UMass Amherst
   Chem/Biochem 657: Drug Design Spring 10
T&Th 1:00pm
ISB 329

Instructors:   Lila M. Gierasch (gierasch@biochem.umass.edu, 1224 Lederle Tower, 5-6094)
  Scott C. Garman (garman@biochem.umass.edu, 1021K Lederle Tower, 7-4488)

Today is
Glossary

 

Date Topic Notes

Reading:

required and optional

  Introductory material Course_Syllabus
Instructions for Final Paper
Drug design glossary;

T Jan 19 LMG: Introduction to course; Drug discovery timeline part 1 Lecture1 pdf Drug discovery tutorial;
DrugResearcher.com
Th Jan 21 LMG: Introduction to protein-ligand binding Lecture2 pdf

Drug discovery tutorial;
   (up to Lead Opt/Med Chem)

•Petsko and Ringe
   1.4, 1.12, 1.14, 1.15, 1.16,

   2.1, 2.3, 2.4, 3.1, 4.9

•updates 3.0, 3.1, 3.2
   3.3
, 3.4, 3.5, 3.6, 3.7,
   3.8, 3.9, 3.10

T Jan 26 LMG: Physical methods in drug discovery Lecture3 pdf

•Petsko and Ringe
   5.1-5.3
Fluorescence html;
Cooper SPR pdf;

Freire ITC pdf;
Blundell X-ray pdf;
Giralt NMR pdf;
Pellecchia NMR pdf
   (or .doc version)

Th Jan 28 SCG: Drug discovery timeline part 2: Lead optimization to clinical trials Lecture4 pdf Drug discovery tutorial;
   (from Lead Opt/Med Chem)
Phase 1 mishap html;
Phase 3 withdrawal html
;
ClinicalTrials.gov
T Feb 2 SCG: Pharmacokinetics and pharmacodynamics

Lecture5 pdf

Lecture5 inked pdf

Goodman chapt1 pdf;
Th Feb 4 SCG: Introduction to transmembrane receptors

Lecture6 pdf

Lecture6 inked pdf

SSprang G prot primer pdf;
Fillmore_GPCR_2004 pdf;
Kroeze GPCR pdf;

•Petsko and Ringe
  3.6-3.8, update 1-6

T Feb 9 Quiz

2009 quiz

2010 quiz key

 
Th Feb 11 Preston Hensley, Consultant: Drug Discovery Challenges Hensley pdf (12 MB)  
T Feb 16 No class: Monday class schedule    
Th Feb 18

Discussion: Drug Discovery Challenges

Leaders: Will H., Jan P., Whitney S., Joe W.

   
T Feb 23 Jonathan Greer, Abbott: Structure-Based Drug Design Greer pdf (19 MB)

Anderson_2003 pdf;

Petros_2006 pdf;

Goodwill_2001 pdf;

Hajduk_2007 pdf;

NIH pub pdf (7 MB)

Th Feb 25

Discussion: Structure-based drug design

Leaders: Nilima K., Mark O, Minal P., Stephen P.

   
T Mar 2

Pat Walters, Vertex: Computational chemistry

Walters pdf Virtual screening pdf;
Chemical libraries pdf
Th Mar 4

Discussion: Computational chemistry

Leaders: Andrew C., Dicky G., Sam N., Bryan S.

   
T Mar 9 Chris Lipinski, Melior Discovery: Reducing Lead Time Lipinski pdf Hit-to-lead pdf;
Online resources pdf
Th Mar 11

Discussion: Lead time

Leaders: Mariel F., Dan K., Jamie L., Fabian R., Daniel S.

   
  Spring Break    
T Mar 23 Angela Cacace, Bristol-Myers Squibb: High Throughput Screening Cacace pdf HTS history pdf;
HTS stats pdf;
HTS assays pdf
Th Mar 25

Discussion: HTS

Leaders: Meenal D., Nick F., Adriana K., Lori M., Amit S.

   
T Mar 30 Field Trip to Vertex Pharmaceuticals Vertex Schedule pdf;
Directions to Vertex
 
Th Apr 1

Discussion: Field Trip

Leaders: Sean B., Caroline D., Josh G., Keith R., Joseph Y.

 
T Apr 6 Joanna Swain, Adnexus: Protein Pharmaceuticals Swain preview pdf Fibronectin libraries pdf
Th Apr 8

Discussion: Biologicals

Leaders: Lindsay D., Kari F., Melissa F., Kaitlyn M., Katie S.

   
T Apr 13 Alan Smith, Genzyme: Biologic Case Study Smith CV pdf;
Smith publications pdf

 

Th Apr 15 Frederick Monsma, Merck: GPCR Case Study Monsma pdf Orphan GPCRs pdf;
oGPCR ligand pdf;
GPCR antagonist pdf
T Apr 20

Discussion: Biologics

Leaders: Dave B., Christina M., Dave P., Serap P., Kristine P.

   
Th Apr 22

Discussion: GPCRs

Leaders: Nick B., Brad D., John H, Amanda H., Steve M.

   
T Apr 27 Stewart Fisher, Astra Zeneca: Identifying New Antibacterial Agents Fisher pdf MurI pdf;
MurI review pdf
Th Apr 29

Discussion: Antibacterials

Leaders: Daniella G., Brendan J., Gladys M., Mark Z.

   
T May 4 Wrap up;
Papers due
Plagiarism links  

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