Ateneo - UPO

The course will cover several key sections and related contents to provide students with a comprehensive understanding of protein science and its applications. It will begin with an introductory leveling section where the basic principles and notions of proteins and enzymes, including their properties and functions, will be discussed. Following this, the course will present and discuss the basic principles of drug design and protein engineering on a rational basis. The physical-chemical methods for the study of protein-protein and protein-ligand molecular interactions will also be explored. Additionally, there will be a workshop focusing on DNA damage and repair, as well as protein-based antioxidants. The course will include seminars led by experts from companies engaged in the field of protein science applied to cosmetics. Moreover, the course aims to introduce students to the main principles of computer simulation of chemical entities, including compounds and proteins. Through these integrated sections, students will gain both theoretical knowledge and practical skills essential for simulating chemical-biological structures and understanding their interactions and applications in various fields.

Introduction to Protein Science: Architecture, Function, and Genomics by Arthur Lesk. Oxford 2015.
Biochemistry 10th edition by Jeremy M. Berg, John L. Tymoczko, Lubert Stryer. Macmillan 2023
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: The objective of the course is to enhance the students' knowledge of protein science, with a particular focus on the structure-activity relationship in biological macromolecules and the structural approach for the rational design of potential protein ligand molecules with therapeutic potential. Following an initial phase of consolidation on the fundamental concepts, the course will proceed to contextualize the basic principles of protein science in the cosmetic field, with a didactic path focused on select cosmetic-related topics, including antioxidant agents and DNA damage repair. Additionally, by the end of the course, students will have to know the main methods currently used in the simulation of systems of chemical-biological interest. 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 molecules (drugs, endogenous ligands) and macromolecules (proteins and nucleic acids).

2. Ability to apply knowledge: Students must be able to identify the most appropriate procedure to solve various chemical-biological problems proposed during the course. They should also be proficient in using basic modeling software to predict the three-dimensional structure of proteins and the drug-receptor association. This involves not only understanding the theoretical aspects but also applying practical skills to perform simulations and analyze results effectively.

Basic knowledge of general chemistry, organic chemistry, physics and biochemistry.

Lessons will be conducted ex-cathedra with the support of slides and video material, which will be provided to students at the beginning of the lessons. The classroom setting will be utilized for the execution of problems and quizzes, as well as for discussions on the data presented in the literature. General and specific topics will be introduced, and basic concepts will be provided to facilitate the understanding of each issue. Additionally, students may utilize the recommended textbooks to further explore the topics covered in the classroom. The topics covered in class will also be the subject of exercises and simulations through the use of complex molecular modeling programs, allowing students to apply their theoretical knowledge in a practical context.

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 final assessment consists of a multiple-choice test covering the theoretical parts of the protein module and the molecular modeling module, which accounts for 4/5 of the final grade. Additionally, students are required to submit a brief assay on the modeling part on the day of the exam, which accounts for 1/5 of the final grade.

See the general course information sheet.
Basic principles of protein science:
-Amino acids and proteins: chemical and structural properties
-Peptide bond and protein structure
Structural analysis techniques:
Structural biology: spectroscopic and diffractometric techniques for protein structure investigation
- Protein science and drug design: principles, examples and discussion of scientific publications
-Methods for the analysis of protein-protein and protein-ligand interactions:
- Isothermal titration calorimetry
- Surface plasmon resonance
- Microscale thermophoresis
Case studies “protein at work”:
DNA damage and repair
Oxidative stress and antioxidants
External expert’s seminar:
-Proteostasis
Intro to chemoinformatics. Handling compounds structural information. Public database for compounds.

Compound similarity. Ligand-based virtual screening.
Public database of proteins. Handling proteins structural information.
Protein-ligand interactions.
Pharmacophores. Structure-based virtual screening.

It is expected that the students will be able to argue and engage in discussions on the fundamental principles of the reactivity of biological macromolecules and the structure-function relationship of proteins. Additionally, students should demonstrate a comprehensive understanding of structure-based drug design. By the end of the course, students will have learned the fundamental aspects necessary to correctly simulate chemical-biological structures. They will be able to apply this knowledge to practical problems, showcasing their ability to utilize computational techniques and modeling software effectively.