Chem 162B/262B
Drug Design
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Chem 162B/262B |
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Dr. Kalju Kahn
Office: PSB-N 2623
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.
In Fall 2006/Winter 2007, the Drug Design course at UCSB is being taught first time as a two-quarter series. 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". In particular, students in the class will have more time for hands-on work, especially on structure-based drug discovery. The Fall and Winter Quarter Drug Design courses in 2006-2007 academic year will be taught by Drs. Norbert Reich and Kalju Kahn. Students are allowed to take Chem 162B/262B without taking Chem 162A/262B this academic year.
Lecture: MWF 12:00-12:50 Place: Phelps 1444
Computer Lab: Open day access Place: Chem 1153
| Syllabus | General information about the 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 |
| Chem 162A | Drug Design (by Dr. Norbert Reich) website for Fall 2007 | Link |
| Last Years | Drug Design (by Dr. Kalju Kahn) website for Winter 2007 | Link |
| Last Years | Drug Design (by Dr. Kalju Kahn) website for Fall 2005 | Link |
| 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 PDF files | Link |
| Exam | Exam Preparation Guide | |
| Exam Sample I | Sample questions with answers from Spring 2004 | |
| Exam Key | Final Exam Questions (W 2007) | |
| Poster Session | Poster Session Presentations: March 16, 2007 | |
| Poster Session | Some pictures from the 2005 Student Poster Session | Link |
Course notes will be posted here before 7:30 a.m. of the lecture day. The lecture slides are password-protected. Contact your instructor to obtain the password.
| Notes | Lecture Notes. Powerpoint Pages in PDF | Acrobat |
| Jan 7 | Overview of the course. Review of Key Concepts from 162A | |
| Jan 9 | ADMET Challanges | |
| Jan 11 | Receptors as Drug Targets: Ion Channels | |
| Jan 14 | Receptors as Drug Targets: Ion Channels | |
| Jan 14-16 | Receptors as Drug Targets: GPCRs | |
| Jan 16-18 | Study of Membrane Receptors | |
| Jan 23 | Ligand-based drug design and optimization | |
| Jan 25 | Ligand-based drug design and optimization | |
| Jan 28 | Fragment-based drug design and optimization | |
| Jan 30 | Structure-Based Drug Design: Intermolecular Interactions | |
| Feb 4 | Structure-Based Drug Design: Protein Structure Analysis | |
| Feb 7 | Structure-Based Drug Design: Docking | |
| Feb 11 | Structure-Based Drug Design: Modeling Protein Flexibility | |
| Feb 14 | Case Study: Nuclear Hormone Receptors | |
| Feb 20-23 | Drug Metabolism: Principles | |
| Feb 25 | Drug Metabolism: P450 | |
| Feb 27 | Drug Metabolism: Design Strategies | |
| Feb 29 | P450 Pharmacogenetics, Drug Toxicity & Interactions | |
| Mar 10 | Prodrugs and Drug Delivery |
| 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 | |
| General | Antibacterial discover strategy: GSK story | |
| Receptors | Epibatidine: Impact on Nicotinic Receptor Research (Dukat & Glennon, 2003) | |
| Receptors | How Antidepressants Block Neurotransmitter Reuptake | |
| LBDD Design | Molecular Superposition (Miller, 1998) | |
| LBDD Design | Fragment-Based Drug Discovery (Erlanson, 2004)) | |
| Leads | HIV Protease Inhibitors | |
| SBDD | The Process of Structure-Based Drug Design | |
| SBDD | The Many Roles of Computation in Drug Discovery | |
| SBDD | Protein-ligand docking: Current Status and Future Challanges | |
| SBDD | High-throughput docking | |
| SBDD | High-throughput docking: thyroid hormone receptor | |
| Metabolism | Coupled Bioreactor-HPLC-MS metabolite analysis of SERMs | |
| Prodrugs | Lessons Learned from Marketed and Investigational Prodrugs | |
| Drug Delivery | Targeted Nanoparticles for Cancer Therapy |
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 | Receptors: general features and ligand design | |
| 2 | Ligand-Based Drug Design: Pharmacophores and Similarity | |
| 3 | Ligand-Based Drug Design: Conformation of Reverse Transcriptase Inhibitors | Link |
| 4 | Target-Based Drug Design: Visualization Tutorial and Homework | Link |
| 5 | Target-Based Drug Design: Docking | Link |
| 6 | Nuclear Hormone Receptors, Drug Metabolism and Prodrugs |
The assignment keys are typically posted one week after the due date.
| Keys | PDF files | Acrobat |
| 1 | Receptors: general features and ligand design | |
| 2 | Ligand-Based Drug Design: Pharmacophores and Similarity | |
| 3 | Ligand-Based Drug Design: Conformation of HIV RT Inhibitors | |
| 6 | Nuclear Hormone Receptors, Drug Metabolism and Prodrugs |
The project milestone guides are typically posted two weeks before they are due.
| Project Tips | General Guidelines to Project Development |
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
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UCSB Gold Login
UCSB Umail Access
UCSB Environmental Health and Safety