Toray Industries, Inc.
Co-creation to open new frontiers, being inspired by quantum phenomena
While the performance of conventional general-purpose computers appears to be reaching its limits, interest in quantum computing technologies is increasing rapidly. However, quantum computing still has the challenge of overcoming the stability of the ‘quantum bit’ as well as increasing its scale. Digital Annealer is a unique computing architecture, inspired by quantum phenomena, which is able to rapidly solve combinational optimization problems on a practical level. Toray Industries, a materials and pharmaceuticals manufacturer, is working together with Fujitsu to develop commercial uses for Digital Annealer. The technology has the potential to transform the pharmaceutical industry and the principles of research and development.
With computing capabilities moving ahead in leaps and bounds, calculations that were once thought beyond reach have now become possible. We believe that the Digital Annealer and the co-creation initiative with Fujitsu will help us break through to the next level, where the winners are determined not by the scale and size but rather by the intelligence.
Ryuji Tanimura, Ph.D.
Senior Molecular Designer
Head of Computer-Aided Drug Design
Pharmaceutical Research Laboratories
Toray Industries, Inc.
Digital Annealer expected to solve complex optimization problems
The limit to increases in computer performance, as expressed in Moore’s Law*1 , is fast approaching. It is anticipated that quantum computing will provide the solution to this, becoming the next generation of computing architecture. However, few actual solutions are currently available. Fujitsu’s Digital Annealer is one such solution, designed for solving combinatorial optimization problems by adopting a general purpose solution called the ‘simulated annealing’ method. It brings advantages of quantum computer into the digital circuit. Fujitsu is already conducting joint research with a number of companies to discover groundbreaking ways of using the Digital Annealer in business, and Toray Industries (Toray) is one of partners.
The first theme of the joint research between Toray and Fujitsu was the optimization of molecular structures. They verified predictions of the most stable structures of proteins by using Digital Annealer. According to Dr. Ryuji Tanimura, Head of Computer-Aided Drug Design, Pharmaceutical Research Laboratories at Toray, “Proteins, which include enzymes, antibodies and receptors, form complex structures and experimentation to analyze them is extremely labor-intensive.”
To determine the structure of a protein through experimentation, crystals with stable molecular structures must be created and analyzed with X-rays or other techniques. However, crystallizing and stabilizing proteins is a difficult process. Growing protein crystals is a time-consuming process. It can take anywhere from a few months to half a year, or even more in some cases and it is not uncommon to discover, even after investing all this time that the process has failed. Consequently, to overcome such lengthy intervals, researchers are looking to computation as a means of predicting the optimal combinations of different, novel molecular arrangements, what is known technically as the side chain*2 conformation*3 of proteins.
Dr. Tanimura explains, “Combination algorithms capable of predicting optimal structures have been available before. The performance of conventional general-purpose computers has allowed us to use these to make predictions for small proteins, but as the combinations of the side chain conformation increase, it was hard to reach answers in practical time.”
Toray looked to the Digital Annealer as a means of potentially overcoming this problem.
- *1Moore’s Law is a prediction that the number of elements in an integrated circuit would double every 18 months in Semiconductor industry
- *2A spot where branches from main chain of proteins
- *3The spatial arrangement of the atoms affording distinction between stereoisomers which can be interconverted by rotations about formally single bonds
The story so far
Previously impossible to find optimal solutions of large combinatorial problems becomes now possible
Two main steps were taken to enable the Digital Annealer to predict the most stable structures for side chain conformation of proteins. First, the known optimal combinations of side chain conformations for structures of small proteins were compared with the optimal combination solutions for the same proteins provided by the Digital Annealer, to confirm that they matched. Next, the Digital Annealer was used to predict the structures of large proteins that previously were unable to be realistically computed.
From September 2018, Digital Annealer specialists from Fujitsu, and researchers with knowledge of protein simulations from Fujitsu Laboratories, worked together for around three months to predict the structure. The side chain structures of large proteins would be tons of combinations. For instance, the possible combinations would be 10 to the power of 100 when identifying proteins which have100 side chains with 10 different conformations. The goal of this research is to reach the most stable structures among the large numbers of identified possible structures in just a few minutes.
Reflecting on the project, Dr. Tanimura comments, “We already had the algorithm formulas for computation, and an interface for transferring them to the Digital Annealer, so we progressed easily to the implementation phase.” The answer for the known optimal combinations was verified, and the problem of the large proteins, which a general-purpose computer failed to solve after three to four hours of computation, was solved in about 20 seconds by Digital Annealer.
Dr. Tanimura emphasized the most important outcome was that, “We were able to arrive at answers which were out of reach using the conventional way.” The significant progress made through this project gave the research team confidence in using Digital Annealer as a means of designing proteins with desirable characteristics.
Designing a desired protein entails the ability to change its properties, structures, and functions. This ability also aids in the design of molecules able to bind easily with proteins and becomes a powerful tool in drug discovery.
Outcome and next step
A shift to “in silico” is changing the rules of the market competition
This co-creation project between Toray and Fujitsu provided confidence in the ability of the Digital Annealer to design proteins, so the development of a design program for predicting desired protein structures is being considered as the next step. Meanwhile, Toray and Fujitsu are currently planning their next joint research project to conduct trials in the area of new materials, which accounts for a large share of Toray’s sales. The two companies have also begun to investigate the formulation of new algorithms to use the Digital Annealer for simulating the development of polymers and other materials.
Digital Annealer used in this project had 1,024 bits connectivity, and will evolve into a second generation with 8,192 bits, which will expand the scope of its application. It is also expected to be able to solve more complex problems.
Dr. Tanimura explains his vision, “In the past, drug candidates were evaluated randomly, with verification through animal testing at the end. There can be up to a million possibilities. By narrowing numbers of evaluating methods down through the computation as much as possible, we hope to reduce the number of possibilities down to 1,000 or even 100.” This represents a shift from in vivo (animal experiments) through to in vitro (test tube experiments) and now to in silico (computer experiments).
This shift changes the principles of research and development of new medicine competition. “If we can improve the precision of in silico, it will become a contest of intelligence rather than scale and size. That is the world that I wish to see,” concludes Dr. Tanimura enthusiastically. Fujitsu and Toray have launched a co-creation initiative that will open frontiers and bring us to the next level.
Toray Industries, Inc.
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［Published in 2019］