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Dutta S, Shukla D. Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting method. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.29.560261. [PMID: 37873328 PMCID: PMC10592854 DOI: 10.1101/2023.09.29.560261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
New psychoactive substances (NPS) targeting cannabinoid receptor 1 pose a significant threat to society as recreational abusive drugs that have pronounced physiological side effects. These greater adverse effects compared to classical cannabinoids have been linked to the higher downstream β-arrestin signaling. Thus, understanding the mechanism of differential signaling will reveal important structure-activity relationship essential for identifying and potentially regulating NPS molecules. In this study, we simulate the slow (un)binding process of NPS MDMB-Fubinaca and classical cannabinoid HU-210 from CB1 using multi-ensemble simulation to decipher the effects of ligand binding dynamics on downstream signaling. The transition-based reweighing method is used for the estimation of transition rates and underlying thermodynamics of (un)binding processes of ligands with nanomolar affinities. Our analyses reveal major interaction differences with transmembrane TM7 between NPS and classical cannabinoids. A variational autoencoder-based approach, neural relational inference (NRI), is applied to assess the allosteric effects on intracellular regions attributable to variations in binding pocket interactions. NRI analysis indicate a heightened level of allosteric control of NPxxY motif for NPS-bound receptors, which contributes to the higher probability of formation of a crucial triad interaction (Y7.53-Y5.58-T3.46) necessary for stronger β-arrestin signaling. Hence, in this work, MD simulation, data-driven statistical methods, and deep learning point out the structural basis for the heightened physiological side effects associated with NPS, contributing to efforts aimed at mitigating their public health impact.
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Affiliation(s)
- Soumajit Dutta
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
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2
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Liu Y, Xu Y, Xu Y, Zhao Z, Cheng GJ, Ren R, Chiang YC. Identifying Residues for Substrate Recognition in Human GPAT4 by Molecular Dynamics Simulations. Int J Mol Sci 2024; 25:3729. [PMID: 38612541 PMCID: PMC11011501 DOI: 10.3390/ijms25073729] [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: 01/25/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the first step in triacylglycerol synthesis. Understanding its substrate recognition mechanism may help to design drugs to regulate the production of glycerol lipids in cells. In this work, we investigate how the native substrate, glycerol-3-phosphate (G3P), and palmitoyl-coenzyme A (CoA) bind to the human GPAT isoform GPAT4 via molecular dynamics simulations (MD). As no experimentally resolved GPAT4 structure is available, the AlphaFold model is employed to construct the GPAT4-substrate complex model. Using another isoform, GPAT1, we demonstrate that once the ligand binding is properly addressed, the AlphaFold complex model can deliver similar results to the experimentally resolved structure in MD simulations. Following the validated protocol of complex construction, we perform MD simulations using the GPAT4-substrate complex. Our simulations reveal that R427 is an important residue in recognizing G3P via a stable salt bridge, but its motion can bring the ligand to different binding hotspots on GPAT4. Such high flexibility can be attributed to the flexible region that exists only on GPAT4 and not on GPAT1. Our study reveals the substrate recognition mechanism of GPAT4 and hence paves the way towards designing GPAT4 inhibitors.
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Affiliation(s)
- Yulan Liu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yunong Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yinuo Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Zhihao Zhao
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Gui-Juan Cheng
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Ruobing Ren
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200438, China
- Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - Ying-Chih Chiang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
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Zantza I, Pyrris Y, Raniolo S, Papadaki GF, Lambrinidis G, Limongelli V, Diallinas G, Mikros E. Uracil/H + Symport by FurE Refines Aspects of the Rocking-bundle Mechanism of APC-type Transporters. J Mol Biol 2023; 435:168226. [PMID: 37544358 DOI: 10.1016/j.jmb.2023.168226] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Transporters mediate the uptake of solutes, metabolites and drugs across the cell membrane. The eukaryotic FurE nucleobase/H+ symporter of Aspergillus nidulans has been used as a model protein to address structure-function relationships in the APC transporter superfamily, members of which are characterized by the LeuT-fold and seem to operate by the so-called 'rocking-bundle' mechanism. In this study, we reveal the binding mode, translocation and release pathway of uracil/H+ by FurE using path collective variable, funnel metadynamics and rational mutational analysis. Our study reveals a stepwise, induced-fit, mechanism of ordered sequential transport of proton and uracil, which in turn suggests that FurE, functions as a multi-step gated pore, rather than employing 'rocking' of compact domains, as often proposed for APC transporters. Finally, our work supports that specific residues of the cytoplasmic N-tail are involved in substrate translocation, in line with their essentiality for FurE function.
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Affiliation(s)
- Iliana Zantza
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
| | - Yiannis Pyrris
- Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15781, Greece.
| | - Stefano Raniolo
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano 6900, Switzerland.
| | - Georgia F Papadaki
- Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15781, Greece
| | - George Lambrinidis
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece.
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), Lugano 6900, Switzerland; Department of Pharmacy, University of Naples "Federico II", Naples 80131, Italy.
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15781, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion 70013, Greece.
| | - Emmanuel Mikros
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15771, Greece; Athena Research and Innovation Center in Information Communication & Knowledge Technologies, Marousi 15125, Greece.
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Sharma R, Singh S, Whiting ZM, Molitor M, Vernall AJ, Grimsey NL. Novel Cannabinoid Receptor 2 (CB2) Low Lipophilicity Agonists Produce Distinct cAMP and Arrestin Signalling Kinetics without Bias. Int J Mol Sci 2023; 24:ijms24076406. [PMID: 37047385 PMCID: PMC10094510 DOI: 10.3390/ijms24076406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Cannabinoid Receptor 2 (CB2) is a promising target for treating inflammatory diseases. We designed derivatives of 3-carbamoyl-2-pyridone and 1,8-naphthyridin-2(1H)-one-3-carboxamide CB2-selective agonists with reduced lipophilicity. The new compounds were measured for their affinity (radioligand binding) and ability to elicit cyclic adenosine monophosphate (cAMP) signalling and β-arrestin-2 translocation with temporal resolution (BRET-based biosensors). For the 3-carbamoyl-2-pyridone derivatives, we found that modifying the previously reported compound UOSS77 (also known as S-777469) by appending a PEG2-alcohol via a 3-carbomylcyclohexyl carboxamide (UOSS75) lowered lipophilicity, and preserved binding affinity and signalling profile. The 1,8-naphthyridin-2(1H)-one-3-carboxamide UOMM18, containing a cis configuration at the 3-carboxamide cyclohexyl and with an alcohol on the 4-position of the cyclohexyl, had lower lipophilicity but similar CB2 affinity and biological activity to previously reported compounds of this class. Relative to CP55,940, the new compounds acted as partial agonists and did not exhibit signalling bias. Interestingly, while all compounds shared similar temporal trajectories for maximal efficacy, differing temporal trajectories for potency were observed. Consequently, when applied at sub-maximal concentrations, CP55,940 tended to elicit sustained (cAMP) or increasing (arrestin) responses, whereas responses to the new compounds tended to be transient (cAMP) or sustained (arrestin). In future studies, the compounds characterised here may be useful in elucidating the consequences of differential temporal signalling profiles on CB2-mediated physiological responses.
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Affiliation(s)
- Raahul Sharma
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand; (R.S.)
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand
| | - Sameek Singh
- Department of Chemistry, University of Otago, Dunedin 9016, New Zealand (M.M.); (A.J.V.)
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zak M. Whiting
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand; (R.S.)
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand
| | - Maximilian Molitor
- Department of Chemistry, University of Otago, Dunedin 9016, New Zealand (M.M.); (A.J.V.)
- Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt, Germany
| | - Andrea J. Vernall
- Department of Chemistry, University of Otago, Dunedin 9016, New Zealand (M.M.); (A.J.V.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Natasha L. Grimsey
- Department of Pharmacology and Clinical Pharmacology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand; (R.S.)
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
- Correspondence:
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Zargari F, Nikfarjam Z, Nakhaei E, Ghorbanipour M, Nowroozi A, Amiri A. Study of tyramine-binding mechanism and insecticidal activity of oil extracted from Eucalyptus against Sitophilus oryzae. Front Chem 2022; 10:964700. [PMID: 36212071 PMCID: PMC9538504 DOI: 10.3389/fchem.2022.964700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 12/02/2022] Open
Abstract
The rice weevil, Sitophilus oryzae (L.), is a major pest of stored grains throughout the world, which causes quantitative and qualitative losses of food commodities. Eucalyptus essential oils (EOs) possess insecticidal and repellent properties, which make them a potential option for insect control in stored grains with environmentally friendly properties. In the current study, the binding mechanism of tyramine (TA) as a control compound has been investigated by funnel metadynamics (FM) simulation toward the homology model of tyramine1 receptor (TyrR) to explore its binding mode and key residues involved in the binding mechanism. EO compounds have been extracted from the leaf and flower part of Eucalyptus camaldulensis and characterized by GC/MS, and their effectiveness has been evaluated by molecular docking and conventional molecular dynamic (CMD) simulation toward the TyrR model. The FM results suggested that Asp114 followed by Asp80, Asn91, and Asn427 are crucial residues in the binding and the functioning of TA toward TyrR in Sitophilus Oryzae. The GC/MS analysis confirmed a total of 54 and 31 constituents in leaf and flower, respectively, where most of the components (29) are common in both groups. This analysis also revealed the significant concentration of Eucalyptus and α-pinene in leaves and flower EOs. The docking followed by CMD was performed to find the most effective compound in Eucalyptus EOs. In this regard, butanoic acid, 3-methyl-, 3-methyl butyl ester (B12) and 2-Octen-1-ol, 3,7-dimethyl- (B23) from leaf and trans- β-Ocimene (G04) from flower showed the maximum dock score and binding free energy, making them the leading candidates to replace tyramine in TyrR. The MM-PB/GBSA and MD analysis proved that the B12 structure is the most effective compound in inhibition of TyrR.
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Affiliation(s)
- Farshid Zargari
- Pharmacology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), Zahedan, Iran
| | - Zahra Nikfarjam
- Department of Physical & Computational Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
- *Correspondence: Zahra Nikfarjam,
| | - Ebrahim Nakhaei
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), Zahedan, Iran
| | - Masoumeh Ghorbanipour
- Department of Physical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Alireza Nowroozi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), Zahedan, Iran
| | - Azam Amiri
- College of Geography and Environmental Planning, University of Sistan and Baluchestan, Zahedan, Iran
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6
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Mechanistic Origin of Partial Agonism of Tetrahydrocannabinol for Cannabinoid Receptors. J Biol Chem 2022; 298:101764. [PMID: 35227761 PMCID: PMC8965160 DOI: 10.1016/j.jbc.2022.101764] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 01/14/2023] Open
Abstract
Cannabinoid receptor 1 (CB1) is a therapeutically relevant drug target for controlling pain, obesity, and other central nervous system disorders. However, full agonists and antagonists of CB1 have been reported to cause serious side effects in patients. Therefore, partial agonists have emerged as a viable alternative as they can mitigate overstimulation and side effects. One of the key bottlenecks in the design of partial agonists, however, is the lack of understanding of the molecular mechanism of partial agonism itself. In this study, we examine two mechanistic hypotheses for the origin of partial agonism in cannabinoid receptors and predict the mechanistic basis of partial agonism exhibited by Δ9-Tetrahydrocannabinol (THC) against CB1. In particular, we inspect whether partial agonism emerges from the ability of THC to bind in both agonist and antagonist-binding poses or from its ability to only partially activate the receptor. We used extensive molecular dynamics simulations and Markov state modeling to capture the THC binding in both antagonist and agonist-binding poses in the CB1 receptor. Furthermore, we predict that binding of THC in the agonist-binding pose leads to rotation of toggle switch residues and causes partial outward movement of intracellular transmembrane helix 6 (TM6). Our simulations also suggest that the alkyl side chain of THC plays a crucial role in determining partial agonism by stabilizing the ligand in the agonist and antagonist-like poses within the pocket. Taken together, this study provides important insights into the mechanistic origin of the partial agonism of THC.
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Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Morales P, Navarro G, Gómez‐Autet M, Redondo L, Fernández‐Ruiz J, Pérez‐Benito L, Cordomí A, Pardo L, Franco R, Jagerovic N. Discovery of Homobivalent Bitopic Ligands of the Cannabinoid CB 2 Receptor*. Chemistry 2020; 26:15839-15842. [PMID: 32794211 PMCID: PMC7756656 DOI: 10.1002/chem.202003389] [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: 07/19/2020] [Revised: 08/12/2020] [Indexed: 12/21/2022]
Abstract
Single chemical entities with potential to simultaneously interact with two binding sites are emerging strategies in medicinal chemistry. We have designed, synthesized and functionally characterized the first bitopic ligands for the CB2 receptor. These compounds selectively target CB2 versus CB1 receptors. Their binding mode was studied by molecular dynamic simulations and site-directed mutagenesis.
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Affiliation(s)
- Paula Morales
- Medicinal Chemistry InstituteSpanish Research CouncilMadridSpain
| | - Gemma Navarro
- Department of Biochemistry and Physiology, CIBERNEDFaculty of Pharmacy and Food SciencesUniversitat de BarcelonaBarcelonaSpain
| | - Marc Gómez‐Autet
- Laboratory of Computational Medicine, Biostatistics UnitFaculty of MedicineUniversitat Autónoma de BarcelonaBarcelonaSpain
| | - Laura Redondo
- Medicinal Chemistry InstituteSpanish Research CouncilMadridSpain
| | - Javier Fernández‐Ruiz
- Department of Biochemistry and Molecular Biology, CIBERNED, IRYCISFaculty of MedicineUniversidad Complutense de MadridMadridSpain
| | - Laura Pérez‐Benito
- Laboratory of Computational Medicine, Biostatistics UnitFaculty of MedicineUniversitat Autónoma de BarcelonaBarcelonaSpain
- Present address: Computational ChemistryJanssen Research & Development, Janssen Pharmaceutica N.V.Belgium
| | - Arnau Cordomí
- Laboratory of Computational Medicine, Biostatistics UnitFaculty of MedicineUniversitat Autónoma de BarcelonaBarcelonaSpain
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics UnitFaculty of MedicineUniversitat Autónoma de BarcelonaBarcelonaSpain
| | - Rafael Franco
- Department of Biochemistry and Physiology, CIBERNEDFaculty of Pharmacy and Food SciencesUniversitat de BarcelonaBarcelonaSpain
- Department of Biochemistry and Molecular Biology, CIBERNEDSchool of ChemistryUniversitat de BarcelonaBarcelonaSpain
| | - Nadine Jagerovic
- Medicinal Chemistry InstituteSpanish Research CouncilMadridSpain
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Conrad M, Söldner CA, Miao Y, Sticht H. Agonist Binding and G Protein Coupling in Histamine H 2 Receptor: A Molecular Dynamics Study. Int J Mol Sci 2020; 21:ijms21186693. [PMID: 32932742 PMCID: PMC7554837 DOI: 10.3390/ijms21186693] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
The histamine H2 receptor (H2R) plays an important role in the regulation of gastric acid secretion. Therefore, it is a main drug target for the treatment of gastroesophageal reflux or peptic ulcer disease. However, there is as of yet no 3D-structural information available hampering a mechanistic understanding of H2R. Therefore, we created a model of the histamine-H2R-Gs complex based on the structure of the ternary complex of the β2-adrenoceptor and investigated the conformational stability of this active GPCR conformation. Since the physiologically relevant motions with respect to ligand binding and conformational changes of GPCRs can only partly be assessed on the timescale of conventional MD (cMD) simulations, we also applied metadynamics and Gaussian accelerated molecular dynamics (GaMD) simulations. A multiple walker metadynamics simulation in combination with cMD was applied for the determination of the histamine binding mode. The preferential binding pose detected is in good agreement with previous data from site directed mutagenesis and provides a basis for rational ligand design. Inspection of the H2R-Gs interface reveals a network of polar interactions that may contribute to H2R coupling selectivity. The cMD and GaMD simulations demonstrate that the active conformation is retained on a μs-timescale in the ternary histamine-H2R-Gs complex and in a truncated complex that contains only Gs helix α5 instead of the entire G protein. In contrast, histamine alone is unable to stabilize the active conformation, which is in line with previous studies of other GPCRs.
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Affiliation(s)
- Marcus Conrad
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Christian A. Söldner
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Yinglong Miao
- Department of Computational Biology and Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA;
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany; (M.C.); (C.A.S.)
- Correspondence:
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10
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Ibrahim P, Clark T. Metadynamics simulations of ligand binding to GPCRs. Curr Opin Struct Biol 2019; 55:129-137. [PMID: 31100549 DOI: 10.1016/j.sbi.2019.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/28/2019] [Accepted: 04/05/2019] [Indexed: 11/17/2022]
Abstract
Recent developments in metadynamics simulation techniques for ligand binding to Class A GPCRs are described and the results obtained elucidated. The computational protocol makes good use of modern massively parallel hardware, making simulations of the binding/unbinding process routine. The simulations reveal unprecedented details of the ligand-binding pathways, including multiple binding sites in many cases. Free energies of binding are reproduced very well and the simulations allow prediction of the efficacy (agonist, antagonist etc.) of ligands.
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Affiliation(s)
- Passainte Ibrahim
- Computer-Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany
| | - Timothy Clark
- Computer-Chemistry Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany.
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Lu D, Immadi SS, Wu Z, Kendall DA. Translational potential of allosteric modulators targeting the cannabinoid CB 1 receptor. Acta Pharmacol Sin 2019; 40:324-335. [PMID: 30333554 DOI: 10.1038/s41401-018-0164-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022] Open
Abstract
The cannabinoid type-1 (CB1) receptor, a G-protein-coupled receptor, is an attractive target for drug discovery due to its involvement in many physiological processes. Historically, drug discovery efforts targeting the CB1 receptor have focused on the development of orthosteric ligands that interact with the active site to which endogenous cannabinoids bind. Research performed over the last several decades has revealed substantial difficulties in translating CB1 orthosteric ligands into druggable candidates. The difficulty is mainly due to the adverse effects associated with orthosteric CB1 ligands. Recent discoveries of allosteric CB1 modulators provide tremendous opportunities to develop CB1 ligands with novel mechanisms of action; these ligands may potentially improve the pharmacological effects and enhance drug safety in treating the disorders by regulating the functions of the CB1 receptor. In this paper, we review and summarize the complex pharmacological profiles of each class of CB1 allosteric modulators, the development of new classes of CB1 allosteric modulators and the results from in vivo assessments of their therapeutic value.
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