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Fu L, Luo Y, Niu L, Lin Y, Chen X, Zhang J, Tang W, Chen Y, Jiao Y. M 1/M 4 receptors as potential therapeutic treatments for schizophrenia: A comprehensive study. Bioorg Med Chem 2024; 105:117728. [PMID: 38640587 DOI: 10.1016/j.bmc.2024.117728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/03/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
Muscarinic acetylcholine receptors (mAChRs) play a significant role in the pathophysiology of schizophrenia. Although activating mAChRs holds potential in addressing the full range of schizophrenia symptoms, clinical application of many non-selective mAChR agonists in cognitive deficits, positive and negative symptoms is hindered by peripheral side effects (gastrointestinal disturbances and cardiovascular effects) and dosage restrictions. Ligands binding to the allosteric sites of mAChRs, particularly the M1 and M4 subtypes, demonstrate activity in improving cognitive function and amelioration of positive and negative symptoms associated with schizophrenia, enhancing our understanding of schizophrenia. The article aims to critically examine current design concepts and clinical advancements in synthesizing and designing small molecules targeting M1/M4, providing theoretical insights and empirical support for future research in this field.
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Affiliation(s)
- Lingsheng Fu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yi Luo
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Longyan Niu
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Ying Lin
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Xingru Chen
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Junhao Zhang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Weifang Tang
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China..
| | - Yadong Chen
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China..
| | - Yu Jiao
- School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China..
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2
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Colombo G. Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design. Curr Opin Struct Biol 2023; 83:102702. [PMID: 37716095 DOI: 10.1016/j.sbi.2023.102702] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The concept of allostery has become a central tenet in the study of biological systems. In parallel, the discovery of allosteric drugs is generating new opportunities to selectively modulate difficult targets involved in pathologic mechanisms. Molecular simulations can provide atomistically detailed insight into the processes involved in allosteric regulation and signaling, and at the same time, they have the potential to unveil regulatory hotspots or cryptic sites that are not immediately evident from the analysis of static structures. In this context, computational approaches should be able to connect the study of allosteric regulation at different scales to the possibility of leveraging this knowledge to expand the chemical space of new, active drugs. Here, we will discuss recent advances in the study of allosteric regulation via computational methods and connect the mechanistic knowledge generated to the possibility of designing new small molecules that can tweak the functions of their receptors.
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Affiliation(s)
- Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy.
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3
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Seong SH, Kim SH, Ryu JH, Jeong JW, Jung HA, Choi JS. Effects of Icariin and Its Metabolites on GPCR Regulation and MK-801-Induced Schizophrenia-Like Behaviors in Mice. Molecules 2023; 28:7300. [PMID: 37959720 PMCID: PMC10647531 DOI: 10.3390/molecules28217300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Icariin, a major bioactive compound found in the Epimedium genus, has been reported to exert protective effects against neurodegenerative disorders. In the current study, we aimed to investigate the regulatory effect of icariin and its active metabolites (icariside II and icaritin) against prime G-protein-coupled receptor targets, considering their association with neuronal disorders. Icariside II exhibited selective agonist activity towards the dopamine D3 receptor (D3R), with half-maximal effective concentrations of 13.29 μM. Additionally, they effectively inhibited the specific binding of radioligands to D3R. Molecular docking analysis revealed that icariside II potentially exerts its agonistic effect through hydrogen-bonding interaction with Asp110 of the D3R, accompanied by negative binding energy. Conversely, icaritin demonstrated selective antagonist effects on the muscarinic acetylcholine M2 receptor (M2R). Radioligand binding assay and molecular docking analysis identified icaritin as an orthosteric ligand for M2R. Furthermore, all three compounds, icariin and its two metabolites, successfully mitigated MK-801-induced schizophrenia-like symptoms, including deficits in prepulse inhibition and social interaction, in mice. In summary, these findings highlight the potential of icariin and its metabolites as promising lead structures for the discovery of new drugs targeting cognitive and neurodegenerative disorders.
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Affiliation(s)
- Su Hui Seong
- Division of Natural Products Research, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea; (S.H.S.); (J.-W.J.)
| | - Seo Hyun Kim
- Division of Research Management, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea;
| | - Jong Hoon Ryu
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea;
| | - Jin-Woo Jeong
- Division of Natural Products Research, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea; (S.H.S.); (J.-W.J.)
| | - Hyun Ah Jung
- Department of Food Science and Human Nutrition, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Jae Sue Choi
- Department of Food and Life Science, Pukyong National University, Busan 48513, Republic of Korea
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Kovyazina IV, Khamidullina AA. Muscarinic Cholinoreceptors in Skeletal Muscle: Localization and Functional Role. Acta Naturae 2023; 15:44-55. [PMID: 38234599 PMCID: PMC10790362 DOI: 10.32607/actanaturae.25259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/24/2023] [Indexed: 01/19/2024] Open
Abstract
The review focuses on the modern concepts of the functions of muscarinic cholinoreceptors in skeletal muscles, particularly, in neuromuscular contacts, and that of the signaling pathways associated with the activation of various subtypes of muscarinic receptors in the skeletal muscles of cold-blooded and warm-blooded animals. Despite the long history of research into the involvement of muscarinic receptors in the modulation of neuromuscular transmission, many aspects of such regulation and the associated intracellular mechanisms remain unclear. Now it is obvious that the functions of muscarinic receptors in skeletal muscle are not limited to the autoregulation of neurosecretion from motor nerve endings but also extend to the development and morphological rearrangements of the synaptic apparatus, coordinating them with the degree of activity. The review discusses various approaches to the study of the functions of muscarinic receptors in motor synapses, as well as the problems arising when interpreting experimental data. The final part of the review is devoted to an analysis of some of the intracellular mechanisms and signaling pathways that mediate the effects of muscarinic agents on neuromuscular transmission.
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Affiliation(s)
- I. V. Kovyazina
- Kazan State Medical University, Kazan, 420012 Russian Federation
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, 420111 Russian Federation
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Biswas D, Chakraborty A, Mukherjee S, Ghosh B. Hairy root culture: a potent method for improved secondary metabolite production of Solanaceous plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1197555. [PMID: 37731987 PMCID: PMC10507345 DOI: 10.3389/fpls.2023.1197555] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/13/2023] [Indexed: 09/22/2023]
Abstract
Secondary metabolites synthesized by the Solanaceous plants are of major therapeutic and pharmaceutical importance, many of which are commonly obtained from the roots of these plants. 'Hairy roots', mirroring the same phytochemical pattern of the corresponding root of the parent plant with higher growth rate and productivity, are therefore extensively studied as an effective alternative for the in vitro production of these metabolites. Hairy roots are the transformed roots, generated from the infection site of the wounded plants with Agrobacterium rhizogenes. With their fast growth, being free from pathogen and herbicide contamination, genetic stability, and autotrophic nature for plant hormones, hairy roots are considered as useful bioproduction systems for specialized metabolites. Lately, several elicitation methods have been employed to enhance the accumulation of these compounds in the hairy root cultures for both small and large-scale production. Nevertheless, in the latter case, the cultivation of hairy roots in bioreactors should still be optimized. Hairy roots can also be utilized for metabolic engineering of the regulatory genes in the metabolic pathways leading to enhanced production of metabolites. The present study summarizes the updated and modern biotechnological aspects for enhanced production of secondary metabolites in the hairy root cultures of the plants of Solanaceae and their respective importance.
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Affiliation(s)
- Diptesh Biswas
- Plant Biotechnology Laboratory, Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
| | - Avijit Chakraborty
- Plant Biotechnology Laboratory, Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
| | - Swapna Mukherjee
- Department of Microbiology, Dinabandhu Andrews College, Kolkata, India
| | - Biswajit Ghosh
- Plant Biotechnology Laboratory, Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
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Fink EA, Bardine C, Gahbauer S, Singh I, Detomasi TC, White K, Gu S, Wan X, Chen J, Ary B, Glenn I, O'Connell J, O'Donnell H, Fajtová P, Lyu J, Vigneron S, Young NJ, Kondratov IS, Alisoltani A, Simons LM, Lorenzo‐Redondo R, Ozer EA, Hultquist JF, O'Donoghue AJ, Moroz YS, Taunton J, Renslo AR, Irwin JJ, García‐Sastre A, Shoichet BK, Craik CS. Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors. Protein Sci 2023; 32:e4712. [PMID: 37354015 PMCID: PMC10364469 DOI: 10.1002/pro.4712] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/29/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023]
Abstract
Antiviral therapeutics to treat SARS-CoV-2 are needed to diminish the morbidity of the ongoing COVID-19 pandemic. A well-precedented drug target is the main viral protease (MPro ), which is targeted by an approved drug and by several investigational drugs. Emerging viral resistance has made new inhibitor chemotypes more pressing. Adopting a structure-based approach, we docked 1.2 billion non-covalent lead-like molecules and a new library of 6.5 million electrophiles against the enzyme structure. From these, 29 non-covalent and 11 covalent inhibitors were identified in 37 series, the most potent having an IC50 of 29 and 20 μM, respectively. Several series were optimized, resulting in low micromolar inhibitors. Subsequent crystallography confirmed the docking predicted binding modes and may template further optimization. While the new chemotypes may aid further optimization of MPro inhibitors for SARS-CoV-2, the modest success rate also reveals weaknesses in our approach for challenging targets like MPro versus other targets where it has been more successful, and versus other structure-based techniques against MPro itself.
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Affiliation(s)
- Elissa A. Fink
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- Graduate Program in BiophysicsUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Conner Bardine
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- Graduate Program in Chemistry and Chemical BiologyUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Stefan Gahbauer
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Isha Singh
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Tyler C. Detomasi
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Kris White
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Global Health and Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Shuo Gu
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Xiaobo Wan
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Jun Chen
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Beatrice Ary
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Isabella Glenn
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Joseph O'Connell
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Henry O'Donnell
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California‐San DiegoSan DiegoCaliforniaUSA
| | - Jiankun Lyu
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Seth Vigneron
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Nicholas J. Young
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Ivan S. Kondratov
- Enamine Ltd.KyïvUkraine
- V.P. Kukhar Institute of Bioorganic Chemistry and PetrochemistryNational Academy of Sciences of UkraineKyïvUkraine
| | - Arghavan Alisoltani
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Lacy M. Simons
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Ramon Lorenzo‐Redondo
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Egon A. Ozer
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Center for Pathogen Genomics and Microbial Evolution, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California‐San DiegoSan DiegoCaliforniaUSA
| | - Yurii S. Moroz
- National Taras Shevchenko University of KyïvKyïvUkraine
- Chemspace LLCKyïvUkraine
| | - Jack Taunton
- Department of Cellular and Molecular PharmacologyUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Adam R. Renslo
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - John J. Irwin
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
| | - Adolfo García‐Sastre
- Department of MicrobiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Global Health and Emerging Pathogens InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Medicine, Division of Infectious DiseasesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Tisch Cancer Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Pathology, Molecular and Cell‐Based MedicineIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
| | - Brian K. Shoichet
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
| | - Charles S. Craik
- Department of Pharmaceutical ChemistryUniversity of California‐San FranciscoSan FranciscoCaliforniaUSA
- QBI COVID‐19 Research Group (QCRG)San FranciscoCaliforniaUSA
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7
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Deng S, Zhang H, Gou R, Luo D, Liu Z, Zhu F, Xue W. Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter. J Chem Inf Model 2023. [PMID: 37410882 DOI: 10.1021/acs.jcim.3c00477] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Human dopamine transporter (hDAT) regulates the reuptake of extracellular dopamine (DA) and is an essential therapeutic target for central nervous system (CNS) diseases. The allosteric modulation of hDAT has been identified for decades. However, the molecular mechanism underlying the transportation is still elusive, which hinders the rational design of allosteric modulators against hDAT. Here, a systematic structure-based method was performed to explore allosteric sites on hDAT in inward-open (IO) conformation and to screen compounds with allosteric affinity. First, the model of the hDAT structure was constructed based on the recently reported Cryo-EM structure of the human serotonin transporter (hSERT) and Gaussian-accelerated molecular dynamics (GaMD) simulation was further utilized for the identification of intermediate energetic stable states of the transporter. Then, with the potential druggable allosteric site on hDAT in IO conformation, virtual screening of seven enamine chemical libraries (∼440,000 compounds) was processed, resulting in 10 compounds being purchased for in vitro assay and with Z1078601926 discovered to allosterically inhibit hDAT (IC50 = 0.527 [0.284; 0.988] μM) when nomifensine was introduced as an orthosteric ligand. Finally, the synergistic effect underlying the allosteric inhibition of hDAT by Z1078601926 and nomifensine was explored using additional GaMD simulation and postbinding free energy analysis. The hit compound discovered in this work not only provides a good starting point for lead optimization but also demonstrates the usability of the method for the structure-based discovery of novel allosteric modulators of other therapeutic targets.
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Affiliation(s)
- Shengzhe Deng
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Haiwei Zhang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Department of Pathology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Rongpei Gou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zerong Liu
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical Co., Ltd., Luzhou 646000, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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8
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Nguyen ATN, Tran QL, Baltos JA, McNeill SM, Nguyen DTN, May LT. Small molecule allosteric modulation of the adenosine A 1 receptor. Front Endocrinol (Lausanne) 2023; 14:1184360. [PMID: 37435481 PMCID: PMC10331460 DOI: 10.3389/fendo.2023.1184360] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/23/2023] [Indexed: 07/13/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent the target for approximately a third of FDA-approved small molecule drugs. The adenosine A1 receptor (A1R), one of four adenosine GPCR subtypes, has important (patho)physiological roles in humans. A1R has well-established roles in the regulation of the cardiovascular and nervous systems, where it has been identified as a potential therapeutic target for a number of conditions, including cardiac ischemia-reperfusion injury, cognition, epilepsy, and neuropathic pain. A1R small molecule drugs, typically orthosteric ligands, have undergone clinical trials. To date, none have progressed into the clinic, predominantly due to dose-limiting unwanted effects. The development of A1R allosteric modulators that target a topographically distinct binding site represent a promising approach to overcome current limitations. Pharmacological parameters of allosteric ligands, including affinity, efficacy and cooperativity, can be optimized to regulate A1R activity with high subtype, spatial and temporal selectivity. This review aims to offer insights into the A1R as a potential therapeutic target and highlight recent advances in the structural understanding of A1R allosteric modulation.
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Affiliation(s)
- Anh T. N. Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Quan L. Tran
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Jo-Anne Baltos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Samantha M. McNeill
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Diep T. N. Nguyen
- Department of Information Technology, Faculty of Engineering and Technology, Vietnam National University, Hanoi, Vietnam
| | - Lauren T. May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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Fouillen A, Bous J, Granier S, Mouillac B, Sounier R. Bringing GPCR Structural Biology to Medical Applications: Insights from Both V2 Vasopressin and Mu-Opioid Receptors. MEMBRANES 2023; 13:606. [PMID: 37367810 DOI: 10.3390/membranes13060606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
G-protein coupled receptors (GPCRs) are versatile signaling proteins that regulate key physiological processes in response to a wide variety of extracellular stimuli. The last decade has seen a revolution in the structural biology of clinically important GPCRs. Indeed, the improvement in molecular and biochemical methods to study GPCRs and their transducer complexes, together with advances in cryo-electron microscopy, NMR development, and progress in molecular dynamic simulations, have led to a better understanding of their regulation by ligands of different efficacy and bias. This has also renewed a great interest in GPCR drug discovery, such as finding biased ligands that can either promote or not promote specific regulations. In this review, we focus on two therapeutically relevant GPCR targets, the V2 vasopressin receptor (V2R) and the mu-opioid receptor (µOR), to shed light on the recent structural biology studies and show the impact of this integrative approach on the determination of new potential clinical effective compounds.
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Affiliation(s)
- Aurélien Fouillen
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, 34000 Montpellier, France
- Centre de Biochimie Structurale (CBS), Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Julien Bous
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Sébastien Granier
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, 34000 Montpellier, France
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, 34000 Montpellier, France
| | - Remy Sounier
- Institut de Génomique Fonctionnelle (IGF), Université de Montpellier, CNRS, INSERM, 34000 Montpellier, France
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Xu J, Wang Q, Hübner H, Hu Y, Niu X, Wang H, Maeda S, Inoue A, Tao Y, Gmeiner P, Du Y, Jin C, Kobilka BK. Structural and dynamic insights into supra-physiological activation and allosteric modulation of a muscarinic acetylcholine receptor. Nat Commun 2023; 14:376. [PMID: 36690613 PMCID: PMC9870890 DOI: 10.1038/s41467-022-35726-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 12/21/2022] [Indexed: 01/25/2023] Open
Abstract
The M2 muscarinic receptor (M2R) is a prototypical G-protein-coupled receptor (GPCR) that serves as a model system for understanding GPCR regulation by both orthosteric and allosteric ligands. Here, we investigate the mechanisms governing M2R signaling versatility using cryo-electron microscopy (cryo-EM) and NMR spectroscopy, focusing on the physiological agonist acetylcholine and a supra-physiological agonist iperoxo, as well as a positive allosteric modulator LY2119620. These studies reveal that acetylcholine stabilizes a more heterogeneous M2R-G-protein complex than iperoxo, where two conformers with distinctive G-protein orientations were determined. We find that LY2119620 increases the affinity for both agonists, but differentially modulates agonists efficacy in G-protein and β-arrestin pathways. Structural and spectroscopic analysis suggest that LY211620 stabilizes distinct intracellular conformational ensembles from agonist-bound M2R, which may enhance β-arrestin recruitment while impairing G-protein activation. These results highlight the role of conformational dynamics in the complex signaling behavior of GPCRs, and could facilitate design of better drugs.
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Affiliation(s)
- Jun Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Qinggong Wang
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, Chinese University of Hong Kong, 518172, Shenzhen, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P. R. China
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University, 91058, Erlangen, Germany
| | - Yunfei Hu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, 100084, Beijing, China
- Innovation Academy for Precision Measurement Science and Technology, CAS, 430071, Wuhan, China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, 100084, Beijing, China
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shoji Maeda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pharmacology, Medical School, University of Michigan 1150 Medical Center Dr., 1315 Medical Science Research Bldg III, Ann Arbor, MI, 48109, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Yuyong Tao
- Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P. R. China
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University, 91058, Erlangen, Germany
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, Chinese University of Hong Kong, 518172, Shenzhen, China.
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, 100084, Beijing, China.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Zhu H, Zhang Y, Li W, Huang N. A Comprehensive Survey of Prospective Structure-Based Virtual Screening for Early Drug Discovery in the Past Fifteen Years. Int J Mol Sci 2022; 23:ijms232415961. [PMID: 36555602 PMCID: PMC9781938 DOI: 10.3390/ijms232415961] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Structure-based virtual screening (SBVS), also known as molecular docking, has been increasingly applied to discover small-molecule ligands based on the protein structures in the early stage of drug discovery. In this review, we comprehensively surveyed the prospective applications of molecular docking judged by solid experimental validations in the literature over the past fifteen years. Herein, we systematically analyzed the novelty of the targets and the docking hits, practical protocols of docking screening, and the following experimental validations. Among the 419 case studies we reviewed, most virtual screenings were carried out on widely studied targets, and only 22% were on less-explored new targets. Regarding docking software, GLIDE is the most popular one used in molecular docking, while the DOCK 3 series showed a strong capacity for large-scale virtual screening. Besides, the majority of identified hits are promising in structural novelty and one-quarter of the hits showed better potency than 1 μM, indicating that the primary advantage of SBVS is to discover new chemotypes rather than highly potent compounds. Furthermore, in most studies, only in vitro bioassays were carried out to validate the docking hits, which might limit the further characterization and development of the identified active compounds. Finally, several successful stories of SBVS with extensive experimental validations have been highlighted, which provide unique insights into future SBVS drug discovery campaigns.
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Affiliation(s)
- Hui Zhu
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Yulin Zhang
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Wei Li
- RPXDs (Suzhou) Co., Ltd., Suzhou 215028, China
| | - Niu Huang
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
- National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
- Correspondence:
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12
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Kampen S, Rodríguez D, Jørgensen M, Kruszyk-Kujawa M, Huang X, Collins M, Boyle N, Maurel D, Rudling A, Lebon G, Carlsson J. Structure-Based Discovery of Negative Allosteric Modulators of the Metabotropic Glutamate Receptor 5. ACS Chem Biol 2022; 17:2744-2752. [PMID: 36149353 PMCID: PMC9594040 DOI: 10.1021/acschembio.2c00234] [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] [Indexed: 01/19/2023]
Abstract
Recently determined structures of class C G protein-coupled receptors (GPCRs) revealed the location of allosteric binding sites and opened new opportunities for the discovery of novel modulators. In this work, molecular docking screens for allosteric modulators targeting the metabotropic glutamate receptor 5 (mGlu5) were performed. The mGlu5 receptor is activated by the main excitatory neurotransmitter of the nervous central system, L-glutamate, and mGlu5 receptor activity can be allosterically modulated by negative or positive allosteric modulators. The mGlu5 receptor is a promising target for the treatment of psychiatric and neurodegenerative diseases, and several allosteric modulators of this GPCR have been evaluated in clinical trials. Chemical libraries containing fragment- (1.6 million molecules) and lead-like (4.6 million molecules) compounds were docked to an allosteric binding site of mGlu5 identified in X-ray crystal structures. Among the top-ranked compounds, 59 fragments and 59 lead-like compounds were selected for experimental evaluation. Of these, four fragment- and seven lead-like compounds were confirmed to bind to the allosteric site with affinities ranging from 0.43 to 8.6 μM, corresponding to a hit rate of 9%. The four compounds with the highest affinities were demonstrated to be negative allosteric modulators of mGlu5 signaling in functional assays. The results demonstrate that virtual screens of fragment- and lead-like chemical libraries have complementary advantages and illustrate how access to high-resolution structures of GPCRs in complex with allosteric modulators can accelerate lead discovery.
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Affiliation(s)
- Stefanie Kampen
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - David Rodríguez
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21 Solna, Sweden,H.
Lundbeck A/S, Ottiliavej
9, DK-2500 Valby, Denmark
| | | | | | - Xinyan Huang
- Lundbeck
Research USA, 215 College Road, Paramus, New Jersey 07652 - 1431, United States
| | - Michael Collins
- Lundbeck
Research USA, 215 College Road, Paramus, New Jersey 07652 - 1431, United States
| | - Noel Boyle
- Lundbeck
Research USA, 215 College Road, Paramus, New Jersey 07652 - 1431, United States
| | - Damien Maurel
- IGF,
Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Axel Rudling
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21 Solna, Sweden
| | - Guillaume Lebon
- IGF,
Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Jens Carlsson
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden,
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13
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Allosteric modulation of GPCRs: From structural insights to in silico drug discovery. Pharmacol Ther 2022; 237:108242. [DOI: 10.1016/j.pharmthera.2022.108242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 11/19/2022]
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14
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Wah Tan Z, Tee WV, Berezovsky IN. Learning about allosteric drugs and ways to design them. J Mol Biol 2022; 434:167692. [PMID: 35738428 DOI: 10.1016/j.jmb.2022.167692] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/23/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022]
Abstract
While the accelerating quest for precision medicine requires new individually targeting and selective drugs, and the ability to work with so-called undruggable targets, the realm of allosteric drugs meeting this need remains largely uncharted. Generalizing the observations on two major drug targets with widely observed inherent allostery, GPCRs and kinases, we describe and discuss basic allosteric modes of action that are universally applicable in all types of structures and functions. Using examples of Class A GPCRs and CMGC protein kinases, we show how Allosteric Signalling and Probing Fingerprints can be used to identify potential allosteric sites and reveal effector-leads that may serve as a starting point for the development of allosteric drugs targeting these regulatory sites. A set of distinct characteristics of allosteric ligands was established, which highlights the versatility of their design and make them advantageous before their orthosteric counterparts in personalized medicine. We argue that rational design of allosteric drugs should begin with the search for latent sites or design of non-natural binding sites followed by fragment-based design of allosteric ligands and by the mutual adjustment of the site-ligand pair in order to achieve required effects. On the basis of the perturbative nature and reversibility of allosteric communication, we propose a generic protocol for computational design of allosteric effectors, enabling also the allosteric tuning of biologics, in obtaining allosteric control over protein functions.
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
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15
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Intrinsically disordered proteins and proteins with intrinsically disordered regions in neurodegenerative diseases. Biophys Rev 2022; 14:679-707. [DOI: 10.1007/s12551-022-00968-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/28/2022] [Indexed: 12/14/2022] Open
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16
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Casadó-Anguera V, Casadó V. Unmasking allosteric binding sites: Novel targets for GPCR drug discovery. Expert Opin Drug Discov 2022; 17:897-923. [PMID: 35649692 DOI: 10.1080/17460441.2022.2085684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Unexpected non-apparent and hidden allosteric binding sites are non-classical and non-apparent allosteric centers in 3-D X-ray protein structures until orthosteric or allosteric ligands bind to them. The orthosteric center of one protomer that modulates binding centers of the other protomers within an oligomer is also an unexpected allosteric site. Furthermore, another partner protein can also produce these effects, acting as an unexpected allosteric modulator. AREAS COVERED This review summarizes both classical and non-classical allosterism. The authors focus on G protein-coupled receptor (GPCR) oligomers as a paradigm of allosteric molecules. Moreover, they show several examples of unexpected allosteric sites such as hidden allosteric sites in a protomer that appear after the interaction with other molecules and the allosterism exerted between orthosteric sites within GPCR oligomer, emphasizing on the allosteric modulations that can occur between binding sites. EXPERT OPINION The study of these new non-classical allosteric sites will expand the diversity of allosteric control on the function of orthosteric sites within proteins, whether GPCRs or other receptors, enzymes or transporters. Moreover, the design of new drugs targeting these hidden allosteric sites or already known orthosteric sites acting as allosteric sites in protein homo- or hetero-oligomers will increase the therapeutic potential of allosterism.
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Affiliation(s)
- Verònica Casadó-Anguera
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, and Institute of Biomedicine of the Universitat de Barcelona, Barcelona, Spain.,Laboratory of Neuropharmacology-Neurophar, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Vicent Casadó
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, and Institute of Biomedicine of the Universitat de Barcelona, Barcelona, Spain
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17
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Tastan Bishop Ö, Mutemi Musyoka T, Barozi V. Allostery and missense mutations as intermittently linked promising aspects of modern computational drug discovery. J Mol Biol 2022; 434:167610. [DOI: 10.1016/j.jmb.2022.167610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/15/2022]
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18
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Egyed A, Kiss DJ, Keserű GM. The Impact of the Secondary Binding Pocket on the Pharmacology of Class A GPCRs. Front Pharmacol 2022; 13:847788. [PMID: 35355719 PMCID: PMC8959758 DOI: 10.3389/fphar.2022.847788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/01/2022] [Indexed: 12/19/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are considered important therapeutic targets due to their pathophysiological significance and pharmacological relevance. Class A receptors represent the largest group of GPCRs that gives the highest number of validated drug targets. Endogenous ligands bind to the orthosteric binding pocket (OBP) embedded in the intrahelical space of the receptor. During the last 10 years, however, it has been turned out that in many receptors there is secondary binding pocket (SBP) located in the extracellular vestibule that is much less conserved. In some cases, it serves as a stable allosteric site harbouring allosteric ligands that modulate the pharmacology of orthosteric binders. In other cases it is used by bitopic compounds occupying both the OBP and SBP. In these terms, SBP binding moieties might influence the pharmacology of the bitopic ligands. Together with others, our research group showed that SBP binders contribute significantly to the affinity, selectivity, functional activity, functional selectivity and binding kinetics of bitopic ligands. Based on these observations we developed a structure-based protocol for designing bitopic compounds with desired pharmacological profile.
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Affiliation(s)
- Attila Egyed
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dóra Judit Kiss
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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Ballante F, Kooistra AJ, Kampen S, de Graaf C, Carlsson J. Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You? Pharmacol Rev 2021; 73:527-565. [PMID: 34907092 DOI: 10.1124/pharmrev.120.000246] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome and are important therapeutic targets. During the last decade, the number of atomic-resolution structures of GPCRs has increased rapidly, providing insights into drug binding at the molecular level. These breakthroughs have created excitement regarding the potential of using structural information in ligand design and initiated a new era of rational drug discovery for GPCRs. The molecular docking method is now widely applied to model the three-dimensional structures of GPCR-ligand complexes and screen for chemical probes in large compound libraries. In this review article, we first summarize the current structural coverage of the GPCR superfamily and the understanding of receptor-ligand interactions at atomic resolution. We then present the general workflow of structure-based virtual screening and strategies to discover GPCR ligands in chemical libraries. We assess the state of the art of this research field by summarizing prospective applications of virtual screening based on experimental structures. Strategies to identify compounds with specific efficacy and selectivity profiles are discussed, illustrating the opportunities and limitations of the molecular docking method. Our overview shows that structure-based virtual screening can discover novel leads and will be essential in pursuing the next generation of GPCR drugs. SIGNIFICANCE STATEMENT: Extraordinary advances in the structural biology of G protein-coupled receptors have revealed the molecular details of ligand recognition by this large family of therapeutic targets, providing novel avenues for rational drug design. Structure-based docking is an efficient computational approach to identify novel chemical probes from large compound libraries, which has the potential to accelerate the development of drug candidates.
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Affiliation(s)
- Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Albert J Kooistra
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
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20
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Kricker JA, Page CP, Gardarsson FR, Baldursson O, Gudjonsson T, Parnham MJ. Nonantimicrobial Actions of Macrolides: Overview and Perspectives for Future Development. Pharmacol Rev 2021; 73:233-262. [PMID: 34716226 DOI: 10.1124/pharmrev.121.000300] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Macrolides are among the most widely prescribed broad spectrum antibacterials, particularly for respiratory infections. It is now recognized that these drugs, in particular azithromycin, also exert time-dependent immunomodulatory actions that contribute to their therapeutic benefit in both infectious and other chronic inflammatory diseases. Their increased chronic use in airway inflammation and, more recently, of azithromycin in COVID-19, however, has led to a rise in bacterial resistance. An additional crucial aspect of chronic airway inflammation, such as chronic obstructive pulmonary disease, as well as other inflammatory disorders, is the loss of epithelial barrier protection against pathogens and pollutants. In recent years, azithromycin has been shown with time to enhance the barrier properties of airway epithelial cells, an action that makes an important contribution to its therapeutic efficacy. In this article, we review the background and evidence for various immunomodulatory and time-dependent actions of macrolides on inflammatory processes and on the epithelium and highlight novel nonantibacterial macrolides that are being studied for immunomodulatory and barrier-strengthening properties to circumvent the risk of bacterial resistance that occurs with macrolide antibacterials. We also briefly review the clinical effects of macrolides in respiratory and other inflammatory diseases associated with epithelial injury and propose that the beneficial epithelial effects of nonantibacterial azithromycin derivatives in chronic inflammation, even given prophylactically, are likely to gain increasing attention in the future. SIGNIFICANCE STATEMENT: Based on its immunomodulatory properties and ability to enhance the protective role of the lung epithelium against pathogens, azithromycin has proven superior to other macrolides in treating chronic respiratory inflammation. A nonantibiotic azithromycin derivative is likely to offer prophylactic benefits against inflammation and epithelial damage of differing causes while preserving the use of macrolides as antibiotics.
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Affiliation(s)
- Jennifer A Kricker
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Clive P Page
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Fridrik Runar Gardarsson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Olafur Baldursson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Thorarinn Gudjonsson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Michael J Parnham
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
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21
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Xiong B, Jin G, Xu Y, You W, Luo Y, Fang M, Chen B, Huang H, Yang J, Lin X, Yu C. Identification of Koumine as a Translocator Protein 18 kDa Positive Allosteric Modulator for the Treatment of Inflammatory and Neuropathic Pain. Front Pharmacol 2021; 12:692917. [PMID: 34248642 PMCID: PMC8264504 DOI: 10.3389/fphar.2021.692917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/07/2021] [Indexed: 01/08/2023] Open
Abstract
Koumine is an alkaloid that displays notable activity against inflammatory and neuropathic pain, but its therapeutic target and molecular mechanism still need further study. Translocator protein 18 kDa (TSPO) is a vital therapeutic target for pain treatment, and recent research implies that there may be allostery in TSPO. Our previous competitive binding assay hint that koumine may function as a TSPO positive allosteric modulator (PAM). Here, for the first time, we report the pharmacological characterization of koumine as a TSPO PAM. The results imply that koumine might be a high-affinity ligand of TSPO and that it likely acts as a PAM since it could delay the dissociation of 3H-PK11195 from TSPO. Importantly, the allostery was retained in vivo, as koumine augmented Ro5-4864-mediated analgesic and anti-inflammatory effects in several acute and chronic inflammatory and neuropathic pain models. Moreover, the positive allosteric modulatory effect of koumine on TSPO was further demonstrated in cell proliferation assays in T98G human glioblastoma cells. In summary, we have identified and characterized koumine as a TSPO PAM for the treatment of inflammatory and neuropathic pain. Our data lay a solid foundation for the use of the clinical candidate koumine to treat inflammatory and neuropathic pain, further demonstrate the allostery in TSPO, and provide the first proof of principle that TSPO PAM may be a novel avenue for the discovery of analgesics.
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Affiliation(s)
- Bojun Xiong
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China.,Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Guilin Jin
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Ying Xu
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Wenbing You
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Yufei Luo
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Menghan Fang
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Bing Chen
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Huihui Huang
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Jian Yang
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Xu Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Changxi Yu
- Department of Pharmacology, School of Pharmacy, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, School of Pharmacy, Fujian Medical University, Fuzhou, China
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22
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Concise Synthesis of Both Enantiomers of Pilocarpine. Molecules 2021; 26:molecules26123676. [PMID: 34208623 PMCID: PMC8235342 DOI: 10.3390/molecules26123676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022] Open
Abstract
Furan-2-carboxylic acid was used as a starting material for the synthesis of dehydro-homopilopic acid. Esterification, hydrogenation and enzymatic hydrolysis followed by the reduction of Weinreb amides and a single-step attachment of a 1-methyl-imidazole residue allowed for the concise synthesis of both enantiomers of pilocarpine.
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Abstract
GPCRs remain the most important drug target comprising ~ 34% of the Food and Drug Administration (FDA)-approved drugs. In modern pharmacology of GPCRs, modulating receptor signaling based on requirement of a specific disorder is of immense interest. Classical drugs targeting orthosteric sites in GPCRs completely block the binding of endogenous ligand and consequently inhibit all important signals from a GPCR. Some of many signals elicited by the endogenous ligands may play vital role and inhibiting these may also cause severe side effects in the long run. However, allosteric drugs can modulate GPCR signaling without blocking the endogenous ligand binding. Therefore, allosteric drugs can maintain beneficial signaling of the receptor and prevent unwanted side effects. In this chapter, we will discuss GPCR crystal structures solved with allosteric ligands, advantages of allosteric drugs, and allosteric drugs which are in clinical use or trials.
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Affiliation(s)
- Khuraijam Dhanachandra Singh
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Sadashiva S Karnik
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.
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24
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Abstract
Opioids such as morphine and oxycodone are analgesics frequently prescribed for the treatment of moderate or severe pain. Unfortunately, these medications are associated with exceptionally high abuse potentials and often cause fatal side effects, mainly through the μ-opioid receptor (MOR). Efforts to discover novel, safer, and more efficacious analgesics targeting MOR have encountered challenges. In this review, we summarize alternative strategies and targets that could be used to develop safer nonopioid analgesics. A molecular understanding of G protein-coupled receptor activation and signaling has illuminated not only the complexities of receptor pharmacology but also the potential for pathway-selective agonists and allosteric modulators as safer medications. The availability of structures of pain-related receptors, in combination with high-throughput computational tools, has accelerated the discovery of multitarget ligands with promising pharmacological profiles. Emerging clinical evidence also supports the notion that drugs targeting peripheral opioid receptors have potential as improved analgesic agents.
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Affiliation(s)
- Tao Che
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA; .,Center for Clinical Pharmacology, University of Health Sciences and Pharmacy and Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA;
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25
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Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ. Property-Unmatched Decoys in Docking Benchmarks. J Chem Inf Model 2021; 61:699-714. [PMID: 33494610 PMCID: PMC7913603 DOI: 10.1021/acs.jcim.0c00598] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enrichment of ligands versus property-matched decoys is widely used to test and optimize docking library screens. However, the unconstrained optimization of enrichment alone can mislead, leading to false confidence in prospective performance. This can arise by over-optimizing for enrichment against property-matched decoys, without considering the full spectrum of molecules to be found in a true large library screen. Adding decoys representing charge extrema helps mitigate over-optimizing for electrostatic interactions. Adding decoys that represent the overall characteristics of the library to be docked allows one to sample molecules not represented by ligands and property-matched decoys but that one will encounter in a prospective screen. An optimized version of the DUD-E set (DUDE-Z), as well as Extrema and sets representing broad features of the library (Goldilocks), is developed here. We also explore the variability that one can encounter in enrichment calculations and how that can temper one's confidence in small enrichment differences. The new tools and new decoy sets are freely available at http://tldr.docking.org and http://dudez.docking.org.
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Affiliation(s)
- Reed M Stein
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Ying Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Trent E Balius
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, Maryland 21702, United States
| | - Matt J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Palmer Commons, 100 Washtenaw Ave. #2017, Ann Arbor, Michigan 48109, United States
| | - Jiankun Lyu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Jennifer Young
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Khanh Tang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
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26
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Yang D, Zhou Q, Labroska V, Qin S, Darbalaei S, Wu Y, Yuliantie E, Xie L, Tao H, Cheng J, Liu Q, Zhao S, Shui W, Jiang Y, Wang MW. G protein-coupled receptors: structure- and function-based drug discovery. Signal Transduct Target Ther 2021; 6:7. [PMID: 33414387 PMCID: PMC7790836 DOI: 10.1038/s41392-020-00435-w] [Citation(s) in RCA: 236] [Impact Index Per Article: 78.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023] Open
Abstract
As one of the most successful therapeutic target families, G protein-coupled receptors (GPCRs) have experienced a transformation from random ligand screening to knowledge-driven drug design. We are eye-witnessing tremendous progresses made recently in the understanding of their structure-function relationships that facilitated drug development at an unprecedented pace. This article intends to provide a comprehensive overview of this important field to a broader readership that shares some common interests in drug discovery.
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Affiliation(s)
- Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Qingtong Zhou
- School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
| | - Viktorija Labroska
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Sanaz Darbalaei
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Elita Yuliantie
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Linshan Xie
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Houchao Tao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Qing Liu
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. .,School of Pharmacy, Fudan University, 201203, Shanghai, China.
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27
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Li M, Huang C, Wu X, Ding F, Hu Z, Zhu Y, Zhao L, Hou L, Chen H, Wang H, Xu J, Tang D. The optimization of a novel selective antagonist for human M 2 muscarinic acetylcholine receptor. Bioorg Med Chem Lett 2020; 30:127632. [PMID: 33132116 DOI: 10.1016/j.bmcl.2020.127632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 01/22/2023]
Abstract
Muscarinic acetylcholine receptors (mAChRs) comprise five distinct subtypes denoted M1 to M5. The antagonism of M2 subtype could increase the release of acetylcholine from vesicles into the synaptic cleft and improve postsynaptic functions in the hippocampus via M1 receptor activation, displaying therapeutic potentials for Alzheimer's disease. However, drug development for M2 antagonists is still challenged among different receptor subtypes. In this study, by optimizing a scaffold from virtual screening, we synthesized two focused libraries and generated up to 50 derivatives. By measuring potency and binding selectivity, we discovered a novel M2 antagonist, ligand 47, featuring submicromolar IC50, high M2/M4 selectivity (~30-fold) and suitable lipophilicity (cLogP = 4.55). Further study with these compounds also illustrates the structure-activity relationship of this novel scaffold. Our study could not only provide novel lead structure, which was easy to synthesize, but also offer valuable information for further development of selective M2 ligands.
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Affiliation(s)
- Miaomiao Li
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chen Huang
- Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pu Jian Road, Shanghai 200127, China; College of Medical Imaging, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Xingyu Wu
- College of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Fan Ding
- Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pu Jian Road, Shanghai 200127, China
| | - Zhoumi Hu
- Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pu Jian Road, Shanghai 200127, China
| | - Yan Zhu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lanxue Zhao
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lina Hou
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hongzhuan Chen
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Institute of Interdisciplinary Integrative Biomedical Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hao Wang
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jianrong Xu
- Department of Pharmacology and Chemical Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Dewei Tang
- Department of Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pu Jian Road, Shanghai 200127, China.
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28
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Lazim R, Suh D, Choi S. Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems. Int J Mol Sci 2020; 21:E6339. [PMID: 32882859 PMCID: PMC7504087 DOI: 10.3390/ijms21176339] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently could provide reliable answers to questions pertaining to the structure-function relationship of proteins. Data collated from protein dynamics can be translated into useful statistics that can be exploited to sieve thermodynamics and kinetics crucial for the elucidation of mechanisms responsible for the modulation of biological processes such as protein-ligand binding and protein-protein association. Continuous modernization of simulation tools enables accurate prediction and characterization of the aforementioned mechanisms and these qualities are highly beneficial for the expedition of drug development when effectively applied to structure-based drug design (SBDD). In this review, current all-atom MD simulation methods, with focus on enhanced sampling techniques, utilized to examine protein structure, dynamics, and functions are discussed. This review will pivot around computer calculations of protein-ligand and protein-protein systems with applications to SBDD. In addition, we will also be highlighting limitations faced by current simulation tools as well as the improvements that have been made to ameliorate their efficiency.
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Affiliation(s)
- Raudah Lazim
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
| | - Donghyuk Suh
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
| | - Sun Choi
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Korea
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29
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Maeda S, Xu J, N Kadji FM, Clark MJ, Zhao J, Tsutsumi N, Aoki J, Sunahara RK, Inoue A, Garcia KC, Kobilka BK. Structure and selectivity engineering of the M 1 muscarinic receptor toxin complex. Science 2020; 369:161-167. [PMID: 32646996 DOI: 10.1126/science.aax2517] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 04/21/2020] [Indexed: 12/13/2022]
Abstract
Muscarinic toxins (MTs) are natural toxins produced by mamba snakes that primarily bind to muscarinic acetylcholine receptors (MAChRs) and modulate their function. Despite their similar primary and tertiary structures, MTs show distinct binding selectivity toward different MAChRs. The molecular details of how MTs distinguish MAChRs are not well understood. Here, we present the crystal structure of M1AChR in complex with MT7, a subtype-selective anti-M1AChR snake venom toxin. The structure reveals the molecular basis of the extreme subtype specificity of MT7 for M1AChR and the mechanism by which it regulates receptor function. Through in vitro engineering of MT7 finger regions that was guided by the structure, we have converted the selectivity from M1AChR toward M2AChR, suggesting that the three-finger fold is a promising scaffold for developing G protein-coupled receptor modulators.
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Affiliation(s)
- Shoji Maeda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Jun Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Science, Tsinghua University, Beijing, China
| | | | - Mary J Clark
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Jiawei Zhao
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Junken Aoki
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
| | - Roger K Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Beijing Advanced Innovation Center for Structural Biology, School of Life Science, Tsinghua University, Beijing, China
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30
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Allosteric drugs and mutations: chances, challenges, and necessity. Curr Opin Struct Biol 2020; 62:149-157. [DOI: 10.1016/j.sbi.2020.01.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/16/2020] [Indexed: 12/22/2022]
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31
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Could confounding the allosteric communication of biotic machinery be an alternative path to antibiotics? Proc Natl Acad Sci U S A 2020; 117:8222-8224. [PMID: 32198204 DOI: 10.1073/pnas.2002666117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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32
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Wang H, Reinecke BA, Zhang Y. Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators. J Comput Aided Mol Des 2020; 34:879-895. [PMID: 32193867 DOI: 10.1007/s10822-020-00309-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 03/14/2020] [Indexed: 11/27/2022]
Abstract
Targeting the mu opioid receptor (MOR) by applying orthosteric ligands is the most frequently employed method to treat opioid use disorder (OUD). Unfortunately, most of MOR orthosteric ligands produce severe side effects, mainly due to their low selectivity over other opioid receptors. In contrast, some G protein-coupled receptor allosteric modulators have been reported to exhibit high subtype selectivity and can effectively modulate the potency and/or efficacy of orthosteric ligands. Recently, NAQ and its analog NCQ were identified as novel MOR bitopic modulators. Interestingly, NAQ and NCQ were similar in structure but exhibited different efficacy profiles to the MOR. NAQ exhibited an antagonism activity to the MOR while NCQ showed a partial agonism activity to the MOR. In the present study, molecular modeling methods were applied to explore the putative molecular mechanisms of their different functional profiles to the MOR. When NAQ binding with the inactive MOR, the 'address' portion of NAQ interacted with the MOR allosteric site but showed no significant allosteric modulation of the efficacy of the 'message' portion of NAQ. However, when NCQ binding with the inactive and active MOR, the 'address' portion of NCQ seemed to be able to positively modulate the efficacy of the 'message' portion of NCQ at varying levels. Evidentially, the substituents at the 1'- and 4'-positions of the isoquinoline ring of NCQ seemed to play a critical role in the modulatory function of the 'address' portion of NCQ. These findings will be invaluable to develop our next generation of MOR bitopic modulators with high affinity and subtype selectivity to potentially treat OUD.
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Affiliation(s)
- Huiqun Wang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA
| | - Bethany A Reinecke
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA
| | - Yan Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 E Leigh Street, Richmond, VA, 23298, USA.
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33
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Singh N, Chaput L, Villoutreix BO. Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace. Brief Bioinform 2020; 22:1790-1818. [PMID: 32187356 PMCID: PMC7986591 DOI: 10.1093/bib/bbaa034] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The interplay between life sciences and advancing technology drives a continuous cycle of chemical data growth; these data are most often stored in open or partially open databases. In parallel, many different types of algorithms are being developed to manipulate these chemical objects and associated bioactivity data. Virtual screening methods are among the most popular computational approaches in pharmaceutical research. Today, user-friendly web-based tools are available to help scientists perform virtual screening experiments. This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule docking. This survey first introduces some key concepts and then presents recent and easily accessible virtual screening and related target-fishing tools as well as briefly discusses case studies enabled by some of these web services. Notwithstanding further improvements, already available web-based tools not only contribute to the design of bioactive molecules and assist drug repositioning but also help to generate new ideas and explore different hypotheses in a timely fashion while contributing to teaching in the field of drug development.
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Affiliation(s)
- Natesh Singh
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ludovic Chaput
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Bruno O Villoutreix
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
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34
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Che T, English J, Krumm BE, Kim K, Pardon E, Olsen RHJ, Wang S, Zhang S, Diberto JF, Sciaky N, Carroll FI, Steyaert J, Wacker D, Roth BL. Nanobody-enabled monitoring of kappa opioid receptor states. Nat Commun 2020; 11:1145. [PMID: 32123179 PMCID: PMC7052193 DOI: 10.1038/s41467-020-14889-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 12/22/2022] Open
Abstract
Recent studies show that GPCRs rapidly interconvert between multiple states although our ability to interrogate, monitor and visualize them is limited by a relative lack of suitable tools. We previously reported two nanobodies (Nb39 and Nb6) that stabilize distinct ligand- and efficacy-delimited conformations of the kappa opioid receptor. Here, we demonstrate via X-ray crystallography a nanobody-targeted allosteric binding site by which Nb6 stabilizes a ligand-dependent inactive state. As Nb39 stabilizes an active-like state, we show how these two state-dependent nanobodies can provide real-time reporting of ligand stabilized states in cells in situ. Significantly, we demonstrate that chimeric GPCRs can be created with engineered nanobody binding sites to report ligand-stabilized states. Our results provide both insights regarding potential mechanisms for allosterically modulating KOR with nanobodies and a tool for reporting the real-time, in situ dynamic range of GPCR activity.
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MESH Headings
- Allosteric Site
- Binding Sites
- Biosensing Techniques
- Crystallography, X-Ray
- Cyclic AMP/metabolism
- Dynorphins/chemistry
- Dynorphins/pharmacology
- HEK293 Cells
- Humans
- Luminescent Measurements/methods
- Piperazines/chemistry
- Piperazines/pharmacology
- Piperidines/chemistry
- Piperidines/pharmacology
- Protein Conformation
- Pyrrolidines/chemistry
- Pyrrolidines/pharmacology
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Opioid, kappa/agonists
- Receptors, Opioid, kappa/chemistry
- Receptors, Opioid, kappa/genetics
- Receptors, Opioid, kappa/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/metabolism
- Tetrahydroisoquinolines/chemistry
- Tetrahydroisoquinolines/pharmacology
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Affiliation(s)
- Tao Che
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | - Justin English
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Brian E Krumm
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Kuglae Kim
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, 1050, Belgium
| | - Reid H J Olsen
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Sheng Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Shicheng Zhang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jeffrey F Diberto
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - F Ivy Carroll
- Research Triangle Institute, Research Triangle Park, Durham, NC, USA
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, 1050, Belgium
| | - Daniel Wacker
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Pharmacological Sciences and Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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35
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Jakubik J, El-Fakahany EE. Current Advances in Allosteric Modulation of Muscarinic Receptors. Biomolecules 2020; 10:biom10020325. [PMID: 32085536 PMCID: PMC7072599 DOI: 10.3390/biom10020325] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023] Open
Abstract
Allosteric modulators are ligands that bind to a site on the receptor that is spatially separated from the orthosteric binding site for the endogenous neurotransmitter. Allosteric modulators modulate the binding affinity, potency, and efficacy of orthosteric ligands. Muscarinic acetylcholine receptors are prototypical allosterically-modulated G-protein-coupled receptors. They are a potential therapeutic target for the treatment of psychiatric, neurologic, and internal diseases like schizophrenia, Alzheimer’s disease, Huntington disease, type 2 diabetes, or chronic pulmonary obstruction. Here, we reviewed the progress made during the last decade in our understanding of their mechanisms of binding, allosteric modulation, and in vivo actions in order to understand the translational impact of studying this important class of pharmacological agents. We overviewed newly developed allosteric modulators of muscarinic receptors as well as new spin-off ideas like bitopic ligands combining allosteric and orthosteric moieties and photo-switchable ligands based on bitopic agents.
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Affiliation(s)
- Jan Jakubik
- Department of Neurochemistry, Institute of Physiology CAS, 142 20 Prague, Czech Republic
- Correspondence: (J.J.); (E.E.E.-F.)
| | - Esam E. El-Fakahany
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN 55455, USA
- Correspondence: (J.J.); (E.E.E.-F.)
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36
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MacKerell AD, Jo S, Lakkaraju SK, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochim Biophys Acta Gen Subj 2020; 1864:129519. [PMID: 31911242 DOI: 10.1016/j.bbagen.2020.129519] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/21/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Fragment-based ligand design is used for the development of novel ligands that target macromolecules, most notably proteins. Central to its success is the identification of fragment binding sites that are spatially adjacent such that fragments occupying those sites may be linked to create drug-like ligands. Current experimental and computational approaches that address this problem typically identify only a limited number of sites as well as use a limited number of fragment types. METHODS The site-identification by ligand competitive saturation (SILCS) approach is extended to the identification of fragment bindings sites, with the method termed SILCS-Hotspots. The approach involves precomputation of the SILCS FragMaps following which the identification of Hotspots, performed by identifying of all possible fragment binding sites on the full 3D structure of the protein followed by spatial clustering. RESULTS The SILCS-Hotspots approach identifies a large number of sites on the target protein, including many sites not accessible in experimental structures due to low binding affinities and binding sites on the protein interior. The identified sites are shown to recapitulate the location of known drug-like molecules in both allosteric and orthosteric binding sites on seven proteins including the androgen receptor, the CDK2 and Erk5 kinases, PTP1B phosphatase and three GPCRs; the β2-adrenergic, GPR40 fatty-acid binding and M2-muscarinic receptors. Analysis indicates the importance of considering all possible fragment binding sites, and not just those accessible to experimental methods, when identifying novel binding sites and performing ligand design versus just considering the most favorable sites. The approach is shown to identify a larger number of known binding sites of drug-like molecules versus the commonly used FTMap and Fpocket methods. GENERAL SIGNIFICANCE The present results indicate the potential utility of the SILCS-Hotspots approach for fragment-based rational design of ligands, including allosteric modulators.
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Affiliation(s)
- Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America.
| | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202, United States of America
| | | | - Christoffer Lind
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
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Abstract
Asthma is a heterogeneous inflammatory disease of the airways that is associated with airway hyperresponsiveness and airflow limitation. Although asthma was once simply categorized as atopic or nonatopic, emerging analyses over the last few decades have revealed a variety of asthma endotypes that are attributed to numerous pathophysiological mechanisms. The classification of asthma by endotype is primarily routed in different profiles of airway inflammation that contribute to bronchoconstriction. Many asthma therapeutics target G protein-coupled receptors (GPCRs), which either enhance bronchodilation or prevent bronchoconstriction. Short-acting and long-acting β 2-agonists are widely used bronchodilators that signal through the activation of the β 2-adrenergic receptor. Short-acting and long-acting antagonists of muscarinic acetylcholine receptors are used to reduce bronchoconstriction by blocking the action of acetylcholine. Leukotriene antagonists that block the signaling of cysteinyl leukotriene receptor 1 are used as an add-on therapy to reduce bronchoconstriction and inflammation induced by cysteinyl leukotrienes. A number of GPCR-targeting asthma drug candidates are also in different stages of development. Among them, antagonists of prostaglandin D2 receptor 2 have advanced into phase III clinical trials. Others, including antagonists of the adenosine A2B receptor and the histamine H4 receptor, are in early stages of clinical investigation. In the past decade, significant research advancements in pharmacology, cell biology, structural biology, and molecular physiology have greatly deepened our understanding of the therapeutic roles of GPCRs in asthma and drug action on these GPCRs. This review summarizes our current understanding of GPCR signaling and pharmacology in the context of asthma treatment. SIGNIFICANCE STATEMENT: Although current treatment methods for asthma are effective for a majority of asthma patients, there are still a large number of patients with poorly controlled asthma who may experience asthma exacerbations. This review summarizes current asthma treatment methods and our understanding of signaling and pharmacology of G protein-coupled receptors (GPCRs) in asthma therapy, and discusses controversies regarding the use of GPCR drugs and new opportunities in developing GPCR-targeting therapeutics for the treatment of asthma.
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Affiliation(s)
- Stacy Gelhaus Wendell
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (S.G.W., C.Z.); Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore (H.F.); and Department of Biological Sciences, National University of Singapore, and Center for Computational Biology, DUKE-NUS Medical School, Singapore (H.F.)
| | - Hao Fan
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (S.G.W., C.Z.); Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore (H.F.); and Department of Biological Sciences, National University of Singapore, and Center for Computational Biology, DUKE-NUS Medical School, Singapore (H.F.)
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (S.G.W., C.Z.); Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore (H.F.); and Department of Biological Sciences, National University of Singapore, and Center for Computational Biology, DUKE-NUS Medical School, Singapore (H.F.)
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Molecular Basis of Opioid Action: From Structures to New Leads. Biol Psychiatry 2020; 87:6-14. [PMID: 31653480 PMCID: PMC6898784 DOI: 10.1016/j.biopsych.2019.08.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 02/06/2023]
Abstract
Since the isolation of morphine from the opium poppy over 200 years ago, the molecular basis of opioid action has remained the subject of intense inquiry. The identification of specific receptors responsible for opioid function and the discovery of many chemically diverse molecules with unique opioid-like efficacies have provided glimpses into the molecular logic of opioid action. Recent revolutions in the structural biology of transmembrane proteins have, for the first time, yielded high-resolution views into the 3-dimensional shapes of all 4 opioid receptors. These studies have begun to decode the chemical logic that enables opioids to specifically bind and activate their receptor targets. A combination of spectroscopic experiments and computational simulations has provided a view into the molecular movements of the opioid receptors, which itself gives rise to the complex opioid pharmacology observed at the cellular and behavioral levels. Further diversity in opioid receptor structure is driven by both genetic variation and receptor oligomerization. These insights have enabled computational drug discovery efforts, with some evidence of success in the design of completely novel opioids with unique efficacies. The combined progress over the past few years provides hope for new, efficacious opioids devoid of the side effects that have made them the scourge of humanity for millennia.
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Utilization of Biased G Protein-Coupled ReceptorSignaling towards Development of Safer andPersonalized Therapeutics. Molecules 2019; 24:molecules24112052. [PMID: 31146474 PMCID: PMC6600667 DOI: 10.3390/molecules24112052] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/19/2019] [Accepted: 05/24/2019] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are involved in a wide variety of physiological processes. Therefore, approximately 40% of currently prescribed drugs have targeted this receptor family. Discovery of β-arrestin mediated signaling and also separability of G protein and β-arrestin signaling pathways have switched the research focus in the GPCR field towards development of biased ligands, which provide engagement of the receptor with a certain effector, thus enriching a specific signaling pathway. In this review, we summarize possible factors that impact signaling profiles of GPCRs such as oligomerization, drug treatment, disease conditions, genetic background, etc. along with relevant molecules that can be used to modulate signaling properties of GPCRs such as allosteric or bitopic ligands, ions, aptamers and pepducins. Moreover, we also discuss the importance of inclusion of pharmacogenomics and molecular dynamics simulations to achieve a holistic understanding of the relation between genetic background and structure and function of GPCRs and GPCR-related proteins. Consequently, specific downstream signaling pathways can be enriched while those that bring unwanted side effects can be prevented on a patient-specific basis. This will improve studies that centered on development of safer and personalized therapeutics, thus alleviating the burden on economy and public health.
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40
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Importance of protein dynamics in the structure-based drug discovery of class A G protein-coupled receptors (GPCRs). Curr Opin Struct Biol 2019; 55:147-153. [PMID: 31102980 DOI: 10.1016/j.sbi.2019.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/06/2019] [Accepted: 03/11/2019] [Indexed: 12/11/2022]
Abstract
Demand for novel GPCR modulators is increasing as the association between the GPCR signaling pathway and numerous diseases such as cancers, psychological and metabolic disorders continues to be established. In silico structure-based drug design (SBDD) offers an outlet where researchers could exploit the accumulating structural information of GPCR to expedite the process of drug discovery. The coupling of structure-based approaches such as virtual screening and molecular docking with molecular dynamics and/or Monte Carlo simulation aids in reflecting the dynamics of proteins in nature into previously static docking studies, thus enhancing the accuracy of rationally designed ligands. This review will highlight recent computational strategies that incorporate protein flexibility into SBDD of GPCR-targeted ligands.
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Phua SX, Chan KF, Su CTT, Poh JJ, Gan SKE. Perspective: The promises of a holistic view of proteins-impact on antibody engineering and drug discovery. Biosci Rep 2019; 39:BSR20181958. [PMID: 30630879 PMCID: PMC6398899 DOI: 10.1042/bsr20181958] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/27/2018] [Accepted: 01/09/2019] [Indexed: 12/23/2022] Open
Abstract
The reductionist approach is prevalent in biomedical science. However, increasing evidence now shows that biological systems cannot be simply considered as the sum of its parts. With experimental, technological, and computational advances, we can now do more than view parts in isolation, thus we propose that an increasing holistic view (where a protein is investigated as much as a whole as possible) is now timely. To further advocate this, we review and discuss several studies and applications involving allostery, where distant protein regions can cross-talk to influence functionality. Therefore, we believe that an increasing big picture approach holds great promise, particularly in the areas of antibody engineering and drug discovery in rational drug design.
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Affiliation(s)
- Ser-Xian Phua
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kwok-Fong Chan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jun-Jie Poh
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- APD SKEG Pte Ltd, Singapore
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
- APD SKEG Pte Ltd, Singapore
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
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Wold EA, Chen J, Cunningham KA, Zhou J. Allosteric Modulation of Class A GPCRs: Targets, Agents, and Emerging Concepts. J Med Chem 2019; 62:88-127. [PMID: 30106578 PMCID: PMC6556150 DOI: 10.1021/acs.jmedchem.8b00875] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-protein-coupled receptors (GPCRs) have been tractable drug targets for decades with over one-third of currently marketed drugs targeting GPCRs. Of these, the class A GPCR superfamily is highly represented, and continued drug discovery for this family of receptors may provide novel therapeutics for a vast range of diseases. GPCR allosteric modulation is an innovative targeting approach that broadens the available small molecule toolbox and is proving to be a viable drug discovery strategy, as evidenced by recent FDA approvals and clinical trials. Numerous class A GPCR allosteric modulators have been discovered recently, and emerging trends such as the availability of GPCR crystal structures, diverse functional assays, and structure-based computational approaches are improving optimization and development. This Perspective provides an update on allosterically targeted class A GPCRs and their disease indications and the medicinal chemistry approaches toward novel allosteric modulators and highlights emerging trends and opportunities in the field.
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Affiliation(s)
- Eric A. Wold
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jianping Chen
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Kathryn A. Cunningham
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jia Zhou
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
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43
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Wang J, Miao Y. Recent advances in computational studies of GPCR-G protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 116:397-419. [PMID: 31036298 PMCID: PMC6986689 DOI: 10.1016/bs.apcsb.2018.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions are key in cellular signaling. G protein-coupled receptors (GPCRs), the largest superfamily of human membrane proteins, are able to transduce extracellular signals (e.g., hormones and neurotransmitters) to intracellular proteins, in particular the G proteins. Since GPCRs serve as primary targets of ~1/3 of currently marketed drugs, it is important to understand mechanisms of GPCR signaling in order to design selective and potent drug molecules. This chapter focuses on recent advances in computational studies of the GPCR-G protein interactions using bioinformatics, protein-protein docking and molecular dynamics simulation approaches.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States.
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44
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New Binding Sites, New Opportunities for GPCR Drug Discovery. Trends Biochem Sci 2019; 44:312-330. [PMID: 30612897 DOI: 10.1016/j.tibs.2018.11.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/11/2018] [Accepted: 11/27/2018] [Indexed: 12/29/2022]
Abstract
Many central biological events rely on protein-ligand interactions. The identification and characterization of protein-binding sites for ligands are crucial for the understanding of functions of both endogenous ligands and synthetic drug molecules. G protein-coupled receptors (GPCRs) typically detect extracellular signal molecules on the cell surface and transfer these chemical signals across the membrane, inducing downstream cellular responses via G proteins or β-arrestin. GPCRs mediate many central physiological processes, making them important targets for modern drug discovery. Here, we focus on the most recent breakthroughs in finding new binding sites and binding modes of GPCRs and their potentials for the development of new medicines.
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45
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He X, Ni D, Lu S, Zhang J. Characteristics of Allosteric Proteins, Sites, and Modulators. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:107-139. [DOI: 10.1007/978-981-13-8719-7_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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46
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Kleist AB, Peterson F, Tyler RC, Gustavsson M, Handel TM, Volkman BF. Solution NMR spectroscopy of GPCRs: Residue-specific labeling strategies with a focus on 13C-methyl methionine labeling of the atypical chemokine receptor ACKR3. Methods Cell Biol 2018; 149:259-288. [PMID: 30616824 DOI: 10.1016/bs.mcb.2018.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The past decade has witnessed remarkable progress in the determination of G protein-coupled receptor (GPCR) structures, profoundly expanding our understanding of how GPCRs recognize ligands, become activated, and interact with intracellular signaling components. In recent years, numerous studies have used solution nuclear magnetic resonance (NMR) spectroscopy to investigate GPCRs, providing fundamental insights into GPCR conformational changes, allostery, dynamics, and other facets of GPCR function are challenging to study using other structural techniques. Despite these advantages, NMR-based studies of GPCRs are few relative to the number of published structures, due in part to the challenges and limitations of NMR for the characterization of large membrane proteins. Several studies have circumvented these challenges using a variety of isotopic labeling strategies, including side chain derivatization and metabolic incorporation of NMR-active nuclei. In this chapter, we provide an overview of different isotopic labeling strategies and describe an in-depth protocol for the expression, purification, and NMR studies of the chemokine GPCR atypical chemokine receptor 3 (ACKR3) via 13CH3-methionine incorporation. The goal of this chapter is to provide a resource to the GPCR community for those interested in pursuing NMR studies of GPCRs.
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Affiliation(s)
- Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Francis Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Robert C Tyler
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States.
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Weiss D, Karpiak J, Huang XP, Sassano MF, Lyu J, Roth BL, Shoichet BK. Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets. J Med Chem 2018; 61:6830-6845. [PMID: 29990431 PMCID: PMC6105036 DOI: 10.1021/acs.jmedchem.8b00718] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 12/14/2022]
Abstract
To investigate large library docking's ability to find molecules with joint activity against on-targets and selectivity versus antitargets, the dopamine D2 and serotonin 5-HT2A receptors were targeted, seeking selectivity against the histamine H1 receptor. In a second campaign, κ-opioid receptor ligands were sought with selectivity versus the μ-opioid receptor. While hit rates ranged from 40% to 63% against the on-targets, they were just as good against the antitargets, even though the molecules were selected for their putative lack of binding to the off-targets. Affinities, too, were often as good or better for the off-targets. Even though it was occasionally possible to find selective molecules, such as a mid-nanomolar D2/5-HT2A ligand with 21-fold selectivity versus the H1 receptor, this was the exception. Whereas false-negatives are tolerable in docking screens against on-targets, they are intolerable against antitargets; addressing this problem may demand new strategies in the field.
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Affiliation(s)
- Dahlia
R. Weiss
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California 94158-2550, United States
| | - Joel Karpiak
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California 94158-2550, United States
| | - Xi-Ping Huang
- Department
of Pharmacology and National Institute of Mental Health Psychoactive
Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Maria F. Sassano
- Department
of Pharmacology and National Institute of Mental Health Psychoactive
Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jiankun Lyu
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California 94158-2550, United States
| | - Bryan L. Roth
- Department
of Pharmacology and National Institute of Mental Health Psychoactive
Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California 94158-2550, United States
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Yuan X, Xu Y. Recent Trends and Applications of Molecular Modeling in GPCR⁻Ligand Recognition and Structure-Based Drug Design. Int J Mol Sci 2018; 19:ijms19072105. [PMID: 30036949 PMCID: PMC6073596 DOI: 10.3390/ijms19072105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors represent the largest family of human membrane proteins and are modulated by a variety of drugs and endogenous ligands. Molecular modeling techniques, especially enhanced sampling methods, have provided significant insight into the mechanism of GPCR–ligand recognition. Notably, the crucial role of the membrane in the ligand-receptor association process has earned much attention. Additionally, docking, together with more accurate free energy calculation methods, is playing an important role in the design of novel compounds targeting GPCRs. Here, we summarize the recent progress in the computational studies focusing on the above issues. In the future, with continuous improvement in both computational hardware and algorithms, molecular modeling would serve as an indispensable tool in a wider scope of the research concerning GPCR–ligand recognition as well as drug design targeting GPCRs.
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Affiliation(s)
- Xiaojing Yuan
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China.
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49
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Structural insights into G-protein-coupled receptor allostery. Nature 2018; 559:45-53. [DOI: 10.1038/s41586-018-0259-z] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/17/2018] [Indexed: 01/14/2023]
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