Photo by Michael Longmire on Unsplash
By combining Fujitsu’s proprietary high-speed, quantum-inspired computing technology with PeptiDream ’s advanced knowledge and wealth of experimental data in unique peptides(1), the companies seek to develop revolutionary in silico drug discovery(2) technology. This technology, applied to the field of peptide drug discovery offers researchers the chance to dramatically accelerate the search for drug candidate compounds through improved efficiency.
At present, the most widely distributed drugs are small-molecule drugs, which have the advantages, as oral drugs, of being relatively cost-effective and easy to develop. On the other hand, because their selectivity toward the target is low, they have the disadvantage of acting on off-target areas, making them prone to causing side-effects. In contrast, antibody drugs, which are large-molecule drugs, are costly, but because they are highly selective cause relatively few side-effects. Peptide therapeutics, which have a molecular weight in between small-molecule drugs and antibody drugs, combine the advantages of low-cost with relatively few side effects.
The drug discovery process for peptides involves extracting thousands of candidates from a starting point of several trillions of candidate compounds, and then further whittling that number down to several tens of candidates. This search process requires an iterative process in which, in addition to “dry” experiments that can be simulated with computers, there are “wet” experiments performed in the lab. Ordinarily, this process takes anywhere from a few months to a few years. In the process of narrowing down candidate compounds, it remains important to have an understanding of a molecule’s stable conformation. In an analysis using a conventional computer, however, getting information on the stable conformation of one compound would take several days.
For combinatorial optimization problems, which take into account various combinations of real-world factors to discover an optimal solution, Fujitsu began offering the services of the Digital Annealer in May 2018. Fujitsu Laboratories Ltd. originally developed the hardware using next-generation architecture inspired by quantum phenomena. The Digital Annealer’s ability to rapidly locate optimal solutions for problems that could not be solved using conventional computers, makes it an ideal choice for applications in a wide range of areas, including delivery optimizations in distribution, the optimization of component placement in a factory, portfolio optimization in finance, and narrowing candidate selection in materials and drug discovery.
For drug discovery, PeptiDream has a proprietary drug discovery and development platform called the Peptide Discovery Platform System, which enables it to freely create unique peptides that have a variety of unnatural amino acids and accelerate searches for drug candidate compounds. PeptiDream is leveraging this system to move forward with the development of a large number of drug candidate compounds targeting a wide range of indications that could not be targeted with conventional small-molecule drugs or antibodies.
By introducing the Digital Annealer to these efforts, Fujitsu and PeptiDream aim to accelerate the search process for candidate compounds in PeptiDream’s peptide drug discovery process, jointly developing and validating their peptide drug discovery technology.
Description of the Joint Research
In peptide drug discovery, it is important to obtain information on the peptide’s stable conformation, which is determined by the structure of its main and side chains(3).
In this collaboration between Fujitsu and PeptiDream, combinatorial optimization calculations will be performed using Fujitsu’s Digital Annealer to verify whether stable conformations of unique peptides can be quickly obtained. Researchers will rely on PeptiDream’s huge database of unique peptides,
The joint research seeks to create search technology for the stable conformations of unique peptides and verify the usefulness of the Digital Annealer in peptide drug discovery. By applying the Digital Annealer technology to the search process in PeptiDream’s candidate compound development, the two companies aim to significantly reduce search times from a few days to a fraction of that time, dramatically improving the efficiency of discovering drug candidate compounds, and helping to improve the prospects of bringing about new drugs.
[1] Peptide: A compound in which two or more amino acid molecules are chemically bound together in a chain or a loop. A unique peptide is a compound that includes unnatural amino acids.
[2] In silico drug discovery: Drug discovery performed by a computer using methods for predicting outcomes using calculations, such as from simulations.
[3] Main chain and side chains: In peptides as well as large molecule compounds, such as proteins, the part forming the backbone is called the main chain, while the parts branching off of the main chain are called the side chains.
At present, the most widely distributed drugs are small-molecule drugs, which have the advantages, as oral drugs, of being relatively cost-effective and easy to develop. On the other hand, because their selectivity toward the target is low, they have the disadvantage of acting on off-target areas, making them prone to causing side-effects. In contrast, antibody drugs, which are large-molecule drugs, are costly, but because they are highly selective cause relatively few side-effects. Peptide therapeutics, which have a molecular weight in between small-molecule drugs and antibody drugs, combine the advantages of low-cost with relatively few side effects.
The drug discovery process for peptides involves extracting thousands of candidates from a starting point of several trillions of candidate compounds, and then further whittling that number down to several tens of candidates. This search process requires an iterative process in which, in addition to “dry” experiments that can be simulated with computers, there are “wet” experiments performed in the lab. Ordinarily, this process takes anywhere from a few months to a few years. In the process of narrowing down candidate compounds, it remains important to have an understanding of a molecule’s stable conformation. In an analysis using a conventional computer, however, getting information on the stable conformation of one compound would take several days.
For combinatorial optimization problems, which take into account various combinations of real-world factors to discover an optimal solution, Fujitsu began offering the services of the Digital Annealer in May 2018. Fujitsu Laboratories Ltd. originally developed the hardware using next-generation architecture inspired by quantum phenomena. The Digital Annealer’s ability to rapidly locate optimal solutions for problems that could not be solved using conventional computers, makes it an ideal choice for applications in a wide range of areas, including delivery optimizations in distribution, the optimization of component placement in a factory, portfolio optimization in finance, and narrowing candidate selection in materials and drug discovery.
For drug discovery, PeptiDream has a proprietary drug discovery and development platform called the Peptide Discovery Platform System, which enables it to freely create unique peptides that have a variety of unnatural amino acids and accelerate searches for drug candidate compounds. PeptiDream is leveraging this system to move forward with the development of a large number of drug candidate compounds targeting a wide range of indications that could not be targeted with conventional small-molecule drugs or antibodies.
By introducing the Digital Annealer to these efforts, Fujitsu and PeptiDream aim to accelerate the search process for candidate compounds in PeptiDream’s peptide drug discovery process, jointly developing and validating their peptide drug discovery technology.
Description of the Joint Research
In peptide drug discovery, it is important to obtain information on the peptide’s stable conformation, which is determined by the structure of its main and side chains(3).
In this collaboration between Fujitsu and PeptiDream, combinatorial optimization calculations will be performed using Fujitsu’s Digital Annealer to verify whether stable conformations of unique peptides can be quickly obtained. Researchers will rely on PeptiDream’s huge database of unique peptides,
The joint research seeks to create search technology for the stable conformations of unique peptides and verify the usefulness of the Digital Annealer in peptide drug discovery. By applying the Digital Annealer technology to the search process in PeptiDream’s candidate compound development, the two companies aim to significantly reduce search times from a few days to a fraction of that time, dramatically improving the efficiency of discovering drug candidate compounds, and helping to improve the prospects of bringing about new drugs.
[1] Peptide: A compound in which two or more amino acid molecules are chemically bound together in a chain or a loop. A unique peptide is a compound that includes unnatural amino acids.
[2] In silico drug discovery: Drug discovery performed by a computer using methods for predicting outcomes using calculations, such as from simulations.
[3] Main chain and side chains: In peptides as well as large molecule compounds, such as proteins, the part forming the backbone is called the main chain, while the parts branching off of the main chain are called the side chains.