Rome Center for Molecular Design (CHIM/08)

Attività di ricerca

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) or 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 (www.3d-qsar.com)
- Web site for essential oils and natural compounds (eo.3d-qsar.com)
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
Application of Machine Learning algorithms to complex mixtures (Essential Oils) to identify the most active/toxic components
Application of Machine Learning algorithms for Virtual Screening Campaigns

Collaborazioni nazionali e internazionali

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 algorithms
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

Strumentazione

Several PC either desktop or laptop for data analysis.
Several workstation server for calculation
A four 1080 GPU as Calculation server
A four 2080 GPU as Calculation server
A two 108 GPU and 32 CPU cores as web server
A File system server with 40 TB of disk space
Calculation servers for a total of about 200 cores

Settori ERC

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

Finanziamenti

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

Pubblicazioni

In the following link is the list of publications as found in the scopus database
Scopus

Publications (2019-2021)

Paglia, G., Antonini, L., Cervoni, L., Ragno, R., Sabatino, M., Minacori, M., Rubini, E., Altieri, F.
A comparative analysis of punicalagin interaction with PDIA1 and PDIA3 by biochemical and computational approaches
(2021) Biomedicines, 9 (11), art. no. 1533.
Vrenna, G., Artini, M., Ragno, R., Relucenti, M., Fiscarelli, E.V., Assanti, V.T.G., Papa, R., Selan, L.
Anti- virulence properties of coridothymus capitatus essential oil against pseudomonas aeruginosa clinical isolates from cystic fibrosis patients
(2021) Microorganisms, 9 (11), art. no. 2257.
Mihović, N., Tomašević, N., Matić, S., Mitrović, M.M., Kostić, D.A., 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
(2021) Journal of Chemical Information and Modeling, 61 (10), pp. 5028-5053.
Di Martile, M., Garzoli, S., Sabatino, M., Valentini, E., D’Aguanno, S., Ragno, R., Del Bufalo, D.
Antitumor effect of Melaleuca alternifolia essential oil and its main component terpinen-4-ol in combination with target therapy in melanoma models
(2021) Cell Death Discovery 7 (1), art. no. 127.
Boriero, D., Carcereri de Prati, A., Antonini, L., Ragno, R., Sohji, K., Mariotto, S., Butturini, E.
The anti-STAT1 polyphenol myricetin inhibits M1 microglia activation and counteracts neuronal death
(2021) FEBS Journal, 288 (7), pp. 2347-2359.
Papa, R., Garzoli, S., Vrenna, G., Sabatino, M., Sapienza, F., Relucenti, M., Donfrancesco, O., Fiscarelli, E.V., Artini, M., Selan, L., Ragno, R.
Essential oils biofilm modulation activity, chemical and machine learning analysis. Application on staphylococcus aureus isolates from cystic fibrosis patients
(2020) International Journal of Molecular Sciences, 21 (23), art. no. 9258, pp. 1-20.
Ragno, R., Papa, R., Patsilinakos, A., Vrenna, G., Garzoli, S., Tuccio, V., Fiscarelli, E.V., Selan, L., Artini, M.
Essential oils against bacterial isolates from cystic fibrosis patients by means of antimicrobial and unsupervised machine learning approaches
(2020) Scientific Reports, 10 (1), art. no. 2653.
Di Martile, M., Garzoli, S., Ragno, R., Del Bufalo, D.
Essential oils and their main chemical components: The past 20 years of preclinical studies in Melanoma
(2020) Cancers, 12 (9), art. no. 2650, pp. 1-45.
Ragno, R., Esposito, V., Di Mario, M., Masiello, S., Viscovo, M., Cramer, R.D.
Teaching and Learning Computational Drug Design: Student Investigations of 3D Quantitative Structure-Activity Relationships through Web Applications
(2020) Journal of Chemical Education, 97 (7), pp. 1922-1930.
Božović, M., Garzoli, S., Baldisserotto, A., Andreotti, E., Cesa, S., Pepi, F., Vertuani, S., Manfredini, S., Ragno, R.
Variation in essential oil content and composition of Ridolfia segetum Moris based on 30-hour prolonged fractionated extraction procedure
(2020) Natural Product Research, 34 (13), pp. 1923-1926.
Rinaldi, F., Oliva, A., Sabatino, M., Imbriano, A., Hanieh, P.N., Garzoli, S., Mastroianni, C.M., De Angelis, M., Miele, M.C., Arnaut, M., Di Timoteo, F., Marianecci, C., Ragno, R., Carafa, M.
Antimicrobial essential oil formulation: Chitosan coated nanoemulsions for nose to brain delivery
(2020) Pharmaceutics, 12 (7), art. no. 678, pp. 1-18.
Gütschow, M., Eynde, J.J.V., Jampilek, J., Kang, C., Mangoni, A.A., Fossa, P., Karaman, R., Trabocchi, A., Scott, P.J.H., Reynisson, J., Rapposelli, S., Galdier, S., Winum, J.-Y., Brullo, C., Prokai-Tatrai, K., Sharma, A.K., Schapira, M., Azuma, Y.-T., Cerchia, L., Spete, M., Torri, G., Collina, S., Geronikaki, A., García-Sosa, A.T., Helena Vasconcelos, M., Sousa, M.E., Kosalec, I., Tuccinardi, T., Duarte, I.F., Salvador, J.A.R., Bertinaria, M., Pellecchia, M., Amato, J., Rastelli, G., Gomes, P.A.C., Guedes, R.C., Sabatier, J.-M., Estévez-Braun, A., Pagano, B., Mangani, S., Ragno, R., Kokotos, G., Brindisi, M., González, F.V., Borges, F., Miloso, M., Rautio, J., Muñoz-Torrero, D.
Breakthroughs in medicinal chemistry: New targets and mechanisms, new drugs, new hopes-7
(2020) Molecules, 25 (13), art. no. 2968.
Caroselli, S., Zwergel, C., Pirolli, A., Sabatino, M., Xu, Z., Kirsch, G., Mai, A., Colotti, G., Altieri, F., Canipari, R., Valente, S., Ragno, R.
Discovery of the First Human Arylsulfatase A Reversible Inhibitor Impairing Mouse Oocyte Fertilization
(2020) ACS Chemical Biology, 15 (6), pp. 1349-1357.
Sabatino, M., Fabiani, M., Božović, M., Garzoli, S., Antonini, L., Marcocci, M.E., Palamara, A.T., de Chiara, G., Ragno, R.
Experimental data based machine learning classification models with predictive ability to select in vitro active antiviral and non-toxic essential oils
(2020) Molecules, 25 (10), art. no. 2452.
Bastos, T.M., Soares, M.B.P., Franco, C.H., Alcântara, L., Antonini, L., Sabatino, M., Mautone, N., Freitas- Junior, L.H., Moraes, C.B., Ragno, R., Rotili, D., Schenkman, S., Mai, A., Moretti, N.S.
Identification of inhibitors to trypanosoma cruzi sirtuins based on compounds developed to human enzymes
(2020) International Journal of Molecular Sciences, 21 (10), art. no. 3659.
Di Vito, M., Grazia Bellardi, M., Sanguinetti, M., Mondello, F., Girolamo, A., Barbanti, L., Garzoli, S., Sabatino, M., Ragno, R., Vitali, A., Palucci, I., Posteraro, B., Gasbarrini, A., Maria Prati, G., Aragona, G., Mattarelli, P., Bugli, F.
Potent in vitro activity of citrus aurantium essential oil and vitis vinifera hydrolate against gut yeast isolates from irritable bowel syndrome patients—the right mix for potential therapeutic use
(2020) Nutrients, 12 (5), art. no. 1329.
Nobile, V., Palumbo, F., Lanni, S., Ghisio, V., Vitali, A., Castagnola, M., Marzano, V., Maulucci, G., De Angelis, C., De Spirito, M., Pacini, L., D’Andrea, L., Ragno, R., Stazi, G., Valente, S., Mai, A., Chiurazzi, P., Genuardi, M., Neri, G., Tabolacci, E.
Altered mitochondrial function in cells carrying a premutation or unmethylated full mutation of the FMR1 gene
(2020) Human Genetics, 139 (2), pp. 227-245.
Oliva, A., Garzoli, S., Sabatino, M., Tadić, V., Costantini, S., Ragno, R., Božović, M.
Chemical composition and antimicrobial activity of essential oil of Helichrysum italicum (Roth) G. Don fil. (Asteraceae) from Montenegro
(2020) Natural Product Research, 34 (3), pp. 445-448.
Vanden Eynde, J.J., Mangoni, A.A., Rautio, J., Leprince, J., Azuma, Y.-T., García-Sosa, A.T., Hulme, C., Jampilek, J., Karaman, R., Li, W., Gomes, P.A.C., Hadjipavlou-Litina, D., Capasso, R., Geronikaki, A., Cerchia, L., Sabatier, J.-M., Ragno, R., Tuccinardi, T., Trabocchi, A., Winum, J.-Y., Luque, F.J., Prokai-Tatrai, K., Spetea, M., Gütschow, M., Kosalec, I., Guillou, C., Vasconcelos, M.H., Kokotos, G., Rastelli, G., De Sousa, M.E., Manera, C., Gemma, S., Mangani, S., Siciliano, C., Galdiero, S., Liu, H., Scott, P.J.H., De Los Ríos, C., Agrofoglio, L.A., Collina, S., Guedes, R.C., Muñoz-Torrero, D.
Breakthroughs in medicinal chemistry: New targets and mechanisms, new drugs, new hopes-6
(2020) Molecules, 25 (1), art. no. 119.
Garzoli, S., Antonini, L., Troiani, A., Salvitti, C., Giacomello, P., Patsilinakos, A., Ragno, R., Pepi, F.
Gas-phase structures and thermochemical properties of protonated 5-HMF isomers
(2020) International Journal of Mass Spectrometry, 447, art. no. 116237.
Stazi, G., Taglieri, L., Nicolai, A., Romanelli, A., Fioravanti, R., Morrone, S., Sabatino, M., Ragno, R., Taurone, S., Nebbioso, M., Carletti, R., Artico, M., Valente, S., Scarpa, S., Mai, A.
Dissecting the role of novel EZH2 inhibitors in primary glioblastoma cell cultures: Effects on proliferation, epithelial-mesenchymal transition, migration, and on the pro-inflammatory phenotype
(2019) Clinical Epigenetics, 11 (1), art. no. 173,
Marrocco, I., Altieri, F., Rubini, E., Paglia, G., Chichiarelli, S., Giamogante, F., Macone, A., Perugia, G., Magliocca, F.M., Gurtner, A., Maras, B., Ragno, R., Patsilinakos, A., Manganaro, R., Eufemi, M.
Shmt2: A Stat3 Signaling New Player in Prostate Cancer Energy Metabolism
(2019) Cells, 8 (9).
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
(2019) Journal of Computer-Aided Molecular Design, 33 (9), pp. 855-864.
Stazi, G., Battistelli, C., Piano, V., Mazzone, R., Marrocco, B., Marchese, S., Louie, S.M., Zwergel, C., Antonini, L., Patsilinakos, A., Ragno, R., Viviano, M., Sbardella, G., Ciogli, A., Fabrizi, G., Cirilli, R., Strippoli, R., Marchetti, A., Tripodi, M., Nomura, D.K., Mattevi, A., Mai, A., Valente, S.
Development of alkyl glycerone phosphate synthase inhibitors: Structure-activity relationship and effects on ether lipids and epithelial- mesenchymal transition in cancer cells
(2019) European Journal of Medicinal Chemistry, 163, pp. 722-735.
Nawrozkij, M.B., Forgione, M., Yablokov, A.S., Lucidi, A., Tomaselli, D., Patsilinakos, A., Panella, C., Hailu, G.S., Kirillov, I.A., Badia, R., Riveira-Munoz, E., Crespan, E., Armijos Rivera, J.I., Cirilli, R., Ragno, R., Esté, J.A., Maga, G., Mai, A., Rotili, D.
Effect of α-Methoxy Substitution on the Anti-HIV Activity of Dihydropyrimidin- 4(3 H)-ones
(2019) Journal of Medicinal Chemistry, 62 (2), pp. 604-621.
Mangoni, A.A., Eynde, J.J.V., Jampilek, J., Hadjipavlou-Litina, D., Liu, H., Reynisson, J., Sousa, M.E., Gomes, P.A.C., Prokai-Tatrai, K., Tuccinardi, T., Sabatier, J.-M., Luque, F.J., Rautio, J., Karaman, R., Vasconcelos, M.H., Gemma, S., Galdiero, S., Hulme, C., Collina, S., Gütschow, M., Kokotos, G., Siciliano, C., Capasso, R., Agrofoglio, L.A., Ragno, R., Muñoz-Torrero, D.
Breakthroughs in medicinal chemistry: New targets and mechanisms, New Drugs, New Hopes-5
(2019) Molecules, 24 (13), art. no. 2415.
Patsilinakos, A., Artini, M., Papa, R., Sabatino, M., Božović, M., Garzoli, S., Vrenna, G., Buzzi, R., Manfredini, S., Selan, L., Ragno, R.
Machine Learning Analyses on Data including Essential Oil Chemical Composition and In Vitro Experimental Antibiofilm Activities against Staphylococcus Species
(2019) Molecules, 24 (5), art. no. 890.
Oliva, A., Garzoli, S., De Angelis, M., Marzuillo, C., Vullo, V., Mastroianni, C.M., Ragno, R.
In-vitro evaluation of different antimicrobial combinations with and without colistin against carbapenem-resistant Acinetobacter baumannii
(2019) Molecules, 24 (5), art. no. 886, .
Mangoni, A.A., Guillou, C., Eynde, J.J.V., Hulme, C., Jampilek, J., Li, W., Prokai-Tatrai, K., Rautio, J., Collina, S., Tuccinardi, T., Sousa, M.E., Sabatier, J.-M., Galdiero, S., Karaman, R., Kokotos, G., Torri, G., Javier Luque, F., Helena Vasconcelos, M., Hadjipavlou-Litina, D., Siciliano, C., Gütschow, M., Ragno, R., Gomes, P.A.C., Agrofoglio, L.A., Muñoz-Torrero, D.
Breakthroughs in medicinal chemistry: New targets and mechanisms, new drugs, new hopes-4
(2019) Molecules, 24 (1), pp. 1-12.