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About Us

NADI Team

NADI Team is actively involved in solving scientific queries mainly on the structural and dynamic aspect of a biological problem in a molecular level using the molecular drug targets that are associated with antibacterial and antiviral agents. We also research in structural and functional prediction of interesting hypothetical proteins that could lead to further understanding biological catalytic pathway.

What are we doing?

Drug Target Screening

Malaysia is known for our rich biodiversity along with extensive knowledge on traditional use of herbs and plants provide an optimal platform serving as great resources for natural products discovery. NADI is designed in our own laboratory as a one stop centre for in silico drug discovery from natural products. Meaning “pulse of life” in Malay Language, NADI is a Natural base Drug Discovery resource. At present, NADI has grown with 3 major databases: NADI-CHEM (a collection of 3D chemical structure of compound derived from Malaysian Natural Products), NADI-HERBS (a collection of brief description of medicinal use of Malaysian medicinal plants in Malay language), and NADI-MePS (an integrated database which is the same as NADI-HERBS but in English language). All the databases are integrated with Molecular Modelling Portals-Structure Predictor, Drug Discovery Engine, Protein Structure/Lead Refiner and Reverse Docking Server.

Protein Binding Studies

Knowledge of the interaction between two molecules is important to understand on how these biomolecules interacts thus functioning in our biological system. The prediction of this interaction using computational studies could advance discovery in rapid and low cost prediction. There are two methods of protein biding that are available in our laboratory, molecular docking and molecular dynamics simulations, either to study the protein-ligand or DNA-ligand interactions.

Drug Design (Pharmacophore studies and drug synthesis)

Pharmacophore that describe interactions between biological targets and ligands are useful screening tools of drug discovery. The use of structure-based approaches in drug discovery has a great demand in recent years. We have recently introduced an in silico method that utilises chemical feature-based pharmacophores that approach both the design of novel compounds, and for lead optimisation. We use Accelrys’ platform that allows scientific research groups to access, aggregate and mine data across and development and the discovery of new products and therapeutics materials.

A reasonable prediction of binding can be made by specifying the spatial arrangement of a small number of atoms or functional group. A common use of Pharmacophore is to search 3D databases for molecules that contain pharmacophore. The application of the model shows great success in predicting the activities of some known inhibitors in our NADI database with a good confidence level. Accordingly, our models are reliable in identifying structurally diverse compounds with desired biological activity.

Testing in the lab

The testing of a (series of) molecule(s) against a known biological target that correlates with a cellular or pharmacological activity is known as bioassay – e.g. enzyme inhibition. Our lab also offers this service if required.

Joint Lab/On-site Facilities

  • 16 nodes high-performance parallel linux cluster with IBM server as master node.
  • 9 nodes high-performance parallel linux cluster with Dell server as master node.
  • Enzyme-assy.
  • Protein binding software: AutoDock, DOCK, GOLD, AMBER.
  • Drug design software: Catalyst.
  • Award

  • Gold Medal Award at the 16th International Invention Innovation Industrial Design and Technology Exhibition 2005 (ITEX 2005) in Kuala Lumpur, Malaysia.
  • Silver Medal Award at the 34th International Exhibition of Inventions, New Techniques and Products in Geneva Switzerland (2005).