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Szwabowski GL, Daigle BJ, Baker DL, Parrill AL. Structure-based pharmacophore modeling 2. Developing a novel framework for structure-based pharmacophore model generation and selection. J Mol Graph Model 2023; 122:108488. [PMID: 37121167 DOI: 10.1016/j.jmgm.2023.108488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023]
Abstract
Pharmacophore models are three-dimensional arrangements of molecular features required for biological activity that are used in ligand identification efforts for many biological targets, including G protein-coupled receptors (GPCR). Though GPCR are integral membrane proteins of considerable interest as targets for drug development, many of these receptors lack known ligands or experimentally determined structures necessary for ligand- or structure-based pharmacophore model generation, respectively. Thus, we here present a structure-based pharmacophore modeling approach that uses fragments placed with Multiple Copy Simultaneous Search (MCSS) to generate high-performing pharmacophore models in the context of experimentally determined, as well as modeled GPCR structures. Moreover, we have addressed the oft-neglected topic of pharmacophore model selection via development of a cluster-then-predict machine learning workflow. Herein score-based pharmacophore models were generated in experimentally determined and modeled structures of 13 class A GPCR and resulted in pharmacophore models exhibiting high enrichment factors when used to search a database containing 569 class A GPCR ligands. In addition, classification of pharmacophore models with the best performing cluster-then-predict logistic regression classifier resulted in positive predictive values (PPV) of 0.88 and 0.76 for selecting high enrichment pharmacophore models from among those generated in experimentally determined and modeled structures, respectively.
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Affiliation(s)
| | - Bernie J Daigle
- Departments of Biological Sciences and Computer Science, The University of Memphis, Memphis, TN, 38152, USA
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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2
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Goracci L, Nurisso A, Roussel E, Pérès B, Chaptal V, Falson P, Marminon C, Jose J, Le Borgne M, Boumendjel A. Inhibitors of ABCG2-mediated multidrug resistance: Lead generation through computer-aided drug design. Eur J Med Chem 2023; 248:115070. [PMID: 36628850 DOI: 10.1016/j.ejmech.2022.115070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/10/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
Human breast cancer resistance protein (BCRP), known also as ABCG2, plays a major role in multiple drug resistance (MDR) in tumor cells. Through this ABC transporter, cancer cells acquire the ability of resistance to structurally and functionally unrelated anticancer drugs. Nowadays, the design of ABCG2 inhibitors as potential agents to enhance the chemotherapy efficacy is an interesting strategy. In this context, we have used computer-aided drug design (CADD) based on available data of a large series of potent inhibitors from our groups as an approach in guiding the design of effective ABCG2 inhibitors. We report therein the results on the use of the FLAPpharm method to elucidate the pharmacophoric features of one of the ABCG2 binding sites involved in the regulation of the basal ATPase activity of the transporter. The predictivity of the model was evaluated by testing three predicted compounds which were found to induce high inhibitory activity of BCRP, in the nanomolar range for the best of them.
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Affiliation(s)
- Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Italy
| | - Alessandra Nurisso
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CH-1211, Geneva 4, Switzerland
| | - Emile Roussel
- Université Grenoble Alpes, INSERM, LRB UMR 1039, 38000, Grenoble, France
| | - Basile Pérès
- Université Grenoble Alpes, CNRS, DPM, UMR 5063, 38000, Grenoble, France
| | - Vincent Chaptal
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367, Lyon, France
| | - Pierre Falson
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367, Lyon, France
| | - Christelle Marminon
- Small Molecules for Biological Targets Team, Centre de recherche en cancérologie de Lyon, Centre Léon Bérard, CNRS 5286, INSERM 1052, Université Claude Bernard Lyon 1, Univ Lyon, 69373, Lyon, France
| | - Joachim Jose
- Westfälische Wilhelms-Universität Münster, Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Corrensstr. 48, 48149, Münster, Germany
| | - Marc Le Borgne
- Small Molecules for Biological Targets Team, Centre de recherche en cancérologie de Lyon, Centre Léon Bérard, CNRS 5286, INSERM 1052, Université Claude Bernard Lyon 1, Univ Lyon, 69373, Lyon, France
| | - Ahcène Boumendjel
- Université Grenoble Alpes, INSERM, LRB UMR 1039, 38000, Grenoble, France.
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3
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Smirnova M, Goracci L, Cruciani G, Federici L, Declèves X, Chapy H, Cisternino S. Pharmacophore-Based Discovery of Substrates of a Novel Drug/Proton-Antiporter in the Human Brain Endothelial hCMEC/D3 Cell Line. Pharmaceutics 2022; 14:pharmaceutics14020255. [PMID: 35213988 PMCID: PMC8875908 DOI: 10.3390/pharmaceutics14020255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
A drug/proton-antiporter, whose the molecular structure is still unknown, was previously evidenced at the blood-brain barrier (BBB) by functional experiments. The computational method could help in the identification of substrates of this solute carrier (SLC) transporter. Two pharmacophore models for substrates of this transporter using the FLAPpharm approach were developed. The trans-stimulation potency of 40 selected compounds for already known specific substrates ([3H]-clonidine) were determined and compared in the human brain endothelial cell line hCMEC/D3. Results. The two pharmacophore models obtained were used as templates to screen xenobiotic and endogenous compounds from four databases (e.g., Specs), and 45 hypothetical new candidates were tested to determine their substrate capacity. Psychoactive drugs such as antidepressants (e.g., imipramine, desipramine), antipsychotics/neuroleptics such as phenothiazine derivatives (chlorpromazine), sedatives anti-histamine-H1 drugs (promazine, promethazine, triprolidine, pheniramine), opiates/opioids (e.g., hydrocodone), trihexyphenidyl and sibutramine were correctly predicted as proton-antiporter substrates. The best performing pharmacophore model for the proton-antiporter substrates appeared as a good predictor of known substrates and allowed the identification of new substrate compounds. This model marks a new step in the characterization of this drug/proton-antiporter and will be of great use in uncovering its substrates and designing chemical entities with an improved influx capability to cross the BBB.
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Affiliation(s)
- Maria Smirnova
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
| | - Laura Goracci
- Biology and Biotechnology, Department of Chemistry, University of Perugia, 06123 Perugia, Italy; (L.G.); (G.C.)
| | - Gabriele Cruciani
- Biology and Biotechnology, Department of Chemistry, University of Perugia, 06123 Perugia, Italy; (L.G.); (G.C.)
| | - Laetitia Federici
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
| | - Xavier Declèves
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
- Biologie du Médicament et Toxicologie, AP-HP, Hôpital Cochin, 75014 Paris, France
| | - Hélène Chapy
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
| | - Salvatore Cisternino
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
- Service Pharmacie, AP-HP, Hôpital Necker-Enfants Malades, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-44-495-191
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4
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Nasser M, Salim N, Hamza H, Saeed F, Rabiu I. Improved Deep Learning Based Method for Molecular Similarity Searching Using Stack of Deep Belief Networks. Molecules 2020; 26:E128. [PMID: 33383976 PMCID: PMC7795308 DOI: 10.3390/molecules26010128] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 11/24/2022] Open
Abstract
Virtual screening (VS) is a computational practice applied in drug discovery research. VS is popularly applied in a computer-based search for new lead molecules based on molecular similarity searching. In chemical databases similarity searching is used to identify molecules that have similarities to a user-defined reference structure and is evaluated by quantitative measures of intermolecular structural similarity. Among existing approaches, 2D fingerprints are widely used. The similarity of a reference structure and a database structure is measured by the computation of association coefficients. In most classical similarity approaches, it is assumed that the molecular features in both biological and non-biologically-related activity carry the same weight. However, based on the chemical structure, it has been found that some distinguishable features are more important than others. Hence, this difference should be taken consideration by placing more weight on each important fragment. The main aim of this research is to enhance the performance of similarity searching by using multiple descriptors. In this paper, a deep learning method known as deep belief networks (DBN) has been used to reweight the molecule features. Several descriptors have been used for the MDL Drug Data Report (MDDR) dataset each of which represents different important features. The proposed method has been implemented with each descriptor individually to select the important features based on a new weight, with a lower error rate, and merging together all new features from all descriptors to produce a new descriptor for similarity searching. Based on the extensive experiments conducted, the results show that the proposed method outperformed several existing benchmark similarity methods, including Bayesian inference networks (BIN), the Tanimoto similarity method (TAN), adapted similarity measure of text processing (ASMTP) and the quantum-based similarity method (SQB). The results of this proposed multi-descriptor-based on Stack of deep belief networks method (SDBN) demonstrated a higher accuracy compared to existing methods on structurally heterogeneous datasets.
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Affiliation(s)
- Maged Nasser
- School of Computing, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia; (H.H.); (I.R.)
| | - Naomie Salim
- School of Computing, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia; (H.H.); (I.R.)
| | - Hentabli Hamza
- School of Computing, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia; (H.H.); (I.R.)
| | - Faisal Saeed
- College of Computer Science and Engineering, Taibah University, Medina 344, Saudi Arabia
| | - Idris Rabiu
- School of Computing, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia; (H.H.); (I.R.)
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5
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Deb PK, Deka S, Borah P, Abed SN, Klotz KN. Medicinal Chemistry and Therapeutic Potential of Agonists, Antagonists and Allosteric Modulators of A1 Adenosine Receptor: Current Status and Perspectives. Curr Pharm Des 2020; 25:2697-2715. [PMID: 31333094 DOI: 10.2174/1381612825666190716100509] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/01/2019] [Indexed: 12/28/2022]
Abstract
Adenosine is a purine nucleoside, responsible for the regulation of a wide range of physiological and pathophysiological conditions by binding with four G-protein-coupled receptors (GPCRs), namely A1, A2A, A2B and A3 adenosine receptors (ARs). In particular, A1 AR is ubiquitously present, mediating a variety of physiological processes throughout the body, thus represents a promising drug target for the management of various pathological conditions. Agonists of A1 AR are found to be useful for the treatment of atrial arrhythmia, angina, type-2 diabetes, glaucoma, neuropathic pain, epilepsy, depression and Huntington's disease, whereas antagonists are being investigated for the treatment of diuresis, congestive heart failure, asthma, COPD, anxiety and dementia. However, treatment with full A1 AR agonists has been associated with numerous challenges like cardiovascular side effects, off-target activation as well as desensitization of A1 AR leading to tachyphylaxis. In this regard, partial agonists of A1 AR have been found to be beneficial in enhancing insulin sensitivity and subsequently reducing blood glucose level, while avoiding severe CVS side effects and tachyphylaxis. Allosteric enhancer of A1 AR is found to be potent for the treatment of neuropathic pain, culminating the side effects related to off-target tissue activation of A1 AR. This review provides an overview of the medicinal chemistry and therapeutic potential of various agonists/partial agonists, antagonists and allosteric modulators of A1 AR, with a particular emphasis on their current status and future perspectives in clinical settings.
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Affiliation(s)
- Pran Kishore Deb
- Faculty of Pharmacy, Philadelphia University, PO Box - 1, 19392, Amman, Jordan
| | - Satyendra Deka
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati-26, Assam, India
| | - Sara N Abed
- Faculty of Pharmacy, Philadelphia University, PO Box - 1, 19392, Amman, Jordan
| | - Karl-Norbert Klotz
- University of Würzburg, Department of Pharmacology and Toxicology Versbacher Str. 9, D-97078 Würzburg, Germany
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6
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Ligand-based pharmacophore filtering, atom based 3D-QSAR, virtual screening and ADME studies for the discovery of potential ck2 inhibitors. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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7
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Ansari F, Ghasemi JB, Niazi A. Three Dimensional Quantitative Structure Activity Relationship and Pharmacophore Modeling of Tacrine Derivatives as Acetylcholinesterase Inhibitors in Alzheimer's Treatment. Med Chem 2020; 16:155-168. [DOI: 10.2174/1573406415666190513100646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 03/23/2019] [Accepted: 05/01/2019] [Indexed: 11/22/2022]
Abstract
Background:
Three dimensional quantitative structure activity relationship and pharmacophore
modeling are studied for tacrine derivatives as acetylcholinesterase inhibitors.
Methods:
The three dimensional quantitative structure–activity relationship and pharmacophore
methods were used to model the 68 derivatives of tacrine as human acetylcholinesterase inhibitors.
The effect of the docked conformer of each molecule in the enzyme cavity was investigated on the
predictive ability and statistical quality of the produced models.
Results:
The whole data set was divided into two training and test sets using hierarchical clustering
method. 3D-QSAR model, based on the comparative molecular field analysis has good statistical
parameters as indicated by q2 =0.613, r2 =0.876, and r2pred =0.75. In the case of comparative
molecular similarity index analysis, q2, r2 and r2pred values were 0.807, 0.96, and 0.865 respectively.
The statistical parameters of the models proved that the inhibition data are well fitted and
they have satisfactory predictive abilities.
Conclusion :
The results from this study illustrate the reliability of using techniques in exploring
the likely bonded conformations of the ligands in the active site of the protein target and improve
the understanding over the structural and chemical features of AChE.
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Affiliation(s)
- Fatemeh Ansari
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
| | - Jahan B. Ghasemi
- Drug Design in Silico Lab, School of Sciences, Chemistry Faculty, University of Tehran, Tehran, Iran
| | - Ali Niazi
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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8
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Wei Y, Wang M, Li Y, Hong Z, Li D, Lin J. Identification of new potent A 1 adenosine receptor antagonists using a multistage virtual screening approach. Eur J Med Chem 2019; 187:111936. [PMID: 31855793 DOI: 10.1016/j.ejmech.2019.111936] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 12/24/2022]
Abstract
The use of antagonists for each adenosine receptor (AR) subtype as potent clinical candidates is of growing interest due to their involvement in the treatment of various diseases. The recent resolution of several A1 and A2A ARs X-ray structures provides opportunities for structure-based drug design. In this study, we describe the discovery of novel A1AR antagonists by applying a multistage virtual screening approach, which is based on random forest (RF), e-pharmacophore modeling and docking methods. A multistage virtual screening approach was applied to screen the ChemDiv library (1,492,362 compounds). Among the final hits, 22 compounds were selected for further radioligand binding assay analysis against human A1AR, and 18 compounds (81.82% success) exhibited nanomolar or low micromolar binding potency (Ki). Then, we selected six compounds (pKi > 6) to further evaluate their antagonist profile in a cAMP functional assay, and we found that they had low micromolar antagonistic activity (pIC50 = 5.51-6.38) for the A1AR. Particularly, four of six compounds (pKi > 6) showed very good affinity (pKi = 6.11-7.13) and selectively (>100-fold) for A1AR over A2AAR. Moreover, the novelty analysis suggested that four of six compounds (pKi > 6) were dissimilar to existing A1AR antagonists and hence represented novel A1AR antagonists. Further molecular docking and molecular dynamics (MD) studies showed that the three selective compounds 15, 20 and 22 were stabilized (RMSlig value ≤ 2 Å) inside the binding pocket of A1AR with similar orientations to the docking pose in 100-ns MD simulations, whereas they escaped from the binding area of A2AAR with larger values of RMSlig (RMSlig ≥ 2 Å). We hope that these findings provide new insights into the discovery of drugs targeting A1AR and facilitate research on new drugs and treatments for A1AR-related human pathologies.
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Affiliation(s)
- Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353, China
| | - Mukuo Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353, China
| | - Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353, China
| | - Zhangyong Hong
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Dongmei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353, China.
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin, 300353, China; Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China; Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, China.
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9
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Deb PK. Recent Updates in the Computer Aided Drug Design Strategies for the Discovery of Agonists and Antagonists of Adenosine Receptors. Curr Pharm Des 2019; 25:747-749. [DOI: 10.2174/1381612825999190515120510] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pran Kishore Deb
- Faculty of Pharmacy, Philadelphia University, PO Box 1, 19392, Amman, Jordan
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10
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Samanta PN, Kar S, Leszczynski J. Recent Advances of In-Silico Modeling of Potent Antagonists for the Adenosine Receptors. Curr Pharm Des 2019; 25:750-773. [DOI: 10.2174/1381612825666190304123545] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 11/22/2022]
Abstract
The rapid advancement of computer architectures and development of mathematical algorithms offer a
unique opportunity to leverage the simulation of macromolecular systems at physiologically relevant timescales.
Herein, we discuss the impact of diverse structure-based and ligand-based molecular modeling techniques in
designing potent and selective antagonists against each adenosine receptor (AR) subtype that constitutes multitude
of drug targets. The efficiency and robustness of high-throughput empirical scoring function-based approaches
for hit discovery and lead optimization in the AR family are assessed with the help of illustrative examples
that have led to nanomolar to sub-micromolar inhibition activities. Recent progress in computer-aided drug
discovery through homology modeling, quantitative structure-activity relation, pharmacophore models, and molecular
docking coupled with more accurate free energy calculation methods are reported and critically analyzed
within the framework of structure-based virtual screening of AR antagonists. Later, the potency and applicability
of integrated molecular dynamics (MD) methods are addressed in the context of diligent inspection of intricated
AR-antagonist binding processes. MD simulations are exposed to be competent for studying the role of the membrane
as well as the receptor flexibility toward the precise evaluation of the biological activities of antagonistbound
AR complexes such as ligand binding modes, inhibition affinity, and associated thermodynamic and kinetic
parameters.
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Affiliation(s)
- Pabitra Narayan Samanta
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
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11
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Congreve M, Brown GA, Borodovsky A, Lamb ML. Targeting adenosine A2A receptor antagonism for treatment of cancer. Expert Opin Drug Discov 2018; 13:997-1003. [DOI: 10.1080/17460441.2018.1534825] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Limited, Steinmetz Building, Cambridge, Granta Park, UK
| | - Giles A. Brown
- Heptares Therapeutics Limited, Steinmetz Building, Cambridge, Granta Park, UK
| | | | - Michelle L. Lamb
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
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12
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Vincenzi M, Bednarska K, Leśnikowski ZJ. Comparative Study of Carborane- and Phenyl-Modified Adenosine Derivatives as Ligands for the A2A and A3 Adenosine Receptors Based on a Rigid in Silico Docking and Radioligand Replacement Assay. Molecules 2018; 23:E1846. [PMID: 30044380 PMCID: PMC6222516 DOI: 10.3390/molecules23081846] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 12/16/2022] Open
Abstract
Adenosine receptors are involved in many physiological processes and pathological conditions and are therefore attractive therapeutic targets. To identify new types of effective ligands for these receptors, a library of adenosine derivatives bearing a boron cluster or phenyl group in the same position was designed. The ligands were screened in silico to determine their calculated affinities for the A2A and A3 adenosine receptors. An virtual screening protocol based on the PatchDock web server was developed. In the first screening phase, the effects of the functional group (organic or inorganic modulator) on the adenosine ligand affinity for the receptors were determined. Then, the lead compounds were identified for each receptor in the second virtual screening phase. Two pairs of the most promising ligands, compounds 3 and 4, and two ligands with lower affinity scores (compounds 11 and 12, one with a boron cluster and one with a phenyl group) were synthesized and tested in a radioligand replacement assay for affinity to the A2A and A3 receptors. A reasonable correlation of in silico and biological assay results was observed. In addition, the effects of a phenyl group and boron cluster, which is new adenosine modifiers, on the adenosine ligand binding were compared.
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Affiliation(s)
- Marian Vincenzi
- Laboratory of Molecular Virology and Biological Chemistry, Institute of Medical Biology of the Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland.
| | - Katarzyna Bednarska
- Laboratory of Experimental Immunology, Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland.
| | - Zbigniew J Leśnikowski
- Laboratory of Molecular Virology and Biological Chemistry, Institute of Medical Biology of the Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland.
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13
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Altamura C, Mangiatordi GF, Nicolotti O, Sahbani D, Farinato A, Leonetti F, Carratù MR, Conte D, Desaphy JF, Imbrici P. Mapping ligand binding pockets in chloride ClC-1 channels through an integrated in silico and experimental approach using anthracene-9-carboxylic acid and niflumic acid. Br J Pharmacol 2018; 175:1770-1780. [PMID: 29500929 DOI: 10.1111/bph.14192] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND AND PURPOSE Although chloride channels are involved in several physiological processes and acquired diseases, the availability of compounds selectively targeting CLC proteins is limited. ClC-1 channels are responsible for sarcolemma repolarization after an action potential in skeletal muscle and have been associated with myotonia congenita and myotonic dystrophy as well as with other muscular physiopathological conditions. To date only a few ClC-1 blockers have been discovered, such as anthracene-9-carboxylic acid (9-AC) and niflumic acid (NFA), whereas no activator exists. The absence of a ClC-1 structure and the limited information regarding the binding pockets in CLC channels hamper the identification of improved modulators. EXPERIMENTAL APPROACH Here we provide an in-depth characterization of drug binding pockets in ClC-1 through an integrated in silico and experimental approach. We first searched putative cavities in a homology model of ClC-1 built upon an eukaryotic CLC crystal structure, and then validated in silico data by measuring the blocking ability of 9-AC and NFA on mutant ClC-1 channels expressed in HEK 293 cells. KEY RESULTS We identified four putative binding cavities in ClC-1. 9-AC appears to interact with residues K231, R421 and F484 within the channel pore. We also identified one preferential binding cavity for NFA and propose R421 and F484 as critical residues. CONCLUSIONS AND IMPLICATIONS This study represents the first effort to delineate the binding sites of ClC-1. This information is fundamental to discover compounds useful in the treatment of ClC-1-associated dysfunctions and might represent a starting point for specifically targeting other CLC proteins.
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Affiliation(s)
- C Altamura
- Department of Pharmacy - Drug Sciences, University of Bari 'Aldo Moro', Bari, Italy
| | - G F Mangiatordi
- Department of Pharmacy - Drug Sciences, University of Bari 'Aldo Moro', Bari, Italy
| | - O Nicolotti
- Department of Pharmacy - Drug Sciences, University of Bari 'Aldo Moro', Bari, Italy
| | - D Sahbani
- Department of Pharmacy - Drug Sciences, University of Bari 'Aldo Moro', Bari, Italy
| | - A Farinato
- Department of Pharmacy - Drug Sciences, University of Bari 'Aldo Moro', Bari, Italy
| | - F Leonetti
- Department of Pharmacy - Drug Sciences, University of Bari 'Aldo Moro', Bari, Italy
| | - M R Carratù
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - D Conte
- Department of Pharmacy - Drug Sciences, University of Bari 'Aldo Moro', Bari, Italy
| | - J-F Desaphy
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - P Imbrici
- Department of Pharmacy - Drug Sciences, University of Bari 'Aldo Moro', Bari, Italy
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14
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Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors. Molecules 2017; 22:molecules22111945. [PMID: 29125553 PMCID: PMC6150288 DOI: 10.3390/molecules22111945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022] Open
Abstract
The four receptors that signal for adenosine, A1, A2A, A2B and A3 ARs, belong to the superfamily of G protein-coupled receptors (GPCRs). They mediate a number of (patho)physiological functions and have attracted the interest of the biopharmaceutical sector for decades as potential drug targets. The many crystal structures of the A2A, and lately the A1 ARs, allow for the use of advanced computational, structure-based ligand design methodologies. Over the last decade, we have assessed the efficient synthesis of novel ligands specifically addressed to each of the four ARs. We herein review and update the results of this program with particular focus on molecular dynamics (MD) and free energy perturbation (FEP) protocols. The first in silico mutagenesis on the A1AR here reported allows understanding the specificity and high affinity of the xanthine-antagonist 8-Cyclopentyl-1,3-dipropylxanthine (DPCPX). On the A2AAR, we demonstrate how FEP simulations can distinguish the conformational selectivity of a recent series of partial agonists. These novel results are complemented with the revision of the first series of enantiospecific antagonists on the A2BAR, and the use of FEP as a tool for bioisosteric design on the A3AR.
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15
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Synthesis and phospholipidosis effect of a series of cationic amphiphilic compounds: a case study to evaluate in silico and in vitro assays. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2093-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Chen WL, Wang ZH, Feng TT, Li DD, Wang CH, Xu XL, Zhang XJ, You QD, Guo XK. Discovery, design and synthesis of 6H-anthra[1,9-cd]isoxazol-6-one scaffold as G9a inhibitor through a combination of shape-based virtual screening and structure-based molecular modification. Bioorg Med Chem 2016; 24:6102-6108. [PMID: 27720557 DOI: 10.1016/j.bmc.2016.09.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/29/2016] [Accepted: 09/29/2016] [Indexed: 01/29/2023]
Abstract
Protein lysine methyltransferase G9a is widely considered as an appealing antineoplastic target. Herein we present an integrated workflow combining shape-based virtual screening and structure-based molecular modification for the identification of novel G9a inhibitors. The shape-based similarity screening through ROCS overlay on the basis of the structure of UNC0638 was performed to identify CPUY074001 contained a 6H-anthra[1,9-cd]isoxazol-6-one scaffold as a hit. Analysis of the binding mode of CPUY074001 with G9a and 3D-QSAR results, two series compounds were designed and synthesized. The derivatives were confirmed to be active by in vitro assay and the SAR was explored by docking stimulations. Besides, several analogues showed acceptable anti-proliferative effects against several cancer cell lines. Among them, CPUY074020 displayed potent dual G9a inhibitory activity and anti-proliferative activity. Furthermore, CPUY074020 induced cell apoptosis in a dose-dependent manner and displayed a significant decrease in dimethylation of H3K9. Simultaneously, CPUY074020 showed reasonable in vivo PK properties. Altogether, our workflow supplied a high efficient strategy in the identification of novel G9a inhibitors. Compounds reported here can serve as promising leads for further study.
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Affiliation(s)
- Wei-Lin Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Zhi-Hui Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Tao-Tao Feng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Dong-Dong Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Chu-Hui Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Li Xu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Jin Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China; Department of Organic Chemistry, School of Science, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Xiao-Ke Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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17
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Molecular interaction fingerprint approaches for GPCR drug discovery. Curr Opin Pharmacol 2016; 30:59-68. [PMID: 27479316 DOI: 10.1016/j.coph.2016.07.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 01/23/2023]
Abstract
Protein-ligand interaction fingerprints (IFPs) are binary 1D representations of the 3D structure of protein-ligand complexes encoding the presence or absence of specific interactions between the binding pocket amino acids and the ligand. Various implementations of IFPs have been developed and successfully applied for post-processing molecular docking results for G Protein-Coupled Receptor (GPCR) ligand binding mode prediction and virtual ligand screening. Novel interaction fingerprint methods enable structural chemogenomics and polypharmacology predictions by complementing the increasing amount of GPCR structural data. Machine learning methods are increasingly used to derive relationships between bioactivity data and fingerprint descriptors of chemical and structural information of binding sites, ligands, and protein-ligand interactions. Factors that influence the application of IFPs include structure preparation, binding site definition, fingerprint similarity assessment, and data processing and these factors pose challenges as well possibilities to optimize interaction fingerprint methods for GPCR drug discovery.
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18
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Mangiatordi GF, Alberga D, Trisciuzzi D, Lattanzi G, Nicolotti O. Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future. Int J Mol Sci 2016; 17:ijms17071119. [PMID: 27420052 PMCID: PMC4964494 DOI: 10.3390/ijms17071119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/30/2016] [Accepted: 07/02/2016] [Indexed: 12/26/2022] Open
Abstract
Among the different aquaporins (AQPs), human aquaporin-4 (hAQP4) has attracted the greatest interest in recent years as a new promising therapeutic target. Such a membrane protein is, in fact, involved in a multiple sclerosis-like immunopathology called Neuromyelitis Optica (NMO) and in several disorders resulting from imbalanced water homeostasis such as deafness and cerebral edema. The gap of knowledge in its functioning and dynamics at the atomistic level of detail has hindered the development of rational strategies for designing hAQP4 modulators. The application, lately, of molecular modeling has proved able to fill this gap providing a breeding ground to rationally address compounds targeting hAQP4. In this review, we give an overview of the important advances obtained in this field through the application of Molecular Dynamics (MD) and other complementary modeling techniques. The case studies presented herein are discussed with the aim of providing important clues for computational chemists and biophysicists interested in this field and looking for new challenges.
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Affiliation(s)
- Giuseppe Felice Mangiatordi
- Dipartimento di Farmacia-Scienze del Farmaco, Via Orabona, 4, University of Bari "Aldo Moro", 70126 Bari, Italy.
| | - Domenico Alberga
- Institut de Recherche de Chimie Paris CNRS Chimie ParisTech, PSL Research University, 11 rue P. et M. Curie, F-75005 Paris, France.
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Via Orabona, 4, University of Bari "Aldo Moro", 70126 Bari, Italy.
| | - Gianluca Lattanzi
- INFN-Sez. di Bari and Dipartimento di Medicina Clinica e Sperimentale, University of Foggia, Viale Pinto, 71122 Foggia, Italy.
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Via Orabona, 4, University of Bari "Aldo Moro", 70126 Bari, Italy.
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19
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Goracci L, Deschamps N, Randazzo GM, Petit C, Dos Santos Passos C, Carrupt PA, Simões-Pires C, Nurisso A. A Rational Approach for the Identification of Non-Hydroxamate HDAC6-Selective Inhibitors. Sci Rep 2016; 6:29086. [PMID: 27404291 PMCID: PMC4941420 DOI: 10.1038/srep29086] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/08/2016] [Indexed: 02/07/2023] Open
Abstract
The human histone deacetylase isoform 6 (HDAC6) has been demonstrated to play a major role in cell motility and aggresome formation, being interesting for the treatment of multiple tumour types and neurodegenerative conditions. Currently, most HDAC inhibitors in preclinical or clinical evaluations are non-selective inhibitors, characterised by a hydroxamate zinc-binding group (ZBG) showing off-target effects and mutagenicity. The identification of selective HDAC6 inhibitors with novel chemical properties has not been successful yet, also because of the absence of crystallographic information that makes the rational design of HDAC6 selective inhibitors difficult. Using HDAC inhibitory data retrieved from the ChEMBL database and ligand-based computational strategies, we identified 8 original new non-hydroxamate HDAC6 inhibitors from the SPECS database, with activity in the low μM range. The most potent and selective compound, bearing a hydrazide ZBG, was shown to increase tubulin acetylation in human cells. No effects on histone H4 acetylation were observed. To the best of our knowledge, this is the first report of an HDAC6 selective inhibitor bearing a hydrazide ZBG. Its capability to passively cross the blood-brain barrier (BBB), as observed through PAMPA assays, and its low cytotoxicity in vitro, suggested its potential for drug development.
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Affiliation(s)
- Laura Goracci
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Quai Ernest-Ansermet, 30, CH-1211, Geneva 4, Switzerland.,Laboratory for Cheminformatics and Molecular Modeling, Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Nathalie Deschamps
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Quai Ernest-Ansermet, 30, CH-1211, Geneva 4, Switzerland
| | - Giuseppe Marco Randazzo
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Quai Ernest-Ansermet, 30, CH-1211, Geneva 4, Switzerland
| | - Charlotte Petit
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Quai Ernest-Ansermet, 30, CH-1211, Geneva 4, Switzerland
| | - Carolina Dos Santos Passos
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Quai Ernest-Ansermet, 30, CH-1211, Geneva 4, Switzerland
| | - Pierre-Alain Carrupt
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Quai Ernest-Ansermet, 30, CH-1211, Geneva 4, Switzerland
| | - Claudia Simões-Pires
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Quai Ernest-Ansermet, 30, CH-1211, Geneva 4, Switzerland
| | - Alessandra Nurisso
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne Quai Ernest-Ansermet, 30, CH-1211, Geneva 4, Switzerland.,Département de Biochimie, Université de Montréal, H3C 3J7 Montréal, Québec, Canada
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20
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Jazayeri A, Andrews SP, Marshall FH. Structurally Enabled Discovery of Adenosine A 2A Receptor Antagonists. Chem Rev 2016; 117:21-37. [PMID: 27333206 DOI: 10.1021/acs.chemrev.6b00119] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past decade there has been a revolution in the field of G protein-coupled receptor (GPCR) structural biology. Many years of innovative research from different areas have come together to fuel this significant change in the fortunes of this field, which for many years was characterized by the paucity of high-resolution structures. The determination to succeed has been in part due to the recognized importance of these proteins as drug targets, and although the pharmaceutical industry has been focusing on these receptors, it can be justifiably argued and demonstrated that many of the approved and commercially successful GPCR drugs can be significantly improved to increase efficacy and/or reduce undesired side effects. In addition, many validated targets in this class remain to be drugged. It is widely recognized that application of structure-based drug design approaches can help medicinal chemists a long way toward discovering better drugs. The achievement of structural biologists in providing high-resolution insight is beginning to transform drug discovery efforts, and there are a number of GPCR drugs that have been discovered by use of structural information that are in clinical development. This review aims to highlight the key developments that have brought success to GPCR structure resolution efforts and exemplify the practical application of structural information for the discovery of adenosine A2A receptor antagonists that have potential to treat multiple conditions.
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Affiliation(s)
- Ali Jazayeri
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Stephen P Andrews
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
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21
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Vucicevic J, Srdic-Rajic T, Pieroni M, Laurila JMM, Perovic V, Tassini S, Azzali E, Costantino G, Glisic S, Agbaba D, Scheinin M, Nikolic K, Radi M, Veljkovic N. A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin. Bioorg Med Chem 2016; 24:3174-83. [PMID: 27265687 DOI: 10.1016/j.bmc.2016.05.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/17/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
Abstract
The clonidine-like central antihypertensive agent rilmenidine, which has high affinity for I1-type imidazoline receptors (I1-IR) was recently found to have cytotoxic effects on cultured cancer cell lines. However, due to its pharmacological effects resulting also from α2-adrenoceptor activation, rilmenidine cannot be considered a suitable anticancer drug candidate. Here, we report the identification of novel rilmenidine-derived compounds with anticancer potential and devoid of α2-adrenoceptor effects by means of ligand- and structure-based drug design approaches. Starting from a large virtual library, eleven compounds were selected, synthesized and submitted to biological evaluation. The most active compound 5 exhibited a cytotoxic profile similar to that of rilmenidine, but without appreciable affinity to α2-adrenoceptors. In addition, compound 5 significantly enhanced the apoptotic response to doxorubicin, and may thus represent an important tool for the development of better adjuvant chemotherapeutic strategies for doxorubicin-insensitive cancers.
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Affiliation(s)
- Jelica Vucicevic
- Institute of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Tatjana Srdic-Rajic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Marco Pieroni
- P4T Group, Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Jonne M M Laurila
- Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Vladimir Perovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, POB 522, Mihaila Petrovica Alasa 14, 11001 Belgrade, Serbia
| | - Sabrina Tassini
- P4T Group, Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Elisa Azzali
- P4T Group, Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Gabriele Costantino
- P4T Group, Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Sanja Glisic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, POB 522, Mihaila Petrovica Alasa 14, 11001 Belgrade, Serbia
| | - Danica Agbaba
- Institute of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Mika Scheinin
- Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland; Unit of Clinical Pharmacology, Turku University Hospital, Turku, Finland
| | - Katarina Nikolic
- Institute of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia.
| | - Marco Radi
- P4T Group, Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy.
| | - Nevena Veljkovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, POB 522, Mihaila Petrovica Alasa 14, 11001 Belgrade, Serbia.
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22
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Massari S, Goracci L, Desantis J, Tabarrini O. Polymerase Acidic Protein-Basic Protein 1 (PA-PB1) Protein-Protein Interaction as a Target for Next-Generation Anti-influenza Therapeutics. J Med Chem 2016; 59:7699-718. [PMID: 27046062 DOI: 10.1021/acs.jmedchem.5b01474] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The limited therapeutic options against the influenza virus (flu) and increasing challenges in drug resistance make the search for next-generation agents imperative. In this context, heterotrimeric viral PA/PB1/PB2 RNA-dependent RNA polymerase is an attractive target for a challenging but strategic protein-protein interaction (PPI) inhibition approach. Since 2012, the inhibition of the polymerase PA-PB1 subunit interface has become an active field of research following the publication of PA-PB1 crystal structures. In this Perspective, we briefly discuss the validity of flu polymerase as a drug target and its inhibition through a PPI inhibition strategy, including a comprehensive analysis of available PA-PB1 structures. An overview of all of the reported PA-PB1 complex formation inhibitors is provided, and approaches used for identification of the inhibitors, the hit-to-lead studies, and the emerged structure-activity relationship are described. In addition to highlighting the strengths and weaknesses of all of the PA-PB1 heterodimerization inhibitors, we analyze their hypothesized binding modes and alignment with a pharmacophore model that we have developed.
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Affiliation(s)
- Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia , 06123 Perugia, Italy
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia , 06123 Perugia, Italy
| | - Jenny Desantis
- Department of Pharmaceutical Sciences, University of Perugia , 06123 Perugia, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia , 06123 Perugia, Italy
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23
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Chapy H, Goracci L, Vayer P, Parmentier Y, Carrupt PA, Declèves X, Scherrmann JM, Cisternino S, Cruciani G. Pharmacophore-based discovery of inhibitors of a novel drug/proton antiporter in human brain endothelial hCMEC/D3 cell line. Br J Pharmacol 2015. [PMID: 26220580 DOI: 10.1111/bph.13258] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND AND PURPOSE An influx drug/proton antiporter of unknown structure has been functionally demonstrated at the blood-brain barrier. This transporter, which handles some psychoactive drugs like diphenhydramine, clonidine, oxycodone, nicotine and cocaine, could represent a new pharmacological target in drug addiction therapy. However, at present there are no known drugs/inhibitors that effectively inhibit/modulate this transporter in vivo. EXPERIMENTAL APPROACH The FLAPpharm approach was used to establish a pharmacophore model for inhibitors of this transporter. The inhibitory potency of 44 selected compounds was determined against the specific substrate, [(3)H]-clonidine, in the human cerebral endothelial cell line hCMEC/D3 and ranked as good, medium, weak or non-inhibitor. KEY RESULTS The pharmacophore model obtained was used as a template to screen xenobiotic and endogenous compounds from databases [Specs, Recon2, Human Metabolome Database (HMDB), human intestinal transporter database], and hypothetical candidates were tested in vitro to determine their inhibitory capacity with [(3)H]-clonidine. According to the transporter database, 80% of the proton antiporter inhibitor candidates could inhibit P-glycoprotein/MDR1/ABCB1 and specificity is improved by reducing inhibitor size/shape and increasing water solubility. Virtual screening results using HMDB and Recon2 for endogenous compounds appropriately scored tryptamine as an inhibitor. CONCLUSIONS AND IMPLICATIONS The pharmacophore model for the proton-antiporter inhibitors was a good predictor of known inhibitors and allowed us to identify new good inhibitors. This model marks a new step towards the discovery of this drug/proton antiporter and will be of great use for the discovery and design of potent inhibitors that could potentially help to assess and validate its pharmacological role in drug addiction in vivo.
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Affiliation(s)
- Hélène Chapy
- INSERM U1144, Variabilité de réponse aux psychotropes, Paris, 75006, France.,UMR-S 1144, Université Paris Descartes, Paris, 75006, France.,UMR-S 1144, Université Paris Diderot, Paris, 75013, France
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, 06123, Italy
| | - Philippe Vayer
- Département de recherche biopharmaceutique, Technologie Servier, Orléans, 45000, France
| | - Yannick Parmentier
- Département de recherche biopharmaceutique, Technologie Servier, Orléans, 45000, France
| | - Pierre-Alain Carrupt
- Laboratoire de Pharmacochimie, Université de Genève, Genève, CH-1211, Switzerland
| | - Xavier Declèves
- INSERM U1144, Variabilité de réponse aux psychotropes, Paris, 75006, France.,UMR-S 1144, Université Paris Descartes, Paris, 75006, France.,UMR-S 1144, Université Paris Diderot, Paris, 75013, France.,Assistance Publique des Hôpitaux de Paris (AP-HP), Paris, France
| | - Jean-Michel Scherrmann
- INSERM U1144, Variabilité de réponse aux psychotropes, Paris, 75006, France.,UMR-S 1144, Université Paris Descartes, Paris, 75006, France.,UMR-S 1144, Université Paris Diderot, Paris, 75013, France.,Assistance Publique des Hôpitaux de Paris (AP-HP), Paris, France
| | - Salvatore Cisternino
- INSERM U1144, Variabilité de réponse aux psychotropes, Paris, 75006, France.,UMR-S 1144, Université Paris Descartes, Paris, 75006, France.,UMR-S 1144, Université Paris Diderot, Paris, 75013, France.,Assistance Publique des Hôpitaux de Paris (AP-HP), Paris, France
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, 06123, Italy
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24
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Mangiatordi GF, Alberga D, Siragusa L, Goracci L, Lattanzi G, Nicolotti O. Challenging AQP4 druggability for NMO-IgG antibody binding using molecular dynamics and molecular interaction fields. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1462-71. [PMID: 25839357 DOI: 10.1016/j.bbamem.2015.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/26/2015] [Accepted: 03/23/2015] [Indexed: 11/30/2022]
Abstract
Neuromyelitis optica (NMO) is a multiple sclerosis-like immunopathology disease affecting optic nerves and the spinal cord. Its pathological hallmark is the deposition of a typical immunoglobulin, called NMO-IgG, against the water channel Aquaporin-4 (AQP4). Preventing NMO-IgG binding would represent a valuable molecular strategy for a focused NMO therapy. The recent observation that aspartate in position 69 (D69) is determinant for the formation of NMO-IgG epitopes prompted us to carry out intensive Molecular Dynamics (MD) studies on a number of single-point AQP4 mutants. Here, we report a domino effect originating from the point mutation at position 69: we find that the side chain of T62 is reoriented far from its expected position leaning on the lumen of the pore. More importantly, the strength of the H-bond interaction between L53 and T56, at the basis of the loop A, is substantially weakened. These events represent important pieces of a clear-cut mechanistic rationale behind the failure of the NMO-IgG binding, while the water channel function as well as the propensity to aggregate into OAPs remains unaltered. The molecular interaction fields (MIF)-based analysis of cavities complemented MD findings indicating a putative binding site comprising the same residues determining epitope reorganization. In this respect, docking studies unveiled an intriguing perspective to address the future design of small drug-like compounds against NMO. In agreement with recent experimental observations, the present study is the first computational attempt to elucidate NMO-IgG binding at the molecular level, as well as a first effort toward a less elusive AQP4 druggability.
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Affiliation(s)
| | - Domenico Alberga
- Dipartimento Interateneo di Fisica "M. Merlin", Università di Bari "Aldo Moro" and INFN, Via E. Orabona, 4, I-70126 Bari, Italy; Centro Ricerche TIRES, University of Bari "Aldo Moro", Via Amendola 173, I-70126 Bari, Italy
| | - Lydia Siragusa
- Molecular Discovery Limited, 215 Marsh Road, Pinner, Middlesex, London HA5 5NE, UK
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Gianluca Lattanzi
- Dipartimento Interateneo di Fisica "M. Merlin", Università di Bari "Aldo Moro" and INFN, Via E. Orabona, 4, I-70126 Bari, Italy; Centro Ricerche TIRES, University of Bari "Aldo Moro", Via Amendola 173, I-70126 Bari, Italy
| | - Orazio Nicolotti
- Dipartimento di Farmacia - Scienze del Farmaco, Via Orabona, 4, Università di Bari "Aldo Moro", Bari, Italy; Centro Ricerche TIRES, University of Bari "Aldo Moro", Via Amendola 173, I-70126 Bari, Italy.
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25
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Poli G, Giuntini N, Martinelli A, Tuccinardi T. Application of a FLAP-Consensus Docking Mixed Strategy for the Identification of New Fatty Acid Amide Hydrolase Inhibitors. J Chem Inf Model 2015; 55:667-75. [DOI: 10.1021/ci5006806] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Giulio Poli
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy
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26
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Goracci L, Buratta S, Urbanelli L, Ferrara G, Di Guida R, Emiliani C, Cross S. Evaluating the risk of phospholipidosis using a new multidisciplinary pipeline approach. Eur J Med Chem 2015; 92:49-63. [DOI: 10.1016/j.ejmech.2014.12.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 12/19/2022]
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27
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Siragusa L, Cross S, Baroni M, Goracci L, Cruciani G. BioGPS: Navigating biological space to predict polypharmacology, off-targeting, and selectivity. Proteins 2015; 83:517-32. [DOI: 10.1002/prot.24753] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 12/09/2014] [Accepted: 12/13/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Lydia Siragusa
- Laboratory for Chemometrics and Molecular Modeling, Department of Chemistry, Biology and Biotechnology; University of Perugia; Perugia 06123 Italy
| | - Simon Cross
- Molecular Discovery Limited; Pinner, Middlesex, London HA5 5NE United Kingdom
| | - Massimo Baroni
- Molecular Discovery Limited; Pinner, Middlesex, London HA5 5NE United Kingdom
| | - Laura Goracci
- Laboratory for Chemometrics and Molecular Modeling, Department of Chemistry, Biology and Biotechnology; University of Perugia; Perugia 06123 Italy
| | - Gabriele Cruciani
- Laboratory for Chemometrics and Molecular Modeling, Department of Chemistry, Biology and Biotechnology; University of Perugia; Perugia 06123 Italy
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28
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Congreve M, Dias JM, Marshall FH. Structure-based drug design for G protein-coupled receptors. PROGRESS IN MEDICINAL CHEMISTRY 2014; 53:1-63. [PMID: 24418607 DOI: 10.1016/b978-0-444-63380-4.00001-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Our understanding of the structural biology of G protein-coupled receptors has undergone a transformation over the past 5 years. New protein-ligand complexes are described almost monthly in high profile journals. Appreciation of how small molecules and natural ligands bind to their receptors has the potential to impact enormously how medicinal chemists approach this major class of receptor targets. An outline of the key topics in this field and some recent examples of structure- and fragment-based drug design are described. A table is presented with example views of each G protein-coupled receptor for which there is a published X-ray structure, including interactions with small molecule antagonists, partial and full agonists. The possible implications of these new data for drug design are discussed.
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Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
| | - João M Dias
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
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29
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Cruciani G, Valeri A, Goracci L, Pellegrino RM, Buonerba F, Baroni M. Flavin monooxygenase metabolism: why medicinal chemists should matter. J Med Chem 2014; 57:6183-96. [PMID: 25003501 DOI: 10.1021/jm5007098] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
FMO enzymes (FMOs) play a key role in the processes of detoxification and/or bioactivation of specific pharmaceuticals and xenobiotics bearing nucleophilic centers. The N-oxide and S-oxide metabolites produced by FMOs are often active metabolites. The FMOs are more active than cytochromes in the brain and work in tandem with CYP3A4 in the liver. FMOs might reduce the risk of phospholipidosis of CAD-like drugs, although some FMOs metabolites seem to be neurotoxic and hepatotoxic. However, in silico methods for FMO metabolism prediction are not yet available. This paper reports, for the first time, a substrate-specificity and catalytic-activity model for FMO3, the most relevant isoform of the FMOs in humans. The application of this model to a series of compounds with unknown FMO metabolism is also reported. The model has also been very useful to design compounds with optimal clearance and in finding erroneous literature data, particularly cases in which substances have been reported to be FMO3 substrates when, in reality, the experimentally validated in silico model correctly predicts that they are not.
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Affiliation(s)
- Gabriele Cruciani
- Laboratory for Chemoinformatics and Molecular Modelling, Department of Chemistry, Biology and Biotechnology, University of Perugia , Via Elce di Sotto 8, 06123 Perugia, Italy
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30
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Siragusa L, Spyrakis F, Goracci L, Cross S, Cruciani G. BioGPS: The Music for the Chemo- and Bioinformatics Walzer. Mol Inform 2014; 33:446-53. [DOI: 10.1002/minf.201400028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/19/2014] [Indexed: 01/09/2023]
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31
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Xu XL, Sun HP, Liu F, Jia JM, Guo XK, Pan Y, Huang HZ, Zhang XJ, You QD. Discovery and Bioevaluation of Novel Pyrazolopyrimidine Analogs as Competitive Hsp90 Inhibitors Through Shape-Based Similarity Screening. Mol Inform 2014; 33:293-306. [PMID: 27485776 DOI: 10.1002/minf.201300150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 02/13/2014] [Indexed: 12/14/2022]
Abstract
Hsp90 as a promising therapeutic target for the treatment of cancer has received great attention. Many Hsp90 inhibitors such as BIIB021 and CUDC-305 have been in clinical. In this paper shape-based similarity screening through ROCS overlays on the basis of CUDC-305, BIIB021, PU-H71 and PU-3 were performed to discover HSP90 inhibitors. A set of 19 novel pyrazolopyrimidine analogues was identified and evaluated on enzyme level and cell-based level as Hsp90 inhibitors. The compound HDI4-04 with IC50 0.35 µM in the Hsp90 ATP hydrolysis assay exhibited potent cytotoxicity against five human cancer cell lines. Western blot analysis and Hsp70 luciferase reporter assay further confirmed that HDI4-04 targeted the Hsp90 protein folding machinery. And according to the biological assay, the SAR was discussed and summarized, which will guide us for further optimization of these compounds.
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Affiliation(s)
- Xiao-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Hao-Peng Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271216
| | - Fang Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jian-Min Jia
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xiao-Ke Guo
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yang Pan
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Hao-Ze Huang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xiao-Jin Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Organic Chemistry, School of Science, China Pharmaceutical University, Nanjing, 210009, China
| | - Qi-Dong You
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271351. , .,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China. , .,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, P. R. China fax & tel: +86-25-83271216. ,
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32
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Spyrakis F, Cellini B, Bruno S, Benedetti P, Carosati E, Cruciani G, Micheli F, Felici A, Cozzini P, Kellogg GE, Voltattorni CB, Mozzarelli A. Targeting cystalysin, a virulence factor of treponema denticola-supported periodontitis. ChemMedChem 2014; 9:1501-11. [PMID: 24616267 DOI: 10.1002/cmdc.201300527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/13/2014] [Indexed: 01/01/2023]
Abstract
Cystalysin from Treponema denticola is a pyridoxal 5'-phosphate dependent lyase that catalyzes the formation of pyruvate, ammonia, and sulfide from cysteine. It is a virulence factor in adult periodontitis because its reaction contributes to hemolysis, which sustains the pathogen. Therefore, it was proposed as a potential antimicrobial target. To identify specific inhibitors by structure-based in silico methods, we first validated the crystal structure of cystalysin as a reliable starting point for the design of ligands. By using single-crystal absorption microspectrophotometry, we found that the enzyme in the crystalline state, with respect to that in solution, exhibits: 1) the same absorption spectra for the catalytic intermediates, 2) a close pKa value for the residue controlling the keto enamine ionization, and 3) similar reactivity with glycine, L-serine, L-methionine, and the nonspecific irreversible inhibitor aminoethoxyvinylglycine. Next, we screened in silico a library of 9357 compounds with the Fingerprints for Ligands and Proteins (FLAP) software, by using the three-dimensional structure of cystalysin as a template. From the library, 17 compounds were selected and experimentally evaluated by enzyme assays and spectroscopic methods. Two compounds were found to competitively inhibit recombinant T. denticola cystalysin, with inhibition constant (Ki ) values of 25 and 37 μM. One of them exhibited a minimum inhibitory concentration (MIC) value of 64 μg mL(-1) on Moraxella catarrhalis ATCC 23246, which proves its ability to cross bacterial membranes.
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Affiliation(s)
- Francesca Spyrakis
- Department of Food Sciences, University of Parma, Parma (Italy); Current address: Department of Life Sciences, University of Modena and Reggio Emilia, Modena (Italy)
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33
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Andrews SP, Brown GA, Christopher JA. Structure-Based and Fragment-Based GPCR Drug Discovery. ChemMedChem 2013; 9:256-75. [DOI: 10.1002/cmdc.201300382] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/15/2013] [Indexed: 01/05/2023]
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34
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Massari S, Nannetti G, Goracci L, Sancineto L, Muratore G, Sabatini S, Manfroni G, Mercorelli B, Cecchetti V, Facchini M, Palù G, Cruciani G, Loregian A, Tabarrini O. Structural Investigation of Cycloheptathiophene-3-carboxamide Derivatives Targeting Influenza Virus Polymerase Assembly. J Med Chem 2013; 56:10118-31. [DOI: 10.1021/jm401560v] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Serena Massari
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | - Giulio Nannetti
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Laura Goracci
- Department
of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Luca Sancineto
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | - Giulia Muratore
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Stefano Sabatini
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | - Giuseppe Manfroni
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | | | - Violetta Cecchetti
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
| | - Marzia Facchini
- Department of Infectious, Parasitic, and Immunomediated Diseases,
WHO National Influenza Centre, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Gabriele Cruciani
- Department
of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Oriana Tabarrini
- Department of Chemistry and Technology
of Drugs, University of Perugia, 06123 Perugia, Italy
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35
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Spyrakis F, Singh R, Cozzini P, Campanini B, Salsi E, Felici P, Raboni S, Benedetti P, Cruciani G, Kellogg GE, Cook PF, Mozzarelli A. Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target. PLoS One 2013; 8:e77558. [PMID: 24167577 PMCID: PMC3805590 DOI: 10.1371/journal.pone.0077558] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/03/2013] [Indexed: 01/06/2023] Open
Abstract
The last step of cysteine biosynthesis in bacteria and plants is catalyzed by O-acetylserine sulfhydrylase. In bacteria, two isozymes, O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, have been identified that share similar binding sites, although the respective specific functions are still debated. O-acetylserine sulfhydrylase plays a key role in the adaptation of bacteria to the host environment, in the defense mechanisms to oxidative stress and in antibiotic resistance. Because mammals synthesize cysteine from methionine and lack O-acetylserine sulfhydrylase, the enzyme is a potential target for antimicrobials. With this aim, we first identified potential inhibitors of the two isozymes via a ligand- and structure-based in silico screening of a subset of the ZINC library using FLAP. The binding affinities of the most promising candidates were measured in vitro on purified O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B from Salmonella typhimurium by a direct method that exploits the change in the cofactor fluorescence. Two molecules were identified with dissociation constants of 3.7 and 33 µM for O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, respectively. Because GRID analysis of the two isoenzymes indicates the presence of a few common pharmacophoric features, cross binding titrations were carried out. It was found that the best binder for O-acetylserine sulfhydrylase-B exhibits a dissociation constant of 29 µM for O-acetylserine sulfhydrylase-A, thus displaying a limited selectivity, whereas the best binder for O-acetylserine sulfhydrylase-A exhibits a dissociation constant of 50 µM for O-acetylserine sulfhydrylase-B and is thus 8-fold selective towards the former isozyme. Therefore, isoform-specific and isoform-independent ligands allow to either selectively target the isozyme that predominantly supports bacteria during infection and long-term survival or to completely block bacterial cysteine biosynthesis.
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Affiliation(s)
| | - Ratna Singh
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Pietro Cozzini
- Department of Food Sciences, University of Parma, Parma, Italy
- National Institute of Biostructures and Biosystems, Rome, Italy
| | - Barbara Campanini
- Department of Pharmacy, University of Parma, Parma, Italy
- * E-mail: (BC); (AM)
| | - Enea Salsi
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Paolo Felici
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Samanta Raboni
- Department of Pharmacy, University of Parma, Parma, Italy
| | | | | | - Glen E. Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul F. Cook
- Department of Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma, Parma, Italy
- National Institute of Biostructures and Biosystems, Rome, Italy
- * E-mail: (BC); (AM)
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36
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Poli G, Tuccinardi T, Rizzolio F, Caligiuri I, Botta L, Granchi C, Ortore G, Minutolo F, Schenone S, Martinelli A. Identification of New Fyn Kinase Inhibitors Using a FLAP-Based Approach. J Chem Inf Model 2013; 53:2538-47. [DOI: 10.1021/ci4002553] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Giulio Poli
- Department
of Pharmacy, University of Pisa, 56126 Pisa, Italy
| | | | - Flavio Rizzolio
- Division of Experimental
and Clinical Pharmacology, Department of Molecular Biology
and Translational Research, National Cancer Institute and Center for Molecular Biomedicine, CRO, Aviano, 33081 Pordenone, Italy
| | - Isabella Caligiuri
- Division of Experimental
and Clinical Pharmacology, Department of Molecular Biology
and Translational Research, National Cancer Institute and Center for Molecular Biomedicine, CRO, Aviano, 33081 Pordenone, Italy
| | - Lorenzo Botta
- Dipartimento
Farmaco Chimico Tecnologico, Università di Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy
| | | | | | | | - Silvia Schenone
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Genova, Viale Benedetto
XV 3, 16132 Genova, Italy
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37
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Sun H, Xu X, Wu X, Zhang X, Liu F, Jia J, Guo X, Huang J, Jiang Z, Feng T, Chu H, Zhou Y, Zhang S, Liu Z, You Q. Discovery and design of tricyclic scaffolds as protein kinase CK2 (CK2) inhibitors through a combination of shape-based virtual screening and structure-based molecular modification. J Chem Inf Model 2013; 53:2093-102. [PMID: 23937544 DOI: 10.1021/ci400114f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein kinase CK2 (CK2), a ubiquitous serine/threonine protein kinase for hundreds of endogenous substrates, serves as an attractive anticancer target. One of its most potent inhibitors, CX-4945, has entered a phase I clinical trial. Herein we present an integrated workflow combining shape-based virtual screening for the identification of novel CK2 inhibitors. A shape-based model derived from CX-4945 was built, and the subsequent virtual screening led to the identification of several novel scaffolds with high shape similarity to that of CX-4945. Among them two tricyclic scaffolds named [1,2,4]triazolo[4,3-c]quinazolin and [1,2,4]triazolo[4,3-a]quinoxalin attracted us the most. Combining strictly chemical similarity analysis, a second-round shape-based screening was performed based on the two tricyclic scaffolds, leading to 28 derivatives. These compounds not only targeted CK2 with potent and dose-dependent activities but also showed acceptable antiproliferative effects against a series of cancer cell lines. Our workflow supplies a high efficient strategy in the identification of novel CK2 inhibitors. Compounds reported here can serve as ideal leads for further modifications.
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Affiliation(s)
- Haopeng Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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38
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Jacobson KA. Structure-based approaches to ligands for G-protein-coupled adenosine and P2Y receptors, from small molecules to nanoconjugates. J Med Chem 2013; 56:3749-67. [PMID: 23597047 PMCID: PMC3701956 DOI: 10.1021/jm400422s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Adenosine receptor (ARs) and P2Y receptors (P2YRs) that respond to extracellular nucleosides/nucleotides are associated with new directions for therapeutics. The X-ray structures of the A2AAR complexes with agonists and antagonists are examined in relationship to the G-protein-coupled receptor (GPCR) superfamily and applied to drug discovery. Much of the data on AR ligand structure from early SAR studies now are explainable from the A2AAR X-ray crystallography. The ligand-receptor interactions in related GPCR complexes can be identified by means of modeling approaches, e.g., molecular docking. Thus, molecular recognition in binding and activation processes has been studied effectively using homology modeling and applied to ligand design. Virtual screening has yielded new nonnucleoside AR antagonists, and existing ligands have been improved with knowledge of the receptor interactions. New agonists are being explored for central nervous system and peripheral therapeutics based on in vivo activity, such as chronic neuropathic pain. Ligands for receptors more distantly related to the X-ray template, i.e., P2YRs, have been introduced and are mainly used as pharmacological tools for elucidating the physiological role of extracellular nucleotides. Other ligand tools for drug discovery include fluorescent probes, radioactive probes, multivalent probes, and functionalized nanoparticles.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, USA.
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39
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Artese A, Cross S, Costa G, Distinto S, Parrotta L, Alcaro S, Ortuso F, Cruciani G. Molecular interaction fields in drug discovery: recent advances and future perspectives. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1150] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Anna Artese
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Simon Cross
- Molecular Discovery Ltd, Pinner; Middlesex London United Kingdom
| | - Giosuè Costa
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Simona Distinto
- Dipartimento di Scienze della Vita e dell'Ambiente; Università di Cagliari; Cagliari Italy
| | - Lucia Parrotta
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute; Università degli Studi “Magna Graecia” di Catanzaro; Campus “S. Venuta”; Viale Europa Catanzaro Italy
| | - Gabriele Cruciani
- Laboratory for Chemometrics and Cheminformatics; Chemistry Department; University of Perugia; Perugia Italy
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40
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Soliman MES. A Hybrid Structure/Pharmacophore-Based Virtual Screening Approach to Design Potential Leads: A Computer-Aided Design of South African HIV-1 Subtype C Protease Inhibitors. Drug Dev Res 2013. [DOI: 10.1002/ddr.21078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Mahmoud E. S. Soliman
- School of Health Sciences; University of KwaZulu-Natal; Westville; Durban; 4001; South Africa
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41
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Sirci F, Istyastono EP, Vischer HF, Kooistra AJ, Nijmeijer S, Kuijer M, Wijtmans M, Mannhold R, Leurs R, de Esch IJP, de Graaf C. Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints. J Chem Inf Model 2012; 52:3308-24. [DOI: 10.1021/ci3004094] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Francesco Sirci
- Laboratory for Chemometrics
and Chemoinformatics, Chemistry Department, University of Perugia, Via Elce di Sotto, 10, I-06123 Perugia Italy
| | - Enade P. Istyastono
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Molecular Modeling Division, Pharmaceutical
Technology Laboratory, Universitas Sanata Dharma, Yogyakarta, Indonesia
| | - Henry F. Vischer
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Albert J. Kooistra
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Saskia Nijmeijer
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Martien Kuijer
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Maikel Wijtmans
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Raimund Mannhold
- Department of Laser Medicine,
Molecular Drug Research Group, Heinrich-Heine-Universität, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Rob Leurs
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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