1
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Stein C. Effects of pH on opioid receptor activation and implications for drug design. Biophys J 2024:S0006-3495(24)00446-6. [PMID: 38970252 DOI: 10.1016/j.bpj.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/29/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024] Open
Abstract
G-protein-coupled receptors are integral membrane proteins that transduce chemical signals from the extracellular matrix into the cell. Traditional drug design has considered ligand-receptor interactions only under normal conditions. However, studies on opioids indicate that such interactions are very different in diseased tissues. In such microenvironments, protons play an important role in structural and functional alterations of both ligands and receptors. The pertinent literature strongly suggests that future drug design should take these aspects into account in order to reduce adverse side effects while preserving desired effects of novel compounds.
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Affiliation(s)
- Christoph Stein
- Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Experimental Anaesthesiology, Berlin, Germany.
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2
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Velloso JPL, Kovacs AS, Pires DEV, Ascher DB. AI-driven GPCR analysis, engineering, and targeting. Curr Opin Pharmacol 2024; 74:102427. [PMID: 38219398 DOI: 10.1016/j.coph.2023.102427] [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: 10/26/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024]
Abstract
This article investigates the role of recent advances in Artificial Intelligence (AI) to revolutionise the study of G protein-coupled receptors (GPCRs). AI has been applied to many areas of GPCR research, including the application of machine learning (ML) in GPCR classification, prediction of GPCR activation levels, modelling GPCR 3D structures and interactions, understanding G-protein selectivity, aiding elucidation of GPCRs structures, and drug design. Despite progress, challenges in predicting GPCR structures and addressing the complex nature of GPCRs remain, providing avenues for future research and development.
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Affiliation(s)
- João P L Velloso
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Aaron S Kovacs
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia.
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.
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3
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Kumar S, Teli MK, Kim MH. GPCR-IPL score: multilevel featurization of GPCR-ligand interaction patterns and prediction of ligand functions from selectivity to biased activation. Brief Bioinform 2024; 25:bbae105. [PMID: 38517694 PMCID: PMC10959162 DOI: 10.1093/bib/bbae105] [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: 11/27/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/24/2024] Open
Abstract
G-protein-coupled receptors (GPCRs) mediate diverse cell signaling cascades after recognizing extracellular ligands. Despite the successful history of known GPCR drugs, a lack of mechanistic insight into GPCR challenges both the deorphanization of some GPCRs and optimization of the structure-activity relationship of their ligands. Notably, replacing a small substituent on a GPCR ligand can significantly alter extracellular GPCR-ligand interaction patterns and motion of transmembrane helices in turn to occur post-binding events of the ligand. In this study, we designed 3D multilevel features to describe the extracellular interaction patterns. Subsequently, these 3D features were utilized to predict the post-binding events that result from conformational dynamics from the extracellular to intracellular areas. To understand the adaptability of GPCR ligands, we collected the conformational information of flexible residues during binding and performed molecular featurization on a broad range of GPCR-ligand complexes. As a result, we developed GPCR-ligand interaction patterns, binding pockets, and ligand features as score (GPCR-IPL score) for predicting the functional selectivity of GPCR ligands (agonism versus antagonism), using the multilevel features of (1) zoomed-out 'residue level' (for flexible transmembrane helices of GPCRs), (2) zoomed-in 'pocket level' (for sophisticated mode of action) and (3) 'atom level' (for the conformational adaptability of GPCR ligands). GPCR-IPL score demonstrated reliable performance, achieving area under the receiver operating characteristic of 0.938 and area under the precision-recall curve of 0.907 (available in gpcr-ipl-score.onrender.com). Furthermore, we used the molecular features to predict the biased activation of downstream signaling (Gi/o, Gq/11, Gs and β-arrestin) as well as the functional selectivity. The resulting models are interpreted and applied to out-of-set validation with three scenarios including the identification of a new MRGPRX antagonist.
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Affiliation(s)
- Surendra Kumar
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, 191 Hambakmoeiro, Yeonsu-gu, Incheon, Republic of Korea
| | - Mahesh K Teli
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, 191 Hambakmoeiro, Yeonsu-gu, Incheon, Republic of Korea
| | - Mi-hyun Kim
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, 191 Hambakmoeiro, Yeonsu-gu, Incheon, Republic of Korea
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4
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What Makes GPCRs from Different Families Bind to the Same Ligand? Biomolecules 2022; 12:biom12070863. [PMID: 35883418 PMCID: PMC9313020 DOI: 10.3390/biom12070863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/09/2022] [Accepted: 06/19/2022] [Indexed: 12/10/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of cell-surface receptor proteins with important functions in signal transduction and often serve as therapeutic drug targets. With the rapidly growing public data on three dimensional (3D) structures of GPCRs and GPCR-ligand interactions, computational prediction of GPCR ligand binding becomes a convincing option to high throughput screening and other experimental approaches during the beginning phases of ligand discovery. In this work, we set out to computationally uncover and understand the binding of a single ligand to GPCRs from several different families. Three-dimensional structural comparisons of the GPCRs that bind to the same ligand revealed local 3D structural similarities and often these regions overlap with locations of binding pockets. These pockets were found to be similar (based on backbone geometry and side-chain orientation using APoc), and they correlate positively with electrostatic properties of the pockets. Moreover, the more similar the pockets, the more likely a ligand binding to the pockets will interact with similar residues, have similar conformations, and produce similar binding affinities across the pockets. These findings can be exploited to improve protein function inference, drug repurposing and drug toxicity prediction, and accelerate the development of new drugs.
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5
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Engineered Allosteric Regulation of Protein Function. J Mol Biol 2022; 434:167620. [PMID: 35513109 DOI: 10.1016/j.jmb.2022.167620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/27/2022] [Accepted: 04/26/2022] [Indexed: 11/20/2022]
Abstract
Allosteric regulation of proteins has been utilized to study various aspects of cell signaling, from unicellular events to organism-wide phenotypes. However, traditional methods of allosteric regulation, such as constitutively active mutants and inhibitors, lack tight spatiotemporal control. This often leads to unintended signaling consequences that interfere with data interpretation. To overcome these obstacles, researchers employed protein engineering approaches that enable tight control of protein function through allosteric mechanisms. These methods provide high specificity as well as spatial and temporal precision in regulation of protein activity in vitro and in vivo. In this review, we focus on the recent advancements in engineered allosteric regulation and discuss the various bioengineered allosteric techniques available now, from chimeric GPCRs to chemogenetic and optogenetic switches. We highlight the benefits and pitfalls of each of these techniques as well as areas in which future improvements can be made. Additionally, we provide a brief discussion on implementation of engineered allosteric regulation approaches, demonstrating that these tools can shed light on elusive biological events and have the potential to be utilized in precision medicine.
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6
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In Silico Study Approach on a Series of 50 Polyphenolic Compounds in Plants; A Comparison on the Bioavailability and Bioactivity Data. Molecules 2022; 27:molecules27041413. [PMID: 35209203 PMCID: PMC8878759 DOI: 10.3390/molecules27041413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/31/2022] [Accepted: 02/17/2022] [Indexed: 11/17/2022] Open
Abstract
Fifty (50) phytocompounds from several subclasses of polyphenols, chosen based on their abundance in the plant world, were analyzed through density functional methods, using computational tools to evaluate their oral availability and particular bioactivity on several cell modulators; key descriptors and molecular features related to the electron density and electrostatic potential for the lowest energy conformers of the investigated molecules were computed. An analysis of the bioactivity scores towards six cell modulators (GPCR ligand, ion channel modulator, kinase inhibitor, nuclear receptor ligand, protease inhibitor and enzyme inhibitor) was also achieved, in the context of investigating their potential side effects on the human digestive processes. Summarizing, computational results confirmed in vivo and in vitro data regarding the high bioavailability of soy isoflavones and better bioavailability of free aglycones in comparison with their esterified and glycosylated forms. However, by a computational approach analyzing Lipinski’s rule, apigenin and apigenin-7-O-rhamnoside, naringenin, hesperetin, genistein, daidzin, biochanin A and formonetin in the flavonoid series and all hydroxycinnamic acids and all hydroxybenzoic acids excepting ellagic acid were proved to have the best bioavailability data; rhamnoside derivatives, the predominant glycosides in green plants, which were reported to have the lowest bioavailability values by in vivo studies, were revealed to have the best bioavailability data among the studied flavonoids in the computational approach. Results of in silico screening on the phenolic derivatives series also revealed their real inhibitory potency on the six parameters studied, showing a remarkable similitude between the flavonoid series, while flavonoids were more powerful natural cell modulators than the phenyl carboxylic acids tested. Thus, it can be concluded that there is a need for supplementation with digestive enzymes, mainly in the case of individuals with low digestive efficiency, to obtain the best health benefits of polyphenols in humans.
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7
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Conrad M, Söldner CA, Sticht H. Effect of Ions and Sequence Variants on the Antagonist Binding Properties of the Histamine H 1 Receptor. Int J Mol Sci 2022; 23:ijms23031420. [PMID: 35163341 PMCID: PMC8836275 DOI: 10.3390/ijms23031420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
The histamine H1 receptor (H1R) is a G protein-coupled receptor (GPCR) and represents a main target in the treatment of allergic reactions as well as inflammatory reactions and depressions. Although the overall effect of antagonists on H1 function has been extensively investigated, rather little is known about the potential modulatory effect of ions or sequence variants on antagonist binding. We investigated the dynamics of a phosphate ion present in the crystal structure and of a sodium ion, for which we determined the position in the allosteric pocket by metadynamics simulations. Both types of ions exhibit significant dynamics within their binding site; however, some key contacts remain stable over the simulation time, which might be exploited to develop more potent drugs targeting these sites. The dynamics of the ions is almost unaffected by the presence or absence of doxepin, as also reflected in their small effect (less than 1 kcal·mol-1) on doxepin binding affinity. We also examined the effect of four H1R sequence variants observed in the human population on doxepin binding. These variants cause a reduction in doxepin affinity of up to 2.5 kcal·mol-1, indicating that personalized medical treatments that take into account individual mutation patterns could increase precision in the dosage of GPCR-targeting drugs.
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Affiliation(s)
- Marcus Conrad
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Christian A. Söldner
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (C.A.S.)
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (M.C.); (C.A.S.)
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
- Correspondence:
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8
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Duraisamy K, Singh K, Kumar M, Lefranc B, Bonnafé E, Treilhou M, Leprince J, Chow BKC. P17 induces chemotaxis and differentiation of monocytes via MRGPRX2-mediated mast cell-line activation. J Allergy Clin Immunol 2022; 149:275-291. [PMID: 34111449 DOI: 10.1016/j.jaci.2021.04.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 03/29/2021] [Accepted: 04/23/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND P17, a peptide isolated from Tetramorium bicarinatum ant venom, is known to induce an alternative phenotype of human monocyte-derived macrophages via activation of an unknown G protein-coupled receptor (GPCR). OBJECTIVE We sought to investigate the mechanism of action and the immunomodulatory effects of P17 mediated through MRGPRX2 (Mas-related G protein-coupled receptor X2). METHODS To identify the GPCR for P17, we screened 314 GPCRs. Upon identification of MRGPRX2, a battery of in silico, in vitro, ex vivo, and in vivo assays along with the receptor mutation studies were performed. In particular, to investigate the immunomodulatory actions, we used β-hexosaminidase release assay, cytokine releases, quantification of mRNA expression, cell migration and differentiation assays, immunohistochemical labeling, hematoxylin and eosin, and immunofluorescence staining. RESULTS P17 activated MRGPRX2 in a dose-dependent manner in β-arrestin recruitment assay. In LAD2 cells, P17 induced calcium and β-hexosaminidase release. Quercetin- and short hairpin RNA-mediated knockdown of MRGPRX2 reduced P17-evoked β-hexosaminidase release. In silico and in vitro mutagenesis studies showed that residue Lys8 of P17 formed a cation-π interaction with the Phe172 of MRGPRX2 and [Ala8]P17 lost its activity partially. P17 activated LAD2 cells to recruit THP-1 and human monocytes in Transwell migration assay, whereas MRGPRX2-impaired LAD2 cells cannot. In addition, P17-treated LAD2 cells stimulated differentiation of THP-1 and human monocytes, as indicated by the enhanced expression of macrophage markers cluster of differentiation 11b and TNF-α by quantitative RT-PCR. Immunohistochemical and immunofluorescent staining suggested monocyte recruitment in mice ears injected with P17. CONCLUSIONS Our data provide novel structural information regarding the interaction of P17 with MRGPRX2 and intracellular pathways for its immunomodulatory action.
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Affiliation(s)
- Karthi Duraisamy
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Kailash Singh
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Mukesh Kumar
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Benjamin Lefranc
- INSERM U1239, PRIMACEN, IRIB, Normandy University, Rouen, France
| | - Elsa Bonnafé
- EA7417 BTSB, Université Fédérale Toulouse Midi-Pyrénées, INU Champollion, Albi, France
| | - Michel Treilhou
- EA7417 BTSB, Université Fédérale Toulouse Midi-Pyrénées, INU Champollion, Albi, France
| | - Jérôme Leprince
- INSERM U1239, PRIMACEN, IRIB, Normandy University, Rouen, France.
| | - Billy K C Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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9
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Zhu S, Wu M, Huang Z, An J. Trends in application of advancing computational approaches in GPCR ligand discovery. Exp Biol Med (Maywood) 2021; 246:1011-1024. [PMID: 33641446 PMCID: PMC8113737 DOI: 10.1177/1535370221993422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptors (GPCRs) comprise the most important superfamily of protein targets in current ligand discovery and drug development. GPCRs are integral membrane proteins that play key roles in various cellular signaling processes. Therefore, GPCR signaling pathways are closely associated with numerous diseases, including cancer and several neurological, immunological, and hematological disorders. Computer-aided drug design (CADD) can expedite the process of GPCR drug discovery and potentially reduce the actual cost of research and development. Increasing knowledge of biological structures, as well as improvements on computer power and algorithms, have led to unprecedented use of CADD for the discovery of novel GPCR modulators. Similarly, machine learning approaches are now widely applied in various fields of drug target research. This review briefly summarizes the application of rising CADD methodologies, as well as novel machine learning techniques, in GPCR structural studies and bioligand discovery in the past few years. Recent novel computational strategies and feasible workflows are updated, and representative cases addressing challenging issues on olfactory receptors, biased agonism, and drug-induced cardiotoxic effects are highlighted to provide insights into future GPCR drug discovery.
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Affiliation(s)
- Siyu Zhu
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
- Ciechanover Institute of Precision and Regenerative Medicine, School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Meixian Wu
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ziwei Huang
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
- Ciechanover Institute of Precision and Regenerative Medicine, School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen 518172, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jing An
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
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10
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Lima Neto JX, Bezerra KS, Barbosa ED, Oliveira JIN, Manzoni V, Soares-Rachetti VP, Albuquerque EL, Fulco UL. Exploring the Binding Mechanism of GABAB Receptor Agonists and Antagonists through in Silico Simulations. J Chem Inf Model 2019; 60:1005-1018. [DOI: 10.1021/acs.jcim.9b01025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José X. Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Emmanuel D. Barbosa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Jonas I. N. Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Vinícius Manzoni
- Instituto de Física, Universidade Federal do Alagoas, 57072-970 Maceió-AL, Brazil
| | - Vanessa P. Soares-Rachetti
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Eudenilson L. Albuquerque
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
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11
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Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S. Common activation mechanism of class A GPCRs. eLife 2019; 8:e50279. [PMID: 31855179 PMCID: PMC6954041 DOI: 10.7554/elife.50279] [Citation(s) in RCA: 305] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.
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Affiliation(s)
- Qingtong Zhou
- iHuman InstituteShanghaiTech UniversityShanghaiChina
| | - Dehua Yang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Meng Wu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yu Guo
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Wanjing Guo
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Li Zhong
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Antao Dai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Zhi-Jie Liu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Raymond C Stevens
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ming-Wei Wang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- School of PharmacyFudan UniversityShanghaiChina
| | - Suwen Zhao
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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12
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Federico S, Margiotta E, Paoletta S, Kachler S, Klotz KN, Jacobson KA, Pastorin G, Moro S, Spalluto G. Pyrazolo[4,3- e][1,2,4]triazolo[1,5- c]pyrimidines to develop functionalized ligands to target adenosine receptors: fluorescent ligands as an example. MEDCHEMCOMM 2019; 10:1094-1108. [PMID: 31391881 PMCID: PMC6644567 DOI: 10.1039/c9md00014c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/16/2019] [Indexed: 01/07/2023]
Abstract
A series of adenosine receptor antagonists bearing a reactive linker was developed. Functionalization of these derivatives is useful to easily obtain multi-target ligands, receptor probes, drug delivery systems, and diagnostic or theranostic systems. The pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine scaffold was chosen as a pharmacophore for the adenosine receptors. It was substituted at the 5 position with reactive linkers of different lengths. Then, these compounds were used to synthesise probes for the adenosine receptors by functionalization with a fluorescent moiety. Both series of compounds were evaluated for their binding at the four adenosine receptor subtypes. Different affinity and selectivity profiles were observed towards hA1, hA2A and hA3 adenosine receptors. In particular, fluorescent compounds behave as dual hA2A/hA3 ligands. Computational studies suggested different binding modes for developed compounds at the three receptors. Both molecular docking and supervised molecular dynamics (SuMD) simulations confirmed that the preferred binding mode at the single receptor was driven by the substitution present at the 5 position. Obtained results rationalized the compounds' binding profile at the adenosine receptors and pave the way for the development of more potent conjugable and conjugated ligands targeting these membrane receptors.
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Affiliation(s)
- Stephanie Federico
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , Via Licio Giorgeri 1 , 34127 Trieste , Italy .
| | - Enrico Margiotta
- Molecular Modeling Section (MMS) , Dipartimento di Scienze del Farmaco , Università degli Studi di Padova , Via F. Marzolo 5 , 35131 Padova , Italy
| | - Silvia Paoletta
- Molecular Modeling Section (MMS) , Dipartimento di Scienze del Farmaco , Università degli Studi di Padova , Via F. Marzolo 5 , 35131 Padova , Italy
| | - Sonja Kachler
- Institut für Pharmakologie und Toxicologie , Universität Würzburg , Versbacher Straße 9 , 97078 Würzburg , Germany
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxicologie , Universität Würzburg , Versbacher Straße 9 , 97078 Würzburg , Germany
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry , National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892-0810 , USA
| | - Giorgia Pastorin
- Department of Pharmacy , National University of Singapore , 3 Science Drive 3 , 117543 Singapore
| | - Stefano Moro
- Molecular Modeling Section (MMS) , Dipartimento di Scienze del Farmaco , Università degli Studi di Padova , Via F. Marzolo 5 , 35131 Padova , Italy
| | - Giampiero Spalluto
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , Via Licio Giorgeri 1 , 34127 Trieste , Italy .
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Lammi C, Sgrignani J, Arnoldi A, Lesma G, Spatti C, Silvani A, Grazioso G. Computationally Driven Structure Optimization, Synthesis, and Biological Evaluation of Imidazole-Based Proprotein Convertase Subtilisin/Kexin 9 (PCSK9) Inhibitors. J Med Chem 2019; 62:6163-6174. [DOI: 10.1021/acs.jmedchem.9b00402] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Carmen Lammi
- Dipartimento di Scienze Farmaceutiche, Universitá degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Jacopo Sgrignani
- Istituto di Ricerca in Biomedicina (IRB), Universitá della Svizzera Italiana (USI), Via V. Vela 6, CH-6500 Bellinzona, Switzerland
| | - Anna Arnoldi
- Dipartimento di Scienze Farmaceutiche, Universitá degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Giordano Lesma
- Dipartimento di Chimica, Universitá degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Claudia Spatti
- Dipartimento di Chimica, Universitá degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Alessandra Silvani
- Dipartimento di Chimica, Universitá degli Studi di Milano, Via Golgi 19, 20133 Milan, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Universitá degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milan, Italy
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14
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Al-Shar'i NA, Al-Balas QA. Molecular Dynamics Simulations of Adenosine Receptors: Advances, Applications and Trends. Curr Pharm Des 2019; 25:783-816. [DOI: 10.2174/1381612825666190304123414] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 01/09/2023]
Abstract
:
Adenosine receptors (ARs) are transmembrane proteins that belong to the G protein-coupled receptors
(GPCRs) superfamily and mediate the biological functions of adenosine. To date, four AR subtypes are known,
namely A1, A2A, A2B and A3 that exhibit different signaling pathways, tissue localization, and mechanisms of
activation. Moreover, the widespread ARs and their implication in numerous physiological and pathophysiological
conditions had made them pivotal therapeutic targets for developing clinically effective agents.
:
The crystallographic success in identifying the 3D crystal structures of A2A and A1 ARs has dramatically enriched
our understanding of their structural and functional properties such as ligand binding and signal transduction.
This, in turn, has provided a structural basis for a larger contribution of computational methods, particularly molecular
dynamics (MD) simulations, toward further investigation of their molecular properties and designing
bioactive ligands with therapeutic potential. MD simulation has been proved to be an invaluable tool in investigating
ARs and providing answers to some critical questions. For example, MD has been applied in studying ARs
in terms of ligand-receptor interactions, molecular recognition, allosteric modulations, dimerization, and mechanisms
of activation, collectively aiding in the design of subtype selective ligands.
:
In this review, we focused on the advances and different applications of MD simulations utilized to study the
structural and functional aspects of ARs that can foster the structure-based design of drug candidates. In addition,
relevant literature was briefly discussed which establishes a starting point for future advances in the field of drug
discovery to this pivotal group of drug targets.
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Affiliation(s)
- Nizar A. Al-Shar'i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Qosay A. Al-Balas
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
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15
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Samanta PN, Kar S, Leszczynski J. Recent Advances of In-Silico Modeling of Potent Antagonists for the Adenosine Receptors. Curr Pharm Des 2019; 25:750-773. [DOI: 10.2174/1381612825666190304123545] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 11/22/2022]
Abstract
The rapid advancement of computer architectures and development of mathematical algorithms offer a
unique opportunity to leverage the simulation of macromolecular systems at physiologically relevant timescales.
Herein, we discuss the impact of diverse structure-based and ligand-based molecular modeling techniques in
designing potent and selective antagonists against each adenosine receptor (AR) subtype that constitutes multitude
of drug targets. The efficiency and robustness of high-throughput empirical scoring function-based approaches
for hit discovery and lead optimization in the AR family are assessed with the help of illustrative examples
that have led to nanomolar to sub-micromolar inhibition activities. Recent progress in computer-aided drug
discovery through homology modeling, quantitative structure-activity relation, pharmacophore models, and molecular
docking coupled with more accurate free energy calculation methods are reported and critically analyzed
within the framework of structure-based virtual screening of AR antagonists. Later, the potency and applicability
of integrated molecular dynamics (MD) methods are addressed in the context of diligent inspection of intricated
AR-antagonist binding processes. MD simulations are exposed to be competent for studying the role of the membrane
as well as the receptor flexibility toward the precise evaluation of the biological activities of antagonistbound
AR complexes such as ligand binding modes, inhibition affinity, and associated thermodynamic and kinetic
parameters.
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Affiliation(s)
- Pabitra Narayan Samanta
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
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16
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A Metadynamics-Based Protocol for the Determination of GPCR-Ligand Binding Modes. Int J Mol Sci 2019; 20:ijms20081970. [PMID: 31013635 PMCID: PMC6514967 DOI: 10.3390/ijms20081970] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are a main drug target and therefore a hot topic in pharmaceutical research. One important prerequisite to understand how a certain ligand affects a GPCR is precise knowledge about its binding mode and the specific underlying interactions. If no crystal structure of the respective complex is available, computational methods can be used to deduce the binding site. One of them are metadynamics simulations which have the advantage of an enhanced sampling compared to conventional molecular dynamics simulations. However, the enhanced sampling of higher-energy states hampers identification of the preferred binding mode. Here, we present a novel protocol based on clustering of multiple walker metadynamics simulations which allows identifying the preferential binding mode from such conformational ensembles. We tested this strategy for three different model systems namely the histamine H1 receptor in combination with its physiological ligand histamine, as well as the β2 adrenoceptor with its agonist adrenaline and its antagonist alprenolol. For all three systems, the proposed protocol was able to reproduce the correct binding mode known from the literature suggesting that the approach can more generally be applied to the prediction of GPCR ligand binding in future.
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17
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Panday SK, Sturlese M, Salmaso V, Ghosh I, Moro S. Coupling Supervised Molecular Dynamics (SuMD) with Entropy Estimations To Shine Light on the Stability of Multiple Binding Sites. ACS Med Chem Lett 2019; 10:444-449. [PMID: 30996777 DOI: 10.1021/acsmedchemlett.8b00490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/15/2019] [Indexed: 11/30/2022] Open
Abstract
Exploring at the molecular level, all possible ligand-protein approaching pathways and, consequently, identifying the energetically favorable binding sites is considered crucial to depict a clear picture of the whole scenario of ligand-protein binding. In fact, a ligand can recognize a protein in multiple binding sites, adopting multiple conformations in every single binding site and inducing protein modifications upon binding. In the present work, we would like to present how it is possible to couple a supervised molecular dynamics (SuMD) approach to explore, from an unbound state, the most energetically favorable recognition pathways of the ligand to its protein, with an enthalpic and entropic characterization of the most stable ligand-protein bound states, using the protein kinase CK2α as a prototype study. We identified two accessory binding pockets surrounding the ATP-binding site having a strong enthalpic contribution but a different configurational entropy contribution, suggesting that they play a different role.
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Affiliation(s)
- Shailesh Kumar Panday
- School of Computational and Integrative Sciences (SCIS), Jawaharlal Nehru University, New Delhi 110067, India
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35122 Padova, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35122 Padova, Italy
| | - Veronica Salmaso
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35122 Padova, Italy
| | - Indira Ghosh
- School of Computational and Integrative Sciences (SCIS), Jawaharlal Nehru University, New Delhi 110067, India
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35122 Padova, Italy
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18
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Vijayamahantesh, Vijayalaxmi. Tinkering with targeting nucleotide signaling for control of intracellular Leishmania parasites. Cytokine 2019; 119:129-143. [PMID: 30909149 DOI: 10.1016/j.cyto.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/23/2022]
Abstract
Nucleotides are one of the most primitive extracellular signalling molecules across all phyla and regulate a multitude of responses. The biological effects of extracellular nucleotides/sides are mediated via the specific purinergic receptors present on the cell surface. In mammalian system, adenine nucleotides are the predominant nucleotides found in the extracellular milieu and mediate a constellation of physiological functions. In the context of host-pathogen interaction, extracellular ATP is recognized as a danger signal and potentiates the release of pro-inflammatory mediators from activated immune cells, on the other hand, its breakdown product adenosine exerts potential anti-inflammatory and immunosuppressive actions. Therefore, it is increasingly apparent that the interplay between extracellular ATP/adenosine ratios has a significant role in coordinating the regulation of the immune system in health and diseases. Several pathogens express ectonucleotidases on their surface and exploit the purinergic signalling as one of the mechanisms to modulate the host immune response. Leishmania pathogens are one of the most successful intracellular pathogens which survive within host macrophages and manipulate protective Th1 response into disease promoting Th2 response. In this review, we discuss the regulation of extracellular ATP and adenosine levels, the role of ATP/adenosine counter signalling in regulating the inflammation and immune responses during infection and how Leishmania parasites exploit the purinergic signalling to manipulate host response. We also discuss the challenges and opportunities in targeting purinergic signalling and the future prospects.
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Affiliation(s)
- Vijayamahantesh
- Department of Biochemistry, Indian Institute of Science (IISc), Bengaluru, Karnataka, India.
| | - Vijayalaxmi
- Department of Zoology, Karnatak University, Dharwad, Karnataka, India
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19
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Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A 2A adenosine receptor orthosteric binding site using a molecular docking approach? Insights from Dockbench. J Comput Aided Mol Des 2018; 32:1337-1346. [PMID: 30361971 DOI: 10.1007/s10822-018-0174-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/22/2018] [Indexed: 01/05/2023]
Abstract
The allosteric modulation of G protein-coupled receptors (GPCRs) by sodium ions has received considerable attention as crystal structures of several receptors, in their inactive conformation, show a Na+ ion bound to specific residues which, in the human A2A adenosine receptor (hA2A AR), are Ser913.39, Trp2466.48, Asn2807.45, and Asn2847.49. A cluster of water molecules completes the coordination of the sodium ion in the putative allosteric site. It is absolutely consolidated that the progress made in the field of GPCRs structural determination has increased the adoption of docking-driven approaches for the identification or the optimization of novel potent and selective ligands. Despite the extensive use of docking protocols in virtual screening approaches, to date, almost any of these studies have been carried out without taking into account the presence of the sodium cation and its first solvation shell in the putative allosteric binding site. In this study, we have focused our attention on determining how the presence of sodium ion binding and additionally its first hydration sphere, in hA2AAR could influence the ligand positioning accuracy during molecular docking simulations for most of the available resting and activated hA2A AR crystal structures, using DockBench as a comparative benchmarking tool and implementing a new correlation coefficient (EM). This work provides indications on the evidence that the posing performance (accuracy and/or precision) of the docking protocols in reproducing the crystallographic poses of different hA2A AR antagonists is generally increased in the presence of the sodium cation and its first solvation shell, in agreement with experimental observations. Consequently, the inclusion of sodium ion and its first solvation shell should be considered in order to facilitate the selection of new potential ligands in all molecular docking-based virtual screening protocols that aim to find novel GPCRs antagonists and inverse agonists.
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20
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Pandya AN, Baraiya AB, Jalani HB, Pandya D, Kaila JC, Kachler S, Salmaso V, Moro S, Klotz KN, Vasu KK. Discovery of 2-aminoimidazole and 2-amino imidazolyl-thiazoles as non-xanthine human adenosine A 3 receptor antagonists: SAR and molecular modeling studies. MEDCHEMCOMM 2018; 9:676-684. [PMID: 30108958 DOI: 10.1039/c7md00643h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/27/2018] [Indexed: 01/07/2023]
Abstract
A small-molecule combinatorial library of 24 compounds with 2-aminoimidazole and 2-aminoimidazolyl-thiazole derivatives was synthesized using a 2-chloro trityl resin. The generated compound library was tested against all the human adenosine receptors subtypes. The 2-aminoimidazole derivatives (6a-6l) showed weak to moderate affinity towards the human adenosine receptors. Further modification to 2-aminoimidazolyl-thiazole derivatives (12a-12l) resulted in an improvement of affinity at adenosine A1, A2A and A3 receptor subtypes. Compound 12b was the most potent and selective non-xanthine human adenosine A3 receptor antagonist of this series. A receptor-based modeling study was performed to explore the possible binding mode of these novel 2-aminoimidazole and 2-aminoimidazolyl-thiazole derivatives into human adenosine A1, A2A and A3 receptor subtypes.
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Affiliation(s)
- Amit N Pandya
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Arshi B Baraiya
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Hitesh B Jalani
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Dhaivat Pandya
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Jitendra C Kaila
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
| | - Sonja Kachler
- Institut für Pharmakologie und Toxikologie , Julius-Maximilians-Universität Würzburg , Germany
| | - Veronica Salmaso
- Molecular Modeling Section (MMS) , Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS) , Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo 5 , 35131 Padova , Italy
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxikologie , Julius-Maximilians-Universität Würzburg , Germany
| | - Kamala K Vasu
- Department of Medicinal Chemistry , B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre , Sarkej-Gandhinagar Highway, Thaltej , Ahmedabad 380e054 , Gujarat , India . ;
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21
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Basith S, Cui M, Macalino SJY, Park J, Clavio NAB, Kang S, Choi S. Exploring G Protein-Coupled Receptors (GPCRs) Ligand Space via Cheminformatics Approaches: Impact on Rational Drug Design. Front Pharmacol 2018; 9:128. [PMID: 29593527 PMCID: PMC5854945 DOI: 10.3389/fphar.2018.00128] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/06/2018] [Indexed: 01/14/2023] Open
Abstract
The primary goal of rational drug discovery is the identification of selective ligands which act on single or multiple drug targets to achieve the desired clinical outcome through the exploration of total chemical space. To identify such desired compounds, computational approaches are necessary in predicting their drug-like properties. G Protein-Coupled Receptors (GPCRs) represent one of the largest and most important integral membrane protein families. These receptors serve as increasingly attractive drug targets due to their relevance in the treatment of various diseases, such as inflammatory disorders, metabolic imbalances, cardiac disorders, cancer, monogenic disorders, etc. In the last decade, multitudes of three-dimensional (3D) structures were solved for diverse GPCRs, thus referring to this period as the "golden age for GPCR structural biology." Moreover, accumulation of data about the chemical properties of GPCR ligands has garnered much interest toward the exploration of GPCR chemical space. Due to the steady increase in the structural, ligand, and functional data of GPCRs, several cheminformatics approaches have been implemented in its drug discovery pipeline. In this review, we mainly focus on the cheminformatics-based paradigms in GPCR drug discovery. We provide a comprehensive view on the ligand- and structure-based cheminformatics approaches which are best illustrated via GPCR case studies. Furthermore, an appropriate combination of ligand-based knowledge with structure-based ones, i.e., integrated approach, which is emerging as a promising strategy for cheminformatics-based GPCR drug design is also discussed.
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Affiliation(s)
| | | | | | | | | | - Soosung Kang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, South Korea
| | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, South Korea
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22
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Abstract
Advances in the structural biology of G-protein Coupled Receptors have resulted in a significant step forward in our understanding of how this important class of drug targets function at the molecular level. However, it has also become apparent that they are very dynamic molecules, and moreover, that the underlying dynamics is crucial in shaping the response to different ligands. Molecular dynamics simulations can provide unique insight into the dynamic properties of GPCRs in a way that is complementary to many experimental approaches. In this chapter, we describe progress in three distinct areas that are particularly difficult to study with other techniques: atomic level investigation of the conformational changes that occur when moving between the various states that GPCRs can exist in, the pathways that ligands adopt during binding/unbinding events and finally, the influence of lipids on the conformational dynamics of GPCRs.
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Affiliation(s)
- Naushad Velgy
- Department of Biochemistry, Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - George Hedger
- Department of Biochemistry, Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Philip C Biggin
- Department of Biochemistry, Structural Bioinformatics and Computational Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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23
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Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
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Lee Y, Basith S, Choi S. Recent Advances in Structure-Based Drug Design Targeting Class A G Protein-Coupled Receptors Utilizing Crystal Structures and Computational Simulations. J Med Chem 2017; 61:1-46. [PMID: 28657745 DOI: 10.1021/acs.jmedchem.6b01453] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) represent the largest and most physiologically important integral membrane protein family, and these receptors respond to a wide variety of physiological and environmental stimuli. GPCRs are among the most critical therapeutic targets for numerous human diseases, and approximately one-third of the currently marketed drugs target this receptor family. The recent breakthroughs in GPCR structural biology have significantly contributed to our understanding of GPCR function, ligand binding, and pharmacological action as well as to the design of new drugs. This perspective highlights the latest advances in GPCR structures with a focus on the receptor-ligand interactions of each receptor family in class A nonrhodopsin GPCRs as well as the structural features for their activation, biased signaling, and allosteric mechanisms. The current state-of-the-art methodologies of structure-based drug design (SBDD) approaches in the GPCR research field are also discussed.
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Affiliation(s)
- Yoonji Lee
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Shaherin Basith
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
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25
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Deganutti G, Moro S. Supporting the Identification of Novel Fragment-Based Positive Allosteric Modulators Using a Supervised Molecular Dynamics Approach: A Retrospective Analysis Considering the Human A2A Adenosine Receptor as a Key Example. Molecules 2017; 22:molecules22050818. [PMID: 28509867 PMCID: PMC6154550 DOI: 10.3390/molecules22050818] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/03/2017] [Accepted: 05/10/2017] [Indexed: 12/31/2022] Open
Abstract
Structure-driven fragment-based (SDFB) approaches have provided efficient methods for the identification of novel drug candidates. This strategy has been largely applied in discovering several pharmacological ligand classes, including enzyme inhibitors, receptor antagonists and, more recently, also allosteric (positive and negative) modulators. Recently, Siegal and collaborators reported an interesting study, performed on a detergent-solubilized StaR adenosine A2A receptor, describing the existence of both fragment-like negative allosteric modulators (NAMs), and fragment-like positive allosteric modulators (PAMs). From this retrospective study, our results suggest that Supervised Molecular Dynamics (SuMD) simulations can support, on a reasonable time scale, the identification of fragment-like PAMs following their receptor recognition pathways and characterizing the possible allosteric binding sites.
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Affiliation(s)
- Giuseppe Deganutti
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padua, Italy.
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padua, Italy.
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26
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Squarcialupi L, Betti M, Catarzi D, Varano F, Falsini M, Ravani A, Pasquini S, Vincenzi F, Salmaso V, Sturlese M, Varani K, Moro S, Colotta V. The role of 5-arylalkylamino- and 5-piperazino- moieties on the 7-aminopyrazolo[4,3-d]pyrimidine core in affecting adenosine A 1 and A 2A receptor affinity and selectivity profiles. J Enzyme Inhib Med Chem 2017; 32:248-263. [PMID: 28114825 PMCID: PMC6009979 DOI: 10.1080/14756366.2016.1247060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
New 7-amino-2-phenylpyrazolo[4,3-d]pyrimidine derivatives, substituted at the 5-position with aryl(alkyl)amino- and 4-substituted-piperazin-1-yl- moieties, were synthesized with the aim of targeting human (h) adenosine A1 and/or A2A receptor subtypes. On the whole, the novel derivatives 1–24 shared scarce or no affinities for the off-target hA2B and hA3 ARs. The 5-(4-hydroxyphenethylamino)- derivative 12 showed both good affinity (Ki = 150 nM) and the best selectivity for the hA2A AR while the 5-benzylamino-substituted 5 displayed the best combined hA2A (Ki = 123 nM) and A1 AR affinity (Ki = 25 nM). The 5-phenethylamino moiety (compound 6) achieved nanomolar affinity (Ki = 11 nM) and good selectivity for the hA1 AR. The 5-(N4-substituted-piperazin-1-yl) derivatives 15–24 bind the hA1 AR subtype with affinities falling in the high nanomolar range. A structure-based molecular modeling study was conducted to rationalize the experimental binding data from a molecular point of view using both molecular docking studies and Interaction Energy Fingerprints (IEFs) analysis.
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Affiliation(s)
- Lucia Squarcialupi
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Marco Betti
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Daniela Catarzi
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Flavia Varano
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Matteo Falsini
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
| | - Annalisa Ravani
- b Dipartimento di Scienze Mediche, Sezione di Farmacologia , Università di Ferrara , Ferrara , Italy
| | - Silvia Pasquini
- b Dipartimento di Scienze Mediche, Sezione di Farmacologia , Università di Ferrara , Ferrara , Italy
| | - Fabrizio Vincenzi
- b Dipartimento di Scienze Mediche, Sezione di Farmacologia , Università di Ferrara , Ferrara , Italy
| | - Veronica Salmaso
- c Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco , Università di Padova , Padova , Italy
| | - Mattia Sturlese
- c Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco , Università di Padova , Padova , Italy
| | - Katia Varani
- b Dipartimento di Scienze Mediche, Sezione di Farmacologia , Università di Ferrara , Ferrara , Italy
| | - Stefano Moro
- c Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco , Università di Padova , Padova , Italy
| | - Vittoria Colotta
- a Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, Sezione di Farmaceutica e Nutraceutica , Università di Firenze , Sesto Fiorentino , Italy
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Bartuzi D, Kaczor AA, Targowska-Duda KM, Matosiuk D. Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors. Molecules 2017; 22:molecules22020340. [PMID: 28241450 PMCID: PMC6155844 DOI: 10.3390/molecules22020340] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/27/2017] [Accepted: 02/15/2017] [Indexed: 12/16/2022] Open
Abstract
The growing number of studies on G protein-coupled receptors (GPCRs) family are a source of noticeable improvement in our understanding of the functioning of these proteins. GPCRs are responsible for a vast part of signaling in vertebrates and, as such, invariably remain in the spotlight of medicinal chemistry. A deeper insight into the underlying mechanisms of interesting phenomena observed in GPCRs, such as biased signaling or allosteric modulation, can be gained with experimental and computational studies. The latter play an important role in this process, since they allow for observations on scales inaccessible for most other methods. One of the key steps in such studies is proper computational reconstruction of actual ligand-receptor or protein-protein interactions, a process called molecular docking. A number of improvements and innovative applications of this method were documented recently. In this review, we focus particularly on innovations in docking to GPCRs.
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Affiliation(s)
- Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., PL20093 Lublin, Poland.
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., PL20093 Lublin, Poland.
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | | | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., PL20093 Lublin, Poland.
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Janero DR, Korde A, Makriyannis A. Ligand-Assisted Protein Structure (LAPS): An Experimental Paradigm for Characterizing Cannabinoid-Receptor Ligand-Binding Domains. Methods Enzymol 2017; 593:217-235. [DOI: 10.1016/bs.mie.2017.06.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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Strasser A, Wittmann HJ. Molecular Modelling Approaches for the Analysis of Histamine Receptors and Their Interaction with Ligands. Handb Exp Pharmacol 2017; 241:31-61. [PMID: 28110354 DOI: 10.1007/164_2016_113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Several experimental techniques to analyse histamine receptors are available, e.g. pharmacological characterisation of known or new compounds by different types of assays or mutagenesis studies. To obtain insights into the histamine receptors on a molecular and structural level, crystal structures have to be determined and molecular modelling studies have to be performed. It is widely accepted to generate homology models of the receptor of interest based on an appropriate crystal structure as a template and to refine the resulting models by molecular dynamic simulations. A lot of modelling techniques, e.g. docking, QSAR or interaction fingerprint methods, are used to predict binding modes of ligands and pharmacological data, e.g. affinity or even efficacy. However, within the last years, molecular dynamic simulations got more and more important: First of all, molecular dynamic simulations are very helpful to refine the binding mode of a ligand to a histamine receptor, obtained by docking studies. Furthermore, with increasing computational performance it got possible to simulate complete binding pathways of ions or ligands from the aqueous extracellular phase into the allosteric or orthosteric binding pocket of histamine receptors.
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Affiliation(s)
- Andrea Strasser
- Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Universitäts-Str. 31, Regensburg, 93040, Germany.
| | - Hans-Joachim Wittmann
- Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Universitäts-Str. 31, Regensburg, 93040, Germany
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30
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McRobb FM, Negri A, Beuming T, Sherman W. Molecular dynamics techniques for modeling G protein-coupled receptors. Curr Opin Pharmacol 2016; 30:69-75. [DOI: 10.1016/j.coph.2016.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/28/2016] [Accepted: 07/03/2016] [Indexed: 11/17/2022]
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Heifetz A, James T, Morao I, Bodkin MJ, Biggin PC. Guiding lead optimization with GPCR structure modeling and molecular dynamics. Curr Opin Pharmacol 2016; 30:14-21. [DOI: 10.1016/j.coph.2016.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 01/04/2023]
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32
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Djuric SW, Hutchins CW, Talaty NN. Current status and future prospects for enabling chemistry technology in the drug discovery process. F1000Res 2016; 5:2426. [PMID: 27781094 PMCID: PMC5054812 DOI: 10.12688/f1000research.9515.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/26/2016] [Indexed: 11/20/2022] Open
Abstract
This review covers recent advances in the implementation of enabling chemistry technologies into the drug discovery process. Areas covered include parallel synthesis chemistry, high-throughput experimentation, automated synthesis and purification methods, flow chemistry methodology including photochemistry, electrochemistry, and the handling of "dangerous" reagents. Also featured are advances in the "computer-assisted drug design" area and the expanding application of novel mass spectrometry-based techniques to a wide range of drug discovery activities.
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Affiliation(s)
- Stevan W Djuric
- Discovery Chemistry and Technology, AbbVie, North Chicago, IL, USA
| | | | - Nari N Talaty
- Discovery Chemistry and Technology, AbbVie, North Chicago, IL, USA
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Cuzzolin A, Sturlese M, Deganutti G, Salmaso V, Sabbadin D, Ciancetta A, Moro S. Deciphering the Complexity of Ligand–Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations. J Chem Inf Model 2016; 56:687-705. [DOI: 10.1021/acs.jcim.5b00702] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Alberto Cuzzolin
- Molecular
Modeling Section
(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy
| | - Mattia Sturlese
- Molecular
Modeling Section
(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy
| | - Giuseppe Deganutti
- Molecular
Modeling Section
(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy
| | - Veronica Salmaso
- Molecular
Modeling Section
(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy
| | - Davide Sabbadin
- Molecular
Modeling Section
(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy
| | - Antonella Ciancetta
- Molecular
Modeling Section
(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy
| | - Stefano Moro
- Molecular
Modeling Section
(MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy
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