Chem/Biochem 657: Drug Design Spring 14
T&Th 1:00pm
ISB 329

Instructors:   Lynmarie K. Thompson (, 864 Lederle Tower, 5-0827)
  Scott C. Garman (, 1021K Lederle Tower, 7-4488)
  UMass Moodle site
Today is


Date Topic Notes Reading:

required and optional

  Introductory material


Example summary

Plagiarism links

Drug design glossary;

T Jan 21 LKT: Introduction to course; Drug discovery timeline part 1 Lec 1 notes

Drug discovery tutorial;

Behind the surge

Th Jan 23 LKT: Introduction to protein-ligand binding Lec 2 notes

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, 5.1-5.3

•updates 3.0, 3.1, 3.2
, 3.4, 3.5, 3.6, 3.7,
   3.8, 3.9, 3.10
Fluorescence html;
Cooper SPR pdf;

Freire ITC pdf;
Blundell X-ray pdf;
Giralt NMR pdf;
Pellecchia NMR pdf

T Jan 28 SCG: Drug discovery timeline part 2: Lead optimization to clinical trials Lec 3 notes

Drug discovery tutorial;
   (from Lead Opt/Med Chem)
Phase 1 mishap html;
Phase 3 withdrawal pdf

Cholesterol market html;
Vertex HCV fast track

Th Jan 30 SCG: Pharmacokinetics and pharmacodynamics

Lec 4 notes

Goodman chapt1 pdf;

PK applets

Tox red flags

T Feb 4 SCG: Introduction to transmembrane receptors

Lec 5 notes

SSprang G prot primer pdf;
Fillmore_GPCR_2004 pdf;

Rasmussen_2011 pdf;
Kroeze GPCR pdf;

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

Th Feb 6



2013 Quiz

T Feb 11

Quiz Discussion




Th Feb 13 No class meeting: Snow Day!



T Feb 18 No class meeting: Monday class schedule    
Th Feb 20




T Feb 25

Mark Murcko, Disruptive Biomedical: Overview of Drug Discovery

Murcko pdf (50MB)

Alpha shock

Th Feb 27

Discussion: Murcko

Discussion leaders: Seamus, Keenan, Lexi, David, Josh

Murcko discussion


T Mar 4

Meaghan Richmond, AstraZeneca: Patents and Intellectual Property


IP 101

Patent example 1

Patent example 2

Patents in Pharma

Patents at the Core


Genetics and Patenting

Protecting the Assets

Critics Target Patent Deals

Th Mar 6

Discussion: Richmond

Discussion leaders: Coralie, Liz, Dan, Lauren, Kris K

T Mar 11 Chris Lipinski, Melior Discovery: Reducing Lead Time

Lipinski pdf

Lipinski essay draft

Lipinski essay proof

Hit-to-lead pdf;
False positives pdf

Th Mar 13

Discussion: Lipinski

Discussion leaders: Christina, Jill, Barbara, Carolina, Ilker, Eric

  Spring Break    
T Mar 25 Joanna Swain, Bristol-Myers Squibb: Protein Pharmaceuticals Swain 2008 pdf

Adnectins pdf

Th Mar 27

Discussion: Swain

Discussion leaders: James, Matt, Anthony, Bryan T, Chris W

T Apr 1

Ravi Kurumbail, Pfizer: Applications of Structure-Based Drug Design

Kurumbail pdf

Bunnage_2011 pdf;

Hughes_2008 pdf;

South_2003 pdf;

Kurumbail_1996 pdf

Th Apr 3

Discussion: Kurumbail

Discussion leaders: Molly, Raquel, Cindy, Shaul, Ayesha


T Apr 8 Field Trip to Vertex Pharmaceuticals (optional)

Vertex schedule

Vertex directions


Th Apr 10

Discussion: Vertex trip

Discussion leaders: Wendy, Matteen, Brian K, Iman, Dong Yeop


T Apr 15

Woody Sherman, Schrödinger: Computer-Aided Drug Design

Sherman pdf

Improving selectivity pdf;

Molecular interactions pdf

Th Apr 17

Discussion: Sherman

Discussion leaders: Ryan, Kyle, William, Brian W, Zhe

T Apr 22

Thomas Keating, AstraZeneca: Infectious Disease Drug Discovery

Keating pdf TMK validation pdf;
Sulfonylpiperidines pdf;
TMK inhibitors pdf
Th Apr 24

Discussion: Keating

Discussion leaders: Priyanka, Monifa, Kamal, Tomoko, Joe

T Apr 29

Wrap up

Exam discussion leaders: Bobby, Carolyn, Victoria, Juan, Michael

Exam pdf

Exam word doc


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