Chem 162/262
Drug Design
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Chem 162/262 |
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Dr. Kalju Kahn
Office: PSB-N 1511
Office hours: Tue 11:00-12:00, and Thu 11:00-12:00 PM
Phone: 893-6157
E-mail: kalju@chem.ucsb.edu
Website: http;//www.chem.ucsb.edu
To teach principles that govern the process of modern drug discovery and development. Students in the course 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.
The Drug Design course taught in Fall 2005 will differ significantly from the course that was taught in Winter 2005. The Fall 2005 course will focus on fewer topics but will go more in depth and offer more hands-on work on structure-based drug discovery. The remainder of topics will be covered in "Chem 162B" course in the Winter 2006. The instructors hope that this expansion facilitates the exploration of different aspects of the drug discovery process and gives students more time and tools to work on their "Drug Discovery Course Project". The Fall and Winter Quarter Drug Design courses in 2005-2006 academic year will be team-taught by Dr. Kalju Kahn and Norbert Reich.
Lecture: MWF 12:00-12:50 Place: Phelps 1440
Computer Lab: Open day access Place: Chem 1153
| Syllabus | General information about the course. | |
| Chem 162B | Tentative list of topics that will be covered in Winter 2005 Drug Design course. | |
| Textbook | The Organic Chemistry of Drug Design and Drug Action by Richard B. Silverman (Second Edition) | Amazon |
| Sample Lecture | Target Validation. (No Password Needed) Warning: Large File | PDF WAV |
| Last Years | Drug Design (by Dr. Kalju Kahn) website for Winter 2005 | Link |
| Last Years | Drug Design (by Dr. Kalju Kahn) website for Spring 2004 | Link |
| Last Years | Drug Design (by Dr. Norbert Reich) website for Spring 2003 | Link |
| Upload | Submit your assignments as MS Word or PDF files | Link |
| Exam | Midterm Preparation Guide | |
| Exam | Final Preparation Guide | |
| Exam Sample I | Sample questions with answers from Spring 2004 | |
| Exam Key | Brief Key for selected Questions (F 2005) | No PDF |
| Statistics | Grade Distribution for Fall 2005 | Image |
| Poster Session | Some pictures from 2005 Student Poster Session | Link |
Course notes will be posted here before 7:30 a.m. of the lecture day. See last year's site for old audio files. The lecture slides are password-protected. Contact your instructor to obtain the password.
| Notes | Lecture Notes. Powerpoint Pages in PDF | Acrobat |
| Sep 23-Sep 26 | Overview of the course. History of drug design | |
| Sep 28-Sep 30 | Current trends and future of drug design. Diseases. | |
| Oct 3 | Target Validation: Principles | |
| Oct 5 | Target Validation: Pre-Genomic Methods | |
| Oct 7 | Target Validation: Post-Genomic Methods | |
| Oct 14 | Enzymes as Drug Targets | |
| Oct 17 | Receptors as Drug Targets | |
| Oct 19 | Pharmacokinetics | |
| Oct 21 | Drug Design Software Tutorial | Link |
| Oct 26 | Enzyme Mechanisms | |
| Oct 28 | Enzyme Mechanisms and Kinetics | |
| Nov 2 | Enzyme Inhibition and Inactivation | |
| Nov 7 | Study of Membrane Receptors | |
| Nov 9 | Cell-based Assays: Lead Identification; Molecular Interactions | |
| Nov 15 | Structure-Based Drug Design: Principles | |
| Nov 18 | Structure-Based Drug Design: Energy Evaluation | |
| Nov 18 | Structure-Based Drug Design: Molecular Simulations | |
| Nov 23 | Structure-Based Drug Design: Visualization | |
| Nov 23 | Structure-Based Drug Design: Docking |
| Literature | Required reading in PDF | Acrobat |
| General | From Serendipity to Rational Drug Design | |
| History | Drug Discovery: A Historical Perspective | |
| Future | Drug Research: Myths, Hype and Reality | |
| Future | Cell-based uHTS Chemical Genomic Drug Discovery | |
| Validation | Drug Discovery in the Post-Genomic Era | |
| Validation | DNA Microarrays | |
| Validation | mRNA Knockdown: Antisense, Ribozymes, RNAi | |
| Validation | Proteomics: Proteins Rule | |
| Targets | Protein Kinases as Drug Targets | |
| Targets | Acetylcholine Receptors as Drug Targets | |
| ADME | Predicting Pharmacokinetics | |
| Enzymes | Enzyme Mechanisms: Transition State Binding | |
| Leads | HIV Protease Inhibitors | |
| Leads | Cell-based assay for farnesyl:protein transferase inhibitors | |
| SBDD | The Process of Structure-Based Drug Design | |
| SBDD | The Many Roles of Computation in Drug Discovery | |
| SBDD | High-throughput docking | |
| SBDD | Nicotinic Acetylcholine Receptor: Docking |
Suggested literature can be found now on a separate page
The assignments are posted one week before the due date. Answers shall be submitted electronically no later than the midnight of the due date.
| Assignments | PDF files | Acrobat |
| 1 | Molecular Mechanisms of Diseases. General Principles of Drug Design | |
| 2 | Target Validation Exercise | |
| 3 | Target Validation Techniques | |
| 4 | Enzymes: Mechanism, Kinetics and Inhibition | |
| 5 | Assay Development; Biomolecular Interactions | |
| 6 | Structure-Based Drug Design |
The assignment keys are typically posted one week after the due date.
| Keys | PDF files | Acrobat |
| 1 | Molecular Mechanisms of Diseases. General Principles of Drug Design | |
| 2 | Target Validation Excercise | |
| 3 | Target Validation Techniques | |
| 4 | Enzymes: Mechanism and Inhibition | |
| 5 | Assay Development; Interactions and Thermodynamics | |
| 6 | Structure-Based Drug Design |
The project milestone guides are typically posted two weeks before they are due.
| Project Tips | General Guidelines to Project Development | |
| 1 | Disease selection and Characterization | |
| 2 | Target Validation | |
| 3 | Identification of lead compounds | |
| 4 | Lead characterization |
Students in this course encounter many terms which have specific meaning in the context of drug design and medicine. You may find our glossary helpful when reading some of the assigned papers. If you encounter a term that is not in this dictionary, you could try a specialized medicinal chemistry glossary at www.chem.qmw.ac.uk/iupac/medchem ,an on-line dictionary at www.dictionary.com or an on-line encyclopedia at www.wikipedia.com . Feel free to send any additions and suggestions to Kalju Kahn
PyMOL Home Page
Biomolecular Images for Teaching with PyMOL
SYBYL Tutorial
Short List of Programs
Modern Drug Discovery
Nature Reviews Drug Discovery
Drug Discovery and Development
Drug Design Lecture Notes by Dr. Hugo Kubinyi
Oxford Drug Resistance Group Lectures
Basic Pharmacokinetics
Calcium Channel Blockers
Brain Chemistry
Acetylcholine Receptor
Online Video-Lectures
Dr. Andrew Boa lecture notes
An Overview of Marine Drug Discovery
Electronic Journals at UCSB
Google Web Search Engine
Biology Workbench
ExPASy Molecular Biology Server
Protein Data Bank
Periodic Table of the Elements
Cell and Molecular Biology Protocols Online
UCSB General Catalog
UCSB Campus Map
UCSB Gold Login
UCSB Umail Access
UCSB Environmental Health and Safety
