Education

Biography

Simone Brogi got his “Laurea” in Biological Sciences in 2005. During his Master training, he started the studies in the field of molecular modeling. He obtained the Ph.D. degree in Pharmaceutical Sciences in 2010. During his Ph.D. research activity he used different computational techniques applied to diverse drug target with relevant achievements. At present, he is a research fellow at the University of Siena and he is the head of Molecular Modeling and Simulation Unit at the Department of Biotechnology, Chemistry and Pharmacy. His research activity is focused on the discovery and optimization of novel ligands for different drug targets. Most recently, He focused his activity on parasitic diseases. Beside rational drug design, hit discovery and lead optimization through a wide array of computational techniques, he have in depth knowledge of computational tools able to predict critical drug-like and toxicity-related properties such solubility, protonatability, mutagenicity, hERG activity, and cythochrome-mediated metabolism. He has over 8 years of experience in applying the knowledge of Molecular Modelling to solve problems inherent to Medicinal Chemistry research.
Specifically he have sound knowledge of various computational methodologies: Pharmacophore modeling, Virtual Screening, High throughput Docking (HTD), High throughput QM-Polarized Ligand Docking (HTQPLD), Molecular Docking, Homology Modeling, 3D-QSAR and 3D-QSSR models, Molecular Dynamics, QM/MM calculations, in silico prediction of ADME+T Properties. Furthermore Dr. Brogi possesses expertise in GPU calculation by means of CUDA technology applied to Molecular Dynamics software. Ioperates as reviewer for the Journal of Medicinal Chemistry, European Journal of Medicinal Chemistry, PLoS One, Journal of Computer-Aided Molecular Design, Journal of Molecular Graphics and Modelling, Frontiers in Pharmacology, Frontiers in Chemistry, Frontiers in Genetics, Frontiers in Microbiology, Journal of Natural Products, BMC Pharmacology & Toxicology, Journal of Chemistry, Chemistry Select and Interdisciplinary Sciences: Computational Life Sciences.
From January 2014 he is a Review Editor of “Frontiers in Chemistry”.
From November 2015 he is an Associate Editor of “BMC Pharmacology & Toxicology”.

Research Interest

Discovery and optimization of novel ligands for different drug targets
Parasitic diseases

Professional Activities:

Honors & Awards:

Publications

1. Prokineticin 1 receptor agonists and their uses
   Laurent Désaubry, Gunsel Canan Desaubry, Mounia Boulberdaa, Michel Kindo, Andrea Tafi, Simone Brogi, Kyoji Urayama, Nigel Riberio pub. No.: wo/2012/084999 international application no.: pct/ep2011/073474 http://patentscope.wipo.int/search/en/wo2012084999
2. Polypharmacology of dopamine receptor ligands
   Stefania Butini, Katarina Nikolic, Stefanie Kassel, Hjördis Brückmann, Slavica Filipic, Danica Agbaba, Sandra Gemma, Simone Brogi, Margherita Brindisi, Giuseppe Campiani, Holger Stark Prog. Neurobiol.2016, accepted, pp doi:10.1016/j.pneurobio.2016.03.011
3. Verbascoside inhibits promastigotes growth and arginase activity of leishmania amazonensis claudia c. Maquiaveli, JOÃO F. LUCON-JÚNIOR, SIMONE BROGI, GIUSEPPE CAMPIANI, SANDRA GEMMA, PAULO C. VIEIRA, EDSON R. SILVA J. Nat. Prod. 2016, 79(5), 1459–1463 doi: 10.1021/acs.jnatprod.5b00875
4. Development of novel cyclic peptides as pro-apoptotic agents
   Margherita Brindisi, Samuele Maramai, Simone Brogi, Emanuela Fanigliulo, Stefania Butini, Egeria Guarino, Alice Casagni, Stefania Lamponi, Claudia Bonechi, Seema M Nathwani, Federica Finetti, Francesco Ragonese, Paola Arcidiacono, Pietro Campiglia, Salvatore Valenti, Ettore Novellino, Roberta Spaccapelo, Lucia Morbidelli, Daniela M Zisterer, Clive D Williams, Alessandro Donati, Cosima Baldari, Giuseppe Campiani, Cristina Ulivieri, Sandra Gemma Eur. J. Med. Chem. 2016, 117, 301-320 doi: 10.1016/j.ejmech.2016.04.001
5. Targeting clinically-relevant metallo β lactamases: from high throughput docking to broad-spectrum inhibitors
   Margherita Brindisi, Simone Brogi, Simone Giovani, Sandra Gemma, Stefania Lamponi, Filomena De Luca, Ettore Novellino, Jean-Denis Docquier, Giuseppe Campiani, stefania butini j. Enzyme inhib. Med. Chem. 2016, accepted, pp doi: 10.3109/14756366.2016.1172575
6. Development and pharmacological characterization of selective blockers of 2-arachidonoyl glycerol degradation with efficacy in rodent models of multiple sclerosis and pain
   Margherita Brindisi, Samuele Maramai, Sandra Gemma, Simone Brogi, Alessandro Grillo, Lorenzo Di Cesare Mannelli, Emanuele Gabellieri, Stefania Lamponi, Simona Saponara, Beatrice Gorelli, Daniele Tedesco, Tommaso Bonfiglio, Christophe Landry, Kwang-Mook Jung, Andrea Armirotti, Livio Luongo, Alessia Ligresti, Fabiana Piscitelli, Carlo Bertucci, Marie-Pierre Dehouck, Giuseppe Campiani, Sabatino Maione, Carla Ghelardini, Anna Pittaluga, Daniele Piomelli, Vincenzo Di Marzo, Stefania Butini j. Med. Chem. 2016, 59(6), 2612-2632 doi: 10.1021/acs.jmedchem.5b01812
7. In silico study of subtilisin-like protease 1 (sub1) from different plasmodium species in complex with peptidyl-difluorostatones and characterization of potent pan-sub1 inhibitors
   SIMONE BROGI, SIMONE GIOVANI, MARGHERITA BRINDISI, SANDRA GEMMA, ETTORE NOVELLINO, GIUSEPPE CAMPIANI, MICHAEL j. blackman, stefania butini j. Mol. Graph. Model. 2016, 64, 121–130 doi:10.1016/j.jmgm.2016.01.005
8. Development of a practical and scalable route for the preparation of thedeacetoxytubuvaline (dtuv) fragment of pretubulysin and analogues
   Margherita Brindisi, Samuele Maramai, Alessandro Grillo, Simone Brogi, Stefania Butini, Ettore Novellino, Giuseppe Campiani, Sandra Gemma tetrahedron lett. 2016, 57(8), 920-923 doi: 10.1016/j.tetlet.2016.01.051
9. Donepezil-like multifunctional agents: design, synthesis, molecular modeling and biological evaluation
   Ming-Yu Wu,§ Gerard Esteban,§ Simone Brogi,§ Masahi Shionoya, Li Wang, Giuseppe Campiani, Mercedes Unzeta, Tsutomu Inokuchi, Stefania Butini, Jose Marco-Contelles eur. J. Med. Chem. 2016, accepted, pp doi: 10.1016/j.ejmech.2015.10.001 §equal contribution
10. Multitarget compounds bearing tacrine- and donepezil-like structural and functional motifs for the potential treatment of alzheimer's disease
    Lhassane Ismaili, Bernard Refouvelet, Mohamed Benchekroun, Simone Brogi, Margherita Brindisi, Sandra Gemma, Giuseppe Campiani, Slavica Filipic, Danica Agbaba, Gerard Esteban, Mercedes Unzeta, Katarina Nikolic, Stefania Butini, José Marco-Contelles Prog. Neurobiol. 2016, accepted, pp doi: 10.1016/j.pneurobio.2015.12.003
11. Synthesis and biological evaluation of fluorinated 1,5-diarylpyrrole-3-alkoxyethyl ether derivatives as selective cox-2 inhibitors endowed with antiinflammatory activity
    Angela Di Capua, Claudia Sticozzi, Simone Brogi, Margherita Brindisi, Andrea Cappelli, Lidia Sautebin, Antonietta Rossi, Simona Pace, Carla Ghelardini, Lorenzo Di Cesare Mannelli, Giuseppe Valacchi, Gianluca Giorgi, Antonio Giordani, Giovanna Poce, Mariangela Biava, Maurizio Anzini Eur. J. Med. Chem. 2016, 109,99–106 doi: 10.1016/j.ejmech.2015.12.044
12. Exploring clotrimazole-based pharmacophore: 3d-qsar studies and synthesis of novel antiplasmodial agents
    Simone Brogi, Margherita Brindisi, Bhupendra P Joshi, Salvatore Sanna Coccone, Silvia Parapini, Nicoletta Basilico, Ettore Novellino, Giuseppe Campiani, Sandra Gemma, Stefania Butini Bioorg. Med. Chem. Lett. 2015, 25(22), 5412-5418 doi: 10.1016/j.bmcl.2015.09.007
13. Discovery and cardioprotective effects of the first non-peptide agonists of the g-protein-coupled prokineticin receptor-1
    Adeline Gasser§, Simone Brogi§, Kyoji Urayama, Toshishide Nishi, Hitoshi Kurose, Andrea Tafi, Nigel Ribeiro, Laurent Désaubry, Canan G. Nebigil plos one 2015, 10(4), e0121027 doi: 10.1371/journal.pone.0121027 §equal contribution
14. Structure-based discovery of the first non-covalent inhibitors of leishmania major tryparedoxin peroxidase by high throughput docking
    Margherita Brindisi§, Simone Brogi§, Nicola Relitti, Alessandra Vallone, Stefania Butini, Sandra Gemma, Ettore Novellino, Gianni Colotti, Gabriella Angiulli, Francesco Di Chiaro, Annarita Fiorillo, Andrea Ilari, Giuseppe Campiani Sci. Rep. 2015, 5, 9705 doi:10.1038/srep09705 §equal contribution
15. Plasmodium falciparum subtilisin-like protease 1: discovery of potent difluorostatone-based inhibitors
    Simone Giovani, Maria Penzo, Stefania Butini, Margherita Brindisi, Sandra Gemma, Ettore Novellino, Giuseppe Campiani, Michael J. Blackman, simone brogi rsc adv. 2015, 5(29), 22431-22448 doi: 10.1039/c5ra01170a
16. Development of hupertacrines as non-toxic, cholinesterase inhibitors for the potential treatment of alzheimer’s disease
    Mourad chioua, marta pérez, oscar m. Bautista-aguilera, matilde yañez, manuela g. López, alejandro Romero, Ramón Cacabelos, Raimon Puig De La Bellacasa, Simone Brogi, Stefania Butini, José i.
    Borrell, jose marco-contelles mini rev. Med. Chem. 2015, 15(8), 648-658 doi: 10.2174/1389557515666150219130156
17. Synthetic spirocyclic endoperoxides: new antimalarial scaffolds
    Margherita Brindisi, Sandra Gemma, Sanil Kunjir, Luisa Di Cerbo, Simone Brogi, Silvia Parapini, Sarah D’alessandro, Donatella Taramelli, Annette Habluetzel, Sofia Tapanelli, Stefania Lamponi, Ettore Novellino, Giuseppe Campiani, Stefania Butini med. Chem. Commun. 2015, 6, 357-362 doi: 10.1039/c4md00454j
18.  discovery of gpcr ligands for probing signal transduction pathways
    Simone Brogi, Andrea Tafi, Laurent Désaubry, canan g. Nebigil front. Pharmacol. 2014, 5:255doi:10.3389/fphar.2014.00255
19. Targeting dopamine d3 and serotonin 5-ht1a and 5-ht2a receptors for developing effective antipsychotics: synthesis, biological characterization, and behavioral studies
    Margherita Brindisi, Stefania Butini, Silvia Franceschini, Simone Brogi, Francesco Trotta, Sindu Ros, Alfredo Cagnotto, Mario Salmona, Alice Casagni, Marco Andreassi, Simona Saponara, Beatrice Gorelli, Pia Weikop, Jens d. Mikkelsen, Jorgen Scheel-Kruger, Karin Sandager-Nielsen, Ettore Novellino, Giuseppe Campiani, Sandra Gemma j. Med. Chem. 2014, 57(22), 9578-9597 doi:10.1021/jm501119j
20. Disease modifying anti-alzheimer’s drugs: inhibitors of human cholinesterases interfering with β-amyloid aggregation
    Simone Brogi, Stefania Butini, Samuele Maramai, Raffaella Colombo, Laura Verga, Cristina Lanni, Ersilia De Lorenzi, Stefania Lamponi, Marco Andreassi, Manuela Bartolini, Vincenza Andrisano, Ettore
    Novellino, giuseppe campiani, margherita brindisi, sandra gemma cns neurosci. Ther. 2014, 20(7),624-632 doi:10.1111/cns.12290
21. Rational design of the first difluorostatone-based pfsub1 inhibitors
    Simone Giovani, Maria Penzo, Simone Brogi, Margherita Brindisi, Sandra Gemma, Ettore Novellino, Luisa Savini, Michael j. Blackman, Giuseppe Campiani, Stefania Butini Bioorg. Med. Chem. Lett. 2014, 24(15),3582-3586 doi:10.1016/j.bmcl.2014.05.044
22. Hcv-targeted antivirals: current status and future challenges
    Sandra Gemma, Simone Brogi, Ettore Novellino, Giuseppe    Campiani, Giovanni Maga, Margherita Brindisi, Stefania Butini Curr. Pharm. Des. 2014, 20(21), 3445–3464
    Doi:10.2174/13816128113199990630
23. From (+)-epigallocatechin gallate to a simplified synthetic analogue as a cytoadherence inhibitor for p. Falciparum Sandra Gemma, Simone Brogi, Pradeep r. Patil, Simone Giovani, Stefania Lamponi, Andrea Cappelli, Ettore Novellino, Alan Brown, Matthew Higgins, Khairul Mustafa, Tadge Szestak, alister g. Craig, Giuseppe Campiani, Stefania Butini, Margherita Brindisi rsc adv. 2014, 4, 4769–4781 doi:10.1039/c3ra45933k
24. Multifunctional cholinesterase and amyloid beta fibrillization modulators. Synthesis and biological investigation
    Stefania Butini, Margherita Brindisi, Simone Brogi, Samuele Maramai, Egeria Guarino, Alessandro Panico, Ashima Saxena, Ved Chauhan, Raffaella Colombo, Laura Verga, Ersilia De Lorenzi, Manuela Bartolini, Vincenza Andrisano, Ettore Novellino, Giuseppe Campiani, Sandra Gemma acs med. Chem. Lett. 2013, 4(12), 1178-1182 doi:10.1021/ml4002908
25. A stereoselective approach to peptidomimetic bace1 inhibitors
    Stefania Butini, Emanuele Gabellieri, Margherita Brindisi, Simone Giovani, Samuele Maramai, Giridhar Kshirsagar, Egeria Guarino, Simone Brogi, Valeria La Pietra, Mariateresa Giustiniano, Luciana Marinelli, Ettore Novellino, Giuseppe Campiani, Andrea Cappelli, Sandra Gemma Eur. J. Med. Chem. 2013, 70,233-247 doi:10.1016/j.ejmech.2013.09.056
26. The structural evolution of β-secretase inhibitors: a focus on the development of small-molecule inhibitors 
    Stefania Butini, Simone Brogi, Ettore Novellino, Giuseppe Campiani, Arun K. Ghosh, Margherita Brindisi, Sandra Gemma curr. Top. Med. Chem. 2013, 13(15), 1787-1807 doi:
    10.2174/15680266113139990137
27. 3d-qsar using pharmacophore-based alignment and virtual screening for discovery of novel mcf-7 cell line inhibitors
    Simone Brogi, Panagiota Papazafiri, Vassilios Roussis, Andrea Tafi eur. J. Med. Chem. 2013, 67, 344- 351 doi:10.1016/j.ejmech.2013.06.048
28. Novel analgesic/anti-inflammatory agents: 1,5-diarylpyrrole nitro-oxyalkyl ethers and related compounds as cyclooxygenase-2 inhibiting nitric oxide donors
    Maurizio Anzini, Angela Di Capua, Salvatore Valenti, Simone Brogi, Michele Rovini, Germano Giuliani, Andrea Cappelli, Salvatore Vomero, Luisa Chiasserini, Alessandro Sega, Giovanna Poce, Gianluca Giorgi, Vincenzo Calderone, Alma Martelli, Lara Testai, Lidia Sautebin, Antonietta Rossi, Simona Pace, Carla Ghelardini, Lorenzo Di Cesare Mannelli, Veronica Benetti, Antonio Giordani, Paola Anzellotti,
    Melania Dovizio, Paola Patrignani, Mariangela Biava j. Med. Chem. 2013, 56(8), 3191-3206doi:10.1021/jm301370e
29. Synthesis and structure-activity relationship studies in serotonin 5-ht1a receptor agonists based on fused pyrrolidone scaffolds
    Andrea Cappelli, Monica Manini, Salvatore Valenti, Federica Castriconi, Germano Giuliani, Maurizio
    Anzini, Simone Brogi, Stefania Butini, Sandra Gemma, Giuseppe Campiani, Gianluca Giorgi, Laura Mennuni, Marco Lanza, Antonio Giordani, Gianfranco Caselli, Francesco Makovec eur. J. Med. Chem.2013, 63, 85-94 doi:10.1016/j.ejmech.2013.01.044
30. Mimicking the intramolecular hydrogen bond: synthesis, biological evaluation, and molecular modeling of benzoxazines and quinazolines as potential antimalarial agents
    Sandra Gemma, Caterina Camodeca, Margherita Brindisi, Simone Brogi, Gagan Kukreja, Sanil Kunjir, Emanuele Gabellieri, Leonardo Lucantoni, Annette Habluetzel, Donatella Taramelli, Nicoletta Basilico, Roberta Gualdani, Francesco Tadini-Buoninsegni, Gianluca Bartolommei, Maria Rosa Moncelli, Rowena E Martin, Robert L Summers, Stefania Lamponi, Luisa Savini, Isabella Fiorini, Massimo Valoti, Ettore Novellino, Giuseppe Campiani, Stefania Butini j. Med. Chem. 2012, 55(23),10387-10404doi:10.1021/jm300831b
31. Quinolylhydrazones as novel inhibitors of plasmodium falciparum serine protease pfsub1
    Sandra Gemma, Simone Giovani, Margherita Brindisi, Pierangela Tripaldi, Simone Brogi, Luisa Savini, Isabella Fiorini, Ettore Novellino, Stefania Butini, Giuseppe Campiani, Maria Penzo, Michael j. Blackmanbioorg. Med. Chem. Lett. 2012, 22(16), 5317-5321 doi:10.1016/j.bmcl.2012.06.023
32. Optimization of 4-aminoquinoline/clotrimazole-based hybrid antimalarials: further structure-activity relationships, in vivo studies, and preliminary toxicity profiling
    Sandra Gemma, Caterina Camodeca, Salvatore Sanna Coccone, Bhupendra P Joshi, Matteo Bernetti, Vittoria Moretti, Simone Brogi, María-Cruz Bonache, Luisa Savini, Donatella Taramelli, Nicoletta Basilico, Silvia Parapini, Matthias Rottmann, Reto Brun, Stefania Lamponi, Silvio Caccia, Giovanna Guiso, Robert L. Summer, Rowena E. Martin, Simona Saponara, Beatrice Gorelli, Ettore Novellino, Giuseppe Campiani, Stefania Butini j. Med. Chem. 2012, 55(15), 6948-6967 doi:10.1021/jm300802s
33. Design, synthesis, and pharmacological characterization of indol-3-ylacetamides, indol-3-yloxoacetamides, and indol-3-ylcarboxamides: potent and selective cb2 cannabinoid receptor inverse agonists
    Serena Pasquini, Claudia Mugnaini, Alessia Ligresti, Andrea Tafi, Simone Brogi, Chiara Falciani, Valentina Pedani, Nicolò Pesco, Francesca Guida, Livio Luongo, Katia Varani, Pier Andrea Borea, Sabatino Maione, Vincenzo Di Marzo, Federico Corelli j. Med. Chem. 2012, 55(11), 5391-5402doi:10.1021/jm3003334
34. Characterization of cor627 and cor628, two novel positive allosteric modulators of the gabab receptor
    M. Paola Castelli, Angelo Casu, Paola Casti, Carla Lobina, Mauro A.M. Carai, Giancarlo Colombo, Maurizio Solinas, Daniela Giunta, Claudia Mugnaini, Serena Pasquini, Andrea Tafi, Simone Brogi, Gian
    Luigi Gessa, Federico Corelli j. Pharmacol. Exp. Ther. 2012, 340(3), 529-538doi:10.1124/jpet.111.186460
35. Synthesis and antiplasmodial activity of bicyclic dioxanes as simplified dihydroplakortin analogues
    Sandra Gemma, Sanil Kunjir, Salvatore Sanna Coccone, Margherita Brindisi, Vittoria Moretti, Simone Brogi, Ettore Novellino, Nicoletta Basilico, Silvia Parapini, Donatella Taramelli, Giuseppe Campiani, Stefania Butini J. Med. Chem. 2011, 54(16), 5949-5953 doi:10.1021/jm200686d
36. Three-dimensional quantitative structure– selectivity relationships analysis guided rational design of a highly selective ligand for the cannabinoid receptor 2
    Simone Brogi, Federico Corelli, Vincenzo Di Marzo, Alessia Ligresti, Claudia Mugnaini, Serena Pasquini, Andrea Tafi eur. J. Med. Chem. 2011, 46(2), 547-555 doi:10.1016/j.ejmech.2010.11.034
37. Pharmacophore modeling for qualitative prediction of antiestrogenic activity
    Simone Brogi, Maria Kladi, Constantinos Vagias, Panagiota Papazafiri, Vassilios Roussis, Andrea Tafi j. Chem. Inf. Model. 2009, 49(11), 2489-2497 doi:10.1021/ci900254b
38. Tetrahydrofuran acetogenins from laurencia glandulifera
    Maria Kladi, Constantinos Vagias, Panagiota Papazafiri, Simone Brogi, Andrea Tafi, Vassilios Roussis j. Nat. Prod. 2009, 72(2), 190-193 doi:10.1021/np800481w