Drug Discovery and Formulation

We would like to introduce new features of J-OCTA for the life science and drug discovery fields.

J-OCTA is "multi-scale simulation software" that can calculate phenomena from the atomic and molecular scale (nanometer) to the mesoscale (micrometer) region on the computer. It is based on the free software OCTA, which was originally developed as a Japanese national project to realize multiscale simulations for soft matter (soft materials).

When we think of soft matter, we tend to think of "materials" such as resins and rubbers, but biomolecules and biomembranes are also included in its scope. Recently, we have received an increasing number of inquiries from J-OCTA users related to modeling for life sciences, i.e., drug discovery and drug formulation. In addition, the need for simulation of biomaterials has also been increasing in recent years. In response to these needs, we are expanding J-OCTA's functionality, some of which are introduced below.

J-OCTA provides an interface to GENESIS[4][5][6], a molecular dynamics (MD) engine. GENESIS is molecular dynamics software developed mainly by RIKEN and distributed as free software (LGPLv3). GENESIS Windows version is bundled with J-OCTA. GENESIS supports large-scale parallel computing and GPUs, enabling fast computation of large models. GENESIS also has excellent features such as efficient search for binding structures of proteins and ligands (drugs) using the replica exchange method and free energy calculations to evaluate binding affinity.

J-OCTA offers a new GENESIS Modeler for biomolecular modeling and result analysis. After obtaining the molecular structure of a protein using a database such as PDB or, more recently, AI technology such as AlphaFold2, the force field parameters are set to be suitable for biomolecule calculations. We then apply ionization and other processing to support MD calculations. After the calculation, the user can easily perform various result analyses on the GUI as well as drawings (Figure 2).

In addition, recently there is a demand for the application of simulations not only to small molecules, but also to mid- to high-molecular weight pharmaceuticals. In this case, calculations of large systems are required. J-OCTA has long supported multiscale modeling and results analysis of large systems, and GENESIS' strengths are also demonstrated.

Figure 2. Protein modeling by J-OCTA’s GENESIS Modeler

This field, called In Silico Drug Discovery, requires a variety of methods and know-how, including AI, data science, docking calculations, and molecular simulations such as MD. Since it is difficult for J-OCTA to handle everything immediately, we will provide functions from our areas of expertise such as multi-scale simulation.