COURSE DESCRIPTION AND APPLICATION INFORMATION
| Course Name | Code | Semester | T+A+L (hour/week) | Type (C / O) | Local Credit | ECTS |
|---|---|---|---|---|---|---|
| Pharmacophore Modeling | MBG 319 | Spring | 03+00+00 | Compulsory | 3 | 5 |
| Academic Unit: | Molecular Biology and Genetics |
| Mode of Delivery: | Face to face |
| Prerequisites: | None |
| Language of Instruction: | English |
| Level of Course Unit: | Undergraduate |
| Course Coordinator: | - - |
| Course Objectives: | To provide an overview of pharmacophore and pharmacophore modeling applications in drug discovery and ADME-tox. Two approaches will be studied such as structure based and ligand-based pharmacophore modeling. Also, some docking techniques and virtual screening will be introduced. Finally, to present BIOVIA Discovery Studio (DS) computer program for pharmacophore modeling and drug discovery. |
| Course Contents: | Overview of Ligand- Protein Interactions, Pharmacophore Modeling, Drug Discovery, Current Challenges in Pharmacophore Modeling, Structure Based Pharmacophore Modeling, Ligand Based Pharmacophore Modeling Software’s: Biovia discovery Studio, AutoDock, Virtual Screening |
| Learning Outcomes of the Course Unit (LO): |
|
| Planned Learning Activities and Teaching Methods: | One midterm exam, a final exam, project and Homework (Exercises) |
WEEKLY SUBJECTS AND RELATED PREPARATIONS
| Week | Subjects | Related Preperation |
|---|---|---|
| 1 | Overview of Pharmacophore Modeling | Reading the related chapter from textbook |
| 2 | What is Computer-Aided Drug Design | Reading the related chapter from textbook |
| 3 | Overview of Ligand-Protein Interactions | Reading the related chapter from textbook |
| 4 | Pharmacophore modeling in virtual screening | Reading the related chapter from textbook |
| 5 | Pharmacophore methods in docking simulations | Reading the related chapter from textbook |
| 6 | Applications of pharmacophores in ADME-tox | Study of the chapters covered in weeks 1 through 5 |
| 7 | Pharmacophore-guided drug target identification | Reading the related chapter from textbook |
| 8 | Introduction to software tool AutoDock | Installing AutoDock related programs on your personal computer |
| 9 | Introduction to BIVIA DS | Practical |
| 10 | Virtual Screening | Practical |
| 11 | Midterm Project | Practical |
| 12 | Future perspectives on pharmacophore modeling | Reading the related chapter from textbook |
| 13 | Fragment-based drug design | Reading the related chapter from textbook |
| 14 | Final Project | Study of the chapters covered in weeks 9 through 12 |
At Kadir Has University, a Semester is 14 weeks; The weeks 15 and 16 are reserved for final exams.
REQUIRED AND RECOMMENDED READING
| Pharmacophore modeling: advances, limitations, and current utility in drug discovery; Xiaoyu Qing, Xiao Yin Lee, Joren De Raeymaeker, Jeremy RH Tame, Kam YJ Zhang, Marc De Maeyer, Arnout RD Voet Pharmacophore Approaches In Drug Discovery; Thierry Langer ThreeDimensional Pharmacophore Modelling of Monoamine oxidase-A (MAO-A) inhibitors; Kalapatapu V.V.M. Sairam, Roop K. Khar, Rama Mukherjee and Swatantra K. Jain Synthesis, Structure–Activity Relationship, and Pharmacophore Modeling Studies of Pyrazole-3- Carbohydrazone Derivatives as Dipeptidyl Peptidase IV Inhibitors; Deyan Wu, Fangfang Jin, Weiqiang Lu 1, Jin Zhu, Cui Li, Wei Wang, Yun Tang, Hualiang Jiang, Jin Huang, Guixia Liu and Jian Li |
OTHER COURSE RESOURCES
| AutoDock Tutorial BIOVIA DS Tutorial |
ASSESSMENT METHODS AND CRITERIA
| Semester Requirements | Number | Percentage of Grade (%) |
|---|---|---|
| Attendance / Participation | 14 | 10 |
| Homework Assignments | 2 | 10 |
| Extra-Class Activities (reading, individual study etc.) | 5 | 20 |
| Midterms / Oral Exams / Quizes | 1 | 30 |
| Final Exam | 1 | 30 |
| Total: | 23 | 100 |
WORKLOAD
| Events | Count | Duration (Hours) | Total Workload (hour) |
|---|---|---|---|
| Course Hours | 14 | 3 | 42 |
| Homework Assigments | 5 | 6 | 30 |
| Extra-Class Activities (reading,individiual work, etc.) | 5 | 5 | 25 |
| Midterms / Oral Exams / Quizes | 1 | 10 | 10 |
| Final Exam | 1 | 18 | 18 |
| Total Workload (hour): | 125 | ||
1 ECTS = 25 Hours Workload
THE RELATIONSHIP BETWEEN COURSE LEARNING OUTCOMES (LO) AND PROGRAM QUALIFICATIONS (PQ)
| # | PQ1 | PQ2 | PQ3 | PQ4 | PQ5 | PQ6 | PQ7 | PQ8 | PQ9 | PQ10 | PQ11 | PQ12 | PQ13 |
| LO1 | |||||||||||||
| LO2 | |||||||||||||
| LO3 | |||||||||||||
| LO4 | |||||||||||||
| LO5 | |||||||||||||
| LO6 | |||||||||||||
| LO7 |
Contribution: 1 Low, 2 Average, 3 High