1
|
Isu UH, Badiee SA, Polasa A, Tabari SH, Derakhshani-Molayousefi M, Moradi M. Cholesterol Dependence of the Conformational Changes in Metabotropic Glutamate Receptor 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589854. [PMID: 38659864 PMCID: PMC11042357 DOI: 10.1101/2024.04.17.589854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Metabotropic glutamate receptors (mGluRs) are class C G protein-coupled receptors that function as obligate dimers in regulating neurotransmission and synaptic plasticity in the central nervous system. The mGluR1 subtype has been shown to be modulated by the membrane lipid environment, particularly cholesterol, though the molecular mechanisms remain elusive. In this study, we employed all-atom molecular dynamics simulations to investigate the effects of cholesterol on the conformational dynamics of the mGluR1 seven-transmembrane (7TM) domain in an inactive state model. Simulations were performed with three different cholesterol concentrations (0%, 10%, and 25%) in a palmitoyl-oleoyl phosphatidylcholine (POPC) lipid bilayer system. Our results demonstrate that cholesterol induces conformational changes in the mGluR1 dimer more significantly than in the individual protomers. Notably, cholesterol modulates the dynamics and conformations of the TM1 and TM2 helices at the dimer interface. Interestingly, an intermediate cholesterol concentration of 10% elicits more pronounced conformational changes compared to both cholesterol-depleted (0%) and cholesterol-enriched (25%) systems. Specific electrostatic interaction unique to the 10% cholesterol system further corroborate these conformational differences. Given the high sequence conservation of the 7TM domains across mGluR subtypes, the cholesterol-dependent effects observed in mGluR1 are likely applicable to other members of this receptor family. Our findings provide atomistic insights into how cholesterol modulates the conformational landscape of mGluRs, which could impact their function and signaling mechanisms.
Collapse
|
2
|
Jin H, Xia J, Liu Z, Wang XS, Zhang L. A unique ligand-steered strategy for CC chemokine receptor 2 homology modeling to facilitate structure-based virtual screening. Chem Biol Drug Des 2021; 97:944-961. [PMID: 33386704 PMCID: PMC8048943 DOI: 10.1111/cbdd.13820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/12/2020] [Accepted: 12/13/2020] [Indexed: 12/29/2022]
Abstract
CC chemokine receptor 2 (CCR2) antagonists that disrupt CCR2/MCP-1 interaction are expected to treat a variety of inflammatory and autoimmune diseases. The lack of CCR2 crystal structure limits the application of structure-based drug design (SBDD) to this target. Although a few three-dimensional theoretical models have been reported, their accuracy remains to be improved in terms of templates and modeling approaches. In this study, we developed a unique ligand-steered strategy for CCR2 homology modeling. It starts with an initial model based on the X-ray structure of the closest homolog so far, that is, CXCR4. Then, it uses Elastic Network Normal Mode Analysis (EN-NMA) and flexible docking (FD) by AutoDock Vina software to generate ligand-induced fit models. It selects optimal model(s) as well as scoring function(s) via extensive evaluation of model performance based on a unique benchmarking set constructed by our in-house tool, that is, MUBD-DecoyMaker. The model of 81_04 presents the optimal enrichment when combined with the scoring function of PMF04, and the proposed binding mode between CCR2 and Teijin lead by this model complies with the reported mutagenesis data. To highlight the advantage of our strategy, we compared it with the only reported ligand-steered strategy for CCR2 homology modeling, that is, Discovery Studio/Ligand Minimization. Lastly, we performed prospective virtual screening based on 81_04 and CCR2 antagonist bioassay. The identification of two hit compounds, that is, E859-1281 and MolPort-007-767-945, validated the efficacy of our model and the ligand-steered strategy.
Collapse
Affiliation(s)
- Hongwei Jin
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijingChina
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural MedicinesDepartment of New Drug Research and DevelopmentInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijingChina
| | - Xiang Simon Wang
- Molecular Modeling and Drug Discovery Core for District of Columbia Center for AIDS Research (DC CFAR)Laboratory of Cheminformatics and Drug DesignDepartment of Pharmaceutical SciencesCollege of PharmacyHoward UniversityWashingtonDCUSA
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic DrugsSchool of Pharmaceutical SciencesPeking UniversityBeijingChina
| |
Collapse
|
3
|
Shokri M, Moradi S, Amini S, Shahlaei M, Seidi F, Saedi S. A novel amino cellulose derivative using ATRP method: Preparation, characterization, and investigation of its antibacterial activity. Bioorg Chem 2020; 106:104355. [PMID: 33223200 DOI: 10.1016/j.bioorg.2020.104355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/04/2020] [Accepted: 10/05/2020] [Indexed: 12/29/2022]
Abstract
In this study, we prepared a novel amino cellulose derivative (benzyl cellulose-g-poly [2-(N,N-Dimethylamino)ethyl methacrylate]) via a homogeneous ATRP method. The successful synthesis of the novel amino cellulose was confirmed by FT-IR and 1H NMR. This study addressed the different characteristics of the prepared polymer including the thermal stability, solubility, and X-ray diffraction pattern. The antibacterial activity of the synthesized cellulose derivative was investigated using the diffusion disk method against both gram-negative (Escherichia coli, Salmonella enterica) and gram-positive (Staphylococcus aureus, Bacillus subtilis) bacteria. Based on the inhibition zone, it was confirmed that the prepared benzyl cellulose-g-PDMAEMA possesses acceptable antibacterial activity against Escherichia coli, Salmonella enterica, and Staphylococcus aureus while Bacillus subtilis is resistant to the prepared polymer. Also according to the inhibition zone, it was shown that benzyl cellulose-g-PDMAEMA has more impact on E. coli and Salmonella enterica than Staphylococcus aureus. Molecular dynamics simulation was also used to study the interaction of the synthesized cellulose derivative with a model membrane which presented atomistic details of the polymer-lipid interactions. According to the results obtained from the molecular dynamics simulation, the polymer was able to destabilize the structure of the membrane and clearly express its signs of degradation.
Collapse
Affiliation(s)
- Mastaneh Shokri
- Department of Chemistry, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Sajad Moradi
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sabrieh Amini
- Department of Biology, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Mohsen Shahlaei
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farzad Seidi
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing 210037, China.
| | - Shahab Saedi
- Department of Chemistry, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran.
| |
Collapse
|
4
|
Chang GQ, Karatayev O, Boorgu DSSK, Leibowitz SF. CCL2/CCR2 Chemokine System in Embryonic Hypothalamus: Involvement in Sexually Dimorphic Stimulatory Effects of Prenatal Ethanol Exposure on Peptide-Expressing Neurons. Neuroscience 2019; 424:155-171. [PMID: 31705896 DOI: 10.1016/j.neuroscience.2019.10.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
Abstract
Maternal consumption of ethanol during pregnancy is known to increase the offspring's risk for developing alcohol use disorders and associated behavioral disturbances. Studies in adolescent and adult animals suggest the involvement of neuroimmune and neurochemical systems in the brain that control these behaviors. To understand the origin of these effects during early developmental stages, we examined in the embryo and neonate the effects of maternal intraoral administration of ethanol (2 g/kg/day) from embryonic day 10 (E10) to E15 on the inflammatory chemokine C-C motif ligand 2 (CCL2) and its receptor CCR2 in a specific, dense population of neurons in the lateral hypothalamus (LH), where they are closely related to an orexigenic neuropeptide, melanin-concentrating hormone (MCH), known to promote ethanol consumption and related behaviors. We found that prenatal ethanol exposure increases the expression and density of CCL2 and CCR2 cells along with MCH neurons in the LH and the colocalization of CCL2 with MCH. We also discovered that these effects are sexually dimorphic, consistently stronger in female embryos, and are blocked by maternal administration of a CCL2 antibody (1 and 5 µg/day, i.p., E10-E15) that neutralizes endogenous CCL2 and of a CCR2 antagonist INCB3344 (1 mg/day, i.p., E10-E15) that blocks CCL2's main receptor. These results, which in the embryo anatomically and functionally link the CCL2/CCR2 system to MCH neurons in the LH, suggest an important role for this neuroimmune system in mediating ethanol's sexually dimorphic, stimulatory effect on MCH neurons that may promote higher level of alcohol consumption described in females.
Collapse
|
5
|
Structural basis for ligand modulation of the CCR2 conformational landscape. Proc Natl Acad Sci U S A 2019; 116:8131-8136. [PMID: 30975755 DOI: 10.1073/pnas.1814131116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CC chemokine receptor 2 (CCR2) is a part of the chemokine receptor family, an important class of therapeutic targets. These class A G-protein coupled receptors (GPCRs) are involved in mammalian signaling pathways and control cell migration toward endogenous CC chemokine ligands, named for the adjacent cysteine motif on their N terminus. Chemokine receptors and their associated ligands are involved in a wide range of diseases and thus have become important drug targets. CCR2, in particular, promotes the metastasis of cancer cells and is also implicated in autoimmunity-driven type-1 diabetes, diabetic nephropathy, multiple sclerosis, asthma, atherosclerosis, neuropathic pain, and rheumatoid arthritis. Although promising, CCR2 antagonists have been largely unsuccessful to date. Here, we investigate the effect of an orthosteric and an allosteric antagonist on CCR2 dynamics by coupling long-timescale molecular dynamics simulations with Markov-state model theory. We find that the antagonists shift CCR2 into several stable inactive conformations that are distinct from the crystal structure conformation and disrupt a continuous internal water and sodium ion pathway, preventing transitions to an active-like state. Several metastable conformations present a cryptic drug-binding pocket near the allosteric site that may be amenable to targeting with small molecules. Without antagonists, the apo dynamics reveal intermediate conformations along the activation pathway that provide insight into the basal dynamics of CCR2 and may also be useful for future drug design.
Collapse
|
6
|
Moradi S, Nowroozi A, Shahlaei M. Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study. RSC Adv 2019; 9:4644-4658. [PMID: 35520151 PMCID: PMC9060685 DOI: 10.1039/c8ra08441f] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/12/2019] [Accepted: 01/16/2019] [Indexed: 12/20/2022] Open
Abstract
In recent years, a massive increase has been observed in the number of published articles describing accurate and reliable molecular dynamics simulations of lipid bilayers. This is due to several reasons, including the development of fast and efficient methods for treating long-range electrostatic interactions, significant progress in computer hardware, progress in atomistic simulation algorithms and the development of well-validated empirical molecular mechanical force fields. Although molecular dynamics is an effective approach for investigating different aspects of lipid bilayers, to the best of our knowledge, there is no review in the literature that explains the different analyses that can be carried out with membrane simulation. This review gives an overview about the some of the most important possible analyses, technical challenges, and existing protocols that can be performed on the biological membrane by molecular dynamics simulation. The reviewed analyses include the degree of membrane disruption, average area per lipid, probability distributions for the area per lipid molecule, membrane thickness, membrane area compressibility, lateral diffusion, rotational diffusion, order parameters, head group tilt, electron density profile, mass density profile, electrostatic potential profile, ordering of vicinity waters, number of hydrogen bonds, and radial distribution function.
Collapse
Affiliation(s)
- Sajad Moradi
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences Kermanshah Iran
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Kermanshah University of Medical Sciences Kermanshah Iran
| | - Mohsen Shahlaei
- Medical Biology Research Center, Kermanshah University of Medical Sciences Kermanshah Iran
| |
Collapse
|
7
|
Moradi S, Hosseini E, Abdoli M, Khani S, Shahlaei M. Comparative molecular dynamic simulation study on the use of chitosan for temperature stabilization of interferon αII. Carbohydr Polym 2019; 203:52-59. [DOI: 10.1016/j.carbpol.2018.09.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 02/07/2023]
|
8
|
Raucci R, Polo A, Budillon A, Colonna G, Costantini S. Conformational analysis of the human chemokine receptor CXCR3. Mol Immunol 2017; 92:76-86. [PMID: 29054054 DOI: 10.1016/j.molimm.2017.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/08/2017] [Accepted: 10/13/2017] [Indexed: 11/16/2022]
Abstract
In the last years, some studies showed the patho-genetic role of CXCR3 bound to its ligands in many human inflammatory diseases and cancers. Thus, the blockage of the CXCR3 interaction site to its ligands is seen as a possible therapeutic target for the treatment of cancer. The presence of flexible regions in the chemokine receptors determines their capability to develop specific mechanisms of action. We have recently focused on the features of the N-terminal region of human CXCR3 free in solution, where we demonstrate the presence of numerous conformational ensembles, dynamically stabilized by H-bonds. Since up to now no structure was experimentally determined for CXCR3, we decided to approach the study of its conformational behavior by molecular dynamics simulations, in a lipid bilayer, surrounded of water, at neutral pH and 300K. Furthermore, we modeled the CXCR3/CXCL11 complex, where CXCL11 is one of its natural ligands. The aim of this work is to have a vision as realistic as possible in dynamic terms of the biological mechanism that drives the search for the ligand, its interaction and the formation of a stable complex between CXCR3 and CXCL11. Overall, our approach has been able to describe the structural events which dynamically characterize the molecular mechanisms involved in the binding of CXCR3 to CXCL11 and the critical role exerted by its N-terminal region in "hunting" and capturing the ligand.
Collapse
Affiliation(s)
- Raffaele Raucci
- Dottorato in Biologia Computazionale, Dipartimento di Biochimica, Biofisica e Patologia generale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Andrea Polo
- Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italy
| | - Alfredo Budillon
- Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italy
| | - Giovanni Colonna
- Centro di Informatica Medica, Azienda Ospedaliera Universitaria, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Susan Costantini
- Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, Napoli, Italy.
| |
Collapse
|
9
|
Jafari F, Samadi S, Nowroozi A, Sadrjavadi K, Moradi S, Ashrafi-Kooshk MR, Shahlaei M. Experimental and computational studies on the binding of diazinon to human serum albumin. J Biomol Struct Dyn 2017; 36:1490-1510. [DOI: 10.1080/07391102.2017.1329096] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Fataneh Jafari
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Setareh Samadi
- Department of Toxicology, Shahreza Branch, Islamic Azad University, Shaahreza, Iran
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Komail Sadrjavadi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| |
Collapse
|
10
|
|
11
|
Molecular insight into the Grandivitin- matrix metalloproteinase 9 interactions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:493-499. [PMID: 27454459 DOI: 10.1016/j.jphotobiol.2016.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 07/16/2016] [Indexed: 11/23/2022]
Abstract
Grandivitin (GRA), a natural coumarin, can inhibit Matrix metalloproteinase 9 (MMP9). Binding characteristics are therefore of interest for pharmacodynamics of GRA and coumarin derivatives. A combination of spectroscopic methods and molecular modeling techniques was used to characterize interaction of GRA with MMP9. Fluorescence spectroscopy showed that GRA could quench the MMP9 fluorescence spectra. Changes in the UV-Vis and FT-IR spectra were observed upon ligand binding along with a significant degree of tryptophan fluorescence quenching on complex formation. Fluorescence studies showed that GRA has an ability to quench the intrinsic fluorescence of MMP9. Molecular modeling analysis showed that GRA to be bound in the large hydrophobic cavity of MMP9. Further investigation of the binding site of GRA within the MMP9 molecule suggested that hydrophobic contacts, hydrogen bond formation and electrostatic interactions account for the binding of GRA. According molecular dynamics (MD) simulation results the ligand can interact with the protein, with affecting the secondary structure of MMP9 and with a modification of its tertiary structure. The biological significance of this work is evident because MMP9 serves as a potential target protein for anticancer agents. The binding study of GRA with MMP9 is of great importance in pharmacy, pharmacology and biochemistry. This work can provide some key data to clinical research and supply the theoretical basis for the new drug candidate designing.
Collapse
|
12
|
Nowroozi A, Shahlaei M. A coupling of homology modeling with multiple molecular dynamics simulation for identifying representative conformation of GPCR structures: a case study on human bombesin receptor subtype-3. J Biomol Struct Dyn 2016; 35:250-272. [DOI: 10.1080/07391102.2016.1140593] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Amin Nowroozi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| |
Collapse
|
13
|
Exploring binding properties of sertraline with human serum albumin: Combination of spectroscopic and molecular modeling studies. Chem Biol Interact 2015; 242:235-46. [DOI: 10.1016/j.cbi.2015.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/25/2015] [Accepted: 10/07/2015] [Indexed: 12/20/2022]
|
14
|
Shahlaei M, Mousavi A. A Conformational Analysis Study on the Melanocortin 4 Receptor Using Multiple Molecular Dynamics Simulations. Chem Biol Drug Des 2015; 86:309-21. [DOI: 10.1111/cbdd.12495] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 05/29/2014] [Accepted: 06/13/2014] [Indexed: 12/28/2022]
Affiliation(s)
- Mohsen Shahlaei
- Novel Drug Delivery Research Center; School of Pharmacy; Kermanshah University of Medical Sciences; Parastar Bolvar 6734667149 Kermanshah Iran
| | - Atefeh Mousavi
- Student Research Committee; School of Pharmacy; Kermanshah University of Medical Sciences; Parastar Bolvar 6734667149 Kermanshah Iran
| |
Collapse
|