D3R, with a focus on linker chemical space and stereochemistry through testing six distinct chirally resolved linkers and a simple aliphatic linker. The structure activity relationships (SARs) of these linkers are examined extensively, beyond the conventional level, by characterizing the activation of all putative transducers over a 44 min time course. Our multiparametric analysis reveals previously unappreciated specific linker-dependent effects on primary pharmacophores, receptors, transducer activation kinetics, and bias, highlighting the utility of this comprehensive approach and the significance of the linker type in shaping transducer bias profiles.
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Affiliation(s)
- Ana Semeano
- Department
of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical
Sciences, Bouvé College of Health Sciences, Center for Drug
Discovery, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Rian Garland
- Department
of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical
Sciences, Bouvé College of Health Sciences, Center for Drug
Discovery, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Alessandro Bonifazi
- Medicinal
Chemistry Section, Molecular Targets and Medications Discovery Branch,
National Institute on Drug Abuse − Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Kuo Hao Lee
- Computational
Chemistry and Molecular Biophysics Section, Molecular Targets and
Medications Discovery Branch, National Institute on Drug Abuse −
Intramural Research Program, National Institutes
of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - John Famiglietti
- Department
of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical
Sciences, Bouvé College of Health Sciences, Center for Drug
Discovery, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Wenqi Zhang
- Department
of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical
Sciences, Bouvé College of Health Sciences, Center for Drug
Discovery, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Yoon Jae Jo
- Department
of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical
Sciences, Bouvé College of Health Sciences, Center for Drug
Discovery, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Francisco O. Battiti
- Medicinal
Chemistry Section, Molecular Targets and Medications Discovery Branch,
National Institute on Drug Abuse − Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Lei Shi
- Computational
Chemistry and Molecular Biophysics Section, Molecular Targets and
Medications Discovery Branch, National Institute on Drug Abuse −
Intramural Research Program, National Institutes
of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Amy Hauck Newman
- Medicinal
Chemistry Section, Molecular Targets and Medications Discovery Branch,
National Institute on Drug Abuse − Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Hideaki Yano
- Department
of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical
Sciences, Bouvé College of Health Sciences, Center for Drug
Discovery, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
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2
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Lee KH, Camacho-Hernandez GA, Newman AH, Shi L. The Structural Basis of the Activity Cliff in Modafinil-Based Dopamine Transporter Inhibitors. Biomolecules 2024; 14:713. [PMID: 38927116 PMCID: PMC11202288 DOI: 10.3390/biom14060713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Modafinil analogs with either a sulfoxide or sulfide moiety have improved binding affinities at the human dopamine transporter (hDAT) compared to modafinil, with lead sulfoxide-substituted analogs showing characteristics of atypical inhibition (e.g., JJC8-091). Interestingly, the only distinction between sulfoxide and sulfide substitution is the presence of one additional oxygen atom. To elucidate why such a subtle difference in ligand structure can result in different typical or atypical profiles, we investigated two pairs of analogs. Our quantum mechanical calculations revealed a more negatively charged distribution of the electrostatic potential surface of the sulfoxide substitution. Using molecular dynamics simulations, we demonstrated that sulfoxide-substituted modafinil analogs have a propensity to attract more water into the binding pocket. They also exhibited a tendency to dissociate from Asp79 and form a new interaction with Asp421, consequently promoting an inward-facing conformation of hDAT. In contrast, sulfide-substituted analogs did not display these effects. These findings elucidate the structural basis of the activity cliff observed with modafinil analogs and also enhance our understanding of the functionally relevant conformational spectrum of hDAT.
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Affiliation(s)
| | | | | | - Lei Shi
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse–Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA; (K.-H.L.); (G.A.C.-H.); (A.H.N.)
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3
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Hamlish NX, Abramyan AM, Shah B, Zhang Z, Schepartz A. Incorporation of Multiple β 2-Hydroxy Acids into a Protein In Vivo Using an Orthogonal Aminoacyl-tRNA Synthetase. ACS CENTRAL SCIENCE 2024; 10:1044-1053. [PMID: 38799653 PMCID: PMC11117724 DOI: 10.1021/acscentsci.3c01366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/22/2024] [Accepted: 04/03/2024] [Indexed: 05/29/2024]
Abstract
The programmed synthesis of sequence-defined biomaterials whose monomer backbones diverge from those of canonical α-amino acids represents the next frontier in protein and biomaterial evolution. Such next-generation molecules provide otherwise nonexistent opportunities to develop improved biologic therapies, bioremediation tools, and biodegradable plastic-like materials. One monomer family of particular interest for biomaterials includes β-hydroxy acids. Many natural products contain isolated β-hydroxy acid monomers, and polymers of β-hydroxy acids (β-esters) are found in polyhydroxyalkanoate (PHA) polyesters under development as bioplastics and drug encapsulation/delivery systems. Here we report that β2-hydroxy acids possessing both (R) and (S) absolute configuration are substrates for pyrrolysyl-tRNA synthetase (PylRS) enzymes in vitro and that (S)-β2-hydroxy acids are substrates in cellulo. Using the orthogonal MaPylRS/MatRNAPyl synthetase/tRNA pair, in conjunction with wild-type E. coli ribosomes and EF-Tu, we report the cellular synthesis of model proteins containing two (S)-β2-hydroxy acid residues at internal positions. Metadynamics simulations provide a rationale for the observed preference for the (S)-β2-hydroxy acid and provide mechanistic insights that inform future engineering efforts. As far as we know, this finding represents the first example of an orthogonal synthetase that acylates tRNA with a β2-hydroxy acid substrate and the first example of a protein hetero-oligomer containing multiple expanded-backbone monomers produced in cellulo.
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Affiliation(s)
- Noah X. Hamlish
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
| | - Ara M. Abramyan
- Schrödinger,
Inc., San Diego, California 92121, United States
| | - Bhavana Shah
- Process
Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United
States
| | - Zhongqi Zhang
- Process
Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United
States
| | - Alanna Schepartz
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, Calfornia 94720, United States
- California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
- ARC
Institute, Palo Alto, California 94304, United States
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4
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Lee KH, Shi L. Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors. J Chem Inf Model 2024; 64:1778-1793. [PMID: 38454785 DOI: 10.1021/acs.jcim.3c01956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Effective rational drug discovery hinges on understanding the functional states of the target protein and distinguishing it from homologues. However, for the G protein coupled receptors, both activation-related conformational changes (ACCs) and intrinsic divergence among receptors can be misled or obscured by ligand-specific conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics (MD) simulation results of the receptors bound with various ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors, including the extracellular portion of TM5 (TM5e) and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found more outward tilting of TM6e in the D2R compared to the D3R in both the experimental structures and simulations bound with ligands in different scaffolds. However, this difference was drastically reduced in the simulations bound with nonselective agonist quinpirole, suggesting a misleading effect of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may also obscure intrinsic divergence. Importantly, our MD simulations revealed divergence in the dynamics of these receptors. Specifically, the D2R exhibited heightened flexibility compared to the D3R in the extracellular loops and TMs 5e, 6e, and 7e, associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting the D2R and D3R with more precise pharmacological profiles.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
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5
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Tsai MHM, Chen L, Baumann MH, Canals M, Javitch JA, Lane JR, Shi L. In Vitro Functional Profiling of Fentanyl and Nitazene Analogs at the μ-Opioid Receptor Reveals High Efficacy for Gi Protein Signaling. ACS Chem Neurosci 2024; 15:854-867. [PMID: 38345920 DOI: 10.1021/acschemneuro.3c00750] [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] [Indexed: 02/22/2024] Open
Abstract
Novel synthetic opioids (NSOs), including both fentanyl and non-fentanyl analogs that act as μ-opioid receptor (MOR) agonists, are associated with serious intoxication and fatal overdose. Previous studies proposed that G-protein-biased MOR agonists are safer pain medications, while other evidence indicates that low intrinsic efficacy at MOR better explains the reduced opioid side effects. Here, we characterized the in vitro functional profiles of various NSOs at the MOR using adenylate cyclase inhibition and β-arrestin2 recruitment assays, in conjunction with the application of the receptor depletion approach. By fitting the concentration-response data to the operational model of agonism, we deduced the intrinsic efficacy and affinity for each opioid in the Gi protein signaling and β-arrestin2 recruitment pathways. Compared to the reference agonist [d-Ala2,N-MePhe4,Gly-ol5]enkephalin, we found that several fentanyl analogs were more efficacious at inhibiting cAMP production, whereas all fentanyl analogs were less efficacious at recruiting β-arrestin2. In contrast, the non-fentanyl 2-benzylbenzimidazole (i.e., nitazene) analogs were highly efficacious and potent in both the cAMP and β-arrestin2 assays. Our findings suggest that the high intrinsic efficacy of the NSOs in Gi protein signaling is a common property that may underlie their high risk of intoxication and overdose, highlighting the limitation of using in vitro functional bias to predict the adverse effects of opioids. In addition, the extremely high potency of many NSOs now infiltrating illicit drug markets further contributes to the danger posed to public health.
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Affiliation(s)
- Meng-Hua M Tsai
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Li Chen
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Michael H Baumann
- Designer Drug Research Unit, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Meritxell Canals
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K
- Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands NG7 2UH, U.K
| | - Jonathan A Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York 10032, United States
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, United States
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, United States
| | - J Robert Lane
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K
- Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands NG7 2UH, U.K
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224, United States
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6
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Tsai MHM, Chen L, Baumann MH, Canals M, Javitch JA, Lane JR, Shi L. The in vitro functional profiles of fentanyl and nitazene analogs at the μ-opioid receptor - high efficacy is dangerous regardless of signaling bias. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566672. [PMID: 38014284 PMCID: PMC10680598 DOI: 10.1101/2023.11.10.566672] [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
Novel synthetic opioids (NSOs), including both fentanyl and non-fentanyl analogs that act as the μ-opioid receptor (MOR) agonists, are associated with serious intoxication and fatal overdose. Previous studies proposed that G protein biased MOR agonists are safer pain medications, while other evidence indicates that low intrinsic efficacy at MOR better explains reduced opioid side effects. Here, we characterized the in vitro functional profiles of various NSOs at MOR using adenylate cyclase inhibition and β-arrestin2 recruitment assays, in conjunction with the application of the receptor depletion approach. By fitting the concentration-response data to the operational model of agonism, we deduced the intrinsic efficacy and affinity for each opioid in the Gi protein signaling and β-arrestin2 recruitment pathways. Compared to the reference agonist DAMGO, we found that several fentanyl analogs were more efficacious at inhibiting cAMP production, whereas all fentanyl analogs were less efficacious at recruiting β-arrestin2. In contrast, the non-fentanyl 2-benzylbenzimidazole (i.e., nitazene) analogs were highly efficacious and potent in both the cAMP and β-arrestin2 assays. Our findings suggest that the high intrinsic efficacy of the NSOs in Gi protein signaling is a common property that may underlie their high risk of intoxication and overdose, highlighting the limitation of using in vitro functional bias to predict the adverse effects of opioids. Instead, our results show that, regardless of bias, opioids with sufficiently high intrinsic efficacy can be lethal, especially given the extremely high potency of many of these compounds that are now pervading the illicit drug market.
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Affiliation(s)
- Meng-Hua M. Tsai
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Li Chen
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Michael H. Baumann
- Designer Drug Research Unit, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Meritxell Canals
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands, UK
| | - Jonathan A. Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - J. Robert Lane
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, Midlands, UK
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224, USA
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7
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Lee KH, Shi L. Unraveling activation-related rearrangements and intrinsic divergence from ligand-induced conformational changes of the dopamine D3 and D2 receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566699. [PMID: 38014309 PMCID: PMC10680602 DOI: 10.1101/2023.11.11.566699] [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
Effective rational drug discovery targeting a specific protein hinges on understanding their functional states and distinguishing it from homologs. However, for the G protein coupled receptors, both the activation-related conformational changes (ACCs) and the intrinsic divergence among receptors can be misled or obscured by ligand-induced conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics simulation results of the receptors bound with different ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors including TM5e and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found pronounced outward tilting of TM6e in the D2R compared to the D3R in both experimental structures and simulations with ligands in different scaffolds. This tilting was drastically reduced in the simulations of the receptors bound with nonselective full agonist quinpirole, suggesting a misleading impact of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may obscure intrinsic divergence. In addition, our analysis showed that the impact of the nonconserved TM1 propagated to conserved Trp7.40 and Glu2.65, both are ligand binding residues. We also found that the D2R exhibited heightened flexibility compared to the D3R in the extracellular portions of TMs 5, 6, and 7, potentially associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting D2R or D3R with more precise pharmacological profiles.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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8
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Lee KH, Manning JJ, Javitch J, Shi L. A Novel "Activation Switch" Motif Common to All Aminergic Receptors. J Chem Inf Model 2023; 63:5001-5017. [PMID: 37540602 PMCID: PMC10695015 DOI: 10.1021/acs.jcim.3c00732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
Aminergic receptors are G protein-coupled receptors (GPCRs) that transduce signals from small endogenous biogenic amines to regulate intracellular signaling pathways. Agonist binding in the ligand binding pocket on the extracellular side opens and prepares a cavity on the intracellular face of the receptors to interact with and activate G proteins and β-arrestins. Here, by reviewing and analyzing all available aminergic receptor structures, we seek to identify activation-related conformational changes that are independent of the specific scaffold of the bound agonist, which we define as "activation conformational changes" (ACCs). While some common intracellular ACCs have been well-documented, identifying common extracellular ACCs, including those in the ligand binding pocket, is complicated by local adjustments to different ligand scaffolds. Our analysis shows no common ACCs at the extracellular ends of the transmembrane helices. Furthermore, the restricted access to the ligand binding pocket identified previously in some receptors is not universal. Notably, the Trp6.48 toggle switch and the Pro5.50-Ile3.40-Phe6.44 (PIF) motif at the bottom of the ligand binding pocket have previously been proposed to mediate the conformational consequences of ligand binding to the intracellular side of the receptors. Our analysis shows that common ACCs in the ligand binding pocket are associated with the PIF motif and nearby residues, including Trp6.48, but fails to support a shared rotamer toggle associated with activation. However, we identify two common rearrangements between the extracellular and middle subsegments, and propose a novel "activation switch" motif common to all aminergic receptors. This motif includes the middle subsegments of transmembrane helices 3, 5, and 6 and integrates both the PIF motif and Trp6.48.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jamie J. Manning
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jonathan Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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9
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Goldberg A, Xie B, Shi L. The Molecular Mechanism of Positive Allosteric Modulation at the Dopamine D1 Receptor. Int J Mol Sci 2023; 24:12848. [PMID: 37629030 PMCID: PMC10454769 DOI: 10.3390/ijms241612848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
The dopamine D1 receptor (D1R) is a promising target for treating various psychiatric disorders. While upregulation of D1R activity has shown potential in alleviating motor and cognitive symptoms, orthosteric agonists have limitations, restricting their clinical applications. However, the discovery of several allosteric compounds specifically targeting the D1R, such as LY3154207, has opened new therapeutic avenues. Based on the cryo-EM structures of the D1R, we conducted molecular dynamics simulations to investigate the binding and allosteric mechanisms of LY3154207. Our simulations revealed that LY3154207 preferred the horizontal orientation above intracellular loop 2 (IL2) and stabilized the helical conformation of IL2. Moreover, LY3154207 binding induced subtle yet significant changes in key structural motifs and their neighboring residues. Notably, a cluster of residues centered around the Na+-binding site became more compact, while interactions involving the PIF motif and its neighboring residues were loosened upon LY3154207 binding, consistent with their role in opening the intracellular crevice for receptor activation. Additionally, we identified an allosteric pathway likely responsible for the positive allosteric effect of LY3154207 in enhancing Gs protein coupling. This mechanistic understanding of LY3154207's allosteric action at the D1R paves the way for the rational design of more potent and effective allosteric modulators.
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Affiliation(s)
| | | | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
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10
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Goldberg A, Xie B, Shi L. The molecular mechanism of positive allosteric modulation at the dopamine D1 receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550907. [PMID: 37546785 PMCID: PMC10402154 DOI: 10.1101/2023.07.27.550907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The dopamine D1 receptor (D1R) is a promising target for treating various psychiatric disorders. While upregulation of D1R activity has shown potential in alleviating motor and cognitive symptoms, orthosteric agonists have limitations, restricting their clinical applications. However, the discovery of several allosteric compounds specifically targeting the D1R, such as LY3154207, has opened new therapeutic avenues. Based on the cryo-EM structures of the D1R, we conducted molecular dynamics simulations to investigate the binding and allosteric mechanisms of LY3154207. Our simulations revealed that LY3154207 preferred the horizontal orientation above intracellular loop 2 (IL2) and stabilized the helical conformation of IL2. Moreover, LY3154207 binding induced subtle yet significant changes in key structural motifs and their neighboring residues. Notably, a cluster of residues centered around the Na + binding site became more compact, while interactions involving the PIF motif and its neighboring residues were loosened upon LY3154207 binding, consistent with their role in opening the intracellular crevice for receptor activation. Additionally, we identified an allosteric pathway likely responsible for the positive allosteric effect of LY3154207 in enhancing Gs protein coupling. This mechanistic understanding of LY3154207's allosteric action at the D1R pave the way for the rational design of more potent and effective allosteric modulators.
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Affiliation(s)
- Alexander Goldberg
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
| | - Bing Xie
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
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11
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Xie B, Le Rouzic VP, Goldberg A, Tsai MHM, Chen L, Zhang T, Sinha A, Pan YX, Baumann MH, Shi L. Binding preference at the μ-opioid receptor underlies distinct pharmacology of cyclopropyl versus valeryl analogs of fentanyl. Neuropharmacology 2023; 227:109442. [PMID: 36731721 PMCID: PMC9974845 DOI: 10.1016/j.neuropharm.2023.109442] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/12/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Illicitly manufactured fentanyl is driving the current opioid crisis, and various fentanyl analogs are appearing in recreational drug markets worldwide. To assess the potential health risks posed by fentanyl analogs, it is necessary to understand structure-activity relationships for these compounds. Here we compared the pharmacology of two structurally related fentanyl analogs implicated in opioid overdose: cyclopropylfentanyl and valerylfentanyl. Cyclopropylfentanyl has a three-carbon ring attached to the carbonyl group on the fentanyl scaffold, whereas valerylfentanyl has a four-carbon chain at the same position. In vitro assays examining μ-opioid receptor (MOR) coupling to G proteins in CHO cells showed that cyclopropylfentanyl is a full agonist (EC50 = 8.6 nM, %Emax = 113%), with potency and efficacy similar to fentanyl (EC50 = 10.3 nM, %Emax = 113%). By contrast, valerylfentanyl is a partial agonist at MOR (EC50 = 179.8 nM, %Emax = 60%). Similar results were found in assays assessing MOR-mediated β-arrestin recruitment in HEK cells. In vivo studies in male CD-1 mice demonstrated that both fentanyl analogs induce naloxone-reversible antinociception and respiratory suppression, but cyclopropylfentanyl is 100-times more potent as an antinociceptive agent (ED50 = 0.04 mg/kg, s. c.) than valerylfentanyl (ED50 = 4.0 mg/kg, s. c.). Molecular simulation results revealed that the alkyl chain of valerylfentanyl cannot be well accommodated by the active state of MOR and may transition the receptor toward an inactive state, converting the fentanyl scaffold to a partial agonist. Taken together, our results suggest that cyclopropylfentanyl presents much greater risk of adverse effects when compared to valerylfentanyl. Moreover, the summed findings may provide clues to the design of therapeutic opioids with reduced adverse side effects.
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Affiliation(s)
- Bing Xie
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Valerie P Le Rouzic
- Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Alexander Goldberg
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Meng-Hua M Tsai
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Li Chen
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Tiffany Zhang
- Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Antara Sinha
- Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Ying-Xian Pan
- Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA; Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Michael H Baumann
- Designer Drug Research Unit, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA.
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12
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Free RB, Nilson AN, Boldizsar NM, Doyle TB, Rodriguiz RM, Pogorelov VM, Machino M, Lee KH, Bertz JW, Xu J, Lim HD, Dulcey AE, Mach RH, Woods JH, Lane JR, Shi L, Marugan JJ, Wetsel WC, Sibley DR. Identification and Characterization of ML321: A Novel and Highly Selective D 2 Dopamine Receptor Antagonist with Efficacy in Animal Models That Predict Atypical Antipsychotic Activity. ACS Pharmacol Transl Sci 2023; 6:151-170. [PMID: 36654757 PMCID: PMC9841785 DOI: 10.1021/acsptsci.2c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Indexed: 12/31/2022]
Abstract
We have developed and characterized a novel D2R antagonist with exceptional GPCR selectivity - ML321. In functional profiling screens of 168 different GPCRs, ML321 showed little activity beyond potent inhibition of the D2R and to a lesser extent the D3R, demonstrating excellent receptor selectivity. The D2R selectivity of ML321 may be related to the fact that, unlike other monoaminergic ligands, ML321 lacks a positively charged amine group and adopts a unique binding pose within the orthosteric binding site of the D2R. PET imaging studies in non-human primates demonstrated that ML321 penetrates the CNS and occupies the D2R in a dose-dependent manner. Behavioral paradigms in rats demonstrate that ML321 can selectively antagonize a D2R-mediated response (hypothermia) while not affecting a D3R-mediated response (yawning) using the same dose of drug, thus indicating exceptional in vivo selectivity. We also investigated the effects of ML321 in animal models that are predictive of antipsychotic efficacy in humans. We found that ML321 attenuates both amphetamine- and phencyclidine-induced locomotor activity and restored pre-pulse inhibition (PPI) of acoustic startle in a dose-dependent manner. Surprisingly, using doses that were maximally effective in both the locomotor and PPI studies, ML321 was relatively ineffective in promoting catalepsy. Kinetic studies revealed that ML321 exhibits slow-on and fast-off receptor binding rates, similar to those observed with atypical antipsychotics with reduced extrapyramidal side effects. Taken together, these observations suggest that ML321, or a derivative thereof, may exhibit ″atypical″ antipsychotic activity in humans with significantly fewer side effects than observed with the currently FDA-approved D2R antagonists.
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Affiliation(s)
- R. Benjamin Free
- Molecular
Neuropharmacology Section, National Institute of Neurological Disorders
and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland20892, United States
| | - Ashley N. Nilson
- Molecular
Neuropharmacology Section, National Institute of Neurological Disorders
and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland20892, United States
| | - Noelia M. Boldizsar
- Molecular
Neuropharmacology Section, National Institute of Neurological Disorders
and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland20892, United States
| | - Trevor B. Doyle
- Molecular
Neuropharmacology Section, National Institute of Neurological Disorders
and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland20892, United States
| | - Ramona M. Rodriguiz
- Department
of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine
Analysis Core Facility, Duke University
Medical Center, 354 Sands Building, 303 Research Drive, Durham, North Carolina27710, United States
| | - Vladimir M. Pogorelov
- Department
of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine
Analysis Core Facility, Duke University
Medical Center, 354 Sands Building, 303 Research Drive, Durham, North Carolina27710, United States
| | - Mayako Machino
- Computational
Chemistry and Molecular Biophysics Section, Molecular Targets and
Medications Discovery Branch, National Institute on Drug Abuse, Intramural
Research Program, National Institutes of
Health, 333 Cassell Drive, Baltimore, Maryland21224, United
States
| | - Kuo Hao Lee
- Computational
Chemistry and Molecular Biophysics Section, Molecular Targets and
Medications Discovery Branch, National Institute on Drug Abuse, Intramural
Research Program, National Institutes of
Health, 333 Cassell Drive, Baltimore, Maryland21224, United
States
| | - Jeremiah W. Bertz
- Department
of Pharmacology, University of Michigan
Medical School, 1150 W. Medical Center Dr., Ann Arbor, Michigan48109, United States
| | - Jinbin Xu
- Division
of Radiological Sciences, Department of Radiology, Mallinckrodt Institute
of Radiology, Washington University School
of Medicine, St. Louis, Missouri63110, United States
| | - Herman D. Lim
- Drug Discovery
Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC3052, Australia
| | - Andrés E. Dulcey
- Division
of Pre-Clinical Innovation, National Center for Advancing Translational
Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland20850, United States
| | - Robert H. Mach
- Department
of Radiology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania19104, United States
| | - James H. Woods
- Department
of Pharmacology, University of Michigan
Medical School, 1150 W. Medical Center Dr., Ann Arbor, Michigan48109, United States
| | - J Robert Lane
- Centre
of Membrane Proteins and Receptors, Universities
of Birmingham and Nottingham, NottinghamNG7 2UH, United Kingdom
| | - Lei Shi
- Computational
Chemistry and Molecular Biophysics Section, Molecular Targets and
Medications Discovery Branch, National Institute on Drug Abuse, Intramural
Research Program, National Institutes of
Health, 333 Cassell Drive, Baltimore, Maryland21224, United
States
| | - Juan J. Marugan
- Division
of Pre-Clinical Innovation, National Center for Advancing Translational
Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland20850, United States
| | - William C. Wetsel
- Department
of Psychiatry and Behavioral Sciences, Mouse Behavioral and Neuroendocrine
Analysis Core Facility, Duke University
Medical Center, 354 Sands Building, 303 Research Drive, Durham, North Carolina27710, United States
- Departments
of Neurobiology and Cell Biology, Duke University
Medical Center, 354 Sands Building, 303 Research Drive, Durham, North Carolina27710, United States
| | - David R. Sibley
- Molecular
Neuropharmacology Section, National Institute of Neurological Disorders
and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland20892, United States
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13
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Juza R, Musilek K, Mezeiova E, Soukup O, Korabecny J. Recent advances in dopamine D 2 receptor ligands in the treatment of neuropsychiatric disorders. Med Res Rev 2023; 43:55-211. [PMID: 36111795 DOI: 10.1002/med.21923] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023]
Abstract
Dopamine is a biologically active amine synthesized in the central and peripheral nervous system. This biogenic monoamine acts by activating five types of dopamine receptors (D1-5 Rs), which belong to the G protein-coupled receptor family. Antagonists and partial agonists of D2 Rs are used to treat schizophrenia, Parkinson's disease, depression, and anxiety. The typical pharmacophore with high D2 R affinity comprises four main areas, namely aromatic moiety, cyclic amine, central linker and aromatic/heteroaromatic lipophilic fragment. From the literature reviewed herein, we can conclude that 4-(2,3-dichlorophenyl), 4-(2-methoxyphenyl)-, 4-(benzo[b]thiophen-4-yl)-1-substituted piperazine, and 4-(6-fluorobenzo[d]isoxazol-3-yl)piperidine moieties are critical for high D2 R affinity. Four to six atoms chains are optimal for D2 R affinity with 4-butoxyl as the most pronounced one. The bicyclic aromatic/heteroaromatic systems are most frequently occurring as lipophilic appendages to retain high D2 R affinity. In this review, we provide a thorough overview of the therapeutic potential of D2 R modulators in the treatment of the aforementioned disorders. In addition, this review summarizes current knowledge about these diseases, with a focus on the dopaminergic pathway underlying these pathologies. Major attention is paid to the structure, function, and pharmacology of novel D2 R ligands, which have been developed in the last decade (2010-2021), and belong to the 1,4-disubstituted aromatic cyclic amine group. Due to the abundance of data, allosteric D2 R ligands and D2 R modulators from patents are not discussed in this review.
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Affiliation(s)
- Radomir Juza
- Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kamil Musilek
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.,Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Eva Mezeiova
- Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic.,Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Jan Korabecny
- Experimental Neurobiology, National Institute of Mental Health, Klecany, Czech Republic.,Biomedical Research Centre, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
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14
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Grillo W, Boateng CA, Brady LJ, Gaudier-Diaz MM, Mitchell KA, Ruffin VA, Tejdeda HA, Marshall SA. Reflections of six neuroscientists: The influences of training at minority serving institutions. J Neurosci Res 2022; 100:1529-1537. [PMID: 33527411 PMCID: PMC9942539 DOI: 10.1002/jnr.24796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/28/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Wendy Grillo
- Department of Biological & Biomedical Sciences, North Carolina Central University, Durham, NC, USA
| | - Comfort A. Boateng
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, NC, USA
| | - Lillian J. Brady
- Department of Pharmacology, Vanderbilt Center for Addiction Research, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Monica M. Gaudier-Diaz
- Department of Psychology & Neuroscience, University of North Carolina-Chapel Hill, NC, USA
| | - Kerry-Ann Mitchell
- Department of Plastic & Reconstructive Surgery, The Ohio State University, Columbus, OH, USA
| | - Vernon A. Ruffin
- Department of Natural Sciences, Virginia Union University, Richmond, VA, USA
| | - Hugo A. Tejdeda
- Intramural Research Program, National Institute on Drug Abuse, US National Institutes of Health, Baltimore, MD, USA
| | - S. Alex Marshall
- Department of Biological & Biomedical Sciences, North Carolina Central University, Durham, NC, USA,Department of Psychology & Neuroscience, University of North Carolina-Chapel Hill, NC, USA
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15
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Xie B, Goldberg A, Shi L. A comprehensive evaluation of the potential binding poses of fentanyl and its analogs at the µ-opioid receptor. Comput Struct Biotechnol J 2022; 20:2309-2321. [PMID: 35615021 PMCID: PMC9123087 DOI: 10.1016/j.csbj.2022.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/30/2022] Open
Abstract
Fentanyl and its analogs are selective agonists of the µ-opioid receptor (MOR). Among novel synthetic opioids (NSOs), they dominate the recreational drug market and are the main culprits for the opioid crisis, which has been exacerbated by the COVID-19 pandemic. By taking advantage of the crystal structures of the MOR, several groups have investigated the binding mechanism of fentanyl, but have not reached a consensus, in terms of both the binding orientation and the fentanyl conformation. Thus, the binding mechanism of fentanyl at the MOR remains an unsolved and challenging question. Here, we carried out a systematic computational study to investigate the preferred fentanyl conformations, and how these conformations are being accommodated in the MOR binding pocket. We characterized the free energy landscape of fentanyl conformations with metadynamics simulations, and compared and evaluated several possible fentanyl binding conditions in the MOR with long-timescale molecular dynamics simulations. Our results indicate that the most preferred binding pose in the MOR binding pocket corresponds well with the global minimum on the energy landscape of fentanyl in the absence of the receptor, while the energy landscape can be reconfigured by modifying the fentanyl scaffold. The interactions with the receptor may stabilize a slightly unfavored fentanyl conformation in an alternative binding pose. By extending similar investigations to fentanyl analogs, our findings establish a structure–activity relationship of fentanyl binding at the MOR. In addition to providing a structural basis to understand the potential toxicity of the emerging NSOs, such insights will contribute to developing new, safer analgesics.
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16
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Egyed A, Kiss DJ, Keserű GM. The Impact of the Secondary Binding Pocket on the Pharmacology of Class A GPCRs. Front Pharmacol 2022; 13:847788. [PMID: 35355719 PMCID: PMC8959758 DOI: 10.3389/fphar.2022.847788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/01/2022] [Indexed: 12/19/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are considered important therapeutic targets due to their pathophysiological significance and pharmacological relevance. Class A receptors represent the largest group of GPCRs that gives the highest number of validated drug targets. Endogenous ligands bind to the orthosteric binding pocket (OBP) embedded in the intrahelical space of the receptor. During the last 10 years, however, it has been turned out that in many receptors there is secondary binding pocket (SBP) located in the extracellular vestibule that is much less conserved. In some cases, it serves as a stable allosteric site harbouring allosteric ligands that modulate the pharmacology of orthosteric binders. In other cases it is used by bitopic compounds occupying both the OBP and SBP. In these terms, SBP binding moieties might influence the pharmacology of the bitopic ligands. Together with others, our research group showed that SBP binders contribute significantly to the affinity, selectivity, functional activity, functional selectivity and binding kinetics of bitopic ligands. Based on these observations we developed a structure-based protocol for designing bitopic compounds with desired pharmacological profile.
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Affiliation(s)
| | | | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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17
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Kiss B, Krámos B, Laszlovszky I. Potential Mechanisms for Why Not All Antipsychotics Are Able to Occupy Dopamine D 3 Receptors in the Brain in vivo. Front Psychiatry 2022; 13:785592. [PMID: 35401257 PMCID: PMC8987915 DOI: 10.3389/fpsyt.2022.785592] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/25/2022] [Indexed: 11/29/2022] Open
Abstract
Dysfunctions of the dopaminergic system are believed to play a major role in the core symptoms of schizophrenia such as positive, negative, and cognitive symptoms. The first line of treatment of schizophrenia are antipsychotics, a class of medications that targets several neurotransmitter receptors in the brain, including dopaminergic, serotonergic, adrenergic and/or muscarinic receptors, depending on the given agent. Although the currently used antipsychotics display in vitro activity at several receptors, majority of them share the common property of having high/moderate in vitro affinity for dopamine D2 receptors (D2Rs) and D3 receptors (D3Rs). In terms of mode of action, these antipsychotics are either antagonist or partial agonist at the above-mentioned receptors. Although D2Rs and D3Rs possess high degree of homology in their molecular structure, have common signaling pathways and similar in vitro pharmacology, they have different in vivo pharmacology and therefore behavioral roles. The aim of this review, with summarizing preclinical and clinical evidence is to demonstrate that while currently used antipsychotics display substantial in vitro affinity for both D3Rs and D2Rs, only very few can significantly occupy D3Rs in vivo. The relative importance of the level of endogenous extracellular dopamine in the brain and the degree of in vitro D3Rs receptor affinity and selectivity as determinant factors for in vivo D3Rs occupancy by antipsychotics, are also discussed.
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Affiliation(s)
- Béla Kiss
- Pharmacological and Drug Safety Research, Gedeon Richter Plc., Budapest, Hungary
| | - Balázs Krámos
- Spectroscopic Research Department, Gedeon Richter Plc., Budapest, Hungary
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18
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Battiti FO, Zaidi SA, Katritch V, Newman AH, Bonifazi A. Chiral Cyclic Aliphatic Linkers as Building Blocks for Selective Dopamine D 2 or D 3 Receptor Agonists. J Med Chem 2021; 64:16088-16105. [PMID: 34699207 PMCID: PMC11091832 DOI: 10.1021/acs.jmedchem.1c01433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Linkers are emerging as a key component in regulating the pharmacology of bitopic ligands directed toward G-protein coupled receptors (GPCRs). In this study, the role of regio- and stereochemistry in cyclic aliphatic linkers tethering well-characterized primary and secondary pharmacophores targeting dopamine D2 and D3 receptor subtypes (D2R and D3R, respectively) is described. We introduce several potent and selective D2R (rel-trans-16b; D2R Ki = 4.58 nM) and D3R (rel-cis-14a; D3R Ki = 5.72 nM) agonists while modulating subtype selectivity in a stereospecific fashion, transferring D2R selectivity toward D3R via inversion of the stereochemistry around these cyclic aliphatic linkers [e.g., (-)-(1S,2R)-43 and (+)-(1R,2S)-42]. Pharmacological observations were supported with extensive molecular docking studies. Thus, not only is it an innovative approach to modulate the pharmacology of dopaminergic ligands described, but a new class of optically active cyclic linkers are also introduced, which can be used to expand the bitopic drug design approach toward other GPCRs.
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Affiliation(s)
- Francisco O. Battiti
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Saheem A. Zaidi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, United States
| | - Vsevolod Katritch
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, United States
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
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19
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Shaik AB, Boateng CA, Battiti FO, Bonifazi A, Cao J, Chen L, Chitsazi R, Ravi S, Lee KH, Shi L, Newman AH. Structure Activity Relationships for a Series of Eticlopride-Based Dopamine D 2/D 3 Receptor Bitopic Ligands. J Med Chem 2021; 64:15313-15333. [PMID: 34636551 PMCID: PMC9617622 DOI: 10.1021/acs.jmedchem.1c01353] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The crystal structure of the dopamine D3 receptor (D3R) in complex with eticlopride inspired the design of bitopic ligands that explored (1) N-alkylation of the eticlopride's pyrrolidine ring, (2) shifting of the position of the pyrrolidine nitrogen, (3) expansion of the pyrrolidine ring system, and (4) incorporation of O-alkylations at the 4-position. Structure activity relationships (SAR) revealed that moving the N- or expanding the pyrrolidine ring was detrimental to D2R/D3R binding affinities. Small pyrrolidine N-alkyl groups were poorly tolerated, but the addition of a linker and secondary pharmacophore (SP) improved affinities. Moreover, O-alkylated analogues showed higher binding affinities compared to analogously N-alkylated compounds, e.g., O-alkylated 33 (D3R, 0.436 nM and D2R, 1.77 nM) vs the N-alkylated 11 (D3R, 6.97 nM and D2R, 25.3 nM). All lead molecules were functional D2R/D3R antagonists. Molecular models confirmed that 4-position modifications would be well-tolerated for future D2R/D3R bioconjugate tools that require long linkers and or sterically bulky groups.
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Affiliation(s)
- Anver Basha Shaik
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Comfort A. Boateng
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Francisco O. Battiti
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Jianjing Cao
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Li Chen
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse − Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Rezvan Chitsazi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse − Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Saiprasad Ravi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse − Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse − Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse − Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
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20
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Bonifazi A, Newman AH, Keck TM, Gervasoni S, Vistoli G, Del Bello F, Giorgioni G, Pavletić P, Quaglia W, Piergentili A. Scaffold Hybridization Strategy Leads to the Discovery of Dopamine D 3 Receptor-Selective or Multitarget Bitopic Ligands Potentially Useful for Central Nervous System Disorders. ACS Chem Neurosci 2021; 12:3638-3649. [PMID: 34529404 PMCID: PMC8498988 DOI: 10.1021/acschemneuro.1c00368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
![]()
In the search for
novel bitopic compounds targeting the dopamine
D3 receptor (D3R), the N-(2,3-dichlorophenyl)piperazine
nucleus (primary pharmacophore) has been linked to the 6,6- or 5,5-diphenyl-1,4-dioxane-2-carboxamide
or the 1,4-benzodioxane-2-carboxamide scaffold (secondary pharmacophore)
by an unsubstituted or 3-F-/3-OH-substituted butyl chain. This scaffold
hybridization strategy led to the discovery of potent D3R-selective or multitarget ligands potentially useful for central
nervous system disorders. In particular, the 6,6-diphenyl-1,4-dioxane
derivative 3 showed a D3R-preferential profile,
while an interesting multitarget behavior has been highlighted for
the 5,5-diphenyl-1,4-dioxane and 1,4-benzodioxane derivatives 6 and 9, respectively, which displayed potent
D2R antagonism, 5-HT1AR and D4R agonism,
as well as potent D3R partial agonism. They also behaved
as low-potency 5-HT2AR antagonists and 5-HT2CR partial agonists. Such a profile might be a promising starting
point for the discovery of novel antipsychotic agents.
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Affiliation(s)
- Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, Camerino 62032, Italy
| | - Amy H. Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Thomas M. Keck
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
- Department of Chemistry & Biochemistry, Department of Molecular & Cellular Biosciences, Rowan University, 201 Mullica Hill Rd, Glassboro, New Jersey 08028, United States
| | - Silvia Gervasoni
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, Milano 20133, Italy
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, Milano 20133, Italy
| | - Fabio Del Bello
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, Camerino 62032, Italy
| | - Gianfabio Giorgioni
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, Camerino 62032, Italy
| | - Pegi Pavletić
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, Camerino 62032, Italy
| | - Wilma Quaglia
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, Camerino 62032, Italy
| | - Alessandro Piergentili
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, Camerino 62032, Italy
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21
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Mejia-Gutierrez M, Vásquez-Paz BD, Fierro L, Maza JR. In Silico Repositioning of Dopamine Modulators with Possible Application to Schizophrenia: Pharmacophore Mapping, Molecular Docking and Molecular Dynamics Analysis. ACS OMEGA 2021; 6:14748-14764. [PMID: 34151057 PMCID: PMC8209794 DOI: 10.1021/acsomega.0c05984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/30/2021] [Indexed: 05/17/2023]
Abstract
We have performed theoretical calculations with 70 drugs that have been considered in 231 clinical trials as possible candidates to repurpose drugs for schizophrenia based on their interactions with the dopaminergic system. A hypothesis of shared pharmacophore features was formulated to support our calculations. To do so, we have used the crystal structure of the D2-like dopamine receptor in complex with risperidone, eticlopride, and nemonapride. Linagliptin, citalopram, flunarizine, sildenafil, minocycline, and duloxetine were the drugs that best fit with our model. Molecular docking calculations, molecular dynamics outcomes, blood-brain barrier penetration, and human intestinal absorption were studied and compared with the results. From the six drugs selected in the shared pharmacophore features input, flunarizine showed the best docking score with D2, D3, and D4 dopamine receptors and had high stability during molecular dynamics simulations. Flunarizine is a frequently used medication to treat migraines and vertigo. However, its antipsychotic properties have been previously hypothesized, particularly because of its possible ability to block the D2 dopamine receptors.
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Affiliation(s)
- Melissa Mejia-Gutierrez
- Faculty
of Natural and Exact Sciences, Department of Chemistry, and School
of Basic Sciences, Department of Physiological Sciences, Faculty of
Health, Laboratory and Research group - Pharmacology Univalle Group, Universidad del Valle, 25360 Cali, Colombia
| | - Bryan D. Vásquez-Paz
- Faculty
of Natural and Exact Sciences, Department of Chemistry, Laboratory
and Research group - Pharmacology Univalle Group, Universidad del Valle, 25360 Cali, Colombia
| | - Leonardo Fierro
- Faculty
of Health, School of Basic Sciences, Department of Physiological Sciencesh,
Laboratory and Research group - Pharmacology Univalle Group, Universidad del Valle, 25360 Cali, Colombia
| | - Julio R. Maza
- Faculty
of Basic Sciences, Department of Chemistry, Laboratory and Research
group - Organic Chemistry and Biomedical Group, Universidad del Atlántico, 081001 Puerto Colombia, Colombia
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22
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Bonifazi A, Battiti FO, Sanchez J, Zaidi SA, Bow E, Makarova M, Cao J, Shaik AB, Sulima A, Rice KC, Katritch V, Canals M, Lane JR, Newman AH. Novel Dual-Target μ-Opioid Receptor and Dopamine D 3 Receptor Ligands as Potential Nonaddictive Pharmacotherapeutics for Pain Management. J Med Chem 2021; 64:7778-7808. [PMID: 34011153 DOI: 10.1021/acs.jmedchem.1c00611] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The need for safer pain-management therapies with decreased abuse liability inspired a novel drug design that retains μ-opioid receptor (MOR)-mediated analgesia, while minimizing addictive liability. We recently demonstrated that targeting the dopamine D3 receptor (D3R) with highly selective antagonists/partial agonists can reduce opioid self-administration and reinstatement to drug seeking in rodent models without diminishing antinociceptive effects. The identification of the D3R as a target for the treatment of opioid use disorders prompted the idea of generating a class of ligands presenting bitopic or bivalent structures, allowing the dual-target binding of the MOR and D3R. Structure-activity relationship studies using computationally aided drug design and in vitro binding assays led to the identification of potent dual-target leads (23, 28, and 40), based on different structural templates and scaffolds, with moderate (sub-micromolar) to high (low nanomolar/sub-nanomolar) binding affinities. Bioluminescence resonance energy transfer-based functional studies revealed MOR agonist-D3R antagonist/partial agonist efficacies that suggest potential for maintaining analgesia with reduced opioid-abuse liability.
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Affiliation(s)
- Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Francisco O Battiti
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Julie Sanchez
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K.,Centre of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Midlands NG2 7AG, U.K
| | - Saheem A Zaidi
- Bridge Institute, Michelson Center for Convergent Bioscience, Department of Chemistry, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Eric Bow
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 9800 Medical Center Drive, Bethesda, Maryland 20892, United States
| | - Mariia Makarova
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 9800 Medical Center Drive, Bethesda, Maryland 20892, United States
| | - Jianjing Cao
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Anver Basha Shaik
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Agnieszka Sulima
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 9800 Medical Center Drive, Bethesda, Maryland 20892, United States
| | - Kenner C Rice
- Drug Design and Synthesis Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 9800 Medical Center Drive, Bethesda, Maryland 20892, United States
| | - Vsevolod Katritch
- Bridge Institute, Michelson Center for Convergent Bioscience, Department of Chemistry, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Meritxell Canals
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K.,Centre of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Midlands NG2 7AG, U.K
| | - J Robert Lane
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K.,Centre of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Midlands NG2 7AG, U.K
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
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23
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Hayatshahi HS, Luedtke RR, Taylor M, Chen PJ, Blass BE, Liu J. Factors Governing Selectivity of Dopamine Receptor Binding Compounds for D2R and D3R Subtypes. J Chem Inf Model 2021; 61:2829-2843. [PMID: 33988991 DOI: 10.1021/acs.jcim.1c00036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting the D3 dopamine receptor (D3R) is a promising pharmacotherapeutic strategy for the treatment of many disorders. The structure of the D3R is similar to the D2 dopamine receptor (D2R), especially in the transmembrane spanning regions that form the orthosteric binding site, making it difficult to identify D3R selective pharmacotherapeutic agents. Here, we examine the molecular basis for the high affinity D3R binding and D3R vs D2R binding selectivity of substituted phenylpiperazine thiopheneamides. We show that removing the thiophenearylamide portion of the ligand consistently decreases the affinity of these ligands at D3R, while not affecting their affinity at the D2R. Our long (>10 μs) molecular dynamics simulations demonstrated that both dopamine receptor subtypes adopt two major conformations that we refer to as closed or open conformations, with D3R sampling the open conformation more frequently than D2R. The binding of ligands with conjoined orthosteric-allosteric binding moieties causes the closed conformation to populate more often in the trajectories. Also, significant differences were observed in the extracellular loops (ECL) of these two receptor subtypes leading to the identification of several residues that contribute differently to the ligand binding for the two receptors that could potentially contribute to ligand binding selectivity. Our observations also suggest that the displacement of ordered water in the binding pocket of D3R contributes to the affinity of the compounds containing an allosteric binding motif. These studies provide a better understanding of how a bitopic mode of engagement can determine ligands that bind selectively to D2 and D3 dopamine receptor subtypes.
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Affiliation(s)
- Hamed S Hayatshahi
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Robert R Luedtke
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Michelle Taylor
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Peng-Jen Chen
- Moulder Center for Drug Discovery Research, Department of Pharmaceutical Sciences, Temple University School of Pharmacy, 3307 North Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Benjamin E Blass
- Moulder Center for Drug Discovery Research, Department of Pharmaceutical Sciences, Temple University School of Pharmacy, 3307 North Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
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24
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Chirality of Novel Bitopic Agonists Determines Unique Pharmacology at the Dopamine D3 Receptor. Biomolecules 2021; 11:biom11040570. [PMID: 33924613 PMCID: PMC8069330 DOI: 10.3390/biom11040570] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 02/07/2023] Open
Abstract
The dopamine D2/D3 receptor (D2R/D3R) agonists are used as therapeutics for Parkinson's disease (PD) and other motor disorders. Selective targeting of D3R over D2R is attractive because of D3R's restricted tissue distribution with potentially fewer side-effects and its putative neuroprotective effect. However, the high sequence homology between the D2R and D3R poses a challenge in the development of D3R selective agonists. To address the ligand selectivity, bitopic ligands were designed and synthesized previously based on a potent D3R-preferential agonist PF592,379 as the primary pharmacophore (PP). This PP was attached to various secondary pharmacophores (SPs) using chemically different linkers. Here, we characterize some of these novel bitopic ligands at both D3R and D2R using BRET-based functional assays. The bitopic ligands showed varying differences in potencies and efficacies. In addition, the chirality of the PP was key to conferring improved D3R potency, selectivity, and G protein signaling bias. In particular, compound AB04-88 exhibited significant D3R over D2R selectivity, and G protein bias at D3R. This bias was consistently observed at various time-points ranging from 8 to 46 min. Together, the structure-activity relationships derived from these functional studies reveal unique pharmacology at D3R and support further evaluation of functionally biased D3R agonists for their therapeutic potential.
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25
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Neuronal Dopamine D3 Receptors: Translational Implications for Preclinical Research and CNS Disorders. Biomolecules 2021; 11:biom11010104. [PMID: 33466844 PMCID: PMC7830622 DOI: 10.3390/biom11010104] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
Dopamine (DA), as one of the major neurotransmitters in the central nervous system (CNS) and periphery, exerts its actions through five types of receptors which belong to two major subfamilies such as D1-like (i.e., D1 and D5 receptors) and D2-like (i.e., D2, D3 and D4) receptors. Dopamine D3 receptor (D3R) was cloned 30 years ago, and its distribution in the CNS and in the periphery, molecular structure, cellular signaling mechanisms have been largely explored. Involvement of D3Rs has been recognized in several CNS functions such as movement control, cognition, learning, reward, emotional regulation and social behavior. D3Rs have become a promising target of drug research and great efforts have been made to obtain high affinity ligands (selective agonists, partial agonists and antagonists) in order to elucidate D3R functions. There has been a strong drive behind the efforts to find drug-like compounds with high affinity and selectivity and various functionality for D3Rs in the hope that they would have potential treatment options in CNS diseases such as schizophrenia, drug abuse, Parkinson’s disease, depression, and restless leg syndrome. In this review, we provide an overview and update of the major aspects of research related to D3Rs: distribution in the CNS and periphery, signaling and molecular properties, the status of ligands available for D3R research (agonists, antagonists and partial agonists), behavioral functions of D3Rs, the role in neural networks, and we provide a summary on how the D3R-related drug research has been translated to human therapy.
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26
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Montes JM, Montes P, Hernández-Huerta D. Cariprazine in Three Acute Patients with Schizophrenia: A Real-World Experience. Neuropsychiatr Dis Treat 2021; 17:291-296. [PMID: 33568908 PMCID: PMC7868213 DOI: 10.2147/ndt.s298005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/21/2021] [Indexed: 11/23/2022] Open
Abstract
There are still some unmet needs in the treatment of schizophrenia like the persistence of negative symptoms. Cariprazine is a new-generation antipsychotic with partial agonism of the dopamine receptors, distinct from other antipsychotics by its 10 times greater affinity for D3 receptors. This mechanism of action could be especially favorable on patients with predominant negative symptoms. This report is showing three clinical cases of acute schizophrenia exacerbation that required hospitalization and were successfully treated with cariprazine. All of them had predominant positive symptoms and two of them had substance use. Efficacy of cariprazine was also crucial on negative and cognitive symptoms with excellent tolerability.
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Affiliation(s)
- Jose M Montes
- Psychiatry Service, CIBERSAM, IRYCIS, Hospital Universitario Ramóny Cajal, Madrid, Spain
| | - Paloma Montes
- Psychiatry Service, Hospital Universitario de Móstoles Madrid, Spain
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27
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Peris L, Szerman N. Partial Agonists and Dual Disorders: Focus on Dual Schizophrenia. Front Psychiatry 2021; 12:769623. [PMID: 34975572 PMCID: PMC8716462 DOI: 10.3389/fpsyt.2021.769623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/18/2021] [Indexed: 12/31/2022] Open
Abstract
Dual disorder is a term applied to patients with an addictive disorder and other mental disorder. Epidemiological studies have established that dual disorders are an expectation rather than an exception. They are difficult to diagnose and treat and constitute a huge burden for both patients and their relatives and society. Current treatments are a combination of those needed to treat the addictive disorder with those focused on the co-occurring psychiatric disorder. Focusing specifically on schizophrenia, growing scientific evidence supports the existence of a shared vulnerability for substance use in these patients and those at risk. Various antipsychotics have been found to be useful in the treatment of psychotic symptoms and disorders; however, few effective treatments have been identified until now for substance use disorders in patients with dual schizophrenia. Partial agonism stands as a new pharmacological option available in recent years. Molecules with this kind of action may act as functional agonists or as antagonists, depending on the surrounding levels of the neurotransmitter. Studies have found their efficacy in schizophrenia, addiction, anxiety and depression. Certain partial agonist antipsychotics seem to have a role in the treatment of dual schizophrenia. That could be the case with cariprazine. Because of its higher affinity for dopaminergic D3 receptors compared to D2, a potential to prevent relapse to addiction, added to its antipsychotic efficacy, has been suggested. Here we briefly review current advances and future directions and introduce some personal insights into the role of partial agonists in co-occurring schizophrenia and substance use.
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Affiliation(s)
- Lola Peris
- Centre Neuchâtelois De Psychiatrie, Marin-Epagnier, Switzerland
| | - Nestor Szerman
- Hospital Universitario Gregorio Marañon, Madrid, Spain.,Fundación Patología Dual, WPA Section on Dual Disorders, WADD, Madrid, Spain
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28
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Moritz AE, Bonifazi A, Guerrero AM, Kumar V, Free RB, Lane JR, Verma RK, Shi L, Newman AH, Sibley DR. Evidence for a Stereoselective Mechanism for Bitopic Activity by Extended-Length Antagonists of the D 3 Dopamine Receptor. ACS Chem Neurosci 2020; 11:3309-3320. [PMID: 32969645 PMCID: PMC8262072 DOI: 10.1021/acschemneuro.0c00425] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The D3 dopamine receptor (D3R) has been suggested as a drug target for the treatment of a number of neuropsychiatric disorders, including substance use disorders (SUD). Many D3R-selective antagonists are bivalent in nature in that they engage two distinct sites on the receptor-a primary pharmacophore binds to the orthosteric site, where dopamine binds, whereas a secondary pharmacophore interacts with a unique secondary binding pocket (SBP). When engagement of the secondary pocket exerts allosteric activity, the compound is said to be bitopic. We recently reported the synthesis and characterization of two bitopic antagonists of the D3R, (±)-VK04-87 and (±)-VK05-95, which incorporated a racemic trans-cyclopropylmethyl linking chain. To gain a better understanding of the role of chirality in determining the pharmacology of such compounds, we resolved the enantiomers of (±)-VK04-87. We found that the (+)-isomer displays higher affinity for the D3R and exhibits greater selectivity versus the D2R than the (-)-isomer. Strikingly, using functional assays, we found that (+)-VK04-87 inhibits the D3R in a noncompetitive manner, while (-)-VK04-87 behaves as a purely competitive antagonist, indicating that the apparent allosteric activity of the racemate is due to the (+)-isomer. Molecular dynamic simulations of (+)-VK04-87 and (-)-VK04-87 binding to the D3R suggest that the (+)-isomer is able to interact with the SBP of the receptor whereas the (-)-isomer bends away from this pocket, thus potentially explaining their differing pharmacology. These results emphasize the importance of the linker, and its isomeric conformations, within extended-length molecules for their positioning and engagement within GPCR binding pockets.
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Affiliation(s)
- Amy E. Moritz
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, MD, 20892-3723
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medication Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD, 21224
| | - Adrian M. Guerrero
- Medicinal Chemistry Section, Molecular Targets and Medication Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD, 21224
| | - Vivek Kumar
- Medicinal Chemistry Section, Molecular Targets and Medication Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD, 21224
| | - R. Benjamin Free
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, MD, 20892-3723
| | - J. Robert Lane
- Centre of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Nottingham, United Kingdom
| | - Ravi Kumar Verma
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland, 333 Cassell Drive, Baltimore, MD 21224
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland, 333 Cassell Drive, Baltimore, MD 21224
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medication Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD, 21224
| | - David R. Sibley
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, MD, 20892-3723
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29
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Battiti FO, Newman AH, Bonifazi A. Exception That Proves the Rule: Investigation of Privileged Stereochemistry in Designing Dopamine D 3R Bitopic Agonists. ACS Med Chem Lett 2020; 11:1956-1964. [PMID: 33062179 DOI: 10.1021/acsmedchemlett.9b00660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/28/2020] [Indexed: 01/11/2023] Open
Abstract
In this study, starting from our selective D3R agonist FOB02-04A (5), we investigated the chemical space around the linker portion of the molecule via insertion of a hydroxyl substituent and ring-expansion of the trans-cyclopropyl moiety into a trans-cyclohexyl scaffold. Moreover, to further elucidate the importance of the primary pharmacophore stereochemistry in the design of bitopic ligands, we investigated the chiral requirements of (+)-PD128907 ((+)-(4a R ,10b R )-2)) by synthesizing and resolving bitopic analogues in all the cis and trans combinations of its 9-methoxy-3,4,4a,10b-tetrahydro-2H,5H-chromeno[4,3-b][1,4] oxazine scaffold. Despite the lack of success in obtaining new analogues with improved biological profiles, in comparison to our current leads, a "negative" result due to a poor or simply not improved biological profile is fundamental toward better understanding chemical space and optimal stereochemistry for target recognition. Herein, we identified essential structural information to understand the differences between orthosteric and bitopic ligand-receptor binding interactions, discriminate D3R active and inactive states, and assist multitarget receptor recognition. Exploring stereochemical complexity and developing extended D3R SAR from this new library complements previously described SAR and inspires future structural and computational biology investigation. Moreover, the expansion of chemical space characterization for D3R agonism may be utilized in machine learning and artificial intelligence (AI)-based drug design, in the future.
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Affiliation(s)
- Francisco O. Battiti
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
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30
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Moritz AE, Free RB, Weiner WS, Akano EO, Gandhi D, Abramyan A, Keck TM, Ferrer M, Hu X, Southall N, Steiner J, Aubé J, Shi L, Frankowski KJ, Sibley DR. Discovery, Optimization, and Characterization of ML417: A Novel and Highly Selective D 3 Dopamine Receptor Agonist. J Med Chem 2020; 63:5526-5567. [PMID: 32342685 DOI: 10.1021/acs.jmedchem.0c00424] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To identify novel D3 dopamine receptor (D3R) agonists, we conducted a high-throughput screen using a β-arrestin recruitment assay. Counterscreening of the hit compounds provided an assessment of their selectivity, efficacy, and potency. The most promising scaffold was optimized through medicinal chemistry resulting in enhanced potency and selectivity. The optimized compound, ML417 (20), potently promotes D3R-mediated β-arrestin translocation, G protein activation, and ERK1/2 phosphorylation (pERK) while lacking activity at other dopamine receptors. Screening of ML417 against multiple G protein-coupled receptors revealed exceptional global selectivity. Molecular modeling suggests that ML417 interacts with the D3R in a unique manner, possibly explaining its remarkable selectivity. ML417 was also found to protect against neurodegeneration of dopaminergic neurons derived from iPSCs. Together with promising pharmacokinetics and toxicology profiles, these results suggest that ML417 is a novel and uniquely selective D3R agonist that may serve as both a research tool and a therapeutic lead for the treatment of neuropsychiatric disorders.
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Affiliation(s)
- Amy E Moritz
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland 20892-3723, United States
| | - R Benjamin Free
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland 20892-3723, United States
| | - Warren S Weiner
- University of Kansas Specialized Chemistry Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - Emmanuel O Akano
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland 20892-3723, United States
| | - Disha Gandhi
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Ara Abramyan
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, Maryland, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Thomas M Keck
- Department of Chemistry & Biochemistry, Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Marc Ferrer
- NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Noel Southall
- NIH Chemical Genomics Center, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Joseph Steiner
- NeuroTherapeutics Development Unit, National Institute for Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jeffrey Aubé
- University of Kansas Specialized Chemistry Center, University of Kansas, Lawrence, Kansas 66047, United States.,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, Maryland, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Kevin J Frankowski
- University of Kansas Specialized Chemistry Center, University of Kansas, Lawrence, Kansas 66047, United States.,Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - David R Sibley
- Molecular Neuropharmacology Section, National Institute of Neurological Disorders and Stroke, Intramural Research Program, National Institutes of Health, 35 Convent Drive, MSC-3723, Bethesda, Maryland 20892-3723, United States
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31
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Newman AH, Battiti FO, Bonifazi A. 2016 Philip S. Portoghese Medicinal Chemistry Lectureship: Designing Bivalent or Bitopic Molecules for G-Protein Coupled Receptors. The Whole Is Greater Than the Sum of Its Parts. J Med Chem 2020; 63:1779-1797. [PMID: 31499001 PMCID: PMC8281448 DOI: 10.1021/acs.jmedchem.9b01105] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genesis of designing bivalent or bitopic molecules that engender unique pharmacological properties began with Portoghese's work directed toward opioid receptors, in the early 1980s. This strategy has evolved as an attractive way to engineer highly selective compounds for targeted G-protein coupled receptors (GPCRs) with optimized efficacies and/or signaling bias. The emergence of X-ray crystal structures of many GPCRs and the identification of both orthosteric and allosteric binding sites have provided further guidance to ligand drug design that includes a primary pharmacophore (PP), a secondary pharmacophore (SP), and a linker between them. It is critical to note the synergistic relationship among all three of these components as they contribute to the overall interaction of these molecules with their receptor proteins and that strategically designed combinations have and will continue to provide the GPCR molecular tools of the future.
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Affiliation(s)
- Amy Hauck Newman
- Corresponding author: Amy H. Newman: Phone: (443)-740-2887. Fax: (443)-740-2111.
| | - Francisco O. Battiti
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
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32
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Lane JR, Abramyan AM, Adhikari P, Keen AC, Lee KH, Sanchez J, Verma RK, Lim HD, Yano H, Javitch JA, Shi L. Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism. eLife 2020; 9:e52189. [PMID: 31985399 PMCID: PMC7053997 DOI: 10.7554/elife.52189] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/24/2020] [Indexed: 01/07/2023] Open
Abstract
By analyzing and simulating inactive conformations of the highly homologous dopamine D2 and D3 receptors (D2R and D3R), we find that eticlopride binds D2R in a pose very similar to that in the D3R/eticlopride structure but incompatible with the D2R/risperidone structure. In addition, risperidone occupies a sub-pocket near the Na+ binding site, whereas eticlopride does not. Based on these findings and our experimental results, we propose that the divergent receptor conformations stabilized by Na+-sensitive eticlopride and Na+-insensitive risperidone correspond to different degrees of inverse agonism. Moreover, our simulations reveal that the extracellular loops are highly dynamic, with spontaneous transitions of extracellular loop 2 from the helical conformation in the D2R/risperidone structure to an extended conformation similar to that in the D3R/eticlopride structure. Our results reveal previously unappreciated diversity and dynamics in the inactive conformations of D2R. These findings are critical for rational drug discovery, as limiting a virtual screen to a single conformation will miss relevant ligands.
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Affiliation(s)
- J Robert Lane
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of NottinghamNottinghamUnited Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and NottinghamNottinghamUnited Kingdom
| | - Ara M Abramyan
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Pramisha Adhikari
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Alastair C Keen
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of NottinghamNottinghamUnited Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and NottinghamNottinghamUnited Kingdom
- Drug Discovery Biology, Department of Pharmacology and Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Kuo-Hao Lee
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Julie Sanchez
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of NottinghamNottinghamUnited Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and NottinghamNottinghamUnited Kingdom
| | - Ravi Kumar Verma
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Herman D Lim
- Drug Discovery Biology, Department of Pharmacology and Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Hideaki Yano
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Jonathan A Javitch
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia UniversityNew YorkUnited States
- Division of Molecular Therapeutics, New York State Psychiatric InstituteNew YorkUnited States
- Department of PharmacologyVagelos College of Physicians and Surgeons, Columbia UniversityNew YorkUnited States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
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33
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Ferraro M, Decherchi S, De Simone A, Recanatini M, Cavalli A, Bottegoni G. Multi-target dopamine D3 receptor modulators: Actionable knowledge for drug design from molecular dynamics and machine learning. Eur J Med Chem 2019; 188:111975. [PMID: 31940507 DOI: 10.1016/j.ejmech.2019.111975] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 12/02/2019] [Accepted: 12/16/2019] [Indexed: 10/25/2022]
Abstract
Local changes in the structure of G-protein coupled receptors (GPCR) binders largely affect their pharmacological profile. While the sought efficacy can be empirically obtained by introducing local modifications, the underlining structural explanation can remain elusive. Here, molecular dynamics (MD) simulations of the eticlopride-bound inactive state of the Dopamine D3 Receptor (D3DR) have been clustered using a machine learning-based approach in the attempt to rationalize the efficacy change in four congeneric modulators. Accumulating extended MD trajectories of receptor-ligand complexes, we observed how the increase in ligand flexibility progressively destabilized the crystal structure of the inactivated receptor. To prospectively validate this model, a partial agonist was rationally designed based on structural insights and computational modeling, and eventually synthesized and tested. Results turned out to be in line with the predictions. This case study suggests that the investigation of ligand flexibility in the framework of extended MD simulations can assist and inform drug design strategies, highlighting its potential role as a powerful in silico counterpart to functional assays.
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Affiliation(s)
- Mariarosaria Ferraro
- Istituto di Chimica Del Riconoscimento Molecolare, Consiglio Nazionale Delle Ricerche (ICRM-CNR), Via Mario Bianco 9, 20131, Milan, Italy.
| | - Sergio Decherchi
- Computational & Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163, Genoa, Italy.
| | - Alessio De Simone
- Sygnature Discovery Ltd, Bio City, Pennyfoot St, Nottingham NG1 1GR, United Kingdom.
| | - Maurizio Recanatini
- Dept. of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.
| | - Andrea Cavalli
- Computational & Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163, Genoa, Italy; Dept. of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.
| | - Giovanni Bottegoni
- School of Pharmacy, University of Birmingham, Sir Robert Aitken Institute for Clinical Research, Edgbaston, B15 2TT, United Kingdom.
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34
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Su H, Xue Z, Feng Y, Xie Y, Deng B, Yao Y, Tian X, An Q, Yang L, Yao Q, Xue J, Chen G, Hao C, Zhou T. N-arylpiperazine-containing compound (C2): An enhancer of sunitinib in the treatment of pancreatic cancer, involving D1DR activation. Toxicol Appl Pharmacol 2019; 384:114789. [PMID: 31669811 DOI: 10.1016/j.taap.2019.114789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023]
Abstract
Previous studies showed that dopamine (DA) significantly reduces the frequency of cancer stem-like cells (CSC) and enhances the efficacy of sunitinib (SUN) in the treatment of breast cancer and non-small cell lung cancer (NSCLC). To overcome the shortcomings of DA in clinical practice, the purpose of this study was to investigate the efficacy as well as the underlying mechanism of an orally available, N-arylpiperazine-containing compound C2, in the treatment of pancreatic cancer when used alone or in combination with SUN. Our results showed that C2 and SUN exerted synergistic effects on inhibiting the growth of SW1990 and PANC-1 pancreatic cancer cells. C2 significantly inhibited colony formation and migration of both cells. SW1990 xenograft and patient-derived xenograft (PDX) models were utilized for pharmacodynamic investigation in vivo. C2 alone showed little inhibition effect on tumor growth but increased the anti-tumor efficacy of SUN in both xenografts. Moreover, C2 down-regulated CSC markers (CD133 and ALDH) of both cancer cells and up-regulated the expression of dopamine receptor D1 (D1DR) in tumor. Besides, the SW1990 tumor growth was dose-dependently inhibited when the cells were pretreated with C2 before implantation. C2 increased intratumoral cAMP level, and the combination with D1DR specific antagonist SCH23390 reversed the above-mentioned effects of C2 both in vitro and in vivo, indicating the activation of D1DR may be involved in the underlying mechanism of C2 action. In summary, C2 could reduce the CSC frequency and enhance the anti-cancer effect of SUN in the treatment of pancreatic cancer, demonstrating its potential in cancer therapy.
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Affiliation(s)
- Hong Su
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery System, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zixi Xue
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Yaoyao Feng
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery System, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ying Xie
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery System, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Bo Deng
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery System, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ye Yao
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery System, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiuyun Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Qiming An
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Liang Yang
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery System, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qingyu Yao
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery System, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Junsheng Xue
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery System, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Guoshu Chen
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Chunyi Hao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing 100142, China.
| | - Tianyan Zhou
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery System, Department of Pharmaceutics, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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35
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Pal RK, Gadhiya S, Ramsey S, Cordone P, Wickstrom L, Harding WW, Kurtzman T, Gallicchio E. Inclusion of enclosed hydration effects in the binding free energy estimation of dopamine D3 receptor complexes. PLoS One 2019; 14:e0222902. [PMID: 31568493 PMCID: PMC6768453 DOI: 10.1371/journal.pone.0222902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/30/2019] [Indexed: 01/04/2023] Open
Abstract
Confined hydration and conformational flexibility are some of the challenges encountered for the rational design of selective antagonists of G-protein coupled receptors. We present a set of C3-substituted (-)-stepholidine derivatives as potent binders of the dopamine D3 receptor. The compounds are characterized biochemically, as well as by computer modeling using a novel molecular dynamics-based alchemical binding free energy approach which incorporates the effect of the displacement of enclosed water molecules from the binding site. The free energy of displacement of specific hydration sites is obtained using the Hydration Site Analysis method with explicit solvation. This work underscores the critical role of confined hydration and conformational reorganization in the molecular recognition mechanism of dopamine receptors and illustrates the potential of binding free energy models to represent these key phenomena.
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Affiliation(s)
- Rajat Kumar Pal
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, NY 11210, United States of America
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
| | - Satishkumar Gadhiya
- PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
- Department of Chemistry, Hunter College, 695 Park Avenue, NY 10065, United States of America
| | - Steven Ramsey
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
- Department of Chemistry, Lehman College, 250 Bedford Park Blvd. West, Bronx, NY 10468, United States of America
| | - Pierpaolo Cordone
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
- Department of Chemistry, Hunter College, 695 Park Avenue, NY 10065, United States of America
| | - Lauren Wickstrom
- Department of Science, Borough of Manhattan Community College, 199 Chambers Street, New York, NY 10007, United States of America
| | - Wayne W. Harding
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
- PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
- Department of Chemistry, Hunter College, 695 Park Avenue, NY 10065, United States of America
| | - Tom Kurtzman
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
- PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
- Department of Chemistry, Lehman College, 250 Bedford Park Blvd. West, Bronx, NY 10468, United States of America
| | - Emilio Gallicchio
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, NY 11210, United States of America
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
- PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States of America
- * E-mail:
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36
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Klein Herenbrink C, Verma R, Lim HD, Kopinathan A, Keen A, Shonberg J, Draper-Joyce CJ, Scammells PJ, Christopoulos A, Javitch JA, Capuano B, Shi L, Lane JR. Molecular Determinants of the Intrinsic Efficacy of the Antipsychotic Aripiprazole. ACS Chem Biol 2019; 14:1780-1792. [PMID: 31339684 DOI: 10.1021/acschembio.9b00342] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Partial agonists of the dopamine D2 receptor (D2R) have been developed to treat the symptoms of schizophrenia without causing the side effects elicited by antagonists. The receptor-ligand interactions that determine the intrinsic efficacy of such drugs, however, are poorly understood. Aripiprazole has an extended structure comprising a phenylpiperazine primary pharmacophore and a 1,2,3,4-tetrahydroquinolin-2-one secondary pharmacophore. We combined site-directed mutagenesis, analytical pharmacology, ligand fragments, and molecular dynamics simulations to identify the D2R-aripiprazole interactions that contribute to affinity and efficacy. We reveal that an interaction between the secondary pharmacophore of aripiprazole and a secondary binding pocket defined by residues at the extracellular portions of transmembrane segments 1, 2, and 7 determines the intrinsic efficacy of aripiprazole. Our findings reveal a hitherto unappreciated mechanism for fine-tuning the intrinsic efficacy of D2R agonists.
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Affiliation(s)
| | - Ravi Verma
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | | | | | | | | | | | | | | | | | | | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - J. Robert Lane
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K
- Centre of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Nottingham, United Kingdom
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37
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Battiti FO, Cemaj SL, Guerrero AM, Shaik AB, Lam J, Rais R, Slusher BS, Deschamps JR, Imler GH, Newman AH, Bonifazi A. The Significance of Chirality in Drug Design and Synthesis of Bitopic Ligands as D 3 Receptor (D 3R) Selective Agonists. J Med Chem 2019; 62:6287-6314. [PMID: 31257877 DOI: 10.1021/acs.jmedchem.9b00702] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Because of the large degree of homology among dopamine D2-like receptors, discovering ligands capable of discriminating between the D2, D3, and D4 receptor subtypes remains a significant challenge. Previous work has exemplified the use of bitopic ligands as a powerful strategy in achieving subtype selectivity for agonists and antagonists alike. Inspired by the potential for chemical modification of the D3 preferential agonists (+)-PD128,907 (1) and PF592,379 (2), we synthesized bitopic structures to further improve their D3R selectivity. We found that the (2S,5S) conformation of scaffold 2 resulted in a privileged architecture with increased affinity and selectivity for the D3R. In addition, a cyclopropyl moiety incorporated into the linker and full resolution of the chiral centers resulted in lead compound 53 and eutomer 53a that demonstrate significantly higher D3R binding selectivities than the reference compounds. Moreover, the favorable metabolic stability in rat liver microsomes supports future studies in in vivo models of dopamine system dysregulation.
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Affiliation(s)
- Francisco O Battiti
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program , National Institutes of Health , 333 Cassell Drive , Baltimore , Maryland 21224 , United States
| | - Sophie L Cemaj
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program , National Institutes of Health , 333 Cassell Drive , Baltimore , Maryland 21224 , United States
| | - Adrian M Guerrero
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program , National Institutes of Health , 333 Cassell Drive , Baltimore , Maryland 21224 , United States
| | - Anver Basha Shaik
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program , National Institutes of Health , 333 Cassell Drive , Baltimore , Maryland 21224 , United States
| | - Jenny Lam
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program , National Institutes of Health , 333 Cassell Drive , Baltimore , Maryland 21224 , United States.,Johns Hopkins Drug Discovery Program , Johns Hopkins School of Medicine , 855 N. Wolfe Street , Baltimore , Maryland 21205 , United States
| | - Rana Rais
- Johns Hopkins Drug Discovery Program , Johns Hopkins School of Medicine , 855 N. Wolfe Street , Baltimore , Maryland 21205 , United States
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery Program , Johns Hopkins School of Medicine , 855 N. Wolfe Street , Baltimore , Maryland 21205 , United States
| | - Jeffery R Deschamps
- Naval Research Laboratory , Code 6910, 4555 Overlook Avenue , Washington, DC 20375 , United States
| | - Greg H Imler
- Naval Research Laboratory , Code 6910, 4555 Overlook Avenue , Washington, DC 20375 , United States
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program , National Institutes of Health , 333 Cassell Drive , Baltimore , Maryland 21224 , United States
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program , National Institutes of Health , 333 Cassell Drive , Baltimore , Maryland 21224 , United States
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38
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Abramyan AM, Slack RD, Meena S, Davis BA, Newman AH, Singh SK, Shi L. Computation-guided analysis of paroxetine binding to hSERT reveals functionally important structural elements and dynamics. Neuropharmacology 2018; 161:107411. [PMID: 30391505 DOI: 10.1016/j.neuropharm.2018.10.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/03/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023]
Abstract
The serotonin transporter (SERT) is one of the primary targets for medications to treat neuropsychiatric disorders and functions by exploiting pre-existing ion gradients of Na+, Cl-, and K+ to translocate serotonin from the synaptic cleft into the presynaptic neuron. Although recent hSERT crystal structures represent a milestone for structure-function analyses of mammalian neurotransmitter:sodium symporters, they are all derived from thermostabilized but transport-deficient constructs. Two of these structures are in complex with paroxetine, the most potent selective serotonin reuptake inhibitor known. In this study, by carrying out and analyzing the results of extensive and comparative molecular dynamics simulations while also re-evaluating the transport and binding properties of the thermostabilized constructs, we identified functionally important structural elements that are perturbed by these mutations, revealed unexpected dynamics in the central primary binding site of SERT, and uncovered a conceivable ambiguity in paroxetine's binding orientation. We propose that the favored entropy contribution plays a significant role in paroxetine's extraordinarily high affinity for SERT. Our findings lay the foundation for future mechanistic studies and rational design of high-affinity SERT inhibitors. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.
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Affiliation(s)
- Ara M Abramyan
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD, 21224, United States
| | - Rachel D Slack
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD, 21224, United States
| | - Sitaram Meena
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, United States
| | - Bruce A Davis
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, United States
| | - Amy Hauck Newman
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD, 21224, United States.
| | - Satinder K Singh
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, United States.
| | - Lei Shi
- Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD, 21224, United States.
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39
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Abramyan AM, Quick M, Xue C, Javitch JA, Shi L. Exploring Substrate Binding in the Extracellular Vestibule of MhsT by Atomistic Simulations and Markov Models. J Chem Inf Model 2018; 58:1244-1252. [PMID: 29851339 DOI: 10.1021/acs.jcim.8b00175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Neurotransmitter:sodium symporters (NSS) terminate neurotransmission through Na+-driven reuptake of cognate neurotransmitters. Crystallographically, whereas both substrates and inhibitors have been found to bind in the central binding (S1) site of NSS, inhibitors were found to bind to a second binding (S2) site in the extracellular vestibule (EV) of transporters for leucine (LeuT) and serotonin. On the basis of computational and experimental studies, we proposed that substrates bind to the S2 site of LeuT as well and that substrate binding to the S2 site is essential for Na+-coupled symport. Recent binding experiments show that substrate (l-Trp) binding in the S2 site of MhsT, another bacterial NSS, is also central to the allosteric transport mechanism. Here, we used extensive molecular dynamics simulations combined with Markov state model analysis to investigate the interaction of l-Trp with the EV of MhsT and identified potential binding poses of l-Trp as well as induced conformational changes in the EV. Our computational findings were validated by experimental mutagenesis studies and shed light on the ligand binding characteristics of the EV of NSS, which may facilitate development of allosteric ligands targeting NSS.
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Affiliation(s)
- Ara M Abramyan
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program , National Institutes of Health , Baltimore , Maryland 21224 , United States
| | - Matthias Quick
- Division of Molecular Therapeutics , New York State Psychiatric Institute , New York , New York 10032 , United States
| | - Catherine Xue
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program , National Institutes of Health , Baltimore , Maryland 21224 , United States
| | - Jonathan A Javitch
- Division of Molecular Therapeutics , New York State Psychiatric Institute , New York , New York 10032 , United States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program , National Institutes of Health , Baltimore , Maryland 21224 , United States
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40
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Yano H, Bonifazi A, Xu M, Guthrie DA, Schneck SN, Abramyan AM, Fant AD, Hong WC, Newman AH, Shi L. Pharmacological profiling of sigma 1 receptor ligands by novel receptor homomer assays. Neuropharmacology 2018; 133:264-275. [PMID: 29407216 PMCID: PMC5858991 DOI: 10.1016/j.neuropharm.2018.01.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/06/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022]
Abstract
The sigma 1 receptor (σ1R) is a structurally unique transmembrane protein that functions as a molecular chaperone in the endoplasmic reticulum (ER), and has been implicated in cancer, neuropathic pain, and psychostimulant abuse. Despite physiological and pharmacological significance, mechanistic underpinnings of structure-function relationships of σ1R are poorly understood, and molecular interactions of selective ligands with σ1R have not been elucidated. The recent crystallographic determination of σ1R as a homo-trimer provides the foundation for mechanistic elucidation at the molecular level. Here we report novel bioluminescence resonance energy transfer (BRET) assays that enable analyses of ligand-induced multimerization of σ1R and its interaction with BiP. Haloperidol, PD144418, and 4-PPBP enhanced σ1R homomer BRET signals in a dose dependent manner, suggesting their significant effects in stabilizing σ1R multimerization, whereas (+)-pentazocine and several other ligands do not. In non-denaturing gels, (+)-pentazocine significantly decreased whereas haloperidol increased the fraction of σ1R multimers, consistent with the results from the homomer BRET assay. Further, BRET assays examining heteromeric σ1R-BiP interaction revealed that (+)-pentazocine and haloperidol induced opposite trends of signals. From molecular modeling and simulations of σ1R in complex with the tested ligands, we identified initial clues that may lead to the differed responses of σ1R upon binding of structurally diverse ligands. By combining multiple in vitro pharmacological and in silico molecular biophysical methods, we propose a novel integrative approach to analyze σ1R-ligand binding and its impact on interaction of σ1R with client proteins.
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Affiliation(s)
- Hideaki Yano
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA.
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Min Xu
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Daryl A Guthrie
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Stephanie N Schneck
- Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Ara M Abramyan
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Andrew D Fant
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - W Conrad Hong
- Department of Pharmaceutical Sciences, Butler University, Indianapolis, IN 46208, USA
| | - Amy H Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse, Intramural Research Program, National Institute of Health, 333 Cassell Drive, Baltimore, MD 21224, USA.
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41
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Yano H, Cai NS, Xu M, Verma RK, Rea W, Hoffman AF, Shi L, Javitch JA, Bonci A, Ferré S. Gs- versus Golf-dependent functional selectivity mediated by the dopamine D 1 receptor. Nat Commun 2018; 9:486. [PMID: 29402888 PMCID: PMC5799184 DOI: 10.1038/s41467-017-02606-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 12/09/2017] [Indexed: 12/13/2022] Open
Abstract
The two highly homologous subtypes of stimulatory G proteins Gαs (Gs) and Gαolf (Golf) display contrasting expression patterns in the brain. Golf is predominant in the striatum, while Gs is predominant in the cortex. Yet, little is known about their functional distinctions. The dopamine D1 receptor (D1R) couples to Gs/olf and is highly expressed in cortical and striatal areas, making it an important therapeutic target for neuropsychiatric disorders. Using novel drug screening methods that allow analysis of specific G-protein subtype coupling, we found that, relative to dopamine, dihydrexidine and N-propyl-apomorphine behave as full D1R agonists when coupled to Gs, but as partial D1R agonists when coupled to Golf. The Gs/Golf-dependent biased agonism by dihydrexidine was consistently observed at the levels of cellular signaling, neuronal function, and behavior. Our findings of Gs/Golf-dependent functional selectivity in D1R ligands open a new avenue for the treatment of cortex-specific or striatum-specific neuropsychiatric dysfunction.
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Affiliation(s)
- Hideaki Yano
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA.
| | - Ning-Sheng Cai
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Min Xu
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ravi Kumar Verma
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - William Rea
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Alexander F Hoffman
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Lei Shi
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Jonathan A Javitch
- Department of Psychiatry, College of Physicians & Surgeons, Columbia University, New York, NY, 10032, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Antonello Bonci
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Sergi Ferré
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
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42
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Draper-Joyce CJ, Verma RK, Michino M, Shonberg J, Kopinathan A, Klein Herenbrink C, Scammells PJ, Capuano B, Abramyan AM, Thal DM, Javitch JA, Christopoulos A, Shi L, Lane JR. The action of a negative allosteric modulator at the dopamine D 2 receptor is dependent upon sodium ions. Sci Rep 2018; 8:1208. [PMID: 29352161 PMCID: PMC5775417 DOI: 10.1038/s41598-018-19642-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/19/2017] [Indexed: 01/11/2023] Open
Abstract
Sodium ions (Na+) allosterically modulate the binding of orthosteric agonists and antagonists to many class A G protein-coupled receptors, including the dopamine D2 receptor (D2R). Experimental and computational evidences have revealed that this effect is mediated by the binding of Na+ to a conserved site located beneath the orthosteric binding site (OBS). SB269652 acts as a negative allosteric modulator (NAM) of the D2R that adopts an extended bitopic pose, in which the tetrahydroisoquinoline moiety interacts with the OBS and the indole-2-carboxamide moiety occupies a secondary binding pocket (SBP). In this study, we find that the presence of a Na+ within the conserved Na+-binding pocket is required for the action of SB269652. Using fragments of SB269652 and novel full-length analogues, we show that Na+ is required for the high affinity binding of the tetrahydroisoquinoline moiety within the OBS, and that the interaction of the indole-2-carboxamide moiety with the SBP determines the degree of Na+-sensitivity. Thus, we extend our understanding of the mode of action of this novel class of NAM by showing it acts synergistically with Na+ to modulate the binding of orthosteric ligands at the D2R, providing opportunities for fine-tuning of modulatory effects in future allosteric drug design efforts.
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Affiliation(s)
- Christopher J Draper-Joyce
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Ravi Kumar Verma
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland, 21224, United States
| | - Mayako Michino
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland, 21224, United States.,Tri-Institutional Therapeutics Discovery Institute, 413 E 69th St, New York, NY, 10021, United States
| | - Jeremy Shonberg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Anitha Kopinathan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Carmen Klein Herenbrink
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Ara M Abramyan
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland, 21224, United States
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Jonathan A Javitch
- Departments of Psychiatry and Pharmacology, New York State Psychiatric Institute, New York, New York, 10032, United States.,College of Physicians and Surgeons, Columbia University, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York, 10032, United States
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland, 21224, United States.
| | - J Robert Lane
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia.
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Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. Sci Rep 2018; 8:897. [PMID: 29343833 PMCID: PMC5772633 DOI: 10.1038/s41598-018-19345-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/27/2017] [Indexed: 12/20/2022] Open
Abstract
The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments. We overcame the limitations of static docking by using large-scale high-throughput molecular dynamics (MD) simulations and Markov state models (MSMs) to determine an alternative pose consistent with the mutation data. The new pose maintains critical interactions observed in the D3R/eticlopride X-ray crystal structure and suggests that a cryptic pocket forms due to the shift of a highly conserved residue, F6.52. Our study highlights the importance of GPCR dynamics to understand ligand binding and provides new opportunities for drug discovery.
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Verma RK, Abramyan AM, Michino M, Free RB, Sibley DR, Javitch JA, Lane JR, Shi L. The E2.65A mutation disrupts dynamic binding poses of SB269652 at the dopamine D2 and D3 receptors. PLoS Comput Biol 2018; 14:e1005948. [PMID: 29337986 PMCID: PMC5786319 DOI: 10.1371/journal.pcbi.1005948] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/26/2018] [Accepted: 12/30/2017] [Indexed: 12/15/2022] Open
Abstract
The dopamine D2 and D3 receptors (D2R and D3R) are important targets for antipsychotics and for the treatment of drug abuse. SB269652, a bitopic ligand that simultaneously binds both the orthosteric binding site (OBS) and a secondary binding pocket (SBP) in both D2R and D3R, was found to be a negative allosteric modulator. Previous studies identified Glu2.65 in the SBP to be a key determinant of both the affinity of SB269652 and the magnitude of its cooperativity with orthosteric ligands, as the E2.65A mutation decreased both of these parameters. However, the proposed hydrogen bond (H-bond) between Glu2.65 and the indole moiety of SB269652 is not a strong interaction, and a structure activity relationship study of SB269652 indicates that this H-bond may not be the only element that determines its allosteric properties. To understand the structural basis of the observed phenotype of E2.65A, we carried out molecular dynamics simulations with a cumulative length of ~77 μs of D2R and D3R wild-type and their E2.65A mutants bound to SB269652. In combination with Markov state model analysis and by characterizing the equilibria of ligand binding modes in different conditions, we found that in both D2R and D3R, whereas the tetrahydroisoquinoline moiety of SB269652 is stably bound in the OBS, the indole-2-carboxamide moiety is dynamic and only intermittently forms H-bonds with Glu2.65. Our results also indicate that the E2.65A mutation significantly affects the overall shape and size of the SBP, as well as the conformation of the N terminus. Thus, our findings suggest that the key role of Glu2.65 in mediating the allosteric properties of SB269652 extends beyond a direct interaction with SB269652, and provide structural insights for rational design of SB269652 derivatives that may retain its allosteric properties. G protein-coupled receptors (GPCRs) are targets of more than 25% of prescription drugs on the market. Due to their critical roles in human physiology, competitive modulation of these receptors has been found to be associated with many undesired side effects. Allosteric modulation holds the promise of retaining normal receptor function and improving selectivity. However, the underlying molecular mechanisms of the allosteric modulation of GPCRs have remained largely uncharted. The dopamine D2-like receptors have been implicated in voluntary movement, reward, sleep, learning, and memory. Based on previous experimental findings, we computationally characterized the binding of a negative allosteric modulator of dopamine D2 and D3 receptors, and revealed the dynamic binding mode of this modulator in a secondary binding pocket (SBP) of the receptors. Our results highlight the key role of a Glu in mediating the allosteric properties of the modulator by shaping the dynamically formed SBP, and shed light on rational design and optimization of allosteric modulators of GPCRs.
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Affiliation(s)
- Ravi Kumar Verma
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States
| | - Ara M. Abramyan
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States
| | - Mayako Michino
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States
| | - R. Benjamin Free
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States
| | - David R. Sibley
- Molecular Neuropharmacology Section, National Institute of Neurologic Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States
| | - Jonathan A. Javitch
- Departments of Psychiatry and Pharmacology, College of Physicians and Surgeons, Columbia University, New York, New York, United States
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York, United States
| | - J. Robert Lane
- Drug Discovery Biology, Department of Pharmacology and Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), Parkville, Victoria, Australia
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse—Intramural Research Program, National Institutes of Health, Baltimore, Maryland, United States
- * E-mail:
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45
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Draper-Joyce CJ, Michino M, Verma RK, Klein Herenbrink C, Shonberg J, Kopinathan A, Scammells PJ, Capuano B, Thal DM, Javitch JA, Christopoulos A, Shi L, Lane JR. The structural determinants of the bitopic binding mode of a negative allosteric modulator of the dopamine D 2 receptor. Biochem Pharmacol 2018; 148:315-328. [PMID: 29325769 DOI: 10.1016/j.bcp.2018.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/02/2018] [Indexed: 01/11/2023]
Abstract
SB269652 is a negative allosteric modulator of the dopamine D2 receptor (D2R) yet possesses structural similarity to ligands with a competitive mode of interaction. In this study, we aimed to understand the ligand-receptor interactions that confer its allosteric action. We combined site-directed mutagenesis with molecular dynamics simulations using both SB269652 and derivatives from our previous structure activity studies. We identify residues within the conserved orthosteric binding site (OBS) and a secondary binding pocket (SBP) that determine affinity and cooperativity. Our results indicate that interaction with the SBP is a requirement for allosteric pharmacology, but that both competitive and allosteric derivatives of SB269652 can display sensitivity to the mutation of a glutamate residue (E952.65) within the SBP. Our findings provide the molecular basis for the differences in affinity between SB269652 derivatives, and reveal how changes to interactions made by the primary pharmacophore of SB269652 in the orthosteric pocket can confer changes in the interactions made by the secondary pharmacophore in the SBP. Our insights provide a structure-activity framework towards rational optimization of bitopic ligands for D2R with tailored competitive versus allosteric properties.
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Affiliation(s)
- Christopher J Draper-Joyce
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Mayako Michino
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Ravi Kumar Verma
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - Carmen Klein Herenbrink
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Jeremy Shonberg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Anitha Kopinathan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Jonathan A Javitch
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York State Psychiatric Institute, New York, NY 10032, United States; Department of Pharmacology, College of Physicians and Surgeons, Columbia University, New York State Psychiatric Institute, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States.
| | - J Robert Lane
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia.
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Abramyan AM, Stolzenberg S, Li Z, Loland CJ, Noé F, Shi L. The Isomeric Preference of an Atypical Dopamine Transporter Inhibitor Contributes to Its Selection of the Transporter Conformation. ACS Chem Neurosci 2017; 8:1735-1746. [PMID: 28441487 DOI: 10.1021/acschemneuro.7b00094] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cocaine, a widely abused psychostimulant, inhibits the dopamine transporter (DAT) by trapping the protein in an outward-open conformation, whereas atypical DAT inhibitors such as benztropine have low abuse liability and prefer less outward-open conformations. Here, we use a spectrum of computational modeling and simulation approaches to obtain the underlying molecular mechanism in atomistic detail. Interestingly, our quantum mechanical calculations and molecular dynamics (MD) simulations suggest that a benztropine derivative JHW007 prefers a different stereoisomeric conformation of tropane in binding to DAT compared to that of a cocaine derivative, CFT. To further investigate the different inhibition mechanisms of DAT, we carried out MD simulations in combination with Markov state modeling analysis of wild-type and Y156F DAT in the absence of any ligand or the presence of CFT or JHW007. Our results indicate that the Y156F mutation and CFT shift the conformational equilibrium toward an outward-open conformation, whereas JHW007 prefers an inward-occluded conformation. Our findings reveal the mechanistic details of DAT inhibition by JHW007 at the atomistic level, which provide clues for rational design of atypical inhibitors.
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Affiliation(s)
- Ara M. Abramyan
- Computational
Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications
Discovery Branch, NIH/NIDA/IRP, Baltimore, Maryland 21224, United States
| | - Sebastian Stolzenberg
- Computational
Molecular Biology group, Institute for Mathematics, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Zheng Li
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
| | - Claus J. Loland
- Molecular
Neuropharmacology Group, Department of Neuroscience and Pharmacology,
The Faculty of Health Sciences, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Frank Noé
- Computational
Molecular Biology group, Institute for Mathematics, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Lei Shi
- Computational
Chemistry and Molecular Biophysics Unit, Molecular Targets and Medications
Discovery Branch, NIH/NIDA/IRP, Baltimore, Maryland 21224, United States
- Department
of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States
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