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Pawnikar S, Akhter S, Miao Y. Structural dynamics of chemokine receptors. VITAMINS AND HORMONES 2023; 123:645-662. [PMID: 37718001 DOI: 10.1016/bs.vh.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Membrane proteins such as G protein-coupled receptors (GPCRs) are involved in awide range of physiological and pathological cellular processes. Binding of extracellular signals to GPCRs, including hormones, neurotransmitters, peptides and proteins, can activate intracellular signaling cascades via G protein interaction. Chemokine receptors are key GPCRs implicated in cancers, immune responses, cell migration and inflammation. Specifically, the CCR5 and CXCR4 chemokine receptors serve as important therapeutic targets against Human Immunodeficiency virus (HIV) entry into human cells. Maraviroc and Vicriviroc, two clinically used HIV entry inhibitors, are antagonists of the CCR5 receptor. These drugs block HIV entry, but ultimately resistance develops, due to emergence of viruses that can utilize the CXCR4 co-receptor. Unfortunately, development of chemokine receptor antagonists as selective drugs of HIV infection has been greatly hindered as their target orthosteric site is conserved among different receptor subtypes. Accordingly, it is important to understand the structural dynamics of these receptors to develop more effective therapeutics. In this chapter, we describe the latest advances in studies of these two key chemokine receptors with respect to their structures, dynamics and function.
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Affiliation(s)
- Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Sana Akhter
- 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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2
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Goode-Romero G, Dominguez L. Computational study of the structural ensemble of CC chemokine receptor type 5 (CCR5) and its interactions with different ligands. PLoS One 2022; 17:e0275269. [PMID: 36251708 PMCID: PMC9576088 DOI: 10.1371/journal.pone.0275269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
CC Chemokine receptor 5 (CCR5), a member of the Superfamily of G Protein-Coupled Receptors (GPCRs), is an important effector in multiple physiopathological processes such as inflammatory and infectious entities, including central nervous system neuroinflammatory diseases such as Alzheimer's disease, recovery from nervous injuries, and in the HIV-AIDS infective processes. Thus, CCR5 is an attractive target for pharmacological modulation. Since maraviroc was described as a CCR5 ligand that modifies the HIV-AIDS progression, multiple efforts have been developed to describe the functionality of the receptor. In this work, we characterized key structural features of the CCR5 receptor employing extensive atomistic molecular dynamics (MD) in its apo form and in complex with an endogenous agonist, the chemokine CCL5/RANTES, an HIV entry inhibitor, the partial inverse agonist maraviroc, and the experimental antagonists Compound 21 and 34, aiming to elucidate the structural features and mechanistic processes that constitute its functional states, contributing with structural details and a general understanding of this relevant system.
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Affiliation(s)
- Guillermo Goode-Romero
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Dominguez
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
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3
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Bresso E, Fernandez D, Amora DX, Noel P, Petitot AS, de Sa MEL, Albuquerque EVS, Danchin EGJ, Maigret B, Martins NF. A Chemosensory GPCR as a Potential Target to Control the Root-Knot Nematode Meloidogyne incognita Parasitism in Plants. Molecules 2019; 24:E3798. [PMID: 31652525 PMCID: PMC6832152 DOI: 10.3390/molecules24203798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 01/10/2023] Open
Abstract
Root-knot nematodes (RKN), from the Meloidogyne genus, have a worldwide distribution and cause severe economic damage to many life-sustaining crops. Because of their lack of specificity and danger to the environment, most chemical nematicides have been banned from use. Thus, there is a great need for new and safe compounds to control RKN. Such research involves identifying beforehand the nematode proteins essential to the invasion. Since G protein-coupled receptors GPCRs are the target of a large number of drugs, we have focused our research on the identification of putative nematode GPCRs such as those capable of controlling the movement of the parasite towards (or within) its host. A datamining procedure applied to the genome of Meloidogyne incognita allowed us to identify a GPCR, belonging to the neuropeptide GPCR family that can serve as a target to carry out a virtual screening campaign. We reconstructed a 3D model of this receptor by homology modeling and validated it through extensive molecular dynamics simulations. This model was used for large scale molecular dockings which produced a filtered limited set of putative antagonists for this GPCR. Preliminary experiments using these selected molecules allowed the identification of an active compound, namely C260-2124, from the ChemDiv provider, which can serve as a starting point for further investigations.
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Affiliation(s)
- Emmanuel Bresso
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France.
- EMBRAPA Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil.
| | - Diana Fernandez
- EMBRAPA Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil.
- IRD, CIRAD, Université de Montpellier, IPME, F-34398 Montpellier, France.
| | - Deisy X Amora
- EMBRAPA Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil.
| | - Philippe Noel
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France.
| | | | | | | | - Etienne G J Danchin
- INRA, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, F-06903 Sophia-Antipolis, France.
| | - Bernard Maigret
- Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France.
| | - Natália F Martins
- EMBRAPA Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil.
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4
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Mostashari Rad T, Saghaie L, Fassihi A. HIV-1 Entry Inhibitors: A Review of Experimental and Computational Studies. Chem Biodivers 2018; 15:e1800159. [PMID: 30027572 DOI: 10.1002/cbdv.201800159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/18/2018] [Indexed: 12/18/2022]
Abstract
The HIV-1 life cycle consists of different events, such as cell entry and fusion, virus replication, assembly and release of the newly formed virions. The more logical way to inhibit HIV transmission among individuals is to inhibit its entry into the immune host cells rather than targeting the intracellular viral enzymes. Both viral and host cell surface receptors and co-receptors are regarded as potential targets in anti-HIV-1 drug design process. Because of the importance of this topic it was decided to summarize recent reports on small-molecule HIV-1 entry inhibitors that have not been considered in the latest released reviews. All the computational studies reported in the literature regarding HIV-1 entry inhibitors since 2014 was also considered in this review.
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Affiliation(s)
- Tahereh Mostashari Rad
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, 81746-73461, Isfahan, Iran
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, 81746-73461, Isfahan, Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, 81746-73461, Isfahan, Iran.,Bioinformatics and Systems Biology Department, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, 81746-73461, Isfahan, Iran
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5
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Zhang F, Yuan Y, Li H, Shen L, Guo Y, Wen Z, Pu X. Using accelerated molecular dynamics simulation to shed light on the mechanism of activation/deactivation upon mutations for CCR5. RSC Adv 2018; 8:37855-37865. [PMID: 35558583 PMCID: PMC9089863 DOI: 10.1039/c8ra07686c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/06/2018] [Indexed: 12/27/2022] Open
Abstract
In this work, accelerated molecular dynamics (aMD) simulations were used to study different effects of G286F and R126 mutations on the activity of CCR5. Potential of Mean Force (PMF) results indicate that there are stable inactive-like states and active-like ones existing in the conformation space of the wild type (WT), confirming that CCR5 could possess to some extent constitutive activity. But the R126N mutation could constrain CCR5 in the inactive state through influencing the TXP motif and limiting the movements of TM5 and TM6. In contrast, the G286F mutation promotes the activity of the receptor by increasing the distance of TM2–TM6 and the flexibility of the intracellular part of TM5 and changing the H-bonding in the TXP motif. The observations from the cross correlation analysis further show that the R126N mutation dramatically reduces the motion correlations between TMs, which should partly contribute to the deactivation of CCR5. Compared with the WT system, TM6 and TM7 in the G286F mutant are loosely correlated with other regions, which should be conducive to drive the movement of TM6 and TM7 toward the active conformation. In addition, the result from the protein structure network (PSN) analysis reveals that the shortest pathways connecting the extracellular and the intracellular domains are highly conserved in the three systems despite the different mutations, in which the hydrogen bond plays a pivotal role. However, the G286F mutation shortens the lifetime of the pathway with respect to the R126N mutation, which may be associated with the different activities of the two mutants. The pathway connecting the ligand-binding site and the G-protein region reveals that the allosteric communication between TM6 and TM7 is enhanced by the R126N mutation while the G286F mutation induces the activation of the G-protein pocket by arousing more residues in the NPxxY region to participate in the pathway. In this work, accelerated molecular dynamics (aMD) simulations were used to study different effects of G286F and R126 mutations on the activity of CCR5.![]()
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Affiliation(s)
- Fuhui Zhang
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu 610041
- P. R. China
| | - Haiyan Li
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Liting Shen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Zhining Wen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Xuemei Pu
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
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6
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Guryanov I, Cipriani S, Fiorucci S, Zashikhina N, Marchianò S, Scarpelli P, Korzhikov-Vlakh V, Popova E, Korzhikova-Vlakh E, Biondi B, Formaggio F, Tennikova T. Nanotraps with biomimetic surface as decoys for chemokines. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2017; 13:2575-2585. [DOI: 10.1016/j.nano.2017.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/28/2017] [Accepted: 07/14/2017] [Indexed: 12/28/2022]
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7
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Arimont M, Sun SL, Leurs R, Smit M, de Esch IJP, de Graaf C. Structural Analysis of Chemokine Receptor-Ligand Interactions. J Med Chem 2017; 60:4735-4779. [PMID: 28165741 PMCID: PMC5483895 DOI: 10.1021/acs.jmedchem.6b01309] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
This
review focuses on the construction and application of structural chemokine
receptor models for the elucidation of molecular determinants of chemokine
receptor modulation and the structure-based discovery and design of
chemokine receptor ligands. A comparative analysis of ligand binding
pockets in chemokine receptors is presented, including a detailed
description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures,
and their implication for modeling molecular interactions of chemokine
receptors with small-molecule ligands, peptide ligands, and large
antibodies and chemokines. These studies demonstrate how the integration
of new structural information on chemokine receptors with extensive
structure–activity relationship and site-directed mutagenesis
data facilitates the prediction of the structure of chemokine receptor–ligand
complexes that have not been crystallized. Finally, a review of structure-based
ligand discovery and design studies based on chemokine receptor crystal
structures and homology models illustrates the possibilities and challenges
to find novel ligands for chemokine receptors.
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Affiliation(s)
- Marta Arimont
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Shan-Liang Sun
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Martine Smit
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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8
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Bresso E, Togawa R, Hammond-Kosack K, Urban M, Maigret B, Martins NF. GPCRs from fusarium graminearum detection, modeling and virtual screening - the search for new routes to control head blight disease. BMC Bioinformatics 2016; 17:463. [PMID: 28105916 PMCID: PMC5249037 DOI: 10.1186/s12859-016-1342-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGOUND Fusarium graminearum (FG) is one of the major cereal infecting pathogens causing high economic losses worldwide and resulting in adverse effects on human and animal health. Therefore, the development of new fungicides against FG is an important issue to reduce cereal infection and economic impact. In the strategy for developing new fungicides, a critical step is the identification of new targets against which innovative chemicals weapons can be designed. As several G-protein coupled receptors (GPCRs) are implicated in signaling pathways critical for the fungi development and survival, such proteins could be valuable efficient targets to reduce Fusarium growth and therefore to prevent food contamination. RESULTS In this study, GPCRs were predicted in the FG proteome using a manually curated pipeline dedicated to the identification of GPCRs. Based on several successive filters, the most appropriate GPCR candidate target for developing new fungicides was selected. Searching for new compounds blocking this particular target requires the knowledge of its 3D-structure. As no experimental X-Ray structure of the selected protein was available, a 3D model was built by homology modeling. The model quality and stability was checked by 100 ns of molecular dynamics simulations. Two stable conformations representative of the conformational families of the protein were extracted from the 100 ns simulation and were used for an ensemble docking campaign. The model quality and stability was checked by 100 ns of molecular dynamics simulations previously to the virtual screening step. The virtual screening step comprised the exploration of a chemical library with 11,000 compounds that were docked to the GPCR model. Among these compounds, we selected the ten top-ranked nontoxic molecules proposed to be experimentally tested to validate the in silico simulation. CONCLUSIONS This study provides an integrated process merging genomics, structural bioinformatics and drug design for proposing innovative solutions to a world wide threat to grain producers and consumers.
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Affiliation(s)
- Emmanuel Bresso
- EMBRAPA Genetic Resources and Biotechnology, Brasília, DF 70770-917 Brazil
| | - Roberto Togawa
- EMBRAPA Genetic Resources and Biotechnology, Brasília, DF 70770-917 Brazil
| | - Kim Hammond-Kosack
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Martin Urban
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ UK
| | - Bernard Maigret
- EMBRAPA Genetic Resources and Biotechnology, Brasília, DF 70770-917 Brazil
- CAPSID Team, LORIA, UMR 7503, CNRS, Lorraine University, Vandœuvre-lès-Nancy, 54506 France
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9
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Swinney DC, Beavis P, Chuang KT, Zheng Y, Lee I, Gee P, Deval J, Rotstein DM, Dioszegi M, Ravendran P, Zhang J, Sankuratri S, Kondru R, Vauquelin G. A study of the molecular mechanism of binding kinetics and long residence times of human CCR5 receptor small molecule allosteric ligands. Br J Pharmacol 2015; 171:3364-75. [PMID: 24628038 DOI: 10.1111/bph.12683] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 02/04/2014] [Accepted: 02/26/2014] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND AND PURPOSE The human CCR5 receptor is a co-receptor for HIV-1 infection and a target for anti-viral therapy. A greater understanding of the binding kinetics of small molecule allosteric ligand interactions with CCR5 will lead to a better understanding of the binding process and may help discover new molecules that avoid resistance. EXPERIMENTAL APPROACH Using [(3) H] maraviroc as a radioligand, a number of different binding protocols were employed in conjunction with simulations to determine rate constants, kinetic mechanism and mutant kinetic fingerprints for wild-type and mutant human CCR5 with maraviroc, aplaviroc and vicriviroc. KEY RESULTS Kinetic characterization of maraviroc binding to the wild-type CCR5 was consistent with a two-step kinetic mechanism that involved an initial receptor-ligand complex (RA), which transitioned to a more stable complex, R'A, with at least a 13-fold increase in affinity. The dissociation rate from R'A, k-2 , was 1.2 × 10(-3) min(-1) . The maraviroc time-dependent transition was influenced by F85L, W86A, Y108A, I198A and Y251A mutations of CCR5. CONCLUSIONS AND IMPLICATIONS The interaction between maraviroc and CCR5 proceeded according to a multi-step kinetic mechanism, whereby initial mass action binding and later reorganizations of the initial maraviroc-receptor complex lead to a complex with longer residence time. Site-directed mutagenesis identified a kinetic fingerprint of residues that affected the binding kinetics, leading to the conclusion that allosteric ligand binding to CCR5 involved the rearrangement of the binding site in a manner specific to each allosteric ligand.
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Affiliation(s)
- David C Swinney
- Roche Palo Alto, Palo Alto, CA, USA; Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, CA, USA
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10
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11
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Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5. Sci Rep 2014; 4:5447. [PMID: 24965094 PMCID: PMC4894430 DOI: 10.1038/srep05447] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/05/2014] [Indexed: 01/01/2023] Open
Abstract
CCL5 (RANTES) is an inflammatory chemokine which binds to chemokine receptor CCR5 and induces signaling. The CCL5:CCR5 associated chemotactic signaling is of critical biological importance and is a potential HIV-1 therapeutic axis. Several studies provided growing evidence for the expression of CCL5 and CCR5 in non-hematological malignancies. Therefore, the delineation of the CCL5:CCR5 complex structure can pave the way for novel CCR5-targeted drugs. We employed a computational protocol which is primarily based on free energy calculations and molecular dynamics simulations, and report, what is to our knowledge, the first computationally derived CCL5:CCR5 complex structure which is in excellent agreement with experimental findings and clarifies the functional role of CCL5 and CCR5 residues which are associated with binding and signaling. A wealth of polar and non-polar interactions contributes to the tight CCL5:CCR5 binding. The structure of an HIV-1 gp120 V3 loop in complex with CCR5 has recently been derived through a similar computational protocol. A comparison between the CCL5 : CCR5 and the HIV-1 gp120 V3 loop : CCR5 complex structures depicts that both the chemokine and the virus primarily interact with the same CCR5 residues. The present work provides insights into the blocking mechanism of HIV-1 by CCL5.
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12
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Gu WG, Zhang X, Yuan JF. Anti-HIV drug development through computational methods. AAPS JOURNAL 2014; 16:674-80. [PMID: 24760437 DOI: 10.1208/s12248-014-9604-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/02/2014] [Indexed: 11/30/2022]
Abstract
Although highly active antiretroviral therapy (HAART) is effective in controlling the progression of AIDS, the emergence of drug-resistant strains increases the difficulty of successful treatment of patients with HIV infection. Increasing numbers of patients are facing the dilemma that comes with the running out of drug combinations for HAART. Computational methods play a key role in anti-HIV drug development. A substantial number of studies have been performed in anti-HIV drug development using various computational methods, such as virtual screening, QSAR, molecular docking, and homology modeling, etc. In this review, we summarize recent advances in the application of computational methods to anti-HIV drug development for five key targets as follows: reverse transcriptase, protease, integrase, CCR5, and CXCR4. We hope that this review will stimulate researchers from multiple disciplines to consider computational methods in the anti-HIV drug development process.
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Affiliation(s)
- Wan-Gang Gu
- Department of Immunology, Zunyi Medical University, Zunyi, 563003, Guizhou, China,
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13
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Moonsamy S, Dash RC, Soliman MES. Integrated computational tools for identification of CCR5 antagonists as potential HIV-1 entry inhibitors: homology modeling, virtual screening, molecular dynamics simulations and 3D QSAR analysis. Molecules 2014; 19:5243-65. [PMID: 24762964 PMCID: PMC6270745 DOI: 10.3390/molecules19045243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/01/2014] [Accepted: 04/09/2014] [Indexed: 11/16/2022] Open
Abstract
Using integrated in-silico computational techniques, including homology modeling, structure-based and pharmacophore-based virtual screening, molecular dynamic simulations, per-residue energy decomposition analysis and atom-based 3D-QSAR analysis, we proposed ten novel compounds as potential CCR5-dependent HIV-1 entry inhibitors. Via validated docking calculations, binding free energies revealed that novel leads demonstrated better binding affinities with CCR5 compared to maraviroc, an FDA-approved HIV-1 entry inhibitor and in clinical use. Per-residue interaction energy decomposition analysis on the averaged MD structure showed that hydrophobic active residues Trp86, Tyr89 and Tyr108 contributed the most to inhibitor binding. The validated 3D-QSAR model showed a high cross-validated rcv2 value of 0.84 using three principal components and non-cross-validated r2 value of 0.941. It was also revealed that almost all compounds in the test set and training set yielded a good predicted value. Information gained from this study could shed light on the activity of a new series of lead compounds as potential HIV entry inhibitors and serve as a powerful tool in the drug design and development machinery.
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Affiliation(s)
- Suri Moonsamy
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
| | - Radha Charan Dash
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa.
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14
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Gadhe CG, Kothandan G, Cho SJ. Computational modeling of human coreceptor CCR5 antagonist as a HIV-1 entry inhibitor: using an integrated homology modeling, docking, and membrane molecular dynamics simulation analysis approach. J Biomol Struct Dyn 2013; 31:1251-76. [DOI: 10.1080/07391102.2012.732342] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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15
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Arumugam K, Crouzy S, Chevigne A, Seguin-Devaux C, Schmit JC. Structure prediction of GPCRs using piecewise homologs and application to the human CCR5 chemokine receptor: validation through agonist and antagonist docking. J Biomol Struct Dyn 2013; 32:1274-89. [DOI: 10.1080/07391102.2013.817952] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Gadhe CG, Kothandan G, Cho SJ. Binding site exploration of CCR5 using in silico methodologies: a 3D-QSAR approach. Arch Pharm Res 2013; 36:6-31. [DOI: 10.1007/s12272-013-0001-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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17
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Vyas VK, Ukawala RD, Ghate M, Chintha C. Homology modeling a fast tool for drug discovery: current perspectives. Indian J Pharm Sci 2012. [PMID: 23204616 PMCID: PMC3507339 DOI: 10.4103/0250-474x.102537] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery.
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Affiliation(s)
- V K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad-382 481, India
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Saxena M, Bhunia SS, Saxena AK. Docking studies of novel pyrazinopyridoindoles class of antihistamines with the homology modelled H(1)-receptor. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:311-325. [PMID: 22463083 DOI: 10.1080/1062936x.2012.664561] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Histamine is an important neurotransmitter as it controls a multitude of physiological functions by activating specific receptors on target cells. It exerts its effects by binding to four different histamine receptors (H(1)-H(4)), which all belong to the large family of G protein-coupled receptors (GPCRs). Research and development of H(1) ligand has largely focused on antagonists which are used for their anti-allergy effects in the periphery. Recent understanding of the clinical importance of H(1) receptors in brain, however, suggests the pharmacotherapeutic potential of H(1) agonists in neurodegenerative and neuropsychiatric disorders. Despite the therapeutic importance of the H(1) receptor, for many years the molecular features of the H(1) receptor protein had been unknown. In view of the recently reported crystal structure of human H(1) receptor and in continuation of our work on 3D-pharmacophore on antihistamine H(1) and homology model of histamine H(1) receptor, docking studies have been carried out on some promising pyrazinopyridoindole class of antihistamine H(1), including two outliers, to validate our earlier reported models/hypotheses on H(1)-receptor, where a good explanation between estimated and observed activities has been obtained. In addition, the docking study also provided insights about the optimal activity of the outliers, for which no explanation was reported previously.
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Affiliation(s)
- M Saxena
- Department of Chemistry, Amity University, Lucknow, India.
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19
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Kothandan G, Gadhe CG, Cho SJ. Structural insights from binding poses of CCR2 and CCR5 with clinically important antagonists: a combined in silico study. PLoS One 2012; 7:e32864. [PMID: 22479344 PMCID: PMC3314010 DOI: 10.1371/journal.pone.0032864] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 01/31/2012] [Indexed: 11/19/2022] Open
Abstract
Chemokine receptors are G protein-coupled receptors that contain seven transmembrane domains. In particular, CCR2 and CCR5 and their ligands have been implicated in the pathophysiology of a number of diseases, including rheumatoid arthritis and multiple sclerosis. Based on their roles in disease, they have been attractive targets for the pharmaceutical industry, and furthermore, targeting both CCR2 and CCR5 can be a useful strategy. Owing to the importance of these receptors, information regarding the binding site is of prime importance. Structural studies have been hampered due to the lack of X-ray crystal structures, and templates with close homologs for comparative modeling. Most of the previous models were based on the bovine rhodopsin and β2-adrenergic receptor. In this study, based on a closer homolog with higher resolution (CXCR4, PDB code: 3ODU 2.5 Å), we constructed three-dimensional models. The main aim of this study was to provide relevant information on binding sites of these receptors. Molecular dynamics simulation was done to refine the homology models and PROCHECK results indicated that the models were reasonable. Here, binding poses were checked with some established inhibitors of high pharmaceutical importance against the modeled receptors. Analysis of interaction modes gave an integrated interpretation with detailed structural information. The binding poses confirmed that the acidic residues Glu291 (CCR2) and Glu283 (CCR5) are important, and we also found some additional residues. Comparisons of binding sites of CCR2/CCR5 were done sequentially and also by docking a potent dual antagonist. Our results can be a starting point for further structure-based drug design.
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Affiliation(s)
- Gugan Kothandan
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju, Korea
| | - Changdev G. Gadhe
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju, Korea
| | - Seung Joo Cho
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju, Korea
- Department of Cellular Molecular Medicine, Research Center for Resistant Cells, College of Medicine, Chosun University, Gwangju, Korea
- * E-mail:
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20
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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21
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Choi WT, An J. Biology and clinical relevance of chemokines and chemokine receptors CXCR4 and CCR5 in human diseases. Exp Biol Med (Maywood) 2011; 236:637-47. [PMID: 21565895 DOI: 10.1258/ebm.2011.010389] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemokines and their receptors are implicated in a wide range of human diseases, including acquired immune deficiency syndrome (AIDS). The entry of human immunodeficiency virus type 1 (HIV-1) into a cell is initiated by the interaction of the virus's surface envelope proteins with two cell surface components of the target cell, namely CD4 and a chemokine co-receptor, usually CXCR4 or CCR5. Typical anti-HIV-1 agents include protease and reverse transcriptase inhibitors, but the targets of these agents tend to show rapid mutation rates. As such, strategies based on HIV-1 co-receptors have appeal because they target invariant host determinants. Chemokines and their receptors are also of general interest since they play important roles in numerous physiological and pathological processes in addition to AIDS. Therefore, intensive basic and translational research is ongoing for the dissection of their structure - function relationships in an effort to understand the molecular mechanism of chemokine - receptor interactions and signal transductions across cellular membranes. This paper reviews and discusses recent advances and the translation of new knowledge and discoveries into novel interventional strategies for clinical application.
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Affiliation(s)
- Won-Tak Choi
- Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA
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22
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Da LT, Wu YD. Theoretical studies on the interactions and interferences of HIV-1 glycoprotein gp120 and its coreceptor CCR5. J Chem Inf Model 2011; 51:359-69. [PMID: 21284403 DOI: 10.1021/ci1003448] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction between the HIV gp120 protein and coreceptor CCR5 or CXCR4 of the host cell is critical in mediating the HIV entry process. A model for the CCR5-gp120 complex has been developed. In the model, the N-terminus of CCR5 binds to three discontinuous domains of gp120, including the fourth conserved (C4) region, β19/β20 connecting loop, and V3 loop. The second extra-cellular loop (ECL2) of CCR5 also interacts with the crown part of the gp120 V3 loop. The bindings of the three CCR5 antagonists, maraviroc, aplaviroc, and vicriviroc, to the trans-membrane domain of CCR5 have been modeled. The bindings are found to affect the conformation of the ECL2 domain, which in turn drives the N-terminus of CCR5 to an altered state. Aplaviroc is more hydrophilic than maraviroc and vicriviroc, and its binding is more interfered by solvent, resulting in a quite different effect to the structure of CCR5 compared with those of the other two molecules. The above results are in accord with experimental observations and provide a structural basis for further design of CCR5 antagonists.
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Affiliation(s)
- Lin-tai Da
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
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23
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Carrieri A, Pérez-Nueno VI, Fano A, Pistone C, Ritchie DW, Teixidó J. Biological profiling of anti-HIV agents and insight into CCR5 antagonist binding using in silico techniques. ChemMedChem 2009; 4:1153-63. [PMID: 19544518 DOI: 10.1002/cmdc.200900101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Molecular requirements and determinants for efficient binding to CCR5 were interpreted by computational techniques based on comparative receptor structure modeling, advanced 3D-QSAR, docking, and shape-based virtual screening of commercially available entry blockers. Results of this study may be valuable for predicting new HIV entry-blocking leads.Acquired immune deficiency syndrome (AIDS) is responsible for more than 31 million deaths, and many more people are affected by this disease worldwide. Novel ligands that are capable of blocking virus-cell fusion are emerging as promising candidate molecules against HIV-1 infection because they have the promise to overcome the major drawbacks of classical highly active antiretroviral (HAART) drugs. However, structure-based design continues to be hampered owing to the paucity of experimentally determined 3D information about HIV-1 cell-surface co-receptors. Using computational techniques based on comparative receptor structure modeling, advanced 3D-QSAR, and protein-ligand docking, we present recent results that define updated molecular requirements and determinants for efficient binding of small-molecule ligands to CCR5, a principal biological target for HIV entry blockers. These results are compared with shape- and property-based virtual screening results for commercially available entry blockers, and will be valuable for predicting new HIV entry-blocking leads.
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Affiliation(s)
- Antonio Carrieri
- Dipartimento Farmaco-Chimico, Università degli Studi di Bari, Via Orabona 4, 70125 Bari, Italy.
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24
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Chapter 12 The Use of Receptor Homology Modeling to Facilitate the Design of Selective Chemokine Receptor Antagonists. Methods Enzymol 2009; 461:249-79. [DOI: 10.1016/s0076-6879(09)05412-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Pérez-Nueno VI, Ritchie DW, Borrell JI, Teixidó J. Clustering and Classifying Diverse HIV Entry Inhibitors Using a Novel Consensus Shape-Based Virtual Screening Approach: Further Evidence for Multiple Binding Sites within the CCR5 Extracellular Pocket. J Chem Inf Model 2008; 48:2146-65. [DOI: 10.1021/ci800257x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Violeta I. Pérez-Nueno
- Grup d’Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, Department of Computing Science, King’s College, University of Aberdeen, Aberdeen, U.K
| | - David W. Ritchie
- Grup d’Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, Department of Computing Science, King’s College, University of Aberdeen, Aberdeen, U.K
| | - Jose I. Borrell
- Grup d’Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, Department of Computing Science, King’s College, University of Aberdeen, Aberdeen, U.K
| | - Jordi Teixidó
- Grup d’Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, Department of Computing Science, King’s College, University of Aberdeen, Aberdeen, U.K
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26
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Liu Y, Su J, Xiao JH, Jiang SB, Lu H, Zhong W, Wang LL, Yang XH, Li S. Synthesis of benzocycloheptene derivatives as CCR5 antagonists with potent anti-HIV activity. CHINESE CHEM LETT 2008. [DOI: 10.1016/j.cclet.2008.01.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Pérez-Nueno VI, Ritchie DW, Rabal O, Pascual R, Borrell JI, Teixidó J. Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape Matching and Ligand−Receptor Docking. J Chem Inf Model 2008; 48:509-33. [DOI: 10.1021/ci700415g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Violeta I. Pérez-Nueno
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, and Department of Computing Science, King's College, University of Aberdeen, Aberdeen, United Kingdom
| | - David W. Ritchie
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, and Department of Computing Science, King's College, University of Aberdeen, Aberdeen, United Kingdom
| | - Obdulia Rabal
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, and Department of Computing Science, King's College, University of Aberdeen, Aberdeen, United Kingdom
| | - Rosalia Pascual
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, and Department of Computing Science, King's College, University of Aberdeen, Aberdeen, United Kingdom
| | - Jose I. Borrell
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, and Department of Computing Science, King's College, University of Aberdeen, Aberdeen, United Kingdom
| | - Jordi Teixidó
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain, and Department of Computing Science, King's College, University of Aberdeen, Aberdeen, United Kingdom
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28
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Wang T, Duan Y. Binding modes of CCR5-targetting HIV entry inhibitors: partial and full antagonists. J Mol Graph Model 2007; 26:1287-95. [PMID: 18249144 DOI: 10.1016/j.jmgm.2007.12.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 12/06/2007] [Accepted: 12/10/2007] [Indexed: 11/25/2022]
Abstract
Since the CC-chemokine receptor 5 (CCR5) was identified as a major co-receptor for human immunodeficiency virus type 1 (HIV-1) entry into a host cell, CCR5-targetting HIV entry inhibitors have been developed and some of them are currently in clinical trials. Most of these inhibitors also inhibit the physiological chemokine reaction function of CCR5, which is so far considered to be safe to patients based on the observation that individuals that naturally lack CCR5 do not show apparent health problems. Nevertheless, to minimize the toxicity and side effects, it would be ideal to preserve the chemokine receptor activity. In this work, we simulated the flexible docking of two small molecule inhibitors to CCR5 in a solvated phospholipid bilayer environment. One of the inhibitors, aplaviroc has a unique feature of preserving two of the natural chemokine ligands binding to CCR5 and subsequent activation whereas the other one, SCH-C fully blocks chemokine-CCR5 interactions. Our results revealed significantly different binding modes of these two inhibitors although both established extensive interaction networks with CCR5. Comparison of the different binding modes suggests that avoiding the deep insertion of inhibitors into the transmembrane helix bundle may be able to preserve chemokine-CCR5 interactions. These results could help design HIV co-receptor activity-specific inhibitors.
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Affiliation(s)
- Ting Wang
- Genome Center and Bioinformatics Program and Department of Applied Science, 431 East Health Science Drive, University of California, Davis, CA 95616-8816, USA.
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29
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Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, Stevens RC. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 2007; 318:1258-65. [PMID: 17962520 PMCID: PMC2583103 DOI: 10.1126/science.1150577] [Citation(s) in RCA: 2539] [Impact Index Per Article: 149.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors constitute the largest family of eukaryotic signal transduction proteins that communicate across the membrane. We report the crystal structure of a human beta2-adrenergic receptor-T4 lysozyme fusion protein bound to the partial inverse agonist carazolol at 2.4 angstrom resolution. The structure provides a high-resolution view of a human G protein-coupled receptor bound to a diffusible ligand. Ligand-binding site accessibility is enabled by the second extracellular loop, which is held out of the binding cavity by a pair of closely spaced disulfide bridges and a short helical segment within the loop. Cholesterol, a necessary component for crystallization, mediates an intriguing parallel association of receptor molecules in the crystal lattice. Although the location of carazolol in the beta2-adrenergic receptor is very similar to that of retinal in rhodopsin, structural differences in the ligand-binding site and other regions highlight the challenges in using rhodopsin as a template model for this large receptor family.
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Affiliation(s)
- Vadim Cherezov
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
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