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Nipper MA, Helms ML, Finn DA, Ryabinin AE. Stress-enhanced ethanol drinking does not increase sensitivity to the effects of a CRF-R1 antagonist on ethanol intake in male and female mice. Alcohol 2024; 120:73-83. [PMID: 38185336 PMCID: PMC11326135 DOI: 10.1016/j.alcohol.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 01/09/2024]
Abstract
Research confirms that stress is associated with alcohol drinking and relapse in males and females and that there are sex differences in the alcohol-related adaptations of stress pathways. The predator stress (PS) model of traumatic stress produces an increase in alcohol drinking or self-administration in a subpopulation of rodents, so it is utilized as an animal model of comorbid alcohol use disorder (AUD) and post-traumatic stress disorder (PTSD). Previous work determined that sensitivity to PS-enhanced drinking produced sex differences in proteins related to stress-regulating systems in the medial prefrontal cortex and hippocampus. The present studies examined whether male and female C57BL/6J mice differ in sensitivity to the ability of the corticotropin releasing factor receptor 1 antagonist CP-376395 to decrease PS-enhanced drinking. In control studies, CP-376395 doses of 5, 10, and 20 mg/kg dose-dependently decreased 4-h ethanol drinking. Next, CP-376395 doses of 5 and 10 mg/kg were tested for effects on ethanol drinking in mice with differential sensitivity to PS-enhanced drinking. Subgroups of "Sensitive" and "Resilient" male and female mice were identified based on changes in ethanol intake in an unrestricted-access ethanol-drinking procedure following four exposures to PS (dirty rat bedding). During the first 2 h post-injection of CP-376395, both doses significantly decreased ethanol licks versus vehicle in the females, with no significant interaction between subgroups, whereas the 10 mg/kg dose significantly decreased ethanol licks versus vehicle in the "Resilient" males. Thus, sensitivity to the suppressive effect of CP-376395 on stress-induced ethanol intake was greater in females versus males, whereas sensitivity and resilience to PS-enhanced drinking produced differential sensitivity to the ability of CP-376395 to decrease ethanol drinking only in male mice. Our results argue against greater efficacy of CRF-R1's ability to decrease ethanol intake in subjects with traumatic stress-enhanced ethanol drinking.
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Affiliation(s)
- Michelle A Nipper
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, United States
| | - Melinda L Helms
- Department of Research, VA Portland Health Care System, Portland, OR 97239, United States
| | - Deborah A Finn
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, United States; Department of Research, VA Portland Health Care System, Portland, OR 97239, United States
| | - Andrey E Ryabinin
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, United States.
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2
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The full activation mechanism of the adenosine A 1 receptor revealed by GaMD and Su-GaMD simulations. Proc Natl Acad Sci U S A 2022; 119:e2203702119. [PMID: 36215480 PMCID: PMC9586258 DOI: 10.1073/pnas.2203702119] [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] [Indexed: 11/18/2022] Open
Abstract
The full activation process of G protein-coupled receptor (GPCR) plays an important role in cellular signal transduction. However, it remains challenging to simulate the whole process in which the GPCR is recognized and activated by a ligand and then couples to the G protein on a reasonable simulation timescale. Here, we developed a molecular dynamics (MD) approach named supervised (Su) Gaussian accelerated MD (GaMD) by incorporating a tabu-like supervision algorithm into a standard GaMD simulation. By using this Su-GaMD method, from the active and inactive structure of adenosine A1 receptor (A1R), we successfully revealed the full activation mechanism of A1R, including adenosine (Ado)-A1R recognition, preactivation of A1R, and A1R-G protein recognition, in hundreds of nanoseconds of simulations. The binding of Ado to the extracellular side of A1R initiates conformational changes and the preactivation of A1R. In turn, the binding of Gi2 to the intracellular side of A1R causes a decrease in the volume of the extracellular orthosteric site and stabilizes the binding of Ado to A1R. Su-GaMD could be a useful tool to reconstruct or even predict ligand-protein and protein-protein recognition pathways on a short timescale. The intermediate states revealed in this study could provide more detailed complementary structural characterizations to facilitate the drug design of A1R in the future.
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Mahamudul Hassan MM, Mondal B, Singh S, Haldar C, Chaturvedi J, Bisht R, Sunoj RB, Chattopadhyay B. Ir-Catalyzed Ligand-Free Directed C–H Borylation of Arenes and Pharmaceuticals: Detailed Mechanistic Understanding. J Org Chem 2022; 87:4360-4375. [DOI: 10.1021/acs.joc.2c00046] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mirja Md Mahamudul Hassan
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Biplab Mondal
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Sukriti Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chabush Haldar
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Jagriti Chaturvedi
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Ranjana Bisht
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Raghavan B. Sunoj
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Buddhadeb Chattopadhyay
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
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Bai Q, Tan S, Pérez-Sánchez H, Feng H, Feng L, Liu H, Yao X. Conformation Transition of Intracellular Part of Glucagon Receptor in Complex With Agonist Glucagon by Conventional and Accelerated Molecular Dynamics Simulations. Front Chem 2019; 7:851. [PMID: 31921774 PMCID: PMC6928006 DOI: 10.3389/fchem.2019.00851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 11/22/2019] [Indexed: 12/17/2022] Open
Abstract
The inactive conformations of glucagon receptor (GCGR) are widely reported by crystal structures that support the precision structure for drug discovery of type 2 diabetes. The previous study shows that the intracellular part is open in the glucagon-bound GCGR (glu-GCGR) and closed in the apo-GCGR by accelerated molecular dynamics (aMD) simulations. However, the crystal structure of GCGR in complex with partial agonist shows that the intracellular part is closed in the inactive conformation. To understand the differences between the studies of aMD simulations and crystal structure, the 2,500 ns conventional molecular dynamics (cMD) simulations are performed on the simulated model of glu-GCGR. The result shows that the transmembrane helices (TMH) 6 of glu-GCGR is outward ~4 Å to drive the intracellular part of glu-GCGR open until ~390 ns cMD simulations. The (TMH) 6 of glu-GCGR becomes closed after ~490 ns cMD simulations, which are consistent with the crystal structure of GCGR in complex with the partial agonist. To further elucidate the activation mechanism of GCGR deeply, the simulated models of glu-GCGR, apo-GCGR, and antagonist-bound GCGR (ant-GCGR) are constructed to perform 10 of parallel 300 ns aMD simulations, respectively. The results show that both of glu-GCGR and apo-GCGR can generate the open conformations of the intracellular part. But the glu-GCGR has the higher percentage of open conformations than apo-GCGR. The ant-GCGR is restricted to generate the open conformations of the intracellular part by antagonist MK-0893. It indicates that the glu-GCGR, apo-GCGR, and ant-GCGR can be distinguished by the aMD simulated method. Free energy landscape shows that the open conformations of the intracellular part of GCGR are in intermediate state. Our results show that aMD simulations enhance the space samplings of open conformations of GCGR via adding extra boost potential. It indicates that the aMD simulations are an effective way for drug discovery of GCGR.
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Affiliation(s)
- Qifeng Bai
- Key Lab of Preclinical Study for New Drugs of Gansu Province, Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Shuoyan Tan
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Horacio Pérez-Sánchez
- Computer Science Department, Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
| | - Haixia Feng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Liya Feng
- Key Lab of Preclinical Study for New Drugs of Gansu Province, Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - HuanXiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- Key Lab of Preclinical Study for New Drugs of Gansu Province, Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
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5
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Zou Y, Ewalt J, Ng HL. Recent Insights from Molecular Dynamics Simulations for G Protein-Coupled Receptor Drug Discovery. Int J Mol Sci 2019; 20:E4237. [PMID: 31470676 PMCID: PMC6747122 DOI: 10.3390/ijms20174237] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are critical drug targets. GPCRs convey signals from the extracellular to the intracellular environment through G proteins. Some ligands that bind to GPCRs activate different downstream signaling pathways. G protein activation, or -arrestin biased signaling, involves ligands binding to receptors and stabilizing conformations that trigger a specific pathway. -arrestin biased signaling has become a hot target for structure-based drug discovery. However, challenges include that there are few crystal structures available in the Protein Data Bank and that GPCRs are highly dynamic. Hence, molecular dynamics (MD) simulations are especially valuable for obtaining detailed mechanistic information, including identification of allosteric sites and understanding modulators' interactions with receptors and ligands. Here, we highlight recent MD simulation studies and enhanced sampling methods used to study biased G protein-coupled receptor signaling and their conformational dynamics as well as applications to drug discovery.
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Affiliation(s)
- Ye Zou
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - John Ewalt
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Ho-Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA.
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6
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Zhang J, Bai Q, Pérez-Sánchez H, Shang S, An X, Yao X. Investigation of ECD conformational transition mechanism of GLP-1R by molecular dynamics simulations and Markov state model. Phys Chem Chem Phys 2019; 21:8470-8481. [PMID: 30957116 DOI: 10.1039/c9cp00080a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
As a member of the class B G protein-coupled receptors (GPCRs), the glucagon-like peptide-1 (GLP-1) can regulate the blood glucose level by binding to the glucagon-like peptide-1 receptor (GLP-1R). Since the extracellular domain (ECD) of GLP-1R is considered as one of the binding sites of GLP-1, the open and closed states of ECD play an important role in the binding process of GLP-1. To investigate the transition path of GLP-1R ECD, the crystal structures of GLP-1R in its bound and unbound states (apo-state) are chosen to perform a total of 1.6 μs of molecular dynamics simulations. The simulated results show that the ECD of GLP-1R closes in the GLP-1 bound state and opens in the GLP-1 unbound state. To determine the critical role that GLP-1 played in regulating the open and closed states of the ECD, we applied the independent gradient model (IGM) to the simulation trajectories. We found that the "hand-like" N-terminal of the GLP-1R ECD plays an important role in the GLP-1 binding. In contrast, the apo-state GLP-1R ECD opens and exposes the two ligand binding domains of GLP-1 after 200 ns of simulations. To elucidate the open and closed mechanisms of GLP-1R ECD in the apo-state and GLP-1 bound state, the Markov state model (MSM) is performed on the MD simulation trajectories. Our results provide possible transition pathways from the closed state to open state of the apo-state GLP-1R ECD. Each pathway contains several intermediate states that correspond to different local minima in deep wells. The dynamical relationships and the most possible conversion pathway between two states are detailed through the MSM analysis. Our results profile the conformation transition mechanism of the GLP-1R ECD and will help in hypoglycemic peptide design of GLP-1R.
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Affiliation(s)
- Jintu Zhang
- Key Lab of Preclinical Study for New Drugs of Gansu Province, Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu 730000, P. R. China
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7
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Li Y, Yin C, Liu P, Li D, Lin J. Identification of a Different Agonist-Binding Site and Activation Mechanism of the Human P2Y 1 Receptor. Sci Rep 2017; 7:13764. [PMID: 29062134 PMCID: PMC5653743 DOI: 10.1038/s41598-017-14268-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/09/2017] [Indexed: 02/03/2023] Open
Abstract
The human P2Y1 receptor (P2Y1R) is a purinergic G-protein-coupled receptor (GPCR) that functions as a receptor for adenosine 5'-diphosphate (ADP). An antagonist of P2Y1R might potentially have antithrombotic effects, whereas agonists might serve as antidiabetic agents. On the basis of the antagonist-bound MRS2500-P2Y1R crystal structure, we constructed computational models of apo-P2Y1R and the agonist-receptor complex 2MeSADP-P2Y1R. We then performed conventional molecular dynamics (cMD) and accelerated molecular dynamics (aMD) simulations to study the conformational dynamics after binding with agonist/antagonist as well as the P2Y1R activation mechanism. We identified a new agonist-binding site of P2Y1R that is consistent with previous mutagenesis data. This new site is deeper than those of the agonist ADP in the recently simulated ADP-P2Y1R structure and the antagonist MRS2500 in the MRS2500-P2Y1R crystal structure. During P2Y1R activation, the cytoplasmic end of helix VI shifts outward 9.1 Å, the Ser1463.47-Tyr2375.58 hydrogen bond breaks, a Tyr2375.58-Val2626.37 hydrogen bond forms, and the conformation of the χ1 rotamer of Phe2696.44 changes from parallel to perpendicular to helix VI. The apo-P2Y1R system and the MRS2500-P2Y1R system remain inactive. The newly identified agonist binding site and activation mechanism revealed in this study may aid in the design of P2Y1R antagonists/agonists as antithrombotic/antidiabetic agents, respectively.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353, China
| | - Can Yin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353, China
- Pharmaceutical Intelligence Platform, Tianjin Joint Academy of Biomedicine and Technology, Tianjin, 300457, China
| | - Pi Liu
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dongmei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353, China.
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353, China.
- Pharmaceutical Intelligence Platform, Tianjin Joint Academy of Biomedicine and Technology, Tianjin, 300457, China.
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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8
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Adaptive simulations, towards interactive protein-ligand modeling. Sci Rep 2017; 7:8466. [PMID: 28814780 PMCID: PMC5559483 DOI: 10.1038/s41598-017-08445-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022] Open
Abstract
Modeling the dynamic nature of protein-ligand binding with atomistic simulations is one of the main challenges in computational biophysics, with important implications in the drug design process. Although in the past few years hardware and software advances have significantly revamped the use of molecular simulations, we still lack a fast and accurate ab initio description of the binding mechanism in complex systems, available only for up-to-date techniques and requiring several hours or days of heavy computation. Such delay is one of the main limiting factors for a larger penetration of protein dynamics modeling in the pharmaceutical industry. Here we present a game-changing technology, opening up the way for fast reliable simulations of protein dynamics by combining an adaptive reinforcement learning procedure with Monte Carlo sampling in the frame of modern multi-core computational resources. We show remarkable performance in mapping the protein-ligand energy landscape, being able to reproduce the full binding mechanism in less than half an hour, or the active site induced fit in less than 5 minutes. We exemplify our method by studying diverse complex targets, including nuclear hormone receptors and GPCRs, demonstrating the potential of using the new adaptive technique in screening and lead optimization studies.
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9
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Spierling SR, Zorrilla EP. Don't stress about CRF: assessing the translational failures of CRF 1antagonists. Psychopharmacology (Berl) 2017; 234:1467-1481. [PMID: 28265716 PMCID: PMC5420464 DOI: 10.1007/s00213-017-4556-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 01/27/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Dr. Athina Markou sought treatments for a common neural substrate shared by depression and drug dependence. Antagonists of corticotropin-releasing factor (CRF) receptors, a target of interest to her, have not reached the clinic despite strong preclinical rationale and sustained translational efforts. METHODS We explore potential causes for the failure of CRF1 antagonists and review recent findings concerning CRF-CRF1 systems in psychopathology. RESULTS Potential causes for negative outcomes include (1) poor safety and efficacy of initial drug candidates due to bad pharmacokinetic and physicochemical properties, (2) specificity problems with preclinical screens, (3) the acute nature of screens vs. late-presenting patients, (4) positive preclinical results limited to certain models and conditions with dynamic CRF-CRF1 activation not homologous to tested patients, (5) repeated CRF1 activation-induced plasticity that reduces the importance of ongoing CRF1 agonist stimulation, and (6) therapeutic silencing which may need to address CRF2 receptor or CRF-binding protein molecules, constitutive CRF1 activity, or molecules that influence agonist-independent activity or to target structural regions other than the allosteric site bound by all drug candidates. We describe potential markers of activation towards individualized treatment, human genetic, and functional data that still implicate CRF1 systems in emotional disturbance, sex differences, and suggestive clinical findings for CRF1 antagonists in food craving and CRF-driven HPA-axis overactivation. CONCLUSION The therapeutic scope of selective CRF1 antagonists now appears narrower than had been hoped. Yet, much remains to be learned about CRF's role in the neurobiology of dysphoria and addiction and the potential for novel anti-CRF therapies therein.
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Affiliation(s)
- Samantha R Spierling
- Committee on the Neurobiology of Addictive Disorders, SP30-2400, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Eric P Zorrilla
- Committee on the Neurobiology of Addictive Disorders, SP30-2400, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
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10
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Du J, Liu L, Guo LZ, Yao XJ, Yang JM. Molecular basis of P450 OleT JE: an investigation of substrate binding mechanism and major pathways. J Comput Aided Mol Des 2017; 31:483-495. [PMID: 28342136 DOI: 10.1007/s10822-017-0013-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 02/23/2017] [Indexed: 02/02/2023]
Abstract
Cytochrome P450 OleTJE has attracted much attention for its ability to catalyze the decarboxylation of long chain fatty acids to generate alkenes, which are not only biofuel molecule, but also can be used broadly for making lubricants, polymers and detergents. In this study, the molecular basis of the binding mechanism of P450 OleTJE for arachidic acid, myristic acid, and caprylic acid was investigated by utilizing conventional molecular dynamics simulation and binding free energy calculations. Moreover, random acceleration molecular dynamics (RAMD) simulations were performed to uncover the most probable access/egress channels for different fatty acids. The predicted binding free energy shows an order of arachidic acid < myristic acid < caprylic acid. Key residues interacting with three substrates and residues specifically binding to one of them were identified. The RAMD results suggest the most likely channel for arachidic acid, myristic acid, and caprylic acid are 2e/2b, 2a and 2f/2a, respectively. It is suggested that the reaction is easier to carry out in myristic acid bound system than those in arachidic acid and caprylic acid bound system based on the distance of Hβ atom of substrate relative to P450 OleTJE Compound I states. This study provided novel insight to understand the substrate preference mechanism of P450 OleTJE and valuable information for rational enzyme design for short chain fatty acid decarboxylation.
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Affiliation(s)
- Juan Du
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Liu
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Li Zhong Guo
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiao Jun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Jian Ming Yang
- Key Lab of Applied Mycology, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China.
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11
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Li Y, Sun J, Li D, Lin J. Activation and conformational dynamics of a class B G-protein-coupled glucagon receptor. Phys Chem Chem Phys 2016; 18:12642-50. [PMID: 27094704 DOI: 10.1039/c6cp00798h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human glucagon receptor (GCGR) is a class B G-protein-coupled receptor (GPCR). The GCGR can be activated by glucagon and regulates the release of glucose. The GCGR has been proposed to be an important drug target for type 2 diabetes. Based on the structural model of a full-length glucagon-bound GCGR (glu-GCGR), we performed accelerated molecular dynamics (aMD) simulations, potential of mean force (PMF) calculations, cross-correlation analysis and community network analysis to study the activation mechanism and the conformational dynamics during the activation process. The PMF map depicts three different conformational states of the GCGR: the inactive, intermediate and active states. The activation of the GCGR is characterized by the outward movement of the intracellular side of helix VI. In the active state of the GCGR, the Arg173(2.46)-Ser350(6.41) and Glu245(3.50)-Thr351(6.42) hydrogen bonds break, and the χ1 rotamer of Phe322(5.54) changes from perpendicular to parallel to helix VI. The binding of the agonist glucagon decreases the correlated motions of the extracellular loops (ELCs) and the helices around the glucagon-binding site. During the activation of the GCGR, the connections between the intracellular sides of helices become weaker, and the connections between glucagon and ECLs and the extracellular sides of helices become stronger. These facilitate G-protein coupling on the intracellular side and glucagon binding on the extracellular side, and stabilize the GCGR in the active state. We expect that this study can provide useful information on the activation mechanism of the GCGR and facilitate the future design of GCGR inhibitors.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China.
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12
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Wang DD, Lee VHF, Zhu G, Zou B, Ma L, Yan H. Selectivity profile of afatinib for EGFR-mutated non-small-cell lung cancer. MOLECULAR BIOSYSTEMS 2016; 12:1552-63. [DOI: 10.1039/c6mb00038j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The EGFR mutation-response or mutation-PFS correlation for afatinib in NSCLC treatment was computationally profiled, promoting specialized and innovative drug design.
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Affiliation(s)
- Debby D. Wang
- Caritas Institute of Higher Education
- New Territories
- China
- Department of Electronic Engineering
- City University of Hong Kong
| | - Victor H. F. Lee
- Department of Clinical Oncology
- Li Ka Shing Faculty of Medicine
- The University of Hong Kong
- Pokfulam
- China
| | - Guangyu Zhu
- Department of Biology and Chemistry
- City University of Hong Kong
- Kowloon
- China
| | - Bin Zou
- Department of Electronic Engineering
- City University of Hong Kong
- Kowloon
- China
| | - Lichun Ma
- Department of Electronic Engineering
- City University of Hong Kong
- Kowloon
- China
| | - Hong Yan
- Department of Electronic Engineering
- City University of Hong Kong
- Kowloon
- China
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13
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Niu Y, Li S, Pan D, Liu H, Yao X. Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: insight from random acceleration and steered molecular dynamics simulations. Phys Chem Chem Phys 2016; 18:5622-9. [DOI: 10.1039/c5cp06257h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Random acceleration and steered molecular dynamics simulations reveal the unbinding pathway of B-RAF inhibitors and the difference in the residence time.
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Affiliation(s)
- Yuzhen Niu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Shuyan Li
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Dabo Pan
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | | | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- Key Lab of Preclinical Study for New Drugs of Gansu Province
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14
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Bai Q, Zhang Y, Li X, Chen W, Liu H, Yao X. Computational study on the interaction between CCR5 and HIV-1 entry inhibitor maraviroc: insight from accelerated molecular dynamics simulation and free energy calculation. Phys Chem Chem Phys 2015; 16:24332-8. [PMID: 25296959 DOI: 10.1039/c4cp03331k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
C-C chemokine receptor type 5 (CCR5) is the co-receptor of human immunodeficiency virus type 1 (HIV-1) and plays an important role in HIV-1 virus infection. Maraviroc has been proved to be effective for anti-HIV-1 by targeting CCR5. Understanding the detailed interaction mechanism between CCR5 and Maraviroc will be of great help to the rational design of a more potential inverse agonist to block HIV-1 infection. Here, we performed molecular dynamics (MD) simulation and accelerated MD simulation (aMD) to study the interaction mechanism between CCR5 and Maraviroc based on a recently reported crystal structure. The results of MD simulation demonstrate that Maraviroc can form stable hydrogen bonds with residues Tyr37(1.39), Tyr251(6.51) and Glu283(7.39). The results of aMD simulation indicate that the carboxamide moiety is more flexible than the tropane group of Maraviroc in the pocket of CCR5. The electrostatic potential analysis proves that Maraviroc can escape from the pocket of CCR5 along the negative electrostatic potential pathway during the dissociation process. The free energy calculation illustrates that there exist three binding pockets during the dissociation process of Maraviroc. Our results will be useful for understanding the interaction mechanism between CCR5 and Maraviroc as well as for the rational design of a more potent inverse agonist.
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Affiliation(s)
- Qifeng Bai
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, P. R. China.
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15
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Bai Q, Pérez-Sánchez H, Zhang Y, Shao Y, Shi D, Liu H, Yao X. Ligand induced change of β2 adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analysis. Phys Chem Chem Phys 2015; 16:15874-85. [PMID: 24962153 DOI: 10.1039/c4cp01185f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The reported crystal structures of β2 adrenergic receptor (β2AR) reveal that the open and closed states of the water channel are correlated with the inactive and active conformations of β2AR. However, more details about the process by which the water channel states are affected by the active to inactive conformational change of β2AR remain illusive. In this work, molecular dynamics simulations are performed to study the dynamical inactive and active conformational change of β2AR induced by inverse agonist ICI 118,551. Markov state model analysis and free energy calculation are employed to explore the open and close states of the water channel. The simulation results show that inverse agonist ICI 118,551 can induce water channel opening during the conformational transition of β2AR. Markov state model (MSM) analysis proves that the energy contour can be divided into seven states. States S1, S2 and S5, which represent the active conformation of β2AR, show that the water channel is in the closed state, while states S4 and S6, which correspond to the intermediate state conformation of β2AR, indicate the water channel opens gradually. State S7, which represents the inactive structure of β2AR, corresponds to the full open state of the water channel. The opening mechanism of the water channel is involved in the ligand-induced conformational change of β2AR. These results can provide useful information for understanding the opening mechanism of the water channel and will be useful for the rational design of potent inverse agonists of β2AR.
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Affiliation(s)
- Qifeng Bai
- Department of Chemistry, Lanzhou University, Lanzhou 730000, China.
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16
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Sun X, Cheng J, Wang X, Tang Y, Ågren H, Tu Y. Residues remote from the binding pocket control the antagonist selectivity towards the corticotropin-releasing factor receptor-1. Sci Rep 2015; 5:8066. [PMID: 25628267 PMCID: PMC4308710 DOI: 10.1038/srep08066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/02/2015] [Indexed: 01/01/2023] Open
Abstract
The corticotropin releasing factors receptor-1 and receptor-2 (CRF1R and CRF2R) are therapeutic targets for treating neurological diseases. Antagonists targeting CRF1R have been developed for the potential treatment of anxiety disorders and alcohol addiction. It has been found that antagonists targeting CRF1R always show high selectivity, although CRF1R and CRF2R share a very high rate of sequence identity. This has inspired us to study the origin of the selectivity of the antagonists. We have therefore built a homology model for CRF2R and carried out unbiased molecular dynamics and well-tempered metadynamics simulations for systems with the antagonist CP-376395 in CRF1R or CRF2R to address this issue. We found that the side chain of Tyr(6.63) forms a hydrogen bond with the residue remote from the binding pocket, which allows Tyr(6.63) to adopt different conformations in the two receptors and results in the presence or absence of a bottleneck controlling the antagonist binding to or dissociation from the receptors. The rotameric switch of the side chain of Tyr356(6.63) allows the breaking down of the bottleneck and is a perquisite for the dissociation of CP-376395 from CRF1R.
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Affiliation(s)
- Xianqiang Sun
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Jianxin Cheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xu Wang
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
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17
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Xu J, Wang Z, Liu P, Li D, Lin J. An insight into antagonist binding and induced conformational dynamics of class B GPCR corticotropin-releasing factor receptor 1. MOLECULAR BIOSYSTEMS 2015; 11:2042-50. [DOI: 10.1039/c5mb00159e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The binding of small-molecule antagonists, CP-376395 and MTIP, would induce conformational dynamics behaviors of CRF1R.
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Affiliation(s)
- Junli Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy
- Nankai University
- Tianjin 300071
- China
- Pharmaceutical Intelligence Platform
| | - Zhonghua Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy
- Nankai University
- Tianjin 300071
- China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy
- Nankai University
- Tianjin 300071
- China
| | - Dongmei Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy
- Nankai University
- Tianjin 300071
- China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy
- Nankai University
- Tianjin 300071
- China
- Pharmaceutical Intelligence Platform
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18
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Kooistra AJ, de Graaf C, Timmerman H. The receptor concept in 3D: from hypothesis and metaphor to GPCR-ligand structures. Neurochem Res 2014; 39:1850-61. [PMID: 25103230 DOI: 10.1007/s11064-014-1398-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 12/17/2022]
Abstract
The first mentioning of the word "receptor" for the structure with which a bioactive compound should react for obtaining its specific influence on a physiological system goes back to the years around 1900. The receptor concept was adapted from the lock and key theory for the enzyme substrate and blockers interactions. Through the years the concept, in the beginning rather being a metaphor, not a model, was refined and became reality in recent years. Not only the structures of receptors were elucidated, also the receptor machineries were unraveled. Following a brief historical review we will describe how the recent breakthroughs in the experimental determination of G protein-coupled receptor (GPCR) crystal structures can be complemented by computational modeling, medicinal chemistry, biochemical, and molecular pharmacological studies to obtain new insights into the molecular determinants of GPCR-ligand binding and activation. We will furthermore discuss how this information can be used for structure-based discovery of novel GPCR ligands that bind specific (allosteric) binding sites with desired effects on GPCR functional activity.
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Affiliation(s)
- Albert J Kooistra
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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