The aim of studying and bibliography

The main aim of study: The fundamental purpose is introducing the students to modern methods and computational tools used in drug designing.

The general information about the module: The module is implemented in the second semester: 15 hours of lectures and 30 hours of laboratory. Module ends with an credit

Teaching materials: Instrukcje do ćwiczeń laboratoryjnych dostępne ze strony domowej kkordynatora

Bibliography required to complete the module

Bibliography used during lectures

1	G.Patrick	Chemia leków.Krótkie wykłady	PWN.	2012
2	W. Kołos, J. Sadlej	Atom i cząsteczka	WNT Warszawa.	1998,
3	P. G. Higgs, T. K. Attwood	Bioinformatyka i ewolucja molekularna	PWN, Warszawa.	2008

Bibliography used during classes/laboratories/others

1

Tadeusz Pietryga

Instrukcje laboratoryjne

Katedra Chemii Fizycznej.

2013

Basic requirements in category knowledge/skills/social competences

Formal requirements: Registration for the semester

Basic requirements in category knowledge: General, physical and organic chemistry at a basic level

Basic requirements in category skills: Basic computer skills, the laws of chemical thermodynamics and chemical kinetics, the basics of protein structures.

Basic requirements in category social competences: Ability of the cooperation and the work in the group.

Module outcomes

MEK	The student who completed the module	Types of classes / teaching methods leading to achieving a given outcome of teaching	Methods of verifying every mentioned outcome of teaching	Relationships with KEK	Relationships with PRK
01	Has a basic knowledge of the methods of molecular modeling.	lecture, laboratory	written test, written report	K_W02++	P7S_WG
02	Is able to modeling simple chemical reactions and investigate ligand-receptor interactions.	laboratory	written test, performance monitoring	K_W02++ K_U15++	P7S_UW P7S_WG
03	Has a basic knowledge of homological analysis for drug design and modeling of protein structure.	lecture, laboratory	written test, written report	K_W02++ K_U15++	P7S_UW P7S_WG
04	Has a basic knowledge of biomolecular data bases, used for drug designing.	laboratory	written raport, performance monitoring	K_W02+ K_U15++	P7S_UW P7S_WG
05	Has a basic knowledge of usage of molecular docking in drug design.	lecture, laboratory	written test, written report, performance monitoring	K_W02+ K_U15+	P7S_UW P7S_WG
06	Has a basic knowledge of structure-activity relationships (QSAR) in drug designing.	lecture, laboratory	written test, written report	K_W02+ K_W08+ K_U15+	P7S_UW P7S_WG

Attention: Depending on the epidemic situation, verification of the achieved learning outcomes specified in the study program, in particular credits and examinations at the end of specific classes, can be implemented remotely (real-time meetings).

The syllabus of the module

Sem.	TK	The content	realized in	MEK
2	TK01	Main conceptions and areas of application of molecular modeling in drug design. Fundamentals of molecular modeling methods: molecular mechanics, molecular dynamics, Monte Carlo method. Molecular forces. Basics of molecular quantum mechanics: ab initio methods, semi-empirical methods, methods exploiting density functionals (DFT). Biomolecular geometry optimization. Biomolecular structure data bases (Protein Data Bank PDB, PDBe, PDBj), ligand data bases (PubChem, ZINC, BindingDB), enzyme data bases, others). Information downloading from biological data bases for drug designing. Elements of homological analysis in drug design. Basics of spatial protein structure modeling. Modeling of quantities describing physicochemical properties of biological and chemical systems for drug designing. Ligand conformation analysis in drug design. Application of molecular modeling methods in studies of biochemical system reactivities. study of thermodynamics and transition states of drug reactions. Molecular docking in drug design: docking methods, scored functions of assessment of ligand–receptor (i.e. drug-protein) interaction. Biomolecular modeling in the design of pharmacophores. Examination of structure-biological activity relation in drug design (2D-QSAR, 3D-QSAR, 4D-QSAR, 5D-QSAR, 6D-QSAR). Kinds of structural indexes and techniques of their calculation. CoMFA and CoMSIA methods in drug design.	W15	MEK01 MEK03 MEK04 MEK05 MEK06
2	TK02	1. Biomolecular structure data bases (Protein Data Bank PDB, PDBe, PDBj), ligand data bases (PubChem, ZINC, BindingDB), enzyme data bases, Entrez and ExPASy services, others). Information downloading from biological data bases for drug designing. 2. Visualization of the structure and physicochemical properties of biomolecules. Adjustment of protein and ligand structures in drug design processes. 3. Modeling of quantities describing physicochemical properties of biological and chemical systems. Conformational analysis of ligands in drug design. 4. Modeling of protein structure for drug design. 5. Modeling of chemical reaction (thermodynamics, transition states) using en example of a reaction of a drug with a specific receptor. 6. Calculation of QSAR descriptors. 7. Examination of structure-biological activity relationships (QSAR). 8. Molecular docking processes. Investigation of ligand-receptor (i.e. drug-protein) interaction. 9. Biomolecular modeling in the design of pharmacophores.	L30	MEK01 MEK02 MEK03 MEK04 MEK05 MEK06

The student's effort

The type of classes	The work before classes	The participation in classes	The work after classes
Lecture (sem. 2)		contact hours: 9.00 hours/sem.	complementing/reading through notes: 4.00 hours/sem. Studying the recommended bibliography: 15.00 hours/sem.
Laboratory (sem. 2)	The preparation for a test: 5.00 hours/sem.	contact hours: 18.00 hours/sem.	Finishing/Making the report: 5.00 hours/sem.
Advice (sem. 2)
Credit (sem. 2)	The preparation for a Credit: 30.00 hours/sem.	The written credit: 1.00 hours/sem.

The way of giving the component module grades and the final grade

The type of classes	The way of giving the final grade
Lecture	Written credit of lecture covering the entire range of material of lecture. Evaluation of the test depends on the number of points scored: 3,0 (50,0 %-60,0%) MP ; 3,5 (60,1%-70,0%) MP; 4,0 (70,1%-80,0%) MP; 4,5 (80,1%-90,0%) MP; 5,0 (90,1%-100%) MP. MP- max. points.
Laboratory	Correct performance of laboratory exercises included in the schedule and correct preparation of written reports on every exercise. Carrying out of a computational design (2-projekt team), submission of written report on the project and its positive evaluation (P). Laboratory grade (L): L = P
The final grade	Final grade (K): K = 0,50 * W * w + 0,50 * L * w; where: W, L - positive evaluation of the credit of lecture, laboratory; w - factor related to the time of credit or laboratory, w= 1.0 first term, w = 0.9 second term , w = 0.8 third term.The grade is rounded according to WKZJK.

Sample problems

Required during the exam/when receiving the credit
(-)

Realized during classes/laboratories/projects
(-)

Others
(-)

Can a student use any teaching aids during the exam/when receiving the credit : no

The contents of the module are associated with the research profile: yes

1	K. Rydel-Ciszek	DFT Studies of the Activity and Reactivity of Limonene in Comparison with Selected Monoterpenes	2024
2	P. Chmielarz; T. Pacześniak; K. Rydel-Ciszek; A. Sobkowiak	Bio-Inspired Iron Pentadentate Complexes as Dioxygen Activators in the Oxidation of Cyclohexene and Limonene	2023
3	K. Rydel-Ciszek	The most reactive iron and manganese complexes with N-pentadentate ligands for dioxygen activation—synthesis, characteristics, applications	2021
4	P. Chmielarz; A. Miłaczewska; T. Pacześniak; K. Rydel-Ciszek; A. Sobkowiak	‘Oxygen-Consuming Complexes’–Catalytic Effects of Iron–Salen Complexes with Dioxygen	2021
5	P. Błoniarz; P. Chmielarz; T. Pacześniak; K. Rydel-Ciszek; A. Sobkowiak; K. Surmacz; I. Zaborniak	Iron-Based Catalytically Active Complexes in Preparation of Functional Materials	2020