ELEONORA PROIA

PhD Graduate

PhD program:: XXXVI


supervisor: Prof. Rino Ragno

Thesis title: Computational and machine learning approaches for the rational design and discovery of novel bioactive compounds

The use of computational approaches in drug design and discovery has become an essential tool for identifying, prioritising and optimising biologically active compounds in the last decades. These approaches are a valuable integral part of the preliminary stages of the drug discovery pipeline, helping to expedite the drug development process in a more cost-efficient way. They significantly reduce the time and resources required by conventional experimental strategies, such as chemical synthesis and biological testing, while covering a wider chemical space. The most recent impact of big data handling and artificial intelligence (AI) in the field holds great promise to revolutionise and streamline the entire drug discovery process. The extensive variety of computational tools are broadly classified as ligand-based or structure-based methods, depending on the availability of high-resolution structural data about the target. A combination of these methods often produces the most successful stories. This PhD thesis presents the application of computational approaches, chemometric and machine learning techniques to drug design and discovery projects. These techniques provide valuable support in unravelling information from data, assisting in ligand optimization and clarifying potential mechanisms of action. The combination of computational methods and advanced data analysis offers a comprehensive framework for advancing drug discovery, providing valuable support in navigating the complexities of modern pharmaceutical research.

Research products

11573/1711772 - 2024 - (Heteroarylmethyl)benzoic Acids as a New Class of Bacterial Cystathionine γ-Lyase Inhibitors: Synthesis, Biological Evaluation, and Molecular Modeling
Golovina, Anastasia; Proia, Eleonora; Fiorentino, Francesco; Yunin, Maxim; Kasatkina, Maria; Zigangirova, Nailya; Soloveva, Anna; Sysolyatina, Elena; Ermolaeva, Svetlana; Novikov, Roman; Silonov, Sergei; Pushkin, Sergei; Mladenović, Milan; Isakova, Julia; Belik, Albina; Nawrozkij, Maxim; Rotili, Dante; Ragno, Rino; Ivanov, Roman - 01a Articolo in rivista
paper: ACS INFECTIOUS DISEASES (Washington, DC : American Chemical Society, 2015-) pp. 2127-2150 - issn: 2373-8227 - wos: WOS:001228938600001 (0) - scopus: 2-s2.0-85194084452 (0)

11573/1669898 - 2023 - Pyrimidine thioethers: A novel class of antidepressant agents, endowed with anxiolytic, performance enhancing and nootropic activity
Fioravanti, Rossella; Proia, Eleonora; Tyurenkov, Ivan N; Kurkin, Denis V; Bakulin, Dmitry A; Kovalev, Nikolay S; Sheikin, Dmitry S; Kirillov, Ivan A; Nawrozkij, Maxim B; Vernigora, Andrey A; Brunilina, Leila L; Fiorentino, Francesco; Mladenović, Milan; Rotili, Dante; Ragno, Rino - 01a Articolo in rivista
paper: EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY ([Paris] : Elsevier, [198?]-) pp. 114902- - issn: 1768-3254 - wos: WOS:000993134500001 (2) - scopus: 2-s2.0-85141941686 (3)

11573/1686582 - 2023 - Molecular Docking Assessment of Cathinones as 5-HT2AR Ligands: Developing of Predictive Structure-Based Bioactive Conformations and Three-Dimensional Structure-Activity Relationships Models for Future Recognition of Abuse Drugs
Tomašević, Nevena; Vujović, Maja; Kostić, Emilija; Ragavendran, Venkatesan; Arsić, Biljana; Matić, Sanja Lj.; Božović, Mijat; Fioravanti, Rossella; Proia, Eleonora; Ragno, Rino; Mladenović, Milan - 01a Articolo in rivista
paper: MOLECULES (Basel: MDPI Berlin: Springer, 1996-) pp. - - issn: 1420-3049 - wos: WOS:001065372400001 (1) - scopus: 2-s2.0-85170350278 (3)

11573/1659035 - 2022 - Ligand-based and structure-based studies to develop predictive models for {SARS}-{CoV}-2 main protease inhibitors through the 3d-qsar.com portal
Proia, Eleonora; Ragno, Alessio; Antonini, Lorenzo; Sabatino, Manuela; Mladenović, Milan; Capobianco, Roberto; Ragno, Rino - 01a Articolo in rivista
paper: JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (-SPRINGER, VAN GODEWIJCKSTRAAT 30, DORDRECHT, NETHERLANDS, 3311 GZ -Kluwer Academic Publishers:Journals Department, PO Box 322, 3300 AH Dordrecht Netherlands:011 31 78 6576050, EMAIL: frontoffice@wkap.nl, kluweronline@wkap.nl, INTERNET: http://www.kluwerlaw.com, Fax: 011 31 78 6576254) pp. 483-505 - issn: 0920-654X - wos: WOS:000812582700001 (5) - scopus: 2-s2.0-85132189914 (8)

11573/1652233 - 2022 - Bovine serum amine oxidase and polyamine analogues: chemical synthesis and biological evaluation integrated with molecular docking and 3-D QSAR studies
Ragno, Rino; Anna, Minarini; Proia, Eleonora; Antonini, Lorenzo; Andrea, Milelli; Vincenzo, Tumiatti; Marco, Fiore; Fino, Pasquale; Rutigliano, Lavinia; Fioravanti, Rossella; Tahara, Tomoaki; Pacella, Elena; Greco, Antonio; Canettieri, Gianluca; Maria Luisa Di Paolo, ; Agostinelli, Enzo - 01a Articolo in rivista
paper: JOURNAL OF CHEMICAL INFORMATION AND MODELING (AMER CHEMICAL SOC, 1155 16TH ST, NW, WASHINGTON, USA, DC, 20036) pp. 3910-3927 - issn: 1549-9596 - wos: WOS:000844671100001 (0) - scopus: 2-s2.0-85136242905 (0)

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