AddressSapienza University, Piazzale Aldo Moro 5, RomeItaly
3-D QSAR, COMBINE, ligand-based drug design, structure-based drug design, molecular modeling
Ligand Base and Structure Based Drug Design
Molecular modelling techniques to design new chemical entities. We use free and commercial software and develop new software by programming in several computer languages (C, python, java script, etc).
Collaborations outside COST
The RCMD lab collaborate with several research groups: Garland Marshall at Washington University in St Louis (St Louis – MO – USA), Gilbert Kirsch at Losanne University (Metz – FR), Colosseum Combinatorial Chemistry Centre for Technology (C4T) Tor Vergata University, (Rome - IT).
Short description of ongoing research projects
RCMD apply computational methods to derive QSAR, 3-D QSAR and COMBINE models. Actually several models have been built for the following epigenetic targes: LSD1, KDM4A, DOT1L, human KDACs, PRMT1, other models will be generated for many other epigenetic targes with the perspectives to be able to design new epidrugs. The ongoing models will be built not only to predict the activities of new compounds, but also their selectivity profile among similar enzymes/protein. Along with the development of predictive models RCMD has also the possibility to profile molecules for their ADMET properties. Taken together the ADMET profiles and predictive models allow RCMD to set up database virtual screening to selected possible known compounds as new epigenetic tools and to prioritize the chemical synthesis of new small molecule epigenetic probes.
- 1. Ragno, R.; Ballante, F.; Pirolli, A.; Wickersham, R. B., III; 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, 29, 757-776.
- 2. Silvestri, L.; Ballante, F.; Mai, A.; Marshall, G. R.; Ragno, R., Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction. J. Chem. Inf. Model. 2012, 52, 2215-2235.
- 3. Ballante, F.; Ragno, R., 3-D QSAutogrid/R: An Alternative Procedure To Build 3-D QSAR Models. Methodologies and Applications. J. Chem. Inf. Model. 2012, 52, 1674-1685.
- 4. Ragno, R.; Simeoni, S.; Rotili, D.; Caroli, A.; Botta, G.; Brosch, G.; Massa, S.; Mai, A., Class II-selective histone deacetylase inhibitors. Alignment-independent GRIND 3-D QSAR, homology and docking studies. Eur. J. Med. Chem. 2008, 43, 621-632.
- 5. Ragno, R.; Simeoni, S.; Castellano, S.; Vicidomini, C.; Mai, A.; Caroli, A.; Tramontano, A.; Bonaccini, C.; Trojer, P.; Bauer, I.; Brosch, G.; Sbardella, G., Small Molecule Inhibitors of Histone Arginine Methyltransferases: Homology Modeling, Molecular Docking, Binding Mode Analysis, and Biological Evaluations. J. Med. Chem. 2007, 50, 1241-1253.5. Ragno, R.; Simeoni, S.; Castellano, S.; Vicidomini, C.; Mai, A.; Caroli, A.; Tramontano, A.; Bonaccini, C.; Trojer, P.; Bauer, I.; Brosch, G.; Sbardella, G., Small Molecule Inhibitors of Histone Arginine Methyltransferases: Homology Modeling, Molecular Docking, Binding Mode Analysis, and Biological Evaluations. J. Med. Chem. 2007, 50, 1241-1253.
Other activities of potential interest to others
Extraction of natural bioactive compounds compounds. Develop of internet portal and molecular databases.