In the process of Drug Design, the role of Computational Drug Design has enormous significance in deriving information about understanding the properties of a drug and the structure of the receptor, especially the site of action (active site). The receptor may be an enzyme or DNA or Carbo-hydrate or Lipid Membrane. For this process, the Computers can help a lot, said Dr Shashidhara Rao, senior applications scientist, Schrödinger, a Computational Drug Design Company in the US.
He was speaking at a seminar on 'Computer Aided Drug Design', organized by the PG and Research Department of Chemistry, Thiagarajar College, Madurai.
The scientist said basically there are two types of drug design methods, they are structure-based drug design and pharmacophore-based drug design. The structure based method uses the available knowledge of the structure of the receptor which in most cases is an enzyme. The computer helps to study, scrutinize the active site, calculate the dynamic, and to build appropriate drug molecule inside the active site. The drug may be entirely unknown but still can be made in the lab.
The suitability of the size, structure, potential, energy, shape etc of the drug for a given receptor could be easily understood with the help of a computer. Further, the extent of docking (formation of a complex between a drug and its corresponding receptor) of a drug with the given receptor can be predicted by computation.
The pharmacophore-based (Ligand drug design) is an alternate technique to compare the structures of the available drugs in the absence of the structure of the receptor. By having a set of similar features, one can build a new drug using a computer. Synthesis of such drugs, their modifications, biological in-vivo screening, finding toxicity etc will lead to new drugs. The role of computer here is to make comparison among similar drugs, pharmacophore derivation and modification, Dr Shashidhara Rao said.
Now computers perform these two functions using specialized softwares developed for drug design by various companies such as MOE, SYBYL, and ACCELRYS. They have various modular packages for specific functions but integrated in it. These softwares can be afforded by pharma companies which can employ people with knowledge on molecular modelling, chemi-informatics, bio-informatics, genomics and proteomics, data bases, drug designing techniques, etc.
In the conventional method of drug discovery, according to him, there were various steps which took a minimum of 12 years. He stated that even today the rate of production of successful drugs per company all over the world is not even one. The drugs manufacturing industry is unable to meet the requirements of modern days as newer diseases are emerging every day. Hence, he said, there is a growing need for discovering, developing and designing new drugs at a faster rate. Now this has been made possible only with the help of computer aided drug design, he pointed out.
In olden days, the first step was to collect traditional medicinal plants and extract phytochemicals from them using solvents. Now these are non-green technologies. Then the extract had to be separated into various fractions followed by screening of their activities. Then the structures of compounds were compared with similar biological activities to arrive at the pharmacophore. Followed by several steps were done including synthesis of chemicals, modification of the structures of active compounds, selection of best ones and finally going for clinical trials.
Dr A Thamaraichelvan, head of Department of Chemistry, and the dean of R&D of the research wing of the College, said the college has received a UGC Innovative Programme to conduct a Two Years PG Diploma in Molecular Informatics and Drug Designing. He added that the college was already running a one year PG diploma course in Chemical Information Technology, which is very useful in drug design.
R Raghu, applications scientist, Schrödinger, India, R Raja Govindasamy, principal of the College and Dr Uma Kannan, secretary of the College also spoke on the occasion.