Ateneo - UPO

The aim of the course is to introduce the student to the main principles about computer simulation of chemical entities (compounds, proteins).

Andreas Kukol, "Molecular Modeling of Proteins", English | 2014 | ISBN: 1493914642. https://link.springer.com/book/10.1007/978-1-4939-1465-4

Nathan Brown, "In Silico Medicinal Chemistry: Computational Methods to Support Drug Design", English | 2015 | ISBN: 978-1-78262-163-8. https://pubs.rsc.org/en/content/ebook/978-1-78262-163-8

1. Knowledge. At the end of the course students will have to know the main methods currently used in the simulation of systems of chemical-biological interest. In particular, they must be aware of the main computational techniques useful both for the calculation of energies and molecular geometries, and for the conformational analysis of small (drugs, endogenous ligands) and macromolecules (proteins and nucleic acids).

2. Ability to apply knowledge. The student must be able to identify the most appropriate procedure to solve some chemical-biological problems that will be proposed during the course. He must also be able to use some basic modeling software to predict the three-dimensional protein structure and the drug-receptor association.

None

The course is given with the support of slides, which are given to the students at the beginning of the lessons.
General and specific topics will be introduced, basic concepts will be provided for the understanding of each issue, and discussions with the students will be held. A forum section on the course page on D.I.R. (http://www.dir.uniupo.it) will help the discussions. The topics covered in class will be the subject of exercises/simulations through the use of complex molecular modeling programs.

For further informations, please refer to the course page on D.I.R. at: http://www.dir.uniupo.it

Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities

Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

The exam consists of an oral on the topics covered in class.
The first question may be a short presentation of a case-study prepared previously where the student will have to demonstrate knowledge of principles and methods (theory and practice) of the modeling methodologies as well as having acquired basic knowledge on the methods for the presivione of the protein structure and drug-receptor interactions.

Methods for calculating geometry and molecular energy: Molecular Mechanics. Quantomechanical methods (semi-empirical and ab initio, DFT methods). Mixed Quantum Mechanics / Molecular Mechanics methods for the study of large molecular and supramolecular systems. Use of electron density and electrostatic potential (MEP) for the study of similarity and for molecular recognition.
Molecular simulation methods: Introduction to the problem of simulating molecules of chemical-biological interest. Molecular dynamics: coarse grained and atomistic methods. Solvation methods. Some examples: solvation of amino acids and study of a protein in solution.
Conformational analysis for molecules of biological interest: Systematic methods and statistical methods (Monte Carlo). The problem of conformational analysis for systems with a high number of degrees of freedom.
Applications of the methods: Modeling of molecules of biological interest - introduction to drug design: computational methods applied to biomolecules: Determination of the 3D structure of peptides and proteins (ab initio methods, Homology modeling and folding recognition). Applications to modeling and design of peptidomimetics. The design of a drug. Molecular similarity. Oligonucleotides and single and double strand nucleic acids and the hydrogen bridge bond.
Simulations of peptides and proteins in lipid bilayers: state of the art and application examples. Bibliographic research and how to solve a case study.

At the end of the course the student will have learned the fundamental aspects necessary to correctly simulate the chemical-biological structures.