Description of Individual Course Units
Course Unit CodeCourse Unit TitleType of Course UnitYear of StudySemesterNumber of ECTS Credits
300003432007PHARMACEUTICAL CHEMISTRY ICompulsory356
Level of Course Unit
First Cycle and Second Cycle
Language of Instruction
Objectives of the Course
The purpose of the course is to study basic chemical properties leading to drug activity and examine biological process in terms of qualitative and quantitative aspects; introducing the chemical structures and chemical and phsicochemical properties of the drug groups in course content; to associate those properties with pharmaceutic, pharmacokinetic and pharmacodynamic process and general structure-activity properties; to teach synthesis methods used in industry and approaches of general synthetic methodology. The purpose of the practical course is to synthesize some drugs and drug intermediate molecules, to teach and experience choromatographic methods and the principles of general synthesis laboratory work.
Name of Lecturer(s)
Prof. Dr. Erçin ERCİYAS Assoc. Prof. Dr. Vildan ALPTÜZÜN Assist. Prof. Dr. Ayşe Hande Tarıkoğulları Doğan
Learning Outcomes
11. Being able to understand and interpret the chemical properties causing the pharmaceutical actvity and their relations with biological process.
22. Being able to understand the relations between the chemical structures of pharmaceutically active synthetic and semi-synthetic compounds with therapotic and adverse effects.
33. Capable of giving examples about drug design methodology and approaches.
44. Being able to understand the chemical structures, chemical and physicochemical properties of the synthetic and semi-synthetic (drug) active compounds.
55. Being able to name the synthetic and semisynthetic molecules’ structure according to the nomenclature rules.
66. Being able to understand the relations between pharmacokinetic properties with chemical structures of the synthetic and semisynthetic molecules used as drug active compound and use this knowledge during the treatment.
77. Being able to understand the relations between pharmacodynamic properties with chemical structures of the synthetic and semisynthetic molecules used as drug active compound and use this knowledge during the treatment.
88. Being able to evaluate the potentials of biological response of the molecules in terms of chemical structure and reactivity.
99. To be able to understand the general chemical structure leading to a pharmacological response and predict the structure activity relationship.
1010. Being able to understand and predict the drud-drug interactions by interrelating pharmacodynamic and pharmakokinetic concept with drugs’ chemical and physicochemical properties in biological systems.
1111. Being able to predict the chemical structures and the possible incompatibilities of activemolecules and excipients and use this knowledge in formulatin and treatment process.
1212. Capable of understanding the basic approaches regarding to the methods of obtaining pharmaceutical active molecules and excipiants and solving possible problems suring synthesis.
1313. Capable of understanding and applying the principles, techniques and instrumentation of chemistry lab for qualitative and quantitative analysis.
1414. Being able to understand the principles of (chemistry) synthesis laboratory and capable of using the knowledge when necessary.
Mode of Delivery
Face to Face
Prerequisites and co-requisities
Recommended Optional Programme Components
Being successful in organic chemistry course is recommended
Course Contents
Medicinal Chemistry and metabolism (Quantitative structure-activity relationship, bioisosterism, receptors and drug-receptor interactions, metabolism), Autonomic central nervous system drugs (drugs affecting parasympathetic nervous system, drugs affecting sympathetic nervous system, antiparkinson drugs), Cardiovascular system drugs (Cardiotonics) After 2 demonstrative courses, the synthesis of the compounds written below are performed. After synthesis practices one chomatography practice is performed. Iyodoform, α-nitronaftalene / o-nitrophenol, Benzoin / Benzoik acid, Phenylazo-β-naphtol / Diazoaminobenzene, Phenotiyazin / Kinon, 2-Methyl-1H-benzimidazole, Partition coeficient
Weekly Detailed Course Contents
11. Introduction to Medicinal Chemistry 2. Methods for identifying new lead compounds Laboratory safety and first aid information
23. New Drug Development Process 4. İlaç etkisinin oluşumuna kadar gerçekleşen ana işlemler 4.1. Pharmaceutical stage Principles and methods of working in synthesis laboratory
3 4.2. Pharmacokinetic stage 4.2.1. Blood- brain barrier 4.2.2. Quantitative structure-activity relationship (QSAR) History Method Principles and methods of working in synthesis laboratory
4 Hydrophobic parameters Partition coefficient Ferguson equation Hansch Aromatic substituent constants loaning the equipment and Pre working of one of the purification techniques; christalization
5 Electronic parameters Hammet substituent constants Steric parameters Pre working of one of the purification techniques; christalization
6 Hansch Analysis Topliss approach The degree of ionization The solubility of organic compounds Organic compound synthesis
7 4.3. Metabolism 4.3.1. Importance of metabolism ın drug development studies 4.3.2. Phase I reactions- biotransformation 4.3.3. Phase I reactions -Kongugation Organic compound synthesis
8Midterm exam
9 4.4. Prodrugs 4.4.1. Reasons for preparing pro-drug 4.4.2. Bioprecursor prodrugs 4.4.3. Carrier prodrugs 4.4.4. Salt forms of prodrug 4.4.5. Hard and Soft drugs 4.5.3. Bioisosterism Classical bioisosterism Non- classic bioisosterism Organic compound synthesis
104.6. Pharmacodynamic phase: 4.6. 1Description and general information Bonds involved in drug-receptor interaction bonds: - Description and general information - Mechanisms of the formation of covalent bond - Alkylation - Acylation - Phosphorylation - Examples of drugs that form covalent bonds İonic bonds: - Description and general information Organic compound synthesis bonds 4.6.2 Known types of interaction between receptor and drug İon-dipole and dipole dipole interactions Charge transfer complexs Hydrophobic interaction 4.6.2..4 Van der waals forces 4.6.3 Examples Organic compound synthesis
12d- 4.6.4 Importance of stereochemistry in drug receptor interactions (stereoisomerism, optical isomer, geometrical isomer, etc.) Importance of optical isomerism in drug receptor interactions Importance of geometrical isomerism in drug receptor interactions of conformational isomerism in drug receptor interactions Examples of importance of stereochemistry in drug receptor interactions ratio 4.6.5 Drug-receptor theories theory theory Induced Adaptation theory differentiation theory Allosteric modulation Activation-agregation theory Organic compound synthesis
135. Introduction to Computer Aided Drug Design 5.1General information 5.1.1Description 5.1.2Computer aided chemistry 5.1.3Aim of the rational drug design 5.1.4Advantages of computer aided drug design 5.2Determination of molecular 3D structures 5.2.1X-ray diffraction - Description and general information - History 5.2.2Protein crystallography 5.2.3X-ray crystallography 5.3Homology modelling 5.3.1Protein structure - Primer structure - Seconder structure - Tertiary structure - Quaterner structure Organic compound synthesis
145.3.2 Homology modeling - Description of homolog proteins - Reasons of homology modelling applications - Application tecniques 6. Structure based computer aided drug design 6.1Description 6.2Docking 6.2.1Description and general information 6.2.2Advantages 6.2.3Docking tecniques and applications - Preparation of protein - Preperation of ligand - Components of docking programmes Organic compound synthesis
15 5.3.4 Advantages 5.3.5Difficulties of docking 5.3.6Examples 5.4 Molecular dynamic simulations 5.4.1Description and general information 5.4.2 Aims and basis of molecular Dynamics 5.4.3Application types 5.4.4Example simulations Chromotagraphic purification study
Recommended or Required Reading
1.Farmasötik Kimya I Ders Notları (Medisinal Kimyaya Giriş), Prof. Dr. Erçin Erciyas, İzmir, 2010 2.İlaçların Tanınması ve Kantitatif Tayini, Prof. Dr. Nedime Ergenç, Prof. Dr. Aysel Gürsoy, Prof. Dr. Öznur Ateş, İstanbul Üniversitesi Yayınları, İstanbul, 1966. 3.Türkiyede Üretilen İlaç Etken Maddeleri, Prof. Dr. Nedime Ergenç, Prof. Dr. Serpil Salman, Prof. Dr. Aydın Salman, İstanbul Üniversitesi Yayınları, İstanbul, 1992. 4.İlaçların Metabolizması (Biyotransformasyon), Prof. Dr. Sevim Rollas, Marmara Üniversitesi Yayınları, İstanbul, 1992. 5.Farmasötik Kimya Ders Kitabı Cilt I (Medisinal Kimya), Prof. Dr. Nedime Ergenç, Prof. Dr. Aysel Gürsoy, Prof. Dr. Öznur Ateş, İstanbul Üniversitesi Yayınları, İstanbul, 1997. 6.Farmasötik Kimya Cilt I, Prof. Dr. Hakkı Erdoğan ve arkadaşları, Irmak Matbaası, Ankara, 2000. 7.Farmasötik Kimya Cilt II, Prof. Dr. Hakkı Erdoğan ve arkadaşları,Irmak Matbaası, Ankara, 2000. 8.Farmasötik Kimya Prof. Dr. Hakkı Erdoğan ve arkadaşları, Hacettepe Üniversitesi Yayınları, Ankara, 2004.
Planned Learning Activities and Teaching Methods
Activities are given in detail in the section of "Assessment Methods and Criteria" and "Workload Calculation"
Assessment Methods and Criteria
Term (or Year) Learning ActivitiesQuantityWeight
Midterm Examination1100
End Of Term (or Year) Learning ActivitiesQuantityWeight
Final Sınavı1100
Term (or Year) Learning Activities40
End Of Term (or Year) Learning Activities60
Work Placement(s)
Workload Calculation
ActivitiesNumberTime (hours)Total Work Load (hours)
Midterm Examination111
Final Examination122
Attending Lectures14342
Self Study14228
Individual Study for Mid term Examination12525
Individual Study for Final Examination13030
Contribution of Learning Outcomes to Programme Outcomes
LO1      5      4       
LO2 5          44 3 2   
LO3 3     35          43
LO4 4    5     3 2      
LO5 2    4             4
LO6 3          55       
LO7 3          55       
LO8      55             
LO9       55            
LO10            55 2     
LO11            55 2 3   
LO12        5 4       4  
LO13          5       5 4
LO14          5       5 4
* Contribution Level : 1 Very low 2 Low 3 Medium 4 High 5 Very High
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