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Xiao W, Wang D, Shen Z, Li S, Li H. Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites. Molecules 2018; 23:molecules23092321. [PMID: 30208655 PMCID: PMC6225211 DOI: 10.3390/molecules23092321] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 01/14/2023] Open
Abstract
Water molecules play an important role in modeling protein-ligand interactions. However, traditional molecular docking methods often ignore the impact of the water molecules by removing them without any analysis or keeping them as a static part of the proteins or the ligands. Hence, the accuracy of the docking simulations will inevitably be damaged. Here, we introduce a multi-body docking program which incorporates the fixed or the variable number of the key water molecules in protein-ligand docking simulations. The program employed NSGA II, a multi-objective optimization algorithm, to identify the binding poses of the ligand and the key water molecules for a protein. To this end, a force-field-based hydration-specific scoring function was designed to favor estimate the binding affinity considering the key water molecules. The program was evaluated in aspects of the docking accuracy, cross-docking accuracy, and screening efficiency. When the numbers of the key water molecules were treated as fixed-length optimization variables, the docking accuracy of the multi-body docking program achieved a success rate of 80.58% for the best RMSD values for the recruit of the ligands smaller than 2.0 Å. The cross-docking accuracy was investigated on the presence and absence of the key water molecules by four protein targets. The screening efficiency was assessed against those protein targets. Results indicated that the proposed multi-body docking program was with good performance compared with the other programs. On the other side, when the numbers of the key water molecules were treated as variable-length optimization variables, the program obtained comparative performance under the same three evaluation criterions. These results indicated that the multi-body docking with the variable numbers of the water molecules was also efficient. Above all, the multi-body docking program developed in this study was capable of dealing with the problem of the water molecules that explicitly participating in protein-ligand binding.
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Affiliation(s)
- Wei Xiao
- School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Disha Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Zihao Shen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Honglin Li
- School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
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2
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Smelt CLC, Sanders VR, Newcombe J, Burt RP, Sheppard TD, Topf M, Millar NS. Identification by virtual screening and functional characterisation of novel positive and negative allosteric modulators of the α7 nicotinic acetylcholine receptor. Neuropharmacology 2018; 139:194-204. [PMID: 30009834 PMCID: PMC6078708 DOI: 10.1016/j.neuropharm.2018.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/19/2018] [Accepted: 07/08/2018] [Indexed: 01/01/2023]
Abstract
Several previous studies have demonstrated that the activity of neurotransmitters acting on ligand-gated ion channels such as the nicotinic acetylcholine receptor (nAChR) can be altered by compounds binding to allosteric modulatory sites. In the case of α7 nAChRs, both positive and negative allosteric modulators (PAMs and NAMs) have been identified and have attracted considerable interest. A recent study, employing revised structural models of the transmembrane domain of the α7 nAChR in closed and open conformations, has provided support for an inter-subunit transmembrane allosteric binding site (Newcombe et al 2017). In the present study, we have performed virtual screening of the DrugBank database using pharmacophore queries that were based on the predicted binding mode of PAMs to α7 nAChR structural models. A total of 81 compounds were identified in the DrugBank database, of which the 25 highest-ranked hits corresponded to one of four previously-identified therapeutic compound groups (carbonic anhydrase inhibitors, cyclin-dependent kinase inhibitors, diuretics targeting the Na+-K+-Cl- cotransporter, and fluoroquinolone antibiotics targeting DNA gyrase). The top-ranked compound from each of these four groups (DB04763, DB08122, furosemide and pefloxacin, respectively) was tested for its effects on human α7 nAChR expressed in Xenopus oocytes using two-electrode voltage-clamp electrophysiology. These studies, conducted with wild-type, mutant and chimeric receptors, resulted in all four compounds exerting allosteric modulatory effects. While DB04763, DB08122 and pefloxacin were antagonists, furosemide potentiated ACh responses. Our findings, supported by docking studies, are consistent with these compounds acting as PAMs and NAMs of the α7 nAChR via interaction with a transmembrane site. Identification of α7 nAChR positive and negative allosteric modulators. Furosemide is a positive allosteric modulator of α7 nAChRs. DB04763, DB08122 and pefloxacin are negative allosteric modulators of α7 nAChRs. Modulation of α7 nAChRs by an allosteric transmembrane site.
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Affiliation(s)
| | | | - Joseph Newcombe
- Department of Chemistry, University College London, London, UK; Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Richard P Burt
- Division of Biosciences, University College London, London, UK
| | - Tom D Sheppard
- Department of Chemistry, University College London, London, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Neil S Millar
- Division of Biosciences, University College London, London, UK.
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3
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Malik V, Dhanjal JK, Kumari A, Radhakrishnan N, Singh K, Sundar D. Function and structure-based screening of compounds, peptides and proteins to identify drug candidates. Methods 2017; 131:10-21. [DOI: 10.1016/j.ymeth.2017.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/21/2017] [Accepted: 08/21/2017] [Indexed: 01/01/2023] Open
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4
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Motta S, Bonati L. Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches. J Chem Inf Model 2017; 57:1563-1578. [DOI: 10.1021/acs.jcim.7b00125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental
Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Laura Bonati
- Department of Earth and Environmental
Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
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5
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Abstract
It is widely accepted that protein receptors exist as an ensemble of conformations in solution. How best to incorporate receptor flexibility into virtual screening protocols used for drug discovery remains a significant challenge. Here, stepwise methodologies are described to generate and select relevant protein conformations for virtual screening in the context of the relaxed complex scheme (RCS), to design small molecule libraries for docking, and to perform statistical analyses on the virtual screening results. Methods include equidistant spacing, RMSD-based clustering, and QR factorization protocols for ensemble generation and ROC analysis for ensemble selection.
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6
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Ahmed L, Rasulev B, Turabekova M, Leszczynska D, Leszczynski J. Receptor- and ligand-based study of fullerene analogues: comprehensive computational approach including quantum-chemical, QSAR and molecular docking simulations. Org Biomol Chem 2014; 11:5798-808. [PMID: 23900343 DOI: 10.1039/c3ob40878g] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fullerene and its derivatives have potential antiviral activity due to their specific binding interactions with biological molecules. In this study fullerene derivatives were investigated by the synergic combination of three approaches: quantum-mechanical calculations, protein-ligand docking and quantitative structure-activity relationship methods. The protein-ligand docking studies and improved structure-activity models have been able both to predict binding affinities for the set of fullerene-C60 derivatives and to help in finding mechanisms of fullerene derivative interactions with human immunodeficiency virus type 1 aspartic protease, HIV-1 PR. Protein-ligand docking revealed several important molecular fragments that are responsible for the interaction with HIV-1 PR. In addition, a density functional theory method has been utilized to identify the optimal geometries and predict physico-chemical parameters of the studied compounds. The 5-variable GA-MLRA based model showed the best predictive ability (r(2)training = 0.882 and r(2)test = 0.738), with high internal and external correlation coefficients.
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Affiliation(s)
- Lucky Ahmed
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
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7
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Kombo DC, Bencherif M. Comparative study on the use of docking and Bayesian categorization to predict ligand binding to nicotinic acetylcholine receptors (nAChRs) subtypes. J Chem Inf Model 2013; 53:3212-22. [PMID: 24328365 DOI: 10.1021/ci400493a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We have carried out a comparative study between docking into homology models and Bayesian categorization, as applied to virtual screening of nicotinic ligands for binding at various nAChRs subtypes (human and rat α4β2, α7, α3β4, and α6β2β3). We found that although results vary with receptor subtype, Bayesian categorization exhibits higher accuracy and enrichment than unconstrained docking into homology models. However, docking accuracy is improved when one sets up a hydrogen-bond (HB) constraint between the cationic center of the ligand and the main-chain carbonyl group of the conserved Trp-149 or its homologue (a residue involved in cation-π interactions with the ligand basic nitrogen atom). This finding suggests that this HB is a hallmark of nicotinic ligands binding to nAChRs. Best predictions using either docking or Bayesian were obtained with the human α7 nAChR, when 100 nM was used as cutoff for biological activity. We also found that ligand-based Bayesian-derived enrichment factors and structure-based docking-derived enrichment factors highly correlate to each other. Moreover, they correlate with the mean molecular fractional polar surface area of actives ligands and the fractional hydrophobic/hydrophilic surface area of the binding site, respectively. This result is in agreement with the fact that hydrophobicity strongly contributes in promoting nicotinic ligands binding to their cognate nAChRs.
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Affiliation(s)
- David C Kombo
- Targacept, Inc., 100 North Main Street, Winston-Salem, North Carolina 27101, United States
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8
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Selvam B, Porter SL, Tikhonova IG. Addressing Selective Polypharmacology of Antipsychotic Drugs Targeting the Bioaminergic Receptors through Receptor Dynamic Conformational Ensembles. J Chem Inf Model 2013; 53:1761-74. [DOI: 10.1021/ci400282q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Balaji Selvam
- Molecular Therapeutics,
School of Pharmacy, Medical
Biology Centre, 97 Lisburn Road, Queen’s University Belfast, BT9 7BL, Northern Ireland, United Kingdom
| | - Simon L. Porter
- Molecular Therapeutics,
School of Pharmacy, Medical
Biology Centre, 97 Lisburn Road, Queen’s University Belfast, BT9 7BL, Northern Ireland, United Kingdom
| | - Irina G. Tikhonova
- Molecular Therapeutics,
School of Pharmacy, Medical
Biology Centre, 97 Lisburn Road, Queen’s University Belfast, BT9 7BL, Northern Ireland, United Kingdom
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9
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Barakat KH, Jordheim LP, Perez-Pineiro R, Wishart D, Dumontet C, Tuszynski JA. Virtual screening and biological evaluation of inhibitors targeting the XPA-ERCC1 interaction. PLoS One 2012; 7:e51329. [PMID: 23272099 PMCID: PMC3522735 DOI: 10.1371/journal.pone.0051329] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 10/10/2012] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Nucleotide excision repair (NER) removes many types of DNA lesions including those induced by UV radiation and platinum-based therapy. Resistance to platinum-based therapy correlates with high expression of ERCC1, a major element of the NER machinery. The interaction between ERCC1 and XPA is essential for a successful NER function. Therefore, one way to regulate NER is by inhibiting the activity of ERCC1 and XPA. METHODOLOGY/PRINCIPAL FINDINGS Here we continued our earlier efforts aimed at the identification and characterization of novel inhibitors of the ERCC1-XPA interaction. We used a refined virtual screening approach combined with a biochemical and biological evaluation of the compounds for their ability to interact with ERCC1 and to sensitize cells to UV radiation. Our findings reveal a new validated ERCC1-XPA inhibitor that significantly sensitized colon cancer cells to UV radiation indicating a strong inhibition of the ERCC1-XPA interaction. CONCLUSIONS NER is a major factor in acquiring resistance to platinum-based therapy. Regulating the NER pathway has the potential of improving the efficacy of platinum treatments. One approach that we followed is to inhibit the essential interaction between the two NER elements, ERCC1 and XPA. Here, we performed virtual screening against the ERCC1-XPA interaction and identified novel inhibitors that block the XPA-ERCC1 binding. The identified inhibitors significantly sensitized colon cancer cells to UV radiation indicating a strong inhibition of the ERCC1-XPA interaction.
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Affiliation(s)
- Khaled H. Barakat
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Engineering Mathematics and Physics, Fayoum University, Fayoum, Egypt
| | - Lars P. Jordheim
- Université de Lyon, Lyon, France
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | | | - David Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Charles Dumontet
- Université de Lyon, Lyon, France
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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10
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Galland N, Kone S, Le Questel JY. Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry. J Comput Aided Mol Des 2012; 26:1111-26. [PMID: 22972560 DOI: 10.1007/s10822-012-9602-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/05/2012] [Indexed: 11/29/2022]
Abstract
A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.
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Affiliation(s)
- Nicolas Galland
- UMR CNRS 6230, Chimie Et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UFR Sciences & Techniques, Université de Nantes, NANTES Cedex, France
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11
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Saur M, Moeller V, Kapetanopoulos K, Braukmann S, Gebauer W, Tenzer S, Markl J. Acetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits). PLoS One 2012; 7:e43685. [PMID: 22916297 PMCID: PMC3423370 DOI: 10.1371/journal.pone.0043685] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/24/2012] [Indexed: 11/20/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChR) play important neurophysiological roles and are of considerable medical relevance. They have been studied extensively, greatly facilitated by the gastropod acetylcholine-binding proteins (AChBP) which represent soluble structural and functional homologues of the ligand-binding domain of nAChR. All these proteins are ring-like pentamers. Here we report that AChBP exists in the hemolymph of the planorbid snail Biomphalaria glabrata (vector of the schistosomiasis parasite) as a regular pentagonal dodecahedron, 22 nm in diameter (12 pentamers, 60 active sites). We sequenced and recombinantly expressed two ∼25 kDa polypeptides (BgAChBP1 and BgAChBP2) with a specific active site, N-glycan site and disulfide bridge variation. We also provide the exon/intron structures. Recombinant BgAChBP1 formed pentamers and dodecahedra, recombinant BgAChBP2 formed pentamers and probably disulfide-bridged di-pentamers, but not dodecahedra. Three-dimensional electron cryo-microscopy (3D-EM) yielded a 3D reconstruction of the dodecahedron with a resolution of 6 Å. Homology models of the pentamers docked to the 6 Å structure revealed opportunities for chemical bonding at the inter-pentamer interfaces. Definition of the ligand-binding pocket and the gating C-loop in the 6 Å structure suggests that 3D-EM might lead to the identification of functional states in the BgAChBP dodecahedron.
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Affiliation(s)
- Michael Saur
- Institute of Zoology, Johannes Gutenberg University, Mainz, Germany
| | - Vanessa Moeller
- Institute of Zoology, Johannes Gutenberg University, Mainz, Germany
| | | | - Sandra Braukmann
- Institute of Zoology, Johannes Gutenberg University, Mainz, Germany
| | - Wolfgang Gebauer
- Institute of Zoology, Johannes Gutenberg University, Mainz, Germany
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jürgen Markl
- Institute of Zoology, Johannes Gutenberg University, Mainz, Germany
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12
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Abstract
Structure-based drug design has become an essential tool for rapid lead discovery and optimization. As available structural information has increased, researchers have become increasingly aware of the importance of protein flexibility for accurate description of the native state. Typical protein-ligand docking efforts still rely on a single rigid receptor, which is an incomplete representation of potential binding conformations of the protein. These rigid docking efforts typically show the best performance rates between 50 and 75%, while fully flexible docking methods can enhance pose prediction up to 80-95%. This review examines the current toolbox for flexible protein-ligand docking and receptor surface mapping. Present limitations and possibilities for future development are discussed.
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Affiliation(s)
- Katrina W. Lexa
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
| | - Heather A. Carlson
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
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13
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Yu R, Kaas Q, Craik DJ. Delineation of the unbinding pathway of α-conotoxin ImI from the α7 nicotinic acetylcholine receptor. J Phys Chem B 2012; 116:6097-105. [PMID: 22571488 DOI: 10.1021/jp301352d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
α-Conotoxins potently and specifically inhibit isoforms of nicotinic acetylcholine receptors (nAChRs) and are used as molecular probes and as drugs or drug leads. Interactions occurring during binding and unbinding events are linked to binding kinetics, and knowledge of these interactions could help in the development of α-conotoxins as drugs. Here, the unbinding process for the prototypical α-conotoxin ImI/α7-nAChR system was investigated theoretically, and three exit routes were identified using random accelerated molecular dynamics simulations. The route involving the smallest conformation perturbation was further divided into three subpathways, which were studied using steered molecular dynamics simulations. Of the three subpathways, two had better experimental support and lower potential of mean force, indicating that they might be sampled more frequently. Additionally, these subpathways were supported by previous experimental studies. Several pairwise interactions, including a cation-π interaction and charge and hydrogen bond interactions, were identified as potentially playing important roles in the unbinding event.
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Affiliation(s)
- Rilei Yu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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14
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da Silva JCA, Ducati LC, Rittner R. Conformational and stereoeletronic investigations of muscarinic agonists of acetylcholine by NMR and theoretical calculations. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Computational Approaches in the Design of Synthetic Receptors. SPRINGER SERIES ON CHEMICAL SENSORS AND BIOSENSORS 2012. [DOI: 10.1007/5346_2012_22] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ivetac A, McCammon JA. Molecular recognition in the case of flexible targets. Curr Pharm Des 2011; 17:1663-71. [PMID: 21619526 DOI: 10.2174/138161211796355056] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 05/05/2011] [Indexed: 11/22/2022]
Abstract
A protein's flexibility is well recognized to underlie its capacity to engage in critical functions, such as signal transduction, biomolecular transport and biochemical reactivity. Molecular recognition is also tightly linked to the dynamics of the binding partners, yet protein flexibility has largely been ignored by the growing field of structure-based drug design (SBDD). In combination with experimentally determined structures, a number of computational methods have been proposed to model protein movements, which may be important for small molecule binding. Such techniques have the ability to expose new binding site conformations, which may in turn recognize and lead to the discovery of more potent and selective drugs through molecular docking. In this article, we discuss various methods and focus on the Relaxed Complex Scheme (RCS), which uses Molecular Dynamics (MD) simulations to model full protein flexibility and enhance virtual screening programmes. We review practical applications of the RCS and use a recent study of the HIV-1 reverse transcriptase to illustrate the various phases of the scheme. We also discuss some encouraging developments, aimed at addressing current weaknesses of the RCS.
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Affiliation(s)
- Anthony Ivetac
- Department of Chemistry and Biochemistry University of California San Diego, La Jolla, CA 92093-0365, USA.
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17
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Veljkovic N, Glisic S, Perovic V, Veljkovic V. The role of long-range intermolecular interactions in discovery of new drugs. Expert Opin Drug Discov 2011; 6:1263-70. [PMID: 22647065 DOI: 10.1517/17460441.2012.638280] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Long-range intermolecular interactions (interactions at distances between 100 and 1000 Å) play an important role in the interaction between drugs and therapeutic targets, and design techniques based on this concept could significantly improve and accelerate new drug discovery. Understanding these long-range intermolecular interactions will also help further our understanding of the molecular mechanisms and the underlying basic biological processes. AREAS COVERED This article looks at the physical bases of long-range intermolecular interactions in biological systems with a brief review of the literature data to support this concept. The article also gives some examples of techniques used in drug discovery that were based on the long-range intermolecular interaction concept. EXPERT OPINION The electron-ion interaction potential (EIIP) and average quasivalence number (AQVN) concepts shed new light on the role of long-range intermolecular interactions in biological systems. Further research of physicochemical mechanisms underlying long-range interactions between biological molecules is necessary for a better understanding of the basic biological processes. The addition of the computer-aided design techniques based on the EIIP/AQVN concept to the research and development will lead not only to a significant reduction in cost but also to an acceleration in the development of new drugs.
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Affiliation(s)
- Nevena Veljkovic
- University of Belgrade, Institute of Nuclear Sciences Vinca , Center for Multidisciplinary Research, P.O.Box 522, 11001 Belgrade , Serbia +381 11 2453 686 ; +381 11 3440 100 ;
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Mahasenan KV, Pavlovicz RE, Henderson BJ, González-Cestari TF, Yi B, McKay DB, Li C. Discovery of Novel α4β2 Neuronal Nicotinic Receptor Modulators through Structure-Based Virtual Screening. ACS Med Chem Lett 2011; 2:855-60. [PMID: 24936233 DOI: 10.1021/ml2001714] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 09/18/2011] [Indexed: 01/05/2023] Open
Abstract
We performed a hierarchical structure-based virtual screening utilizing a comparative model of the human α4β2 neuronal nicotinic acetylcholine receptor (nAChR) extracellular domain. Compounds were selected for experimental testing based on structural diversity, binding pocket location, and standard error of the free energy scoring function used in the screening. Four of the eleven in silico hit compounds showed promising activity with low micromolar IC50 values in a calcium accumulation assay. Two of the antagonists were also proven to be selective for human α4β2 vs human α3β4 nAChRs. This is the first report of successful discovery of novel nAChR antagonists through the use of structure-based virtual screening with a human nAChR homology model. These compounds may serve as potential novel scaffolds for further development of selective nAChR antagonists.
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Affiliation(s)
- Kiran V. Mahasenan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, ‡Biophysics Program, and §Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ryan E. Pavlovicz
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, ‡Biophysics Program, and §Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Brandon J. Henderson
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, ‡Biophysics Program, and §Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Tatiana F. González-Cestari
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, ‡Biophysics Program, and §Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bitna Yi
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, ‡Biophysics Program, and §Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dennis B. McKay
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, ‡Biophysics Program, and §Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chenglong Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, ‡Biophysics Program, and §Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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Durrant JD, McCammon JA. Molecular dynamics simulations and drug discovery. BMC Biol 2011; 9:71. [PMID: 22035460 PMCID: PMC3203851 DOI: 10.1186/1741-7007-9-71] [Citation(s) in RCA: 724] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 10/27/2011] [Indexed: 02/08/2023] Open
Abstract
This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule ligands can play in drug discovery, including the identification of cryptic or allosteric binding sites, the enhancement of traditional virtual-screening methodologies, and the direct prediction of small-molecule binding energies. The limitations of current simulation methodologies, including the high computational costs and approximations of molecular forces required, are also discussed. With constant improvements in both computer power and algorithm design, the future of computer-aided drug design is promising; molecular dynamics simulations are likely to play an increasingly important role.
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Affiliation(s)
- Jacob D Durrant
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
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Akdemir A, Rucktooa P, Jongejan A, Elk RV, Bertrand S, Sixma TK, Bertrand D, Smit AB, Leurs R, de Graaf C, de Esch IJ. Acetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors. Bioorg Med Chem 2011; 19:6107-19. [DOI: 10.1016/j.bmc.2011.08.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 08/10/2011] [Accepted: 08/12/2011] [Indexed: 12/22/2022]
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Pavlovicz RE, Henderson BJ, Bonnell AB, Boyd RT, McKay DB, Li C. Identification of a negative allosteric site on human α4β2 and α3β4 neuronal nicotinic acetylcholine receptors. PLoS One 2011; 6:e24949. [PMID: 21949802 PMCID: PMC3174232 DOI: 10.1371/journal.pone.0024949] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 08/24/2011] [Indexed: 12/11/2022] Open
Abstract
Acetylcholine-based neurotransmission is regulated by cationic, ligand-gated ion channels called nicotinic acetylcholine receptors (nAChRs). These receptors have been linked to numerous neurological diseases and disorders such as Alzheimer's disease, Parkinson's disease, and nicotine addiction. Recently, a class of compounds has been discovered that antagonize nAChR function in an allosteric fashion. Models of human α4β2 and α3β4 nicotinic acetylcholine receptor (nAChR) extracellular domains have been developed to computationally explore the binding of these compounds, including the dynamics and free energy changes associated with ligand binding. Through a blind docking study to multiple receptor conformations, the models were used to determine a putative binding mode for the negative allosteric modulators. This mode, in close proximity to the agonist binding site, is presented in addition to a hypothetical mode of antagonism that involves obstruction of C loop closure. Molecular dynamics simulations and MM-PBSA free energy of binding calculations were used as computational validation of the predicted binding mode, while functional assays on wild-type and mutated receptors provided experimental support. Based on the proposed binding mode, two residues on the β2 subunit were independently mutated to the corresponding residues found on the β4 subunit. The T58K mutation resulted in an eight-fold decrease in the potency of KAB-18, a compound that exhibits preferential antagonism for human α4β2 over α3β4 nAChRs, while the F118L mutation resulted in a loss of inhibitory activity for KAB-18 at concentrations up to 100 µM. These results demonstrate the selectivity of KAB-18 for human α4β2 nAChRs and validate the methods used for identifying the nAChR modulator binding site. Exploitation of this site may lead to the development of more potent and subtype-selective nAChR antagonists which may be used in the treatment of a number of neurological diseases and disorders.
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Affiliation(s)
- Ryan E. Pavlovicz
- Biophysics Program, Ohio State University, Columbus, Ohio, United States of America
| | - Brandon J. Henderson
- Division of Pharmacology, College of Pharmacy, Ohio State University, Columbus, Ohio, United States of America
| | - Andrew B. Bonnell
- Department of Neuroscience, Ohio State University, Columbus, Ohio, United States of America
| | - R. Thomas Boyd
- Department of Neuroscience, Ohio State University, Columbus, Ohio, United States of America
| | - Dennis B. McKay
- Division of Pharmacology, College of Pharmacy, Ohio State University, Columbus, Ohio, United States of America
| | - Chenglong Li
- Biophysics Program, Ohio State University, Columbus, Ohio, United States of America
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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22
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Taly A, Colas C, Malliavin T, Blondel A, Nilges M, Corringer PJ, Joseph D. Discrimination of agonists versus antagonists of nicotinic ligands based on docking onto AChBP structures. J Mol Graph Model 2011; 30:100-9. [PMID: 21764343 DOI: 10.1016/j.jmgm.2011.06.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 05/27/2011] [Accepted: 06/22/2011] [Indexed: 11/26/2022]
Abstract
Numerous high-resolution crystallographic structures of the acetylcholine binding protein (AChBP), a molluscan cholinergic protein, homologous to the extracellular domain of nicotinic acetylcholine receptors, are available. This offers opportunities to model the interaction between various ligands and the acetylcholine binding site. Herein we present a study of the interplay between ligand binding and motions of the C-loop capping the binding site. Nicotinic agonists and antagonists were docked on AChBP X-ray structures. It is shown that the studied agonists and antagonists can be discriminated according to their higher affinities for structures respectively obtained in the presence of agonists or antagonists, highlighting the fact that AChBP structures retain a pharmacological footprint of the compound used in crystallography experiments. A detailed analysis of the binding site cavities suggests that this property is mainly related to the shape of the cavities.
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Affiliation(s)
- Antoine Taly
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, 74 Route du Rhin-BP 60024, 67401 Illkirch Cedex, France.
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Geitmann M, Retra K, de Kloe GE, Homan E, Smit AB, de Esch IJP, Danielson UH. Interaction Kinetic and Structural Dynamic Analysis of Ligand Binding to Acetylcholine-Binding Protein. Biochemistry 2010; 49:8143-54. [DOI: 10.1021/bi1006354] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Kim Retra
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of BioMolecular Analysis, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University, Amsterdam, The Netherlands
| | - Gerdien E. de Kloe
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University, Amsterdam, The Netherlands
| | - Evert Homan
- Beactica AB, Box 567, SE-751 22 Uppsala, Sweden
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University, Amsterdam, The Netherlands
| | - U. Helena Danielson
- Beactica AB, Box 567, SE-751 22 Uppsala, Sweden
- Department of Biochemistry and Organic Chemistry, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
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