MD (Molecular discovery) by HPC

(27th-January-2020)

There is a supercomputer based drugs discovery is common approach in current medicine development. Let's take a look at how supercomputers can help in drug design and what is planned for the supercomputer "Futake", a successor to the "Kyo" the case of in Japan HPC field.

Related issues: Priority issues (1) Building an innovative drug discovery platform by controlling the functions of biomolecular systems

• How medicines are made

• Search for compounds that close the keyhole by calculation

• Brush up candidate compounds with calculations

"Kyo" has achieved practical results as well as cutting-edge results

“Fugaku” aiming to develop unprecedented drugs

How medicine is made

Do you know why medicine works? When we get sick, molecules that cause the disease (mainly proteins) are active in our bodies. The drug binds to the disease-causing molecule and suppresses its activity. For example, cimetidine, a drug for gastric ulcer, suppresses the action of proteins that stimulate secretion of gastric acid. Therefore, the secretion of stomach acid is stopped, and upset and lean stomach are cured.

More specifically, this protein is a histamine receptor. This protein has a cavity that exactly fits a compound called histamine in the body. This can be said of the relationship between keys and keyholes. And when the key, histamine, enters the keyhole of the receptor, it stimulates the release of gastric acid. This is a necessary function for our lives, but a drug called cimetidine prevents stomach acid from being released as histamine comes more and more. Cimetidine is very similar to histamine and enters the keyhole before histamine comes. In that case, histamine could not get into the keyhole and gastric acid secretion would be suppressed.