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Title: Application of Medicinal Chemistry Methods on Different Classes of Drugs
Keywords: Drug Design
Mobility Shift Assay
Molecular Modeling
Molecular Docking
Issue Date: 27-Jan-2014
Abstract: The present doctoral thesis is the result of the work carried out during the three years of my PhD scholarship at the Rome Center for Molecular Design laboratory (RCMD, Department of Chemistry and Drug Technologies, Sapienza University of Rome), under the supervision of Prof. Rino Ragno. The research activity was focused mainly on the design, optimization and application of computational strategies to derive quantitative structure-activity relationships (QSAR, 3-D QSAR, and COMBINE) on different molecular classes of current interest, such as: opioid receptor antagonists (OPAs), Hepatitis C Virus NS5B-Polymerase Inhibitors (NS5B-NNIs), Hystone Deacetylase Inhibitors (HDACIs), Anti- tubercular agents, vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors, HSP90 inhibitors, HIV-1 reverse transcriptase inhibitors (NNRTIs), Bovine Serum Amine Oxidase (BSAO) substrates, etc... Moreover two research periods abroad were performed: the first framed in a LLP Erasmus program collaboration, was conducted for six months at the Laboratoire d'Ingénierie et Moléculaire Pharmacologique Biochimie (LIMBP) of the Université de Lorraine Metz (France), directed by Prof. Gilbert Kirsch, and characterized by the application of organic synthesis to obtain new thienopyrimidinone derivatives as potential inhibitors of vascular endothelial growth factor receptor-2 (VEGFR-2); the second took place, for three months, at the Department of Biochemistry and Molecular Biophysics in Washington University School of Medicine in Saint Louis (MO, USA), under the supervision of Prof. Garland R. Marshall, investigating the activity profile of new Histone Deacetylases (HDACs) inhibitors by the application of the Mobility Shift Assay Technology. Main purpose of this doctoral thesis is to highlight the activities carried out in the different research projects, the applied methodologies and the obtained results. The text starts describing those studies whose results were published in scientific journals (chapters I-VI): the author decided to omit some procedural details, completely reported in the published papers, that would make the text too long, tedious and redundant; therefore readers who want to delve these aspects can also refer to Chapter XII in which is possible to read the original papers; on the contrary for studies that have not yet been published, as those characterizing the Chapters VII and VIII, discussion is adequately detailed. Chapters IX and X report the scientific activities carried out in France and in USA respectively; Chapter XI summarizes all the scientific activities accomplished during the entire PhD course, whereas Chapter XII, as mentioned, contains the published articles.
Research interests: The research of Dr. Flavio Ballante is addressed to: 1) the development, validation and application of new computational procedures that allow to derive quantitative structure-activity relationships (i.e. 3-D QSAutogrid/R and COMBINEr procedures); 2) the design, optimization and synthesis of bioactive compounds; 3) determination of biological activity by the application of the Mobility Shift Assay Technology. His studies are mainly directed to: HDAC inhibitors, HIV-RT inhibitors, D3DAR antagonists, VEGFR-2 inhibitors, substrates of amino oxidases (BSAO), anti-tubercular and antiparasitic agents, D3DAR antagonists, HSP90 inhibitors, hepatitis C virus NS5B polymerase inhibitors.
Personal skills keywords: Medicinal Chemistry
QSAR, 3-D QSAR, R CRAN, Bash Scripting, Python, Multivariate Analysis
Organic Synthesis
Electrophoretic Mobility Shift Assay
Drug Design

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