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Salmaso V, Persico M, Da Ros T, Spalluto G, Kachler S, Klotz KN, Moro S, Federico S. Pyrazolo-triazolo-pyrimidine Scaffold as a Molecular Passepartout for the Pan-Recognition of Human Adenosine Receptors. Biomolecules 2023; 13:1610. [PMID: 38002292 PMCID: PMC10669182 DOI: 10.3390/biom13111610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Adenosine receptors are largely distributed in our organism and are promising therapeutic targets for the treatment of many pathologies. In this perspective, investigating the structural features of the ligands leading to affinity and/or selectivity is of great interest. In this work, we have focused on a small series of pyrazolo-triazolo-pyrimidine antagonists substituted in positions 2, 5, and N8, where bulky acyl moieties at the N5 position and small alkyl groups at the N8 position are associated with affinity and selectivity at the A3 adenosine receptor even if a good affinity toward the A2B adenosine receptor has also been observed. Conversely, a free amino function at the 5 position induces high affinity at the A2A and A1 receptors with selectivity vs. the A3 subtype. A molecular modeling study suggests that differences in affinity toward A1, A2A, and A3 receptors could be ascribed to two residues: one in the EL2, E168 in human A2A/E172 in human A1, that is occupied by the hydrophobic residue V169 in the human A3 receptor; and the other in TM6, occupied by H250/H251 in human A2A and A1 receptors and by a less bulky S247 in the A3 receptor. In the end, these findings could help to design new subtype-selective adenosine receptor ligands.
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Affiliation(s)
- Veronica Salmaso
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, I-35131 Padova, Italy;
| | - Margherita Persico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Licio Giorgieri 1, I-34127 Trieste, Italy; (M.P.); (T.D.R.); (G.S.)
| | - Tatiana Da Ros
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Licio Giorgieri 1, I-34127 Trieste, Italy; (M.P.); (T.D.R.); (G.S.)
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Licio Giorgieri 1, I-34127 Trieste, Italy; (M.P.); (T.D.R.); (G.S.)
| | - Sonja Kachler
- Institut für Pharmakologie, Universität of Würzburg, Versbacher Str. 9, D-97078 Würzburg, Germany; (S.K.); (K.-N.K.)
| | - Karl-Norbert Klotz
- Institut für Pharmakologie, Universität of Würzburg, Versbacher Str. 9, D-97078 Würzburg, Germany; (S.K.); (K.-N.K.)
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, I-35131 Padova, Italy;
| | - Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Licio Giorgieri 1, I-34127 Trieste, Italy; (M.P.); (T.D.R.); (G.S.)
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2
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Issa NT, Stathias V, Schürer S, Dakshanamurthy S. Machine and deep learning approaches for cancer drug repurposing. Semin Cancer Biol 2021; 68:132-142. [PMID: 31904426 PMCID: PMC7723306 DOI: 10.1016/j.semcancer.2019.12.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/31/2019] [Accepted: 12/15/2019] [Indexed: 02/07/2023]
Abstract
Knowledge of the underpinnings of cancer initiation, progression and metastasis has increased exponentially in recent years. Advanced "omics" coupled with machine learning and artificial intelligence (deep learning) methods have helped elucidate targets and pathways critical to those processes that may be amenable to pharmacologic modulation. However, the current anti-cancer therapeutic armamentarium continues to lag behind. As the cost of developing a new drug remains prohibitively expensive, repurposing of existing approved and investigational drugs is sought after given known safety profiles and reduction in the cost barrier. Notably, successes in oncologic drug repurposing have been infrequent. Computational in-silico strategies have been developed to aid in modeling biological processes to find new disease-relevant targets and discovering novel drug-target and drug-phenotype associations. Machine and deep learning methods have especially enabled leaps in those successes. This review will discuss these methods as they pertain to cancer biology as well as immunomodulation for drug repurposing opportunities in oncologic diseases.
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Affiliation(s)
- Naiem T Issa
- Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami School of Medicine, Miami, FL, USA
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, USA
| | - Stephan Schürer
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, USA
| | - Sivanesan Dakshanamurthy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA.
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3
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Wen M, Deng ZK, Jiang SL, Guan YD, Wu HZ, Wang XL, Xiao SS, Zhang Y, Yang JM, Cao DS, Cheng Y. Identification of a Novel Bcl-2 Inhibitor by Ligand-Based Screening and Investigation of Its Anti-cancer Effect on Human Breast Cancer Cells. Front Pharmacol 2019; 10:391. [PMID: 31057406 PMCID: PMC6478794 DOI: 10.3389/fphar.2019.00391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/29/2019] [Indexed: 01/23/2023] Open
Abstract
Bcl-2 family protein is an important factor in regulating apoptosis and is associated with cancer. The anti-apoptotic proteins of Bcl-2 family, such as Bcl-2, are overexpression in numerous tumors, and contribute to cancer formation, development, and therapy resistance. Therefore, Bcl-2 is a promising target for drug development, and several Bcl-2 inhibitors are currently undergoing clinical trials. In this study, we carried out a QSAR-based virtual screening approach to develop potential Bcl-2 inhibitors from the SPECS database. Surface plasmon resonance (SPR) binding assay was performed to examine the interaction between Bcl-2 protein and the screened inhibitors. After that, we measured the anti-tumor activities of the 8 candidate compounds, and found that compound M1 has significant cytotoxic effect on breast cancer cells. We further proved that compound M1 downregulated Bcl-2 expression and activated apoptosis by inducing mitochondrial dysfunction. In conclusion, we identified a novel Bcl-2 inhibitor by QSAR screening, which exerted significant cytotoxic activity in breast cancer cells through inducing mitochondria-mediated apoptosis.
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Affiliation(s)
- Mei Wen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zhen-Ke Deng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Shi-Long Jiang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Yi-di Guan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Hai-Zhou Wu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Xin-Luan Wang
- Translational Medicine R&D Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Song-Shu Xiao
- Department of Gynecology and Obstetrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zhang
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Jin-Ming Yang
- Department of Pharmacology, The Penn State Hershey Cancer Institute, The Pennsylvania State University College of Medicine and Milton S Hershey Medical Center, Hershey, PA, United States
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Yan Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
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4
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Cruz-Monteagudo M, Borges F, Cordeiro MNDS, Helguera AM, Tejera E, Paz-Y-Mino C, Sanchez-Rodriguez A, Perera-Sardina Y, Perez-Castillo Y. Chemoinformatics Profiling of the Chromone Nucleus as a MAO-B/A2AAR Dual Binding Scaffold. Curr Neuropharmacol 2018; 15:1117-1135. [PMID: 28093976 PMCID: PMC5725544 DOI: 10.2174/1570159x15666170116145316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 03/14/2016] [Accepted: 11/03/2016] [Indexed: 11/22/2022] Open
Abstract
Background: In the context of the current drug discovery efforts to find disease modifying therapies for Parkinson´s disease (PD) the current single target strategy has proved inefficient. Consequently, the search for multi-potent agents is attracting more and more attention due to the multiple pathogenetic factors implicated in PD. Multiple evidences points to the dual inhibition of the monoamine oxidase B (MAO-B), as well as adenosine A2A receptor (A2AAR) blockade, as a promising approach to prevent the neurodegeneration involved in PD. Currently, only two chemical scaffolds has been proposed as potential dual MAO-B inhibitors/A2AAR antagonists (caffeine derivatives and benzothiazinones). Methods: In this study, we conduct a series of chemoinformatics analysis in order to evaluate and advance the potential of the chromone nucleus as a MAO-B/A2AAR dual binding scaffold. Results: The information provided by SAR data mining analysis based on network similarity graphs and molecular docking studies support the suitability of the chromone nucleus as a potential MAO-B/A2AAR dual binding scaffold. Additionally, a virtual screening tool based on a group fusion similarity search approach was developed for the prioritization of potential MAO-B/A2AAR dual binder candidates. Among several data fusion schemes evaluated, the MEAN-SIM and MIN-RANK GFSS approaches demonstrated to be efficient virtual screening tools. Then, a combinatorial library potentially enriched with MAO-B/A2AAR dual binding chromone derivatives was assembled and sorted by using the MIN-RANK and then the MEAN-SIM GFSS VS approaches. Conclusion: The information and tools provided in this work represent valuable decision making elements in the search of novel chromone derivatives with a favorable dual binding profile as MAO-B inhibitors and A2AAR antagonists with the potential to act as a disease-modifying therapeutic for Parkinson´s disease.
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Affiliation(s)
- Maykel Cruz-Monteagudo
- CIQUP/Departamento de Quimica e Bioquimica, Faculdade de Ciencias, Universidade do Porto, Porto 4169-007, Portugal.,Instituto de Investigaciones Biomedicas (IIB), Universidad de Las Americas, 170513 Quito, Ecuador
| | - Fernanda Borges
- CIQUP/Departamento de Quimica e Bioquimica, Faculdade de Ciencias, Universidade do Porto, Porto 4169-007, Portugal
| | - M Natalia D S Cordeiro
- REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Aliuska Morales Helguera
- Molecular Simulation and Drug Design Group, Centro de Bioactivos Quimicos (CBQ), Universidad Central "Marta Abreu" de Las Villas, Santa Clara, 54830, Cuba
| | - Eduardo Tejera
- Instituto de Investigaciones Biomedicas (IIB), Universidad de Las Americas, 170513 Quito, Ecuador
| | - Cesar Paz-Y-Mino
- Instituto de Investigaciones Biomedicas (IIB), Universidad de Las Americas, 170513 Quito, Ecuador
| | - Aminael Sanchez-Rodriguez
- Departamento de Ciencias Naturales, Universidad Tecnica Particular de Loja, Calle Paris S/N, EC1101608 Loja, Ecuador
| | - Yunier Perera-Sardina
- Departamento de Ciencias Quimicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago de Chile, Chile
| | - Yunierkis Perez-Castillo
- Molecular Simulation and Drug Design Group, Centro de Bioactivos Quimicos (CBQ), Universidad Central "Marta Abreu" de Las Villas, Santa Clara, 54830, Cuba.,Seccion Fisico Quimica y Matematicas, Departamento de Quimica, Universidad Tecnica Particular de Loja, San Cayetano Alto S/N, EC1101608 Loja, Ecuador
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5
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Sagawa T, Mashiko R, Yokota Y, Naruse Y, Okada M, Kojima H. Logistic Regression of Ligands of Chemotaxis Receptors Offers Clues about Their Recognition by Bacteria. Front Bioeng Biotechnol 2018; 5:88. [PMID: 29404321 PMCID: PMC5786873 DOI: 10.3389/fbioe.2017.00088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/26/2017] [Indexed: 11/13/2022] Open
Abstract
Because of relative simplicity of signal transduction pathway, bacterial chemotaxis sensory systems have been expected to be applied to biosensor. Tar and Tsr receptors mediate chemotaxis of Escherichia coli and have been studied extensively as models of chemoreception by bacterial two-transmembrane receptors. Such studies are typically conducted using two canonical ligands: l-aspartate for Tar and l-serine for Tsr. However, Tar and Tsr also recognize various analogs of aspartate and serine; it remains unknown whether the mechanism by which the canonical ligands are recognized is also common to the analogs. Moreover, in terms of engineering, it is important to know a single species of receptor can recognize various ligands to utilize bacterial receptor as the sensor for wide range of substances. To answer these questions, we tried to extract the features that are common to the recognition of the different analogs by constructing classification models based on machine-learning. We computed 20 physicochemical parameters for each of 38 well-known attractants that act as chemoreception ligands, and 15 known non-attractants. The classification models were generated by utilizing one or more of the seven physicochemical properties as descriptors. From the classification models, we identified the most effective physicochemical parameter for classification: the minimum electron potential. This descriptor that occurred repeatedly in classification models with the highest accuracies, This descriptor used alone could accurately classify 42/53 of compounds. Among the 11 misclassified compounds, eight contained two carboxyl groups, which is analogous to the structure of characteristic of aspartate analog. When considered separately, 16 of the 17 aspartate analogs could be classified accurately based on the distance between their two carboxyl groups. As shown in these results, we succeed to predict the ligands for bacterial chemoreceptors using only a few descriptors; single descriptor for single receptor. This result might be due to the relatively simple topology of bacterial two-transmembrane receptors compared to the G-protein-coupled receptors of seven-transmembrane receptors. Moreover, this distance between carboxyl groups correlated with the receptor binding affinity of the aspartate analogs. In view of this correlation, we propose a common mechanism underlying ligand recognition by Tar of compounds with two carboxyl groups.
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Affiliation(s)
- Takashi Sagawa
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
| | - Ryota Mashiko
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan.,Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yusuke Yokota
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
| | - Yasushi Naruse
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
| | - Masato Okada
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan.,Department of Complexity Science and Engineering, The University of Tokyo, Kashiwa, Japan
| | - Hiroaki Kojima
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
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6
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He SB, Ben Hu, Kuang ZK, Wang D, Kong DX. Predicting Subtype Selectivity for Adenosine Receptor Ligands with Three-Dimensional Biologically Relevant Spectrum (BRS-3D). Sci Rep 2016; 6:36595. [PMID: 27812030 PMCID: PMC5095671 DOI: 10.1038/srep36595] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/18/2016] [Indexed: 02/02/2023] Open
Abstract
Adenosine receptors (ARs) are potential therapeutic targets for Parkinson’s disease, diabetes, pain, stroke and cancers. Prediction of subtype selectivity is therefore important from both therapeutic and mechanistic perspectives. In this paper, we introduced a shape similarity profile as molecular descriptor, namely three-dimensional biologically relevant spectrum (BRS-3D), for AR selectivity prediction. Pairwise regression and discrimination models were built with the support vector machine methods. The average determination coefficient (r2) of the regression models was 0.664 (for test sets). The 2B-3 (A2Bvs A3) model performed best with q2 = 0.769 for training sets (10-fold cross-validation), and r2 = 0.766, RMSE = 0.828 for test sets. The models’ robustness and stability were validated with 100 times resampling and 500 times Y-randomization. We compared the performance of BRS-3D with 3D descriptors calculated by MOE. BRS-3D performed as good as, or better than, MOE 3D descriptors. The performances of the discrimination models were also encouraging, with average accuracy (ACC) 0.912 and MCC 0.792 (test set). The 2A-3 (A2Avs A3) selectivity discrimination model (ACC = 0.882 and MCC = 0.715 for test set) outperformed an earlier reported one (ACC = 0.784). These results demonstrated that, through multiple conformation encoding, BRS-3D can be used as an effective molecular descriptor for AR subtype selectivity prediction.
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Affiliation(s)
- Song-Bing He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ben Hu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng-Kun Kuang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Dong Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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7
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Federico S, Redenti S, Sturlese M, Ciancetta A, Kachler S, Klotz KN, Cacciari B, Moro S, Spalluto G. The Influence of the 1-(3-Trifluoromethyl-Benzyl)-1H-Pyrazole-4-yl Moiety on the Adenosine Receptors Affinity Profile of Pyrazolo[4,3-e][1,2,4]Triazolo[1,5-c]Pyrimidine Derivatives. PLoS One 2015; 10:e0143504. [PMID: 26625265 PMCID: PMC4666649 DOI: 10.1371/journal.pone.0143504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/05/2015] [Indexed: 12/03/2022] Open
Abstract
A new series of pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine (PTP) derivatives has been developed in order to explore their affinity and selectivity profile at the four adenosine receptor subtypes. In particular, the PTP scaffold was conjugated at the C2 position with the 1-(3-trifluoromethyl-benzyl)-1H-pyrazole, a group believed to confer potency and selectivity toward the human (h) A2B adenosine receptor (AR) to the xanthine ligand 8-(1-(3-(trifluoromethyl)benzyl)-1H-pyrazol-4-yl)-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione (CVT 6975). Interestingly, the synthesized compounds turned out to be inactive at the hA2B AR but they displayed affinity at the hA3 AR in the nanomolar range. The best compound of the series (6) shows both high affinity (hA3 AR Ki = 11 nM) and selectivity (A1/A3 and A2A/A3 > 9090; A2B/A3 > 909) at the hA3 AR. To better rationalize these results, a molecular docking study on the four AR subtypes was performed for all the synthesized compounds. In addition, CTV 6975 and two close analogues have been subjected to the same molecular docking protocol to investigate the role of the 1-(3-trifluoromethyl-benzyl)-1H-pyrazole on the binding at the four ARs.
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Affiliation(s)
- Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Trieste, Italy
| | - Sara Redenti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Trieste, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Padova, Italy
| | - Antonella Ciancetta
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Padova, Italy
| | - Sonja Kachler
- Institut für Pharmakologie und Toxicologie, Universität Würzburg, Würzburg, Germany
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxicologie, Universität Würzburg, Würzburg, Germany
| | - Barbara Cacciari
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Ferrara, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Padova, Italy
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Trieste, Italy
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8
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Yu X. Prediction of the polarity parameter from transition state structures of radical polymerization of vinyl monomers. POLYMER SCIENCE SERIES B 2013. [DOI: 10.1134/s156009041313006x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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10
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Kalliokoski T, Kramer C, Vulpetti A. Quality Issues with Public Domain Chemogenomics Data. Mol Inform 2013; 32:898-905. [DOI: 10.1002/minf.201300051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/26/2013] [Indexed: 11/11/2022]
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11
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Bacilieri M, Ciancetta A, Paoletta S, Federico S, Cosconati S, Cacciari B, Taliani S, Da Settimo F, Novellino E, Klotz KN, Spalluto G, Moro S. Revisiting a receptor-based pharmacophore hypothesis for human A(2A) adenosine receptor antagonists. J Chem Inf Model 2013; 53:1620-37. [PMID: 23705857 DOI: 10.1021/ci300615u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The application of both structure- and ligand-based design approaches represents to date one of the most useful strategies in the discovery of new drug candidates. In the present paper, we investigated how the application of docking-driven conformational analysis can improve the predictive ability of 3D-QSAR statistical models. With the use of the crystallographic structure in complex with the high affinity antagonist ZM 241385 (4-(2-[7-amino-2-(2-furyl)[1,2,4]-triazolo[2,3-a][1,3,5]triazin-5-ylamino]ethyl)phenol), we revisited a general pharmacophore hypothesis for the human A(2A) adenosine receptor of a set of 751 known antagonists, by applying an integrated ligand- and structure-based approach. Our novel pharmacophore hypothesis has been validated by using an external test set of 29 newly synthesized human adenosine receptor antagonists.
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Affiliation(s)
- Magdalena Bacilieri
- Molecular Modeling Section-MMS, Dipartimento di Scienze del Farmaco, Università di Padova, Via Marzolo 5, Padova, Italy
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12
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Zheng LW, Zhao BX, Liu YR. Expeditious Synthesis and Single Crystal Structure of New Pyrazole-Fused 1,4-Oxazine. J Heterocycl Chem 2012. [DOI: 10.1002/jhet.833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Liang-Wen Zheng
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering; Shandong University; Jinan 250100 People's Republic of China
| | - Bao-Xiang Zhao
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering; Shandong University; Jinan 250100 People's Republic of China
| | - Ying-Rui Liu
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering; Shandong University; Jinan 250100 People's Republic of China
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13
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Mustyala KK, Chitturi AR, Naikal James PS, Vuruputuri U. Pharmacophore mapping and in silico screening to identify new potent leads for A2Aadenosine receptor as antagonists. J Recept Signal Transduct Res 2012; 32:102-13. [DOI: 10.3109/10799893.2012.660532] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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14
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(E)-Ethyl 3-(Dimethylamino)-2-(7,9-diphenyl-7H-pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidin-2-yl)acrylate. MOLBANK 2011. [DOI: 10.3390/m746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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15
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Cheong SL, Federico S, Venkatesan G, Mandel AL, Shao YM, Moro S, Spalluto G, Pastorin G. The A3 adenosine receptor as multifaceted therapeutic target: pharmacology, medicinal chemistry, and in silico approaches. Med Res Rev 2011; 33:235-335. [PMID: 22095687 DOI: 10.1002/med.20254] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Adenosine is an ubiquitous local modulator that regulates various physiological and pathological functions by stimulating four membrane receptors, namely A(1), A(2A), A(2B), and A(3). Among these G protein-coupled receptors, the A(3) subtype is found mainly in the lung, liver, heart, eyes, and brain in our body. It has been associated with cerebroprotection and cardioprotection, as well as modulation of cellular growth upon its selective activation. On the other hand, its inhibition by selective antagonists has been reported to be potentially useful in the treatment of pathological conditions including glaucoma, inflammatory diseases, and cancer. In this review, we focused on the pharmacology and the therapeutic implications of the human (h)A(3) adenosine receptor (AR), together with an overview on the progress of hA(3) AR agonists, antagonists, allosteric modulators, and radioligands, as well as on the recent advances pertaining to the computational approaches (e.g., quantitative structure-activity relationships, homology modeling, molecular docking, and molecular dynamics simulations) applied to the modeling of hA(3) AR and drug design.
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Affiliation(s)
- Siew Lee Cheong
- Department of Pharmacy, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
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16
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Ethyl (1,3-diphenyl-1H-pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidin-5-yl)acetate. MOLBANK 2011. [DOI: 10.3390/m743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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17
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Congreve M, Langmead CJ, Mason JS, Marshall FH. Progress in structure based drug design for G protein-coupled receptors. J Med Chem 2011; 54:4283-311. [PMID: 21615150 PMCID: PMC3308205 DOI: 10.1021/jm200371q] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Indexed: 12/12/2022]
Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Limited, BioPark, Welwyn Garden City, Hertfordshire, UK.
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18
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Michielan L, Moro S. Pharmaceutical Perspectives of Nonlinear QSAR Strategies. J Chem Inf Model 2010; 50:961-78. [DOI: 10.1021/ci100072z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lisa Michielan
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche, Università di Padova, via Marzolo 5, I-35131 Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche, Università di Padova, via Marzolo 5, I-35131 Padova, Italy
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19
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Michielan L, Pireddu L, Floris M, Moro S. Support Vector Machine (SVM) as Alternative Tool to Assign Acute Aquatic Toxicity Warning Labels to Chemicals. Mol Inform 2010; 29:51-64. [DOI: 10.1002/minf.200900005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 11/20/2009] [Indexed: 11/09/2022]
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20
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Michielan L, Federico S, Terfloth L, Hristozov D, Cacciari B, Klotz KN, Spalluto G, Gasteiger J, Moro S. Exploring Potency and Selectivity Receptor Antagonist Profiles Using a Multilabel Classification Approach: The Human Adenosine Receptors as a Key Study. J Chem Inf Model 2009; 49:2820-36. [DOI: 10.1021/ci900311j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lisa Michielan
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Stephanie Federico
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Lothar Terfloth
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Dimitar Hristozov
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Barbara Cacciari
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Karl-Norbert Klotz
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Giampiero Spalluto
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Johann Gasteiger
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche,
Università di Padova, via Marzolo 5, I-35131 Padova, Italy,
Dipartimento di Scienze Farmaceutiche, Università degli Studi
di Trieste, Piazzale Europa 1, I-34127 Trieste, Italy, Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Ferrara,
Via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Institut für
Pharmakologie und Toxikologie, Universität Würzburg,
Versbacher Strasse 9, D-97078 Würzburg, Germany, and Molecular
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