2017 Design of Bioactive Molecules

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Academic unit or major
Graduate major in Life Science and Technology
Urabe Hirokazu  Kobayashi Yuichi  Nakamura Hiroyuki  Hata Takeshi 
Course component(s)
Day/Period(Room No.)
Mon3-4(J221,S223)  Thr3-4(J221,S223)  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
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Course description and aims

This course describes the manipulation of molecules having biological activity as advanced application or utility of organic chemistry, with reviewing its fundamental subjects or mentioning its relationship to bioscience and biotechnology. The contents include classification of bioactive molecules, the necessity and purpose of their investigation, and interpretation of pharmacological activity based on organic chemistry, which are then followed by the origin of naturally occurring products, their structural elucidation and synthesis, metabolism and the expression of activity of natural or artificial pharmaceutical drugs, basic chemical biology, design and chemical synthesis of medicines, basic medicinal chemistry, and the development and production of medicines. In the last four classes, an original research article(s) regarding the course topics is selected and studied, and subsequently it will be the subject of the final report.
In this course, students deepen their understanding in the advanced and various fields of organic chemistry and learn practical knowledge for the application and utility of organic compounds, by unifying the fundamental subjects (nature, analysis, reaction, synthesis, and use of organic compounds). Therefore, students can arrange important topics around organic chemistry, such as the origin of naturally occurring bioactive products and artificial pharmaceutical drugs, pharmacological activity, metabolism, design of molecules, the structure-activity relationship, chemical synthesis, and industrial production, from the general points of view even in conjunction with bioscience, biotechnology, or pharmacy. In the last four classes, students study the latest original research article(s) regarding the above topics to fulfill the aim of this course.

Student learning outcomes

By the end of this course, students will be able to:
1. Understand and explain the study on naturally occurring products
2. Understand and explain the metabolism of pharmaceutical drugs and their molecular modification (fundamental medicinal chemistry)
3. Understand and explain the structure-activity relationship of drugs (fundamental chemical biology)
4. Discuss synthetic organic reactions in a dependable way
5. Make appropriate synthetic plans of naturally occurring products and pharmaceutical drugs
6. Understand and explain the production from laboratory to industry (fundamental process chemistry)
7. Catch up the most recent trends in the design and synthesis of bioactive molecules


naturally occurring product, pharmaceutical drug, organic chemistry, organic synthesis, drug metabolism, structure-activity relationship, medicinal chemistry, chemical biology, process chemistry

Competencies that will be developed

Specialist skills Intercultural skills Communication skills Critical thinking skills Practical and/or problem-solving skills

Class flow

The instructor uses handouts that are distributed in the class. Students are given small exercise problems for the last 10 minutes of each class, and their solutions and remarks will be explained at the beginning of the next class. The 12th to 15th classes are allotted to the reading of the latest original research articles regarding the contents of this course and the students are requested to prepare the final report describing their interpretations and proposals along the above article(s).

Course schedule/Required learning

  Course schedule Required learning
Class 1 Introduction: The purpose and significance of design of bioactive molecules Understand and explain the purpose and significance of design of bioactive molecules from the standpoint of organic and pharmaceutical chemistry.
Class 2 Medicinal chemistry (Basic subjects of pharmacological activity) Understand and explain the fundamental way to handle molecules of pharmaceutical drugs regarding their functions and design.
Class 3 Synthesis of biologically active molecules (A survey) Understand and explain key points for designing synthesis of given targets.
Class 4 Synthesis of biologically active molecules (Effect of stereochemistry) Understand the importance of stereochemical synthesis and explain stereoselective reactions and methods.
Class 5 Synthesis of biologically active molecules (Role of functional groups) Understand and explain protection/deprotection of functional groups in synthesis of target molecules with several total syntheses.
Class 6 Drug metabolism (Classification of metabolic reactions) Understand and explain the important chemical reactions in drug metabolism that should be considered for pharmaceutical drug design.
Class 7 Drug metabolism (Hydrocarbons) Understand and explain the drug metabolism of hydrocarbons, especially typical drugs containing aromatic components.
Class 8 Drug metabolism (Compounds with functionalities) Understand and explain the drug metabolism of compounds with functionalities. In addition, understand the concept of prodrug and chemical biology in drug development.
Class 9 Design and synthesis of pharmaceutical drugs (Overview) Understand and explain biomolecules as targets of drug development, interactions between drug and target biomolecules, and bioactivities.
Class 10 Design and synthesis of pharmaceutical drugs (Structure-activity relationship) Understand and explain quantitative structure-activity relationship (QSAR), bioequivalence, and the drug design in consideration of the pharmacokinetics.
Class 11 Medicinal chemistry (Development and production of pharmaceutical drug) Understand and explain the manipulation of organic molecules for drug development.
Class 12 Reading of the latest research articles-1 (New synthetic methods) Learn the frontiers to develop new synthetic reactions, preferably satisfying an economical and environmentally benign way and exploit them to obtain designed bioactive compounds.
Class 13 Reading of the latest research articles-2 (Synthesis of naturally occurring products) Learn the frontiers to the synthesis of natural products such as lipid metabolites and alkaloids and enhance the skill in drug design.
Class 14 Reading of the latest research articles-3 (Pharmaceutical drug design) Learn the frontiers of drug design including recent development of drug delivery system (DDS) and cultivate practical skills of the drug design.
Class 15 Reading of the latest research articles-4 (Synthesis and bioassay of pharmaceutical drugs) Learn the frontiers of the drug synthesis including the relationship between structure and pharmacological action and acquire practical skills of the drug design.


Course materials are provided during class.

Reference books, course materials, etc.

If necessary, references are shown in class.

Assessment criteria and methods

Students will be assessed on the concise exercise problems in each class (40%) and the final four reports (60%). In the final reports, students’ unique interpretation and proposal to the article(s) studied in the class are welcome.

Related courses

  • LST.A402 : Organic and Bioorganic Chemistry

Prerequisites (i.e., required knowledge, skills, courses, etc.)

No prerequisites.

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