Print syllabusComputer-aided drug design
General data
| Course ID: | 1200-2CHMMO1W1 |
| Erasmus code / ISCED: |
13.3
|
| Course title: | Computer-aided drug design |
| Name in Polish: | Komputerowe wspomaganie projektowania leków |
| Organizational unit: | Faculty of Chemistry |
| Course groups: |
(in Polish) Moduł 1 Leki - od projektowania do wdrożenia (S2-PRK-CHM) |
| ECTS credit allocation (and other scores): |
1.50
|
| Language: | Polish |
| Main fields of studies for MISMaP: | biology |
| Type of course: | obligatory courses |
| Prerequisites: | Molecular modeling for drug design 1200-1CHMMOW6 |
| Prerequisites (description): | Knowledge of the basic methods of modeling and visualization of chemical and biological molecules. |
| Mode: | Blended learning |
| Short description: |
The lecture presents the assumptions and general characteristics of computer methods of drug design. Particular attention will be paid to molecular docking, including the use of large chemical databases, as the primary method used in drug design. |
| Full description: |
During the lecture, the assumptions of drug design methods and examples of their use will be discussed. To show a broader context of the application of these methods, a review of various molecular targets (proteins, DNA, RNA) with ligands/drugs will be made in order to compare their bioactive conformations, the role of individual interactions in the drug binding energy, the role of water molecules and the role of entropy in the drug binding process. A typical vHTS (virtual high-throughput screening) experiment and its individual components will be presented, i.e. molecular docking with an overview of algorithms and software, the use of chemical databases, comparison and evaluation of ligand-receptor conformation using various evaluation methods, confusion matrix, ROC curves, AUC and the enrichment factor. In addition, the machine learning methods in drug design will be presented, as well as the FEP (free energy perturbation) method for the accurate determination of differences in drug binding strength. Methods used in the absence of knowledge of the structure of molecular target, based on properties of ligands themselves (pharmacophore), design of peptide drugs and peptidomimetics, as well as the properties and design of antibodies will also be presented. |
| Bibliography: |
Recommended reading: Graham L. Patrick, “An introduction to medicinal chemistry”, Oxford University Press, 2009; or newer. |
| Learning outcomes: |
Knowledge: the student knows and understands the major methods used in drug design. He knows the limitations of individual methods in terms of their accuracy and speed. He uses his knowledge to select the appropriate methods, or their combinations, for the selected molecular targets. Skills: the student is able to formulate a research hypothesis, make a critical analysis of the results, and make conclusions based on them. Social competences: the student understands and appreciates the importance of intellectual honesty in own and other people's activities; can think and act in an entrepreneurial manner; is able to use the acquired knowledge in other, related fields. |
| Assessment methods and assessment criteria: |
Requirements related to participation in class - none. Permitted number of justified absences – 1 per 7 lectures. Test exam with about 50% of closed questions and 50% of open questions - the same for the correction test. Required minimum 50% of correct answers to pass. |
| Practical placement: |
N/A |
Classes in period "Summer semester 2023/24" (in progress)
| Time span: | 2024-02-19 - 2024-06-16 |
 
MO TU W WYK
TH FR |
| Type of class: |
Lecture, 15 hours
|
|
| Coordinators: | Sławomir Filipek | |
| Group instructors: | Sławomir Filipek | |
| Students list: | (inaccessible to you) | |
| Examination: | Examination |
Copyright by University of Warsaw.
