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Tomašević N, Vujović M, Kostić E, Ragavendran V, Arsić B, Matić SL, Božović M, Fioravanti R, Proia E, Ragno R, Mladenović M. Molecular Docking Assessment of Cathinones as 5-HT 2AR Ligands: Developing of Predictive Structure-Based Bioactive Conformations and Three-Dimensional Structure-Activity Relationships Models for Future Recognition of Abuse Drugs. Molecules 2023; 28:6236. [PMID: 37687065 PMCID: PMC10488745 DOI: 10.3390/molecules28176236] [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: 08/03/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Commercially available cathinones are drugs of long-term abuse drugs whose pharmacology is fairly well understood. While their psychedelic effects are associated with 5-HT2AR, the enclosed study summarizes efforts to shed light on the pharmacodynamic profiles, not yet known at the receptor level, using molecular docking and three-dimensional quantitative structure-activity relationship (3-D QSAR) studies. The bioactive conformations of cathinones were modeled by AutoDock Vina and were used to build structure-based (SB) 3-D QSAR models using the Open3DQSAR engine. Graphical inspection of the results led to the depiction of a 3-D structure analysis-activity relationship (SAR) scheme that could be used as a guideline for molecular determinants by which any untested cathinone molecule can be predicted as a potential 5-HT2AR binder prior to experimental evaluation. The obtained models, which showed a good agreement with the chemical properties of co-crystallized 5-HT2AR ligands, proved to be valuable for future virtual screening campaigns to recognize unused cathinones and similar compounds, such as 5-HT2AR ligands, minimizing both time and financial resources for the characterization of their psychedelic effects.
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Affiliation(s)
- Nevena Tomašević
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia
| | - Maja Vujović
- Department of Pharmacy, Faculty of Medicine, University of Niš, Bulevar Dr. Zorana Đinđića 81, 18000 Niš, Serbia; (M.V.); (E.K.)
| | - Emilija Kostić
- Department of Pharmacy, Faculty of Medicine, University of Niš, Bulevar Dr. Zorana Đinđića 81, 18000 Niš, Serbia; (M.V.); (E.K.)
| | - Venkatesan Ragavendran
- Department of Physics, Sri Chandrasekharendra Saraswathi Viswa Mahavidyalaya, Kanchipuram 631561, Tamil Nadu, India;
| | - Biljana Arsić
- Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Serbia;
| | - Sanja Lj. Matić
- Department of Science, Institute for Informational Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia;
| | - Mijat Božović
- Faculty of Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000 Podgorica, Montenegro;
| | - Rossella Fioravanti
- Department of Drug Chemistry and Technology, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185 Rome, Italy;
| | - Eleonora Proia
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185 Rome, Italy; (E.P.); (R.R.)
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185 Rome, Italy; (E.P.); (R.R.)
| | - Milan Mladenović
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia
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Ragno R, Minarini A, Proia E, Lorenzo A, Milelli A, Tumiatti V, Fiore M, Fino P, Rutigliano L, Fioravanti R, Tahara T, Pacella E, Greco A, Canettieri G, Di Paolo ML, Agostinelli E. Bovine Serum Amine Oxidase and Polyamine Analogues: Chemical Synthesis and Biological Evaluation Integrated with Molecular Docking and 3-D QSAR Studies. J Chem Inf Model 2022; 62:3910-3927. [PMID: 35948439 DOI: 10.1021/acs.jcim.2c00559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural polyamines (PAs) are key players in cellular homeostasis by regulating cell growth and proliferation. Several observations highlight that PAs are also implicated in pathways regulating cell death. Indeed, the PA accumulation cytotoxic effect, maximized with the use of bovine serum amine oxidase (BSAO) enzyme, represents a valuable strategy against tumor progression. In the present study, along with the design, synthesis, and biological evaluation of a series of new spermine (Spm) analogues (1-23), a mixed structure-based (SB) and ligand-based (LB) protocol was applied. Binding modes of BSAO-PA modeled complexes led to clarify electrostatic and steric features likely affecting the BSAO-PA biochemical kinetics. LB and SB three-dimensional quantitative structure-activity relationship (Py-CoMFA and Py-ComBinE) models were developed by means of the 3d-qsar.com portal, and their analysis represents a strong basis for future design and synthesis of PA BSAO substrates for potential application in oxidative stress-induced chemotherapy.
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Affiliation(s)
- Rino Ragno
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Sapienza Università di Roma, P. le A. Moro 5, Roma 00185, Italy
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Eleonora Proia
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Sapienza Università di Roma, P. le A. Moro 5, Roma 00185, Italy
| | - Antonini Lorenzo
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Sapienza Università di Roma, P. le A. Moro 5, Roma 00185, Italy
| | - Andrea Milelli
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto, 237, Rimini 47921, Italy
| | - Vincenzo Tumiatti
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d'Augusto, 237, Rimini 47921, Italy
| | - Marco Fiore
- Department Institute of Biochemistry and Cell Biology, IBBC-CNR, Via E. Ramarini, 32, Monterotondo Scalo Rome 00015, Italy
| | - Pasquale Fino
- UOC of Dermatology, Policlinico Umberto I Hospital, Sapienza Medical School of Rome, Viale del Policlinico 155, Rome I-00161, Italy
| | - Lavinia Rutigliano
- Department of Sensory Organs, Sapienza University of Rome, Policlinico Umberto I, Viale del Policlinico155, Rome I-00161, Italy
| | - Rossella Fioravanti
- Department of Drug Chemistry and Technology, Sapienza Università di Roma, P. le A. Moro 5, Roma 00185, Italy
| | - Tomoaki Tahara
- Department of Sensory Organs, Sapienza University of Rome, Policlinico Umberto I, Viale del Policlinico155, Rome I-00161, Italy
| | - Elena Pacella
- Department of Sensory Organs, Sapienza University of Rome, Policlinico Umberto I, Viale del Policlinico155, Rome I-00161, Italy
| | - Antonio Greco
- Department of Sensory Organs, Sapienza University of Rome, Policlinico Umberto I, Viale del Policlinico155, Rome I-00161, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, Rome 00161, Italy.,Istituto Pasteur, Fondazione Cenci-Bolognetti, Sapienza University of Rome, Viale Regina Elena 291, Rome 00161, Italy
| | - Maria Luisa Di Paolo
- Department of Molecular Medicine, University Padua, Via G. Colombo 3, Padova 35131, Italy
| | - Enzo Agostinelli
- Department of Sensory Organs, Sapienza University of Rome, Policlinico Umberto I, Viale del Policlinico155, Rome I-00161, Italy.,International Polyamines Foundation 'ETS-ONLUS', Via del Forte Tiburtino 98, Rome I-00159, Italy
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Mihović N, Tomašević N, Matić S, Mitrović MM, Kostić DA, Sabatino M, Antonini L, Ragno R, Mladenović M. Human Estrogen Receptor α Antagonists. Part 1: 3-D QSAR-Driven Rational Design of Innovative Coumarin-Related Antiestrogens as Breast Cancer Suppressants through Structure-Based and Ligand-Based Studies. J Chem Inf Model 2021; 61:5028-5053. [PMID: 34648283 DOI: 10.1021/acs.jcim.1c00530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The estrogen receptor α (ERα) represents a 17β-estradiol-inducible transcriptional regulator that initiates the RNA polymerase II-dependent transcriptional machinery, pointed for breast cancer (BC) development via either genomic direct or genomic indirect (i.e., tethered) pathway. To develop innovative ligands, structure-based (SB) three-dimensional (3-D) quantitative structure-activity relationship (QSAR) studies have been undertaken from structural data taken from partial agonists, mixed agonists/antagonists (selective estrogen receptor modulators (SERMs)), and full antagonists (selective ERα downregulators (SERDs)) correlated with either wild-type or mutated ERα receptors. SB and ligand-based (LB) alignments allow us to rule out guidelines for the SB/LB alignment of untested compounds. 3-D QSAR models for ERα ligands, coupled with SB/LB alignment, were revealed to be useful tools to dissect the chemical determinants for ERα-based anticancer activity as well as to predict their potency. The herein developed protocol procedure was verified through the design and potency prediction of 12 new coumarin-based SERMs, namely, 3DQ-1a to 3DQ-1e, that upon synthesis turned to be potent ERα antagonists by means of either in vitro or in vivo assays (described in the second part of this study).
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Affiliation(s)
- Nezrina Mihović
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia
| | - Nevena Tomašević
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia
| | - Sanja Matić
- Institute for Informational Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Marina M Mitrović
- Department of Biochemistry, Faculty of Medical Sciences, University of Kragujevac, Svetozara Markovića 69, 34000 Kragujevac, Serbia
| | - Danijela A Kostić
- Department of Chemistry, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Serbia
| | - Manuela Sabatino
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Lorenzo Antonini
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Milan Mladenović
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia
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Ragno R, Esposito V, Di Mario M, Masiello S, Viscovo M, Cramer RD. Teaching and Learning Computational Drug Design: Student Investigations of 3D Quantitative Structure-Activity Relationships through Web Applications. JOURNAL OF CHEMICAL EDUCATION 2020; 97:1922-1930. [PMID: 33814598 PMCID: PMC8008382 DOI: 10.1021/acs.jchemed.0c00117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/06/2020] [Indexed: 05/27/2023]
Abstract
The increasing use of information technology in the discovery of new molecular entities encourages the use of modern molecular-modeling tools to help teach important concepts of drug design to chemistry and pharmacy undergraduate students. In particular, statistical models such as quantitative structure-activity relationships (QSAR)-often as its 3D QSAR variant-are commonly used in the development and optimization of a leading compound. We describe how these drug discovery methods can be taught and learned by means of free and open-source web applications, specifically the online platform www.3d-qsar.com. This new suite of web applications has been integrated into a drug design teaching course, one that provides both theoretical and practical perspectives. We include the teaching protocol by which pharmaceutical biotechnology master students at Pharmacy Faculty of Sapienza Rome University are introduced to drug design. Starting with a choice among recent articles describing the potencies of a series of molecules tested against a biological target, each student is expected to build a 3D QSAR ligand-based model from their chosen publication, proceeding as follows: creating the initial data set (Py-MolEdit); generating the global minimum conformations (Py-ConfSearch); proposing a promising mutual alignment (Py-Align); and finally, building, and optimizing a robust 3D QSAR models (Py-CoMFA). These student activities also help validate these new molecular modeling tools, especially for their usability by inexperienced hands. To more fully demonstrate the effectiveness of this protocol and its tools, we include the work performed by four of these students (four of the coauthors), detailing the satisfactory 3D QSAR models they obtained. Such scientifically complete experiences by undergraduates, made possible by the efficiency of the 3D QSAR methodology, provide exposure to computational tools in the same spirit as traditional laboratory exercises. With the obsolescence of the classic Comparative Molecular Field Analysis Sybyl host, the 3dqsar web portal offers one of the few available means of performing this well-established 3D QSAR method.
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Affiliation(s)
- Rino Ragno
- Rome
Center for Molecular Design, Department of Drug Chemistry and Technology, Sapienza Rome University, P. le A. Moro 5, 00185 Rome, Italy
| | - Valeria Esposito
- Pharmacy
and Medicine Faculty, Pharmaceutical Biotechnology Master Degree Course, Sapienza Rome University, P. le A. Moro 5, 00185 Rome, Italy
| | - Martina Di Mario
- Pharmacy
and Medicine Faculty, Pharmaceutical Biotechnology Master Degree Course, Sapienza Rome University, P. le A. Moro 5, 00185 Rome, Italy
| | - Stefano Masiello
- Pharmacy
and Medicine Faculty, Pharmaceutical Biotechnology Master Degree Course, Sapienza Rome University, P. le A. Moro 5, 00185 Rome, Italy
| | - Marco Viscovo
- Pharmacy
and Medicine Faculty, Pharmaceutical Biotechnology Master Degree Course, Sapienza Rome University, P. le A. Moro 5, 00185 Rome, Italy
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Ragno R. www.3d-qsar.com: a web portal that brings 3-D QSAR to all electronic devices—the Py-CoMFA web application as tool to build models from pre-aligned datasets. J Comput Aided Mol Des 2019; 33:855-864. [DOI: 10.1007/s10822-019-00231-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 09/28/2019] [Indexed: 11/28/2022]
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Vucicevic J, Nikolic K, Mitchell JB. Rational Drug Design of Antineoplastic Agents Using 3D-QSAR, Cheminformatic, and Virtual Screening Approaches. Curr Med Chem 2019; 26:3874-3889. [DOI: 10.2174/0929867324666170712115411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 01/07/2023]
Abstract
Background:Computer-Aided Drug Design has strongly accelerated the development of novel antineoplastic agents by helping in the hit identification, optimization, and evaluation.Results:Computational approaches such as cheminformatic search, virtual screening, pharmacophore modeling, molecular docking and dynamics have been developed and applied to explain the activity of bioactive molecules, design novel agents, increase the success rate of drug research, and decrease the total costs of drug discovery. Similarity, searches and virtual screening are used to identify molecules with an increased probability to interact with drug targets of interest, while the other computational approaches are applied for the design and evaluation of molecules with enhanced activity and improved safety profile.Conclusion:In this review are described the main in silico techniques used in rational drug design of antineoplastic agents and presented optimal combinations of computational methods for design of more efficient antineoplastic drugs.
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Affiliation(s)
- Jelica Vucicevic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - John B.O. Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, United Kingdom
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Aswathy L, Jisha RS, Masand VH, Gajbhiye JM, Shibi IG. Design of novel amyloid β aggregation inhibitors using QSAR, pharmacophore modeling, molecular docking and ADME prediction. In Silico Pharmacol 2018; 6:12. [PMID: 30607325 PMCID: PMC6314802 DOI: 10.1007/s40203-018-0049-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/07/2018] [Indexed: 02/03/2023] Open
Abstract
The inhibition of abnormal amyloid β (Aβ) aggregation has been regarded as a good target to control Alzheimer's disease. The present study adopted 2D-QSAR, HQSAR and 3D QSAR (CoMFA & CoMSIA) modeling approaches to identify the structural and physicochemical requirements for the potential Aβ aggregation inhibition. A structure-based molecular docking technique is utilized to approve the features that are obtained from the ligand-based techniques on 30 curcumin derivatives. The combined outputs were then used to screen the modified 10 compounds. The 2D QSAR model on curcumin derivatives gave statistical values R2 = 0.9086 and SEE = 0.1837. The model was further confirmed by Y-randomization test and Applicability domain analysis by the standardization approach. The HQSAR study (Q2 = 0.615, Rncv 2 = 0.931, Rpred 2 = 0.956) illustrated the important molecular fingerprints for inhibition. Contour maps of 3D QSAR models, CoMFA (Q2 = 0.687, Rncv 2 = 0.787, Rpred 2 = 0.731) and CoMSIA (Q2 = 0.743, Rncv 2 = 0.972, Rpred 2 = 0.713), depict that the models are robust and provide explanation of the important features, like steric, electrostatic and hydrogen bond acceptor, which play important role for interaction with the receptor site cavity. The molecular docking study of the curcumin derivatives elucidates the important interactions between the amino acid residues at the catalytic site of the receptor and the ligands, indicating the structural requirements of the inhibitors. The ligand-receptor interactions of top hits were analyzed to explore the pharmacophore features of Aβ aggregation inhibition. The Aβ aggregation inhibitory activities of novel chemical entities were then obtained through inverse QSAR. The newly designed molecules were further screened through machine learning, prediction of toxicity and nature of metabolism to get the proposed six lead compounds.
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Affiliation(s)
- Lilly Aswathy
- Department of Chemistry, Sree Narayana College, Chempazhanthy, Thiruvananthapuram, Kerala 695587 India
| | - Radhakrishnan S. Jisha
- Department of Chemistry, Sree Narayana College, Chempazhanthy, Thiruvananthapuram, Kerala 695587 India
| | - Vijay H. Masand
- Department of Chemistry, Vidya Bharati College, Camp, Amravati, Maharashtra 444 602 India
| | - Jayant M. Gajbhiye
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, 411 008 India
| | - Indira G. Shibi
- Department of Chemistry, Sree Narayana College, Chempazhanthy, Thiruvananthapuram, Kerala 695587 India
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Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches. J Comput Aided Mol Des 2018; 32:435-458. [PMID: 29335872 DOI: 10.1007/s10822-018-0096-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/06/2018] [Indexed: 01/25/2023]
Abstract
Chemical inhibition of chromatin-mediated signaling involved proteins is an established strategy to drive expression networks and alter disease progression. Protein methyltransferases are among the most studied proteins in epigenetics and, in particular, disruptor of telomeric silencing 1-like (DOT1L) lysine methyltransferase plays a key role in MLL-rearranged acute leukemia Selective inhibition of DOT1L is an established attractive strategy to breakdown aberrant H3K79 methylation and thus overexpression of leukemia genes, and leukemogenesis. Although numerous DOT1L inhibitors have been several structural data published no pronounced computational efforts have been yet reported. In these studies a first tentative of multi-stage and LB/SB combined approach is reported in order to maximize the use of available data. Using co-crystallized ligand/DOT1L complexes, predictive 3-D QSAR and COMBINE models were built through a python implementation of previously reported methodologies. The models, validated by either modeled or experimental external test sets, proved to have good predictive abilities. The application of these models to an internal library led to the selection of two unreported compounds that were found able to inhibit DOT1L at micromolar level. To the best of our knowledge this is the first report of quantitative LB and SB DOT1L inhibitors models and their application to disclose new potential epigenetic modulators.
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Ballante F. Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection. Methods Mol Biol 2018; 1824:67-88. [PMID: 30039402 DOI: 10.1007/978-1-4939-8630-9_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Main goal in drug discovery is the identification of drug-like compounds capable to modulate specific biological targets. Thus, the prediction of reliable binding poses of candidate ligands, through molecular docking simulations, represents a key step to be pursued in structure-based drug design (SBDD). Since the increasing number of resolved three-dimensional ligand-protein structures, together with the expansion of computational power and software development, the comprehensive and systematic use of experimental data can be proficiently employed to validate the docking performance. This allows to select and refine the protocol to adopt when predicting the binding pose of trial compounds in a target. Given the availability of multiple docking software, a comparative docking assessment in an early research stage represents a must-use step to minimize fails in molecular modeling. This chapter describes how to perform a docking assessment, using freely available tools, in a semiautomated fashion.
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Affiliation(s)
- Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA. .,Department of Cell and Molecular Biology, Uppsala Biomedicinska Centrum BMC, Uppsala University, Uppsala, Sweden.
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Carradori S, Bizzarri B, D'Ascenzio M, De Monte C, Grande R, Rivanera D, Zicari A, Mari E, Sabatino M, Patsilinakos A, Ragno R, Secci D. Synthesis, biological evaluation and quantitative structure-active relationships of 1,3-thiazolidin-4-one derivatives. A promising chemical scaffold endowed with high antifungal potency and low cytotoxicity. Eur J Med Chem 2017; 140:274-292. [PMID: 28963991 DOI: 10.1016/j.ejmech.2017.09.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 01/04/2023]
Abstract
With reference to recent studies reporting on the various biological properties of the thiazolidinone scaffold, we synthesized more than a hundred compounds characterized by a 1,3-thiazolidin-4-one nucleus derivatised at the C2 with a hydrazine bridge linked to (cyclo)aliphatic or hetero(aryl) moieties, and their N-benzylated derivatives. These molecules were assayed as potential anti-Candida agents and they were shown to possess comparable, and in some cases higher biological activity than well-established topical and systemic antimycotic drugs (i.e. clotrimazole, fluconazole, ketoconazole, miconazole, tioconazole, amphotericin B). Compounds endowed with the lowest MICs underwent further testing in order to assess their cytotoxic effect (CC50) on Hep2 cells, which demonstrated their relative safety. Finally, QSAR and 3-D QSAR models were used to predict putative chemical modifications of the 1,3-thiazolidin-4-one scaffold in order to design new and potential more active compounds against Candida spp.
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Affiliation(s)
- Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy.
| | - Bruna Bizzarri
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Melissa D'Ascenzio
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Celeste De Monte
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Rossella Grande
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; Center for Aging Science and Translational Medicine (CeSI-MeT), Via dei Vestini 31, 66100 Chieti, Italy
| | - Daniela Rivanera
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessanda Zicari
- Dipartimento di Medicina Sperimentale, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Emanuela Mari
- Dipartimento di Medicina Sperimentale, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Manuela Sabatino
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alexandros Patsilinakos
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Alchemical Dynamics s.r.l., 00125 Rome, Italy
| | - Rino Ragno
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Alchemical Dynamics s.r.l., 00125 Rome, Italy
| | - Daniela Secci
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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Zwergel C, Czepukojc B, Evain-Bana E, Xu Z, Stazi G, Mori M, Patsilinakos A, Mai A, Botta B, Ragno R, Bagrel D, Kirsch G, Meiser P, Jacob C, Montenarh M, Valente S. Novel coumarin- and quinolinone-based polycycles as cell division cycle 25-A and -C phosphatases inhibitors induce proliferation arrest and apoptosis in cancer cells. Eur J Med Chem 2017; 134:316-333. [DOI: 10.1016/j.ejmech.2017.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 01/06/2023]
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12
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Structural insights of SmKDAC8 inhibitors: Targeting Schistosoma epigenetics through a combined structure-based 3D QSAR, in vitro and synthesis strategy. Bioorg Med Chem 2017; 25:2105-2132. [DOI: 10.1016/j.bmc.2017.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/06/2017] [Accepted: 02/09/2017] [Indexed: 11/24/2022]
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13
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Mladenović M, Patsilinakos A, Pirolli A, Sabatino M, Ragno R. Understanding the Molecular Determinant of Reversible Human Monoamine Oxidase B Inhibitors Containing 2H-Chromen-2-One Core: Structure-Based and Ligand-Based Derived Three-Dimensional Quantitative Structure–Activity Relationships Predictive Models. J Chem Inf Model 2017; 57:787-814. [DOI: 10.1021/acs.jcim.6b00608] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Milan Mladenović
- Kragujevac Center
for Computational Biochemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, P.O. Box 60, Serbia
| | - Alexandros Patsilinakos
- Rome Center for Molecular Design, Department of Drug
Chemistry and Technologies, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185, Rome Italy
- Alchemical Dynamics srl, 00125 Rome, Italy
| | - Adele Pirolli
- Rome Center for Molecular Design, Department of Drug
Chemistry and Technologies, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185, Rome Italy
- Department of Information
Technology, IRBM Science Park, Via Pontina km 30, 600, 00071 Pomezia, Rome, Italy
| | - Manuela Sabatino
- Rome Center for Molecular Design, Department of Drug
Chemistry and Technologies, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185, Rome Italy
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Drug
Chemistry and Technologies, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185, Rome Italy
- Alchemical Dynamics srl, 00125 Rome, Italy
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14
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Coluccia A, Passacantilli S, Famiglini V, Sabatino M, Patsilinakos A, Ragno R, Mazzoccoli C, Sisinni L, Okuno A, Takikawa O, Silvestri R, La Regina G. New Inhibitors of Indoleamine 2,3-Dioxygenase 1: Molecular Modeling Studies, Synthesis, and Biological Evaluation. J Med Chem 2016; 59:9760-9773. [PMID: 27690429 DOI: 10.1021/acs.jmedchem.6b00718] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) is an attractive target for anticancer therapy. Herein, we report a virtual screening study which led to the identification of compound 5 as a new IDO1 inhibitor. In order to improve the biological activity of the identified hit, arylthioindoles 6-30 were synthesized and tested. Among these, derivative 21 exhibited an IC50 value of 7 μM, being the most active compound of the series. Furthermore, compounds 5 and 21 induced a dose-dependent growth inhibition in IDO1 expressing cancer cell lines HTC116 and HT29. Three-dimensional quantitative structure-activity relationship studies were carried out in order to rationalize obtained results and suggest new chemical modifications.
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Affiliation(s)
| | | | | | | | | | - Rino Ragno
- Alchemical Dynamics s.r.l. , Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Carmela Mazzoccoli
- Laboratorio di Ricerca Pre-Clinica e Traslazionale, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Centro di Riferimento Oncologico della Basilicata (CROB) , Via Padre Pio 1, I-85028 Rionero in Vulture, Italy
| | - Lorenza Sisinni
- Laboratorio di Ricerca Pre-Clinica e Traslazionale, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Centro di Riferimento Oncologico della Basilicata (CROB) , Via Padre Pio 1, I-85028 Rionero in Vulture, Italy
| | - Alato Okuno
- National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology 35 Gengo, Morioka, Obu, Aichi 474-8511, Japan
| | - Osamu Takikawa
- National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology 35 Gengo, Morioka, Obu, Aichi 474-8511, Japan
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15
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Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions. Int J Mol Sci 2016; 17:ijms17071087. [PMID: 27399692 PMCID: PMC4964463 DOI: 10.3390/ijms17071087] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 02/07/2023] Open
Abstract
Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions.
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16
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Reddy DN, Ballante F, Chuang T, Pirolli A, Marrocco B, Marshall GR. Design and Synthesis of Simplified Largazole Analogues as Isoform-Selective Human Lysine Deacetylase Inhibitors. J Med Chem 2016; 59:1613-33. [PMID: 26681404 DOI: 10.1021/acs.jmedchem.5b01632] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Selective inhibition of KDAC isoforms while maintaining potency remains a challenge. Using the largazole macrocyclic depsipeptide structure as a starting point for developing new KDACIs with increased selectivity, a combination of four different simplified largazole analogue (SLA) scaffolds with diverse zinc-binding groups (for a total of 60 compounds) were designed, synthesized, and evaluated against class I KDACs 1, 3, and 8, and class II KDAC6. Experimental evidence as well as molecular docking poses converged to establish the cyclic tetrapeptides (CTPs) as the primary determinant of both potency and selectivity by influencing the correct alignment of the zinc-binding group in the KDAC active site, providing a further basis for developing new KDACIs of higher isoform selectivity and potency.
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Affiliation(s)
- Damodara N Reddy
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Timothy Chuang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Adele Pirolli
- Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Biagina Marrocco
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , 700 South Euclid Avenue, St. Louis, Missouri 63110, United States
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17
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Ballante F, Marshall GR. An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design. J Chem Inf Model 2016; 56:54-72. [PMID: 26682916 DOI: 10.1021/acs.jcim.5b00603] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular docking is a widely used technique in drug design to predict the binding pose of a candidate compound in a defined therapeutic target. Numerous docking protocols are available, each characterized by different search methods and scoring functions, thus providing variable predictive capability on a same ligand-protein system. To validate a docking protocol, it is necessary to determine a priori the ability to reproduce the experimental binding pose (i.e., by determining the docking accuracy (DA)) in order to select the most appropriate docking procedure and thus estimate the rate of success in docking novel compounds. As common docking programs use generally different root-mean-square deviation (RMSD) formulas, scoring functions, and format results, it is both difficult and time-consuming to consistently determine and compare their predictive capabilities in order to identify the best protocol to use for the target of interest and to extrapolate the binding poses (i.e., best-docked (BD), best-cluster (BC), and best-fit (BF) poses) when applying a given docking program over thousands/millions of molecules during virtual screening. To reduce this difficulty, two new procedures called Clusterizer and DockAccessor have been developed and implemented for use with some common and "free-for-academics" programs such as AutoDock4, AutoDock4(Zn), AutoDock Vina, DOCK, MpSDockZn, PLANTS, and Surflex-Dock to automatically extrapolate BD, BC, and BF poses as well as to perform consistent cluster and DA analyses. Clusterizer and DockAccessor (code available over the Internet) represent two novel tools to collect computationally determined poses and detect the most predictive docking approach. Herein an application to human lysine deacetylase (hKDAC) inhibitors is illustrated.
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Affiliation(s)
- Flavio Ballante
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
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18
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In silico exploration of c-KIT inhibitors by pharmaco-informatics methodology: pharmacophore modeling, 3D QSAR, docking studies, and virtual screening. Mol Divers 2015; 20:41-53. [DOI: 10.1007/s11030-015-9635-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/14/2015] [Indexed: 10/23/2022]
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19
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Ragno R, Ballante F, Pirolli A, Wickersham RB, Patsilinakos A, Hesse S, Perspicace E, Kirsch G. Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches. J Comput Aided Mol Des 2015. [PMID: 26194852 DOI: 10.1007/s10822-015-9859-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Vascular endothelial growth factor receptor-2, (VEGFR-2), is a key element in angiogenesis, the process by which new blood vessels are formed, and is thus an important pharmaceutical target. Here, 3-D quantitative structure-activity relationship (3-D QSAR) were used to build a quantitative screening and pharmacophore model of the VEGFR-2 receptors for design of inhibitors with improved activities. Most of available experimental data information has been used as training set to derive optimized and fully cross-validated eight mono-probe and a multi-probe quantitative models. Notable is the use of 262 molecules, aligned following both structure-based and ligand-based protocols, as external test set confirming the 3-D QSAR models' predictive capability and their usefulness in design new VEGFR-2 inhibitors. From a survey on literature, this is the first generation of a wide-ranging computational medicinal chemistry application on VEGFR2 inhibitors.
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Affiliation(s)
- Rino Ragno
- Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P. le A. Moro 5, 00185, Rome, Italy,
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20
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Consalvi S, Alfonso S, Di Capua A, Poce G, Pirolli A, Sabatino M, Ragno R, Anzini M, Sartini S, La Motta C, Di Cesare Mannelli L, Ghelardini C, Biava M. Synthesis, biological evaluation and docking analysis of a new series of methylsulfonyl and sulfamoyl acetamides and ethyl acetates as potent COX-2 inhibitors. Bioorg Med Chem 2015; 23:810-20. [DOI: 10.1016/j.bmc.2014.12.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/14/2014] [Accepted: 12/17/2014] [Indexed: 01/01/2023]
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21
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Ballante F, Caroli A, Wickersham RB, Ragno R. Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening. J Chem Inf Model 2014; 54:956-69. [PMID: 24564321 DOI: 10.1021/ci400759t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The multichaperone heat shock protein (Hsp) 90 complex mediates the maturation and stability of a variety of oncogenic signaling proteins. For this reason, Hsp90 has emerged as a promising target for anticancer drug development. Herein, we describe a complete computational procedure for building several 3-D QSAR models used as a ligand-based (LB) component of a comprehensive ligand-based (LB) and structure-based (SB) virtual screening (VS) protocol to identify novel molecular scaffolds of Hsp90 inhibitors. By the application of the 3-D QSAutogrid/R method, eight SB PLS 3-D QSAR models were generated, leading to a final multiprobe (MP) 3-D QSAR pharmacophoric model capable of recognizing the most significant chemical features for Hsp90 inhibition. Both the monoprobe and multiprobe models were optimized, cross-validated, and tested against an external test set. The obtained statistical results confirmed the models as robust and predictive to be used in a subsequent VS.
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Affiliation(s)
- Flavio Ballante
- Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma , P. le A. Moro 5, 00185 Roma, Italy
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22
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Friggeri L, Ballante F, Ragno R, Musmuca I, De Vita D, Manetti F, Biava M, Scipione L, Di Santo R, Costi R, Feroci M, Tortorella S. Pharmacophore assessment through 3-D QSAR: evaluation of the predictive ability on new derivatives by the application on a series of antitubercular agents. J Chem Inf Model 2013; 53:1463-74. [PMID: 23617317 DOI: 10.1021/ci400132q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pharmacophoric mapping is a useful procedure to frame, especially when crystallographic receptor structures are unavailable as in ligand-based studies, the hypothetical site of interaction. In this study, 71 pyrrole derivatives active against M. tuberculosis were used to derive through a recent new 3-D QSAR protocol, 3-D QSAutogrid/R, several predictive 3-D QSAR models on compounds aligned by a previously reported pharmacophoric application. A final multiprobe (MP) 3-D QSAR model was then obtained configuring itself as a tool to derive pharmacophoric quantitative models. To stress the applicability of the described models, an external test set of unrelated and newly synthesized series of R-4-amino-3-isoxazolidinone derivatives found to be active at micromolar level against M. tuberculosis was used, and the predicted bioactivities were in good agreement with the experimental values. The 3-D QSAutogrid/R procedure proved to be able to correlate by a single multi-informative scenario the different activity molecular profiles thus confirming its usefulness in the rational drug design approach.
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Affiliation(s)
- Laura Friggeri
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P. le A. Moro 5, 00185 Rome, Italy
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23
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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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24
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Perspicace E, Jouan-Hureaux V, Ragno R, Ballante F, Sartini S, La Motta C, Da Settimo F, Chen B, Kirsch G, Schneider S, Faivre B, Hesse S. Design, synthesis and biological evaluation of new classes of thieno[3,2-d]pyrimidinone and thieno[1,2,3]triazine as inhibitor of vascular endothelial growth factor receptor-2 (VEGFR-2). Eur J Med Chem 2013; 63:765-81. [DOI: 10.1016/j.ejmech.2013.03.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/07/2013] [Accepted: 03/10/2013] [Indexed: 11/26/2022]
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25
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Pan Y, Wang Y, Bryant SH. Pharmacophore and 3D-QSAR characterization of 6-arylquinazolin-4-amines as Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) inhibitors. J Chem Inf Model 2013; 53:938-47. [PMID: 23496085 PMCID: PMC3633254 DOI: 10.1021/ci300625c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Indexed: 01/23/2023]
Abstract
Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) are protein kinases that are promising targets for treatment of diseases caused by abnormal gene splicing. 6-Arylquinazolin-4-amines have been recently identified as potent Clk4 and Dyrk1A inhibitors. In order to understand the structure-activity correlation of these analogs, we have applied ligand-based pharmacophore and 3D-QSAR modeling combined with structure-based homology modeling and docking. The high R(2) and Q(2) (0.88 and 0.79 for Clk4, 0.85 and 0.82 for Dyrk1A, respectively) based on validation with training and test set compounds suggested that the generated 3D-QSAR models are reliable in predicting novel ligand activities against Clk4 and Dyrk1A. The binding mode identified through docking ligands to the ATP binding domain of Clk4 was consistent with the structural properties and energy field contour maps characterized by pharmacophore and 3D-QSAR models and gave valuable insights into the structure-activity profile of 6-arylquinazolin-4-amine analogs. The obtained 3D-QSAR and pharmacophore models in combination with the binding mode between inhibitor and residues of Clk4 will be helpful for future lead compound identification and optimization to design potent and selective Clk4 and Dyrk1A inhibitors.
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Affiliation(s)
- Yongmei Pan
- National Center for
Biotechnology Information, National
Library of Medicine, National Institution of Health, 8600 Rockville
Pike, Bethesda, Maryland 20894, United States
| | - Yanli Wang
- National Center for
Biotechnology Information, National
Library of Medicine, National Institution of Health, 8600 Rockville
Pike, Bethesda, Maryland 20894, United States
| | - Stephen H. Bryant
- National Center for
Biotechnology Information, National
Library of Medicine, National Institution of Health, 8600 Rockville
Pike, Bethesda, Maryland 20894, United States
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26
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Pan Y, Wang Y, Bryant SH. Pharmacophore and 3D-QSAR characterization of 6-arylquinazolin-4-amines as Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) inhibitors. J Chem Inf Model 2013. [PMID: 23496085 DOI: 10.1021/ci300635c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) are protein kinases that are promising targets for treatment of diseases caused by abnormal gene splicing. 6-Arylquinazolin-4-amines have been recently identified as potent Clk4 and Dyrk1A inhibitors. In order to understand the structure-activity correlation of these analogs, we have applied ligand-based pharmacophore and 3D-QSAR modeling combined with structure-based homology modeling and docking. The high R(2) and Q(2) (0.88 and 0.79 for Clk4, 0.85 and 0.82 for Dyrk1A, respectively) based on validation with training and test set compounds suggested that the generated 3D-QSAR models are reliable in predicting novel ligand activities against Clk4 and Dyrk1A. The binding mode identified through docking ligands to the ATP binding domain of Clk4 was consistent with the structural properties and energy field contour maps characterized by pharmacophore and 3D-QSAR models and gave valuable insights into the structure-activity profile of 6-arylquinazolin-4-amine analogs. The obtained 3D-QSAR and pharmacophore models in combination with the binding mode between inhibitor and residues of Clk4 will be helpful for future lead compound identification and optimization to design potent and selective Clk4 and Dyrk1A inhibitors.
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Affiliation(s)
- Yongmei Pan
- National Center for Biotechnology Information, National Library of Medicine, National Institution of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
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27
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Putz MV, Dudaş NA. Variational principles for mechanistic quantitative structure–activity relationship (QSAR) studies: application on uracil derivatives’ anti-HIV action. Struct Chem 2013. [DOI: 10.1007/s11224-013-0249-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Ballante F, Musmuca I, Marshall GR, Ragno R. Comprehensive model of wild-type and mutant HIV-1 reverse transciptases. J Comput Aided Mol Des 2012; 26:907-19. [DOI: 10.1007/s10822-012-9586-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
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29
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Silvestri L, Ballante F, Mai A, Marshall GR, Ragno R. Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction. J Chem Inf Model 2012; 52:2215-35. [DOI: 10.1021/ci300160y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Laura Silvestri
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Flavio Ballante
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Antonello Mai
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Garland R. Marshall
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
| | - Rino Ragno
- Rome
Center for Molecular Design Dipartimento di Chimica e Tecnologie del
Farmaco, Facoltà di Farmacia e Medicina, ‡Istituto Pasteur—Fondazione
Cenci Bolognetti Dipartimento di Chimica e Tecnologie del Farmaco,
Facoltà di Farmacia e Medicina, Sapienza Università di Roma, P.le A. Moro 5, 00185 Rome,
Italy
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