Course syllabus for Chemistry 162A / 262A Drug Design (Fall 2009) Class meets: Mon, Wed, Fri 11:00 – 11:50 AM Phelps 3505 Instructor: Professor Kalju Kahn, Office: PSB-N 2623 E-mail: [email protected] Phone: (805) 893-6157 Office Hours: Tue 12:30-1:30 and Thu 12:30-1:30 or by appointment Course website: http://www.chem.ucsb.edu/~kalju/chem162 Teaching Assistant: Robert Levenson, Office Chem 1317 Lecture Textbook: Richard B. Silverman, The Organic Chemistry of Drug Design and Drug Action, 2nd edition The Course: In Chem 162 students learn principles that govern the process of modern drug discovery and development. Students will follow a path similar to that taken by real-life drug developers by learning important elements of the drug design process in a logical order. Some topics that we focus more extensively in 162A are:  Target identification and validation  Receptor mechanisms and receptor targeting  Chemical libraries and screening  Ligand-based drug design Expectations of Students:  Attendance and taking good lecture notes is expected. Submitting completed assignments in time is required.  The textbook provides some necessary background material. Furthermore, students are expected to read modern drug design-related research literature. Required literature will be available on the course website.  Honesty and academic integrity must be always preserved. While discussing your ideas with others is encouraged outside the classroom, you must answer the assignment questions individually. No supplemental material should be used during an exam.  Your grade in the course is based on points you collect from the weekly assignments (10 points each), the mid-term (40 points), the final exam (50 points), and the written research proposal (50 points). Grading will be based on the curve but you have to meet a certain level to get a grade higher than F.  The course requires that you have a solid understanding of basic biology and organic chemistry; good background in biochemistry and physical chemistry will be very helpful.  No student shall give, sell, or otherwise distribute to others or publish any electronically available course materials or recordings made during any course presentation without the written consent of the instructor. Study tips:  I am posting lecture note slides on-line before the class meets so that you can focus on following my talk. The slides are mainly illustrative and you need to follow the lecture in order to fully understand the topics I cover.  Come in class prepared. Read the relevant textbook material and required reading before the class meets. I like to interact with students during our meetings and you enjoy the lectures more if you can think along.  Review (or rewrite) your class notes the same day and supplement them with material from the textbook and other resources (optional reading, Internet). Ask for help if something remains unclear.  This course is not about memorization of names, reactions, or facts. It is about understanding the process, its principles and methods. You should demonstrate good understanding of the material when answering assignment questions and the exam problems. Your creativity and originality are highly important for getting a high score in the final written proposal. Good luck! — KaljuChem162/262 Schedule for the Winter 2009 Sep 25th F Overview and history of drug design Sep 27th M Rational drug design: overview of approaches Sep 30th W Current trends and future of drug design. Diseases. Oct 2nd F Target Identification and Validation: Principles Oct 5th M Target Validation: Pre-genomic methods Oct 7th W Target Validation: Post-genomic methods First assignment due Oct 9th F Tutorial in SGI lab (Chem 1153): Target identification from microarray data Oct 12th M Enzymes as drug targets Oct 14th W Receptors as drug targets: Overview of biosignaling Second assignment due Oct 16th F Receptors as drug targets: Ion channels Oct 19th M Receptors as drug targets: G-protein coupled receptors Oct 21st W Experimental characterization of membrane-bound receptors Third assignment due Oct 23rd F Nuclear hormone receptors Oct 26th M Midterm Exam Oct 28th W Combinatorial chemistry Oct 30th F Chemical libraries Nov 2nd M Principles of assay development Fourth assignment due Nov 4th W High-throughput screening for lead identification Nov 6th M General strategies for lead optimization Nov 9th M Ligand-based drug design and optimization Fifth assignment due Nov 11th W Veteran’s day Nov 13th F Tutorial in SGI lab (Chem 1153): Ligand building and modeling Nov 16th M Ligand-based drug design and optimization Nov 18th W Fragment-based drug design and optimization Sixth assignment due Nov 20th F QSAR: Overview Nov 23th M QSAR: Technical Details Nov 25th W Tutorial: Practical QSAR: tutorial in the SGI lab (Chem 1153) Analysis Nov 27th F Thanksgiving Holiday Nov 30th M Comparative Molecular Field Analysis Dec 2nd W Nucleic Acid Drugs Dec 4th F Course Review and Evaluation Written draft proposals due Assignments (will be posted on Wednesday one week before the due date) 1. Diseases and targets 2. Target validation 3. Receptors: general features 4. Assay development and library design 5. Pharmacophores and molecular similarity 6. Molecular properties, ligand-based