ADVANCEMENTS IN COMPUTER-AIDED
DRUG DESIGN
The research fields in
chemical engineering have always been changing and evolving, from the field of
applied industrial chemistry at the beginning of the last century, through the
revolutionary reformulation of unit operations, transport phenomena and
engineering science in the 1960s, to the extensive use of computing technology
and the incorporation of molecular biology over the last two decades. Indeed,
the integration of computational force and molecular biology, such as to
simulate the behavior of molecules, is becoming a mainstream in the chemical
engineering research and has received much attention from the pharmaceutical
industries.
The two major application
areas of CADD, include structure-based drug
design and ligand-based drug design. Structure-based drug design
relies on three-dimensional knowledge of the receptor structure and its active
sites to investigate interaction, binding energy and steric relationship
between ligand and receptor. Ligand-based designing approach, on the other
hand, relies on knowledge of ligands that interact with target of interest.
This technique employs statistical methods to link structural features to
biological activities and attempts to identify specific structural features of
a ligand required for interacting with its target. Both structure-based and
ligand-based techniques can be applied in the initial drug discovery process
and aid the discovery of a lead compound which serves as the starting basis for
further modification to improve pharmacokinetics, solubility, selectivity,
potency or stability. Two of the great advantages of CADD lie in the ability of
fast screening a large molecule databank and the accelerated time steps of
identifying notable medicinal chemistry features. These characteristics are
extremely beneficial in designing multi-target medicinal products.
System biology,
proteomics, molecular biology, bioinformatics, and materials science now a days
using the application of advancement in molecular biology and information
technology aided rich molecular simulations. Computing techniques, protein structure
modeling, docking, binding site prediction, quantitative structure–activity
relationship (QSAR), and molecular dynamics simulation are the present
developments in drug design. Present docking issues includes accuracy of
protein structure and protein–ligand interaction.
It is easy to see that molecular
simulation has a vital role in drug design and CADD, whether it is in protein
modeling, in docking or in molecular dynamics. In addition to these, we hope our
flexibility concept can greatly increase the hit rate and the accuracy of
protein–ligand interaction.
With the advancement in
computing facilities and software algorithms, many simulations works that
require supercomputer in the past can be done in a workstation. By implementing
molecular simulation into biomolecular researches, not only the research steps
can be accelerated, but also the vast investment in money can be saved. In the
future, molecular simulation and computer-aided drug design can greatly influence
the development of pharmaceutical industry and become a necessity before
molecular experiments.
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