ELRAZI UNIVERSITY

Faculty of Pharmacy

Drug Design Training

Program

Prepared By: Dr. Talal Ahmed Awad Adlan

September 2021

1 Prepared by Dr. Talal Awad Sep. 2021

 Computer-Aided Drug Design

Background
Computer-aided drug design (CADD) approaches can use the information in the 3D
structures of biological target molecules to identify chemicals with a high potential for
binding to these target molecules. The selected compounds are referred to as lead
compounds and may then be subjected to additional structural optimization via structural
biology, CADD and novel organic synthetic methods to obtain compounds with improved
activities. Both the lead compounds and their optimized analogs represent chemical entities
with a high probability of being developed into therapeutic agents and, therefore, are of
great interest to pharmaceutical companies.

Overview
The specific training areas could cover the following:

1. Finding potential enzyme inhibitors using computational drug design techniques such
as:
a. Molecular docking and molecular dynamics
To study the 3D molecular recognition between small molecules and target enzymes
in order to understand the best fitting between them via analysis of the energetics
of binding and investigation of drug-receptor interactions.
b. Structure activity relationships (SAR) and Quantitative structure activity
relationships (QSAR)
To study the relationships between the molecular structure (functional groups and
substituents) and the activity of the compounds, and to quantify the effects of these
functions via building statistical models that allow the prediction of biological
activities of suggested compounds, using specific software designed carefully for this
purpose.
2. Prediction of physicochemical ADMET (Absorption, distribution, metabolism, excretion
and toxicity) properties of chemical compounds.

2 Prepared by Dr. Talal Awad Sep. 2021

Trainings
 The Drug design training courses will provide a 5 to one week workshop on drug design
approaches and methods. Courses includes lectures and practicals which are focused on
molecular modeling molecular docking and QSAR methods
 The targeted persons are research students from the various disciplines and
backgrounds.
 The courses enable students to acquire the basic knowledge in molecular modeling and
drug design, which needed for accomplishment of researches in the various fields.
 All courses are computer based, as the students will be able to have and access to the
many drug design packages.

Training Course Outlines

(I) Theoretical Background
 Part 1: Drug Discovery and Development
 Part 2: Molecular Modeling simulation: Optimization and Energy minimization of
molecules.
 Part 3: Docking and interaction studies in terms of Binding energy, Structure based
Drug Design (SBDD).

(II) Practical
All Tutorials will be conducted using Molecular Operating Environment (MOE) package.

 Generating 3D-structures of small molecules:

• By simple sketching
• By downloading from web molecular databases (PubChem as an example)
• Using SMILES notations

 Dealing with molecular databases

 Dealing with Protein Databank
 Preparing protein structure for docking
 Protein-ligand docking tutorial
 Docking results analysis

3 Prepared by Dr. Talal Awad Sep. 2021