Virtual Docking for Drug Discovery
http://pecet-colombia.org/en/medios/Afiche-Curso-Virtual-Docking-1-150×150.jpg
Course Virtual Docking for Drug Discovery
INSCRIPCIONES CERRADAS
August 31 – September 3, 2010
Hosted by:
Program for the Study and Control of Tropical Diseases, University of Antioquia,
Sponsored by: PECET-WSAID and Colciencias.
Medellín, Colombia
Technical Information
Schedule:
8 sessions, 4 hours/session, 32 hours (Four days)
Number of participants:
15-20
Target public:
Graduate students, Professors, Researchers from Biology, Chemistry or computational sciences.
Background required:
Basic concepts in Chemistry and Physics
Basic skills in Scientific software
Cost:
$80,000 Pesos (Local currency)
Date:
August 31 to September 3, 2010
Instructors:
- Stan Watowich PhD. Associate Professor
Dept. of Biochemistry & Molecular Biology
University of Texas Medical Branch.
- Robert Malmstrom, Research Associate.
Dept. of Biochemistry & Molecular Biology
University of Texas Medical Branch.
Certification:
Yes
Justification:
The drug discovery process implies a combination of different disciplines with the main goal of bringing a drug to the market that can be employed to solve health problems. However the current experimental strategy takes long time to be completed and most of the drugs have problems on the clinical trials especially because of toxicity issues. Additionally the cost of this process is very high which limits developing countries to discover new drugs. Computational alternatives like Virtual docking constitutes an advantageous strategy that allow discovering new compounds with biological activity to be tested in the lab with less investment of money and time. There is an increasing interest of the Colombian scientific community (especially in Antioquia) to apply this computational strategies for drug discovery which motivate us to develop this course targeting those needs.
General Purpose:
To give an introduction to drug and target databases, techniques and tools employed on virtual docking with a particular focus on Drug Discovery.
Learning Objectives:
- Learn how to use some drug and target databases to extract information of interest (about drugs)).
- Understand the molecular concepts of Virtual Docking and its applications.
- Develop skills in using the most common programs in Virtual docking applied to solve specific biological problems.
Contents:
1. Introduction to Docking (Day 1)
Responsible: Stan Watowich and Robert Malmstrom
Morning session
Drug discovery & development overview
Review of protein and chemical structures
Introduction to molecular graphics programs
Introduction to protein and chemical structure databases (e.g., Protein Data Bank, Cambridge Data bank)
Review of protein-ligand chemistry, energetics, kinetics, equilibrium
Interactive: visualizing proteins and analyzing protein-ligand interactions on individual PCs
Afternoon session
Computer-based drug discovery
Docking overview
Scoring methods & energy calculations
Docking procedure using AutoDock Vina tools
Interactive: docking experiments with test ligands on individual PCs
2. Virtual Screening Tutorial (Day 2)
Responsible: Stan Watowich and Robert Malmstrom
Morning session
Ligand preparation tools
Ligand libraries for virtual screening
Docking tools
Metrics for analyzing virtual screening programs
Comparison of docking programs
Docking applications for toxicity testing
Afternoon session
Experience with the project Discovering Dengue Drugs – Together
Interactive virtual screening and structure analysis on individual PCs
3. Experimental Validation of “Hits” and High-Throughput Screening (Day 3)
Responsible: Robert Malmstrom
Morning session
Enzyme structure-function
Protein-ligand binding
Enzyme kinetics
Rate orders
Assay design
Considerations for biochemical assays in high-throughput screening
Afternoon session
Data interpretation and quantitative modeling
Interactive: fitting interaction models to kinetic data (using coupled differential equations) on individual PCs
4. Free energy calculations and data filtering (Day 4)
Responsible: Stan Watowich
Morning session
Drawbacks and limitations of virtual screening and docking
Filtering screening “hits” for experimental validation
Free energy calculations to reduce false positive “hits”
Filtering “hits” for solubility, drug-like characteristics
Cluster and similarity analysis
Data-mining for lead analogs to develop SAR
Afternoon session
Interactive: structure-based drug optimization and automated analog generation on individual PCs
Requirements:
Accepted participants must be able communicate in English and bring their own labtops. No Labtops would be provided in course.
All programs to be worked in course would be downloaded from the web the first day of the course.
Address:
The course will be held at the “Sede de Investigacion Universitaria” of the Universidad de Antioquia in the auditorium area, located in the first floor of the building.
Calle 62 No 52.-59
Phone: 219-6507 / 02
Application procedure
The first 15 persons that send the receipt of payment will be selected. Five extra applicants may be considered.
Important: To confirm your inscription remember sends the receipt marked with your personal information (complete name and surnames, document of identity, telephone number and city) to comunicaciones.pecet@siu.udea.edu.co or to the fax number (4 219-6511).
Payment deadline: 25 AUGUST, 2010.
Deposit or electronic transfer
Name of the Bank: BANCOLOMBIA
Type of account: CURRENT
Account number: 008522396-50
Name of the account: FUNDACIÓN UNIVERSIDAD DE ANTIOQUIA
NIT. 811.004.659-3
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