(2nd-February-2020)
Aiming at long-term simulations targeting even larger causative molecules.
"Long time" means to extend the time to move atoms. In the molecular dynamics method, atoms are moved little by little at a time interval of about 1 femtosecond (femto is 10 −15). Therefore, even with "K computer", the simulation time is about 10 microseconds (micro is 10-6) (still 10 billion calculations are required). However, a truly accurate calculation of the strength of a bond requires 100 times this, a millisecond calculation. It takes about 1 millisecond for the compound to approach the causal molecule and repeatedly bond and separate.
The goal of “Futake” is to perform a 1-ms molecular dynamics simulation for each combination. If realized, what would have been previously seen as a "trailer" that only took out the scenes of binding of the causal molecule and the compound would be seen as a single movie from beginning to end. Researchers are looking forward to seeing what kind of world this will open.
And "large" means increasing the number of combinations that can be examined. "K computer" can perform one hundred microsecond molecular dynamics simulations in one week, but "Fugaku" should be able to perform tens of thousands of calculations in one week. In that case, the compound may bind to another molecule and cause side effects, or it may bind to a molecule that was not expected and find another medicinal effect. Molecular dynamics simulations at "Fugaku" have the potential to be a powerful weapon for pharmaceutical companies to design real medicines.
On the other hand, Tomitake is also working on designing new types of drugs that are difficult for pharmaceutical companies to tackle. For example, it has recently been discovered that the attachment of one protein to another between surfaces is the cause of the disease. In this case, the medicine cannot be designed with the conventional “key and keyhole” model. Therefore, it is conceivable that the state of binding between proteins will be first clarified by long-term molecular dynamics simulations, and then that will be used as a clue to the design of compounds that hinder the binding.
The development of medicines cannot be done only by calculation, but it takes more than 10 years for many elemental technologies to be linked together. In order to increase the speed of development, it is necessary to sharpen each elemental technology and incorporate cutting-edge technologies. “Futake” will be increasingly important in the future as one of them
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