The course consists of 8 lectures, presented below:

1. Introduction: Bacterial resistance – A global perspective.
2. Extended-spectrum beta-lactamases. Structural analysis of CTX-M.
3. Introduction to nucleotide and amino acid bioinformatics analysis.
4. Protein visualization based on PyMOL.
5. Homology modeling based on SWISS-MODEL and MODELLER.
6. Evaluation of models based on Verify3D and PROCHECK.
7. Theoretical basis of Molecular Docking.
8. Molecular docking using AutoDock Vina.

Content

1. Introduction: Bacterial resistance – A global perspective.

Teaching: Edgar Gonzales Escalante

 The class will present an updated global perspective on bacterial resistance with an emphasis on the epidemiology of bacterial resistance in Peru.

2. Extended-spectrum beta-lactamases. Structural analysis of CTX-M.

Teaching: Pablo Power

The class will review the main extended-spectrum beta-lactamases (ESBLs), focusing primarily on CTX-M type ESBLs, and will present an analysis of their structure using the bioinformatics programs that will be analyzed in the following classes.

3. Introduction to nucleotide and amino acid bioinformatics analysis.

Teaching: Guillermo Uceda Campos

This session will teach participants how to perform a bioinformatics analysis based on a previously sequenced CTX-M sequence in its raw state. Participants will also learn how to perform electropherogram analysis using Chromas. Finally, various data analyses will be conducted using BLAST and UNIPROT to expand their understanding of the sequence of interest.

4. Protein visualization based on PyMOL.

Teaching: Juan Faya Castillo

The session will focus on exploring the RCSB database and analyzing the information recorded in the PDB. Following this, students will be taught how to use the PyMOL program, which will enable them to perform three-dimensional structural analyses of proteins.

5. Homology modeling based on SWISS-MODEL and MODELLER.

Teaching: Juan Faya Castillo

This topic will cover theoretical concepts of the predictive technique for protein homology modeling, as well as the step-by-step process for obtaining an atomic structure based on known structures stored in specialized databases (RSCB). Two different strategies using the SWISS-MODEL and MODELLER programs will be presented.

6. Evaluation of models based on Verify3D and PROCHECK.

Teaching: Diego Leonardo Cabrejos

The session will focus on evaluating protein structures obtained using techniques in silico. In addition, the importance of this procedure and the different concepts on which these methods are based will be explained.

7. Theoretical basis of Molecular Docking.

Teaching: Diego Leonardo Cabrejos

This class will explain in detail the theoretical basis behind the computational technique of molecular docking; as well as the use of docking algorithms for predicting binding between ligands and receptors.

8. Molecular docking using AutoDock Vina.

Teaching: Pablo Power

In this final topic, the student will learn to prepare both the protein and ligand of interest for molecular docking using the AutoDock Tools and AutoDock Vina programs, respectively. AutoDock Vina is an open-source program for drug discovery., molecular docking and virtual screening, which features compatibility with input and output files used in AutoDock Tools, is easy to use and achieves significant improvements in the average accuracy of predictions.

Methodological strategies:

• Virtual classroom

Pre-recorded videos of the instructors' presentations will be shown in the days leading up to the synchronous session. During the synchronous session, questions from participants will be addressed by an instructor. Questions must be submitted beforehand in the course forum.

The recorded sessions will begin with an introduction to the specific topics to be covered, followed by a review of the theoretical foundations of the points initially mentioned, accompanied by real-world examples demonstrating the application of the concepts to be developed. Afterward, you will receive recordings explaining the operation of the bioinformatics program to be used in each class.

The teaching methods will focus on the visualization of bioinformatics programs, according to the session, graphics and annotations on the virtual whiteboard and, in an auxiliary way, projected slides (the latter, preferably for complex drawings, videos or graphics).