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    Michele SAVIANO


    Corso di laurea magistrale in MOLECULAR BIOTECHNOLOGY

    SSD: CHIM/08

    CFU: 6,00


    Periodo di Erogazione: Primo Semestre


    Lingua di insegnamento



    Teaching language



    Structural biology of pharmacological targets and their ligands (Experimental versus computation approaches);
    Properties of protein structures;
    Rational Design of bioactive molecules;
    Ligand-protein interactions;
    Structure-based drug discovery;
    Ligand-based drug discovery;
    Fragment-based drug discovery;
    Molecular recognition in biomolecules
    Biomolecules as Drug;
    The word of Peptide and its analogues for Drug Design;
    Secondary structure in protein and in peptide
    Molecular Recognition: the structural and chemical physics basis;
    Drugs the function in biological systems;
    The Drug Design;
    Molecular Tools for design of peptides: Examples: Helix Design, Protein Structure, Prediction and its application to thermostable proteins, Design of selective bioactive

    Textbook and course materials

    Bibliography provided by the teacher

    Course objectives

    The aim of this course is to introduce the theory and practice for the design of bioactive compounds using different theoretical and experimental techniques of Structural Chemistry and Biology (X-ray diffraction, NMR spectroscopy, Computational techniques). At the end of the course,the student knows the chemical basis of the structure and structural and functional properties of natural and synthetic peptide systems and is able to understand the logic that governs their design to perform specific biological functions. It is able to find information on the structure of peptide systems and complexes with proteins and nucleic acids in databases and to analyze their spatial structure. Understands the importance, through specific examples, of knowledge of peptide chemistry in application fields such as diagnostics and pharmaceuticals.


    No propaedeutic
    Basic knowledge of Inorganic and Organic Chemistry, Mathematics, Physics, Biochemistry and Biology.

    Teaching methods

    The attendance to the lessons is mandatory. The module is organized in 48 hours of frontal lessons that will be theoretical and practical.

    Evaluation methods

    The final examination will consist in an oral interview, aimed to verify the notions acquired and the ability of the student to re-elaborate the contents presented during the lessons. In particular, these oral examinations are aimed to evaluate the capability of reasoning and connecting the various topics of the course. They will consist of questions about the theoretical part of the course with the twofold scope of evaluating (a) the knowledge of the treated subjects and (b) the capability to expose and connect the diverse topics.

    Other information

    During the course slides and notes of the lectures will be provided to the students via Teams.
    Each Professor is available for student reception during the office hours as reported in the course sheet or upon e-mail request.

    Course Syllabus

    - Structural Biology of targets and ligands-
    The state of the art, Experimental approaches (X-ray crystallography, Electron microscopy) Computational approaches (Protein structure prediction methods, AlphaFold revolution, Molecular dynamics simulations) , Structure validation, Successful examples (he ribosome machinery and the DNA structure)
    - Rational Design of bioactive molecules,
    Properties of protein structures, Ligand-protein interactions, Structure-based drug discovery, Ligand-based drug discovery, Fragment-based drug discovery, Classical and recent successful examples of rational drug design

    - The Peptides. Nomenclature. Non-natural amino acids. Permitted conformations. Ramachandran maps of natural and non-natural amino acids. Characteristics of the peptide bond. Acidity and basicity in peptides, calculation of the isoelectric point.
    -Characterization of peptides. Secondary structure. Turn.. Prediction of the three-dimensional structure using computational techniques. Solid state studies using diffraction and IR techniques. Characterization in solution with circular dichroism, NMR, IR and fluorescence techniques
    - Peptides as drugs and diagnostics: Principles of Drug Design, The design of peptide drugs. Examples of applications in diagnosis and therapy
    - Databases for peptide structures and complexes with proteins and DNA: Protein Data Bank and CCSD.
    - Molecular Tools for design of peptides: Examples: Helix Design, Protein Structure, Prediction and its application to thermostable proteins, Design of selective bioactive molecules for therapeutic applications.

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