Research Groups‎ > ‎

Rome Center for Molecular Design (CHIM/08)

Head of Laboratory: Prof. Rino Ragno
Sito web: www.rcmd.it; www.3d-qsar.com

Main Topics: 


RCMD is involved in several activities:
- Development of theoretical models in the field of medicinal chemistry. The models rely on ligand-based techniques such as quantitative structure activity relationships (QSAR) either bi-dimensional (2D) and three-dimensional (3-D). Moreover structure based models are also built by means of comparative molecular binding energy analyses (COMBINE).
- Implementation of algorithm to be used for the building of QSAR and COMBINE models
- Implementation of scientific websites:
- The 3D-QSAR portal for the automatic building of QSAR, 3-D QSAR and COMBINE models
- Web site for NMR, MS and HPLC data from food and food extracts
- Quantum Chemical calculation to evaluate sugar degradation
- Application of QSAR, 3-D QSAR and COMBINE models in conjunction with molecular docking software in virtual screening to select bioactive compounds
- Essential oil extraction, chemical analysis and their biological evaluation in collaboration with a network of collaborators either national or international

National and International Collaborations:


Mijat Bozovic from Montenegro University: active collaboration in evaluating the essential oils
Milan Mladenovic from Kragujevac University (Serbia): active collaboration in developing 3-D QSAR and COMBINE models to select bioactive compound to be acquired from vendors.
Garland Marshal from Washington University of St Louis (Missouri): active collaboration in the design of new algorothms
Vanja Tadic from Belgrade University (Serbia): active collaboration in chemical characterization of essential oil and plant extracts
Gilbert Kirsch from Université de Lorraine, METZ (Francia): active collaboration in developing the synthesis of compounds designed by computational approaches

Facilities:


Several PC either desktop or laptop for data analysis.
Several workstation server for calculation
A four 1080 GPU server
A File system server with 40 TB of disk space
Calculation servers for a total of about 200 cores

ERC Panels: 


PE4_3 Molecular architecture and Structure
PE4_13 Theoretical and computational chemistry
PE5_18 Molecular chemistry
PE6_4 Theoretical computer science, formal methods, and quantum computing
PE6_7 Artificial intelligence, intelligent systems, multi agent systems
PE6_8 Computer graphics, computer vision, multi media, computer games
PE6_10 Web and information systems, database systems, information retrieval and digital
PE6_11 Machine learning, statistical data processing and applications using signal processing
PE6_12 Scientific computing, simulation and modelling tools
PE6_13 Bioinformatics, biocomputing, and DNA and molecular computation
LS2_10 Bioinformatics
LS2_11 Computational biology
LS7_3 Pharmacology, pharmacogenomics, drug discovery and design, drug therapy
LS9_5 Food sciences

Grants:

Progetti di Ricerca di Università Anno 2015 - prot. C26A15988X
Domanda di finanziamento per Congressi e Convegni dell'anno 2016 Anno: 2015 - prot. C26C152KTJ
2016. Computational Medicinal Chemistry WorkShop Finanziamenti per convegni, seminari, workshop - Classe a Responsabile: RAGNO Rino Numero protocollo: CC216154A6F13C39
2016. MOTYA and the INTERACTION OF MEDITERRANEAN CULTURES in the Second and First Millennium BC - interdisciplinary approaches Scavi Archeologici - Scavi Archeologici Responsabile: NIGRO Lorenzo - 10 Doc./Ric. - 11 Dott./Ass./Spec. - 2 Altro Numero protocollo: SA116154BE659EEC
2016. Targeting the lysine-specific histone demethylase LSD1 for development of new anticancer agents Progetti di Ricerca Grandi - Progetti Grandi Responsabile: MAI Antonello - 4 Doc./Ric. - 1 Dott./Ass./Spec. - 0 Altro Numero protocollo: RG116154BED07FE9
2017. Motya: investigating ancient Mediterranean cultures. Excavation, interdisciplinary study and analyses, interpretation and outreach. Scavi Archeologici - Scavi Archeologici Responsabile: NIGRO Lorenzo - 7 Doc./Ric. - 12 Dott./Ass./Spec. - 43 Altro Numero protocollo: SA11715C7D7BF225
2017. Disruptor of Telomeric Silencing 1-Like (DOT1L): identificazione di nuova classe di inibitori non nucleosidici mediante approacci ligand-based e structured-based. Progetti per Avvio alla Ricerca - Tipo 1 Responsabile: SABATINO MANUELA - 1 Tutor - 0 Dott./Ass./Spec. Numero protocollo: AR11715C81EEA2F2


Laboratory members:

SABATINO Manuela
PATSILINAKOS Alexandros

Publications (2015-2018):


1. Rosa Sessa, Marisa Di Pietro, Fiorenzo De Santis, Simone Filardo, Rino Ragno, and Letizia Angiolella, “Effects ofMentha suaveolens Essential Oil on Chlamydia trachomatis,”BioMed Research International, vol. 2015, Article ID 508071, 7 pages, 2015. doi:10.1155/2015/508071

2. S. Consalvi, S. Alfonso, A. Di Capua, G. Poce, A. Pirolli, M. Sabatino, R. Ragno, M. Anzini, S. Sartini, C. La Motta, L. Di Cesare Mannelli, C. Ghelardini, M. Biava. Synthesis, biological evaluation and docking analysis of a new series of methylsulfonyl and sulfamoyl acetamides and ethyl acetates as potent COX-2 inhibitors. Bioorganic Medicinal Chemistry (2015). Feb 15;23(4):810-20. doi: 10.1016/j.bmc.2014.12.041. Epub 2014 Dec 26

3. Ragno, Rino; Marshall, Garland R.; Ballante, Flavio. Three-dimensional structure-based modeling predicting target selectivity in drug design. PCT Int. Appl. (2015), WO 2015002860 A1 20150108. Language: English, Database: CAPLUS

4. Alberto De Petris, Maria Elisa Crestoni, Adele Pirolli, Carme Rovira, Javier Iglesias-Fernández, Barbara Chiavarino, Rino Ragno*, and Simonetta Fornarini**. Binding of azole drugs to heme: A combined MS/MS and computational approach. Polyhedron (2015) doi: 10.1016/j.poly.2015.02.011

5. Elisabetta Vavala, Claudio Passariello, Federico Pepi, Marisa Colone, Stefania Garzoli, Rino Ragno, Adele Pirolli, Annarita Stringaro, Letizia Angiolella. Antibacterial activity of essential oils mixture against PSA. Natural Product Research. (2015). DOI:10.1080/14786419.2015.1022543

6. Bozovic, Mijat; Pirolli, Adele; Ragno, Rino. Mentha suaveolens Ehrh. (Lamiaceae) essential oil and its main constituent piperitenone oxide: biological activities and chemistry. Molecules (2015), 20(5), 8605-8633

7. Garzoli, S., Pirolli, A., Vavala, E., Di Sotto, A., Sartorelli, G., Božović, M., Angiolella,
L., Mazzanti, G., Pepi, F., Ragno, R. Multidisciplinary approach to determine the optimal time and period for extracting the essential oil from mentha suaveolens ehrh. Molecules (2015), 20 (6), 9640-9655

8. Ragno, R., Ballante, F., Pirolli, A., Wickersham, R.B., 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. Journal of Computer-Aided Molecular Design (2015), 29 (8), 757-776

9. Consalvi, S.; Poce, G.; Ragno, R.; Sabatino, M.; La Motta, C.; Sartini, S.; Calderone, V.; Martelli, A.; Ghelardini, C.; Di Cesare Mannelli, L.; Biava, M., A Series of COX-2 Inhibitors Endowed with NO-Releasing Properties: Synthesis, Biological Evaluation, and Docking Analysis. ChemMedChem 2016, 11, 1804-11

10. 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.

11. Bozovic, M.; Garzoli, S.; Sabatino, M.; Pepi, F.; Baldisserotto, A.; Andreotti, E.; Romagnoli, C.; Mai, A.; Manfredini, S.; Ragno, R., Essential Oil Extraction, Chemical Analysis and Anti-Candida Activity of Calamintha nepeta (L.) Savi subsp. glandulosa (Req.) Ball-New Approaches. Molecules 2017, 22

12. Mollica, A.; Pelliccia, S.; Famiglini, V.; Stefanucci, A.; Macedonio, G.; Chiavaroli, A.; Orlando, G.; Brunetti, L.; Ferrante, C.; Pieretti, S.; Novellino, E.; Benyhe, S.; Zador, F.; Erdei, A.; Szucs, E.; Samavati, R.; Dvrorasko, S.; Tomboly, C.; Ragno, R.; Patsilinakos, A.; Silvestri, R., Exploring the first Rimonabant analog-opioid peptide hybrid compound, as bivalent ligand for CB1 and opioid receptors. J Enzyme Inhib Med Chem 2017, 32, 444-451.

13. Nikolaos Papastavrou, Maria Chatzopoulou, Jana Ballekova, Mario Cappiello, Roberta Moschini, Francesco Balestri, Alexandros Patsilinakos, Rino Ragno, Milan Stefekb, Enhancing activity and selectivity in a series of pyrrol-1-yl-1-hydroxypyrazole-based aldose reductase inhibitors: The case of trifluoroacetylation. European Journal of Medicinal Chemistry, 2017, 130, 328-335

14. Mijat Božović and Rino Ragno Calamintha nepeta (L.) Savi and its Main Essential Oil Constituent Pulegone: Biological Activities and Chemistry. Molecules. 2017 Feb 14;22(2). pii: E290. doi: 10.3390/molecules22020290

15. Mijat Božović, Alberto Navarra & Rino Ragno. 24-Hour Steam Distillation Methodology For Essential Oils Extraction. Natural Product Research. (2017).

16. Milan Mladenovic, Alexandros Patsilinakos, Adele Pirolli, Manuela Sabatino, and Rino Ragno. Understanding the Molecular Determinant of Reversible Human Monoamine Oxidase B Inhibitors Containing 2H-chromen-2-One Core: Structure-Based and Ligand-Based Derived 3-D QSAR Predictive Models. J. Chem. Inf. Model., (2017). Just Accepted Manuscript. DOI: 10.1021/acs.jcim.6b00608. Publication Date (Web): March 14, 201

17. Clemens Zwergel, PhD; Brigitte Czepukojc,; Emilie Evain-Bana, Zhanjie Xu, Giulia Stazi, Mattia Mori, Alexkandros Patsilinakos, Antonello Mai, Bruno Botta, Rino Ragno, Denyse Bagrel, Gilbert Kirsch, Peter Meiser, Claus Jacob, Mathias Montenarh, Sergio Valente. Novel Coumarin- and Quinolinone-Based Polycycles as Cell Division Cycle 25-A and -C Phosphatases Inhibitors Induce Proliferation Arrest and Apoptosis in Cancer Cells. European Journal of Medicinal Chemistry, 2017

18. Antonella Di Sotto, Ph.D.; Silvia Di Giacomo. Lorena Abete; Mijat Božović ; Olga A Parisi; Fabio Barile ; Annabella Vitalone, PhD; Angelo A Izzo; Rino Ragno; Gabriela Mazzanti. Genotoxicity assessment of piperitenone oxide: an in vitro and in silico evaluation. Food Microbiology. 2017

19. Diego Muñoz-Torrero, Arduino A. Mangoni, Catherine Guillou, Simona Collina, Jean Jacques Vanden Eynde, Jarkko Rautio, György M. Keserű, Christopher Hulme, Kelly Chibale, F. Javier Luque, Rafik Karaman, Michael Gütschow, Hong Liu and Rino Ragno. Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes. Molecules 2017, 22(5), 743

20. Stefania Garzolia, Mijat Božović, Anna Baldisserotto, Manuela Sabatino, Stefania Cesa, Federico Pepi, Chiara Beatrice Vicentini, Stefano Manfredini and Rino Ragno. Essential Oil Extraction, Chemical Analysis and Anti-Candida Activity of Foeniculum vulgare Miller – New Approaches. Natural Product Research. (2017)

21. Alessandro Venditti, Claudio Frezza, Giulia Salutari, Mirella di Cecco, Giampiero Ciaschetti, Alessandra Oliva, Massimiliano De Angelis, Vincenzo Vullo, Manuela Sabatino, Stefania Garzoli, Federico Pepi, Rino Ragno, Mauro Serafini, Armandodoriano Bianco. Composition of the Essential Oil of Coristospermum cuneifolium and Antimicrobial Activity Evaluation. Planta Med Int Open 2017

22. Vanja Tadić, Alessandra Oliva, Mijat Božović, Alessia Cipolla, Massimiliano De Angelis, Vincenzo Vullo, Stefania Garzoli, Rino Ragno. Chemical and antimicrobial analyses of Sideritis romana L. subsp. purpurea (Tal. ex Benth.) Heywood, an endemic of the Western Balkan. Molecules 2017, doi: 10.3390/molecules22091395.

23. Simone Carradori, Bruna Bizzarri, Melissa D'Ascenzio, Celeste De Monte, Rossella Grande, Daniela Rivanera, Alessanda Zicari, Emanuela Mari, Manuela Sabatino, Alexandros Pasilinakos, Rino Ragno, Daniela Secci. Eur J Med Chem. 2017 Nov 10;140:274-292. doi: 10.1016/j.ejmech.2017.09.026.

24. Stefania Garzoli, Mijat Božović, Anna Baldisserotto, Elisa Andreotti, Federico Pepi, Vanja Tadić, Stefano Manfredini & Rino Ragno. Sideritis romana L. subsp. purpurea (Tal. ex Benth.) Heywood, a new chemotype from Montenegro. Nat Prod Res. 2017 Sep 19:1-6. doi: 10.1080/14786419.2017.1378212. [Epub ahead of print]

25. Diego Muñoz-Torrero, Arduino A. Mangoni, Hong Liu, Christopher Hulme, Jarkko Rautio, Rafik Karaman, Maria Emília de Sousa, Katalin Prokai-Tatrai, Jean-Marc Sabatier, Carlo Siciliano, F. Javier Luque, George Kokotos, Rino Ragno, Simona Collina, Catherine Guillou, Michael Gütschow and Luigi A. Agrofoglio. Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes–2. Molecules 2018, 23(1), 65; doi:10.3390/molecules23010065

26. Manuela Sabatino, Dante Rotili, Alexandros Patsilinakos, Mariantonietta Forgione, Daniela Tomaselli, Fréderic Alby, Paola B. Arimondo, Antonello Mai, Rino Ragno. J Comput Aided Mol Des (2018). https://doi.org/10.1007/s10822-018-0096-z

27. Alessandra Masci, Simone Carradori, Maria Antonietta Casadei, Patrizia Paolicelli, Stefania Petralito, Rino Ragno, Stefania Cesa. Lycium barbarum polysaccharides: Extraction, purification, structural characterisation and evidence about hypoglycaemic and hypolipidaemic effects. A review. Food Chemistry (2018)

28. L. Antonini, S. Garzoli, A. Ricci, A. Troiani, C. Salvitti, P. Giacomello, R. Ragno, A. Patsilinakos, B.Di Rienzo and F. Pepi. Ab-initio and experimental study of pentose sugar dehydration mechanism in the gas phase. Carbohydrate Research 458-459 (2018) 19-28

29. Marco Artini, Alexandros Patsilinakos, Rosanna Papa, Mijat Božović, Manuela Sabatino, Stefania Garzoli, Gianluca Vrenna, Marco Tilotta, Federico Pepi, Rino Ragno and Laura Selan. Antimicrobial and antibiofilm activity and machine learning classification analysis of essential oils from different Mediterranean plants against Pseudomonas aeruginosa. Molecules (2018)

30.  Vincenzo Carafa , Angela Nebbioso , Francesca Cuomo , Dr. Dante Rotili , Dr. Gilda Cobellis , Dr. Paola Bontempo , Dr. Baldi Alfonso , Dr. Enrico P Spugnini , Dr. Gennaro Citro , Dr. Angela Chambery , Dr. Rosita Russo , Dr. Menotti Ruvo , Dr. Paolo Ciana , Dr. Luca Maravigna , Dr. Jani Shaik , Dr. Enrico Radaelli , Dr. Pasqualino De Antonellis , Dr. Domenico Tarantino , Dr. Adele Pirolli , Dr. Rino Ragno , Dr. Massimo Zollo , Dr. Hendrik G. Stunnenberg , Dr. Antonello Mai. RIP1-HAT1-SirT complex identification and targeting in treatment and prevention of cancer. Clinical Cancer Research MS# CCR-17-3081R (2018)

31. Mijat Božović, Stefania Garzoli, Anna Baldisserotto, Elisa Andreotti, Federico Pepi, Stefania Cesa, Silvia Vertuani, Stefano Manfredini and Rino Ragno. Melissa officinalis L. subsp. altissima (Sibth. & Sm.) Arcang. Essential Oil: Chemical Composition and Preliminary Antimicrobial Investigation of Samples Obtained at Different Harvesting Periods and by Fractionated Extractions. Industrial Crops and Products (2018)