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CompScore: Boosting Structure-Based Virtual Screening Performance by Incorporating Docking Scoring Function Components into Consensus Scoring. J Chem Inf Model 2019; 59:3655-3666. [DOI: 10.1021/acs.jcim.9b00343] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Makhouri FR, Ghasemi JB. In Silico Studies in Drug Research Against Neurodegenerative Diseases. Curr Neuropharmacol 2018; 16:664-725. [PMID: 28831921 PMCID: PMC6080098 DOI: 10.2174/1570159x15666170823095628] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/24/2017] [Accepted: 08/16/2017] [Indexed: 01/14/2023] Open
Abstract
Background Neurodegenerative diseases such as Alzheimer's disease (AD), amyotrophic lateral sclerosis, Parkinson's disease (PD), spinal cerebellar ataxias, and spinal and bulbar muscular atrophy are described by slow and selective degeneration of neurons and axons in the central nervous system (CNS) and constitute one of the major challenges of modern medicine. Computer-aided or in silico drug design methods have matured into powerful tools for reducing the number of ligands that should be screened in experimental assays. Methods In the present review, the authors provide a basic background about neurodegenerative diseases and in silico techniques in the drug research. Furthermore, they review the various in silico studies reported against various targets in neurodegenerative diseases, including homology modeling, molecular docking, virtual high-throughput screening, quantitative structure activity relationship (QSAR), hologram quantitative structure activity relationship (HQSAR), 3D pharmacophore mapping, proteochemometrics modeling (PCM), fingerprints, fragment-based drug discovery, Monte Carlo simulation, molecular dynamic (MD) simulation, quantum-mechanical methods for drug design, support vector machines, and machine learning approaches. Results Detailed analysis of the recently reported case studies revealed that the majority of them use a sequential combination of ligand and structure-based virtual screening techniques, with particular focus on pharmacophore models and the docking approach. Conclusion Neurodegenerative diseases have a multifactorial pathoetiological origin, so scientists have become persuaded that a multi-target therapeutic strategy aimed at the simultaneous targeting of multiple proteins (and therefore etiologies) involved in the development of a disease is recommended in future.
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Affiliation(s)
| | - Jahan B Ghasemi
- Chemistry Department, Faculty of Sciences, University of Tehran, Tehran, Iran
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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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Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
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Yi B, Long S, González-Cestari TF, Henderson BJ, Pavlovicz RE, Werbovetz K, Li C, McKay DB. Discovery of benzamide analogs as negative allosteric modulators of human neuronal nicotinic receptors: pharmacophore modeling and structure-activity relationship studies. Bioorg Med Chem 2013; 21:4730-43. [PMID: 23757208 PMCID: PMC4347880 DOI: 10.1016/j.bmc.2013.03.082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/22/2013] [Accepted: 03/29/2013] [Indexed: 02/05/2023]
Abstract
The present study describes our ongoing efforts toward the discovery of drugs that selectively target nAChR subtypes. We exploited knowledge on nAChR ligands and their binding site that were previously identified by our laboratory through virtual screenings and identified benzamide analogs as a novel chemical class of neuronal nicotinic receptor (nAChR) ligands. The lead molecule, compound 1 (4-(allyloxy)-N-(6-methylpyridin-2-yl)benzamide) inhibits nAChR activity with an IC₅₀ value of 6.0 (3.4-10.6) μM on human α4β2 nAChRs with a ∼5-fold preference against human α3β4 nAChRs. Twenty-six analogs of compound 1 were also either synthesized or purchased for structure-activity relationship (SAR) studies and provided information relating the chemical/structural properties of the molecules to their ability to inhibit nAChR activity. The discovery of subtype-selective ligands of nAChRs described here should contribute significantly to our understanding of the involvement of specific nAChR subtypes in normal and pathophysiological states.
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Affiliation(s)
- Bitna Yi
- Division of Pharmacology, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, USA
| | - Sihui Long
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Tatiana F. González-Cestari
- Division of Pharmacology, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, USA
| | - Brandon J. Henderson
- Division of Pharmacology, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, USA
| | - Ryan E. Pavlovicz
- Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Karl Werbovetz
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Chenglong Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
| | - Dennis B. McKay
- Division of Pharmacology, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, USA
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Durrant JD, Friedman AJ, Rogers KE, McCammon JA. Comparing neural-network scoring functions and the state of the art: applications to common library screening. J Chem Inf Model 2013; 53:1726-35. [PMID: 23734946 PMCID: PMC3735370 DOI: 10.1021/ci400042y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Indexed: 11/29/2022]
Abstract
We compare established docking programs, AutoDock Vina and Schrödinger's Glide, to the recently published NNScore scoring functions. As expected, the best protocol to use in a virtual-screening project is highly dependent on the target receptor being studied. However, the mean screening performance obtained when candidate ligands are docked with Vina and rescored with NNScore 1.0 is not statistically different than the mean performance obtained when docking and scoring with Glide. We further demonstrate that the Vina and NNScore docking scores both correlate with chemical properties like small-molecule size and polarizability. Compensating for these potential biases leads to improvements in virtual screen performance. Composite NNScore-based scoring functions suited to a specific receptor further improve performance. We are hopeful that the current study will prove useful for those interested in computer-aided drug design.
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Affiliation(s)
- Jacob D Durrant
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA.
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Yuriev E, Ramsland PA. Latest developments in molecular docking: 2010-2011 in review. J Mol Recognit 2013; 26:215-39. [PMID: 23526775 DOI: 10.1002/jmr.2266] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/16/2013] [Accepted: 01/19/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; Parkville; VIC; 3052; Australia
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Henderson BJ, González-Cestari TF, Yi B, Pavlovicz RE, Boyd RT, Li C, Bergmeier SC, McKay DB. Defining the putative inhibitory site for a selective negative allosteric modulator of human α4β2 neuronal nicotinic receptors. ACS Chem Neurosci 2012; 3:682-92. [PMID: 23019495 DOI: 10.1021/cn300035f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 05/25/2012] [Indexed: 02/05/2023] Open
Abstract
Neuronal nicotinic receptors (nAChRs) have been implicated in several diseases and disorders such as autism spectrum disorders, Alzheimer's disease, Parkinson's disease, epilepsy, and nicotine addiction. To understand the role of nAChRs in these conditions, it would be beneficial to have selective molecules that target specific nAChRs in vitro and in vivo. Our laboratory has previously identified a novel allosteric site on human α4β2 nAChRs using a series of computational and in vitro approaches. At this site, we have identified negative allosteric modulators that selectively inhibit human α4β2 nAChRs, a subtype implicated in nicotine addiction. This study characterizes the allosteric site via site-directed mutagenesis. Three amino acids (Phe118, Glu60, and Thr58) on the β2 subunit were shown to participate in the inhibitory properties of the selective antagonist KAB-18 and provided insights into its antagonism of human α4β2 nAChRs. SAR studies with KAB-18 analogues and various mutant α4β2 nAChRs also provided information concerning how different physiochemical features influence the inhibition of nAChRs through this allosteric site. Together, these studies identify the amino acids that contribute to the selective antagonism of human α4β2 nAChRs at this allosteric site. Finally, these studies define the physiochemical features of ligands that influence interaction with specific amino acids in this allosteric site.
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Affiliation(s)
- Brandon J. Henderson
- Division of
Biology, California Institute of Technology, Pasadena, California
91125, United States
| | - Tatiana F. González-Cestari
- Division
of Pharmacology, College
of Pharmacy, The Ohio State University,
Columbus, Ohio 43210, United States
| | - Bitna Yi
- Division
of Pharmacology, College
of Pharmacy, The Ohio State University,
Columbus, Ohio 43210, United States
| | - Ryan E. Pavlovicz
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United
States
| | - R. Thomas Boyd
- Department of Neuroscience, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Chenglong Li
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Stephen C. Bergmeier
- Department of Chemistry
and Biochemistry, Ohio University, Athens,
Ohio 45701, United States
| | - Dennis B. McKay
- Division
of Pharmacology, College
of Pharmacy, The Ohio State University,
Columbus, Ohio 43210, United States
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Dandapani S, Rosse G, Southall N, Salvino JM, Thomas CJ. Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening. ACTA ACUST UNITED AC 2012; 4:177-191. [PMID: 26705509 DOI: 10.1002/9780470559277.ch110252] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The selection, acquisition and use of high quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes and environments. The decisions surrounding the make-up of any given small molecule library is informed by a multitude of variables and opinions vary on best-practices. The fitness of any collection relies upon upfront filtering to avoiding problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication and assay objective also play a significant role in the choice of library composition. This overview attempts to offer advice to all organizations engaged in small molecule screening based upon current best practices and theoretical considerations in library selection and acquisition.
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Affiliation(s)
- Sivaraman Dandapani
- Chemical Biology Platform, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge Massachusetts 02142 USA
| | - Gerard Rosse
- Dart NeuroScience LLC, 7473 Lusk Boulevard, San Diego, CA 92121 USA
| | - Noel Southall
- NIH Chemical Genomics Center, National Human Genome Research Institute, 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Joseph M Salvino
- Alliance Discovery, Inc, Biotechnology Center 3805 Old Easton Road, Doylestown, PA 18902 USA
| | - Craig J Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
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Henderson BJ, Carper DJ, González-Cestari TF, Yi B, Mahasenan K, Pavlovicz RE, Dalefield ML, Coleman RS, Li C, McKay DB. Structure-activity relationship studies of sulfonylpiperazine analogues as novel negative allosteric modulators of human neuronal nicotinic receptors. J Med Chem 2011; 54:8681-92. [PMID: 22060139 DOI: 10.1021/jm201294r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Neuronal nicotinic receptors have been implicated in several diseases and disorders such as autism, Alzheimer's disease, Parkinson's disease, epilepsy, and various forms of addiction. To understand the role of nicotinic receptors in these conditions, it would be beneficial to have selective molecules that target specific nicotinic receptors in vitro and in vivo. Our laboratory has previously identified novel negative allosteric modulators of human α4β2 (Hα4β2) and human α3β4 (Hα3β4) nicotinic receptors. The effects of novel sulfonylpiperazine analogues that act as negative allosteric modulators on both Hα4β2 nAChRs and Hα3β4 nAChRs were investigated. This work, through structure-activity relationship (SAR) studies, describes the chemical features of these molecules that are important for both potency and selectivity on Hα4β2 nAChRs.
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Affiliation(s)
- Brandon J Henderson
- Division of Pharmacology, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
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