Fujitsu and PeptiDream Leverage Quantum-Inspired Tech in Joint Research to Accelerate Drug Discovery

September 23, 2019

TOKYO and KAWASAKI, Japan, September 23, 2019 — Fujitsu Limited and PeptiDream Inc. today announced that they have agreed to initiate joint research and development in the area of peptide drug discovery, using Fujitsu’s Digital Annealer, which employs next-generation computing architecture to quickly solve combinatorial optimization problems.

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.

About Fujitsu

Fujitsu is the leading Japanese information and communication technology (ICT) company, offering a full range of technology products, solutions, and services. Approximately 132,000 Fujitsu people support customers in more than 100 countries. We use our experience and the power of ICT to shape the future of society with our customers. Fujitsu Limited (TSE: 6702) reported consolidated revenues of 4.0 trillion yen (US $36 billion) for the fiscal year ended March 31, 2019. For more information, please see www.fujitsu.com.

About PeptiDream

PeptiDream Inc. is a public (Tokyo Stock Exchange 1st Section 4587) biopharmaceutical company founded in 2006 employing our proprietary Peptide Discovery Platform System (PDPS), a state-of-the-art highly versatile discovery platform which enables the production of highly diverse (trillions) non-standard peptide libraries with high efficiency, for the identification of highly potent and selective hit candidates, which then can be developed into peptide-based or small molecule-based therapeutics. PeptiDream aspires to be a world leader in drug discovery and development to address unmet medical needs and improve the quality of life of patients worldwide. For further information, please visit www.peptidream.com.


Source: Fujitsu 

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

IBM, CQC Intro Cloud-based Quantum Random Number Generation

September 21, 2020

IBM and Cambridge Quantum Computing (CQC) have partnered to achieve progress on one of the major business aspirations for quantum computing – the goal of generating verified, truly random numbers that can be used for a Read more…

By Todd R. Weiss

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at current count) across the European Union and supplanting HPC Read more…

By Oliver Peckham

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for high-performance computing, a newly created position that is a Read more…

By Tiffany Trader

Swiss Supercomputer Enables Ultra-Precise Climate Simulations

September 17, 2020

As smoke from the record-breaking West Coast wildfires pours across the globe and tropical storms continue to form at unprecedented rates, the state of the global climate is once again looming in the public eye. Owing to Read more…

By Oliver Peckham

Future of Fintech on Display at HPC + AI Wall Street

September 17, 2020

Those who tuned in for Tuesday's HPC + AI Wall Street event got a peak at the future of fintech and lively discussion of topics like blockchain, AI for risk management, and high-frequency trading, as told by a group of l Read more…

By Alex Woodie,Tiffany Trader and Todd R. Weiss

AWS Solution Channel

Next-generation aerospace modeling and simulation: benchmarking Amazon Web Services High Performance Computing services

The aerospace industry has been using Computational Fluid Dynamics (CFD) for decades to create and optimize designs digitally, from the largest passenger planes and fighter jets to gliders and drones. Read more…

Intel® HPC + AI Pavilion

Berlin Institute of Health: Putting HPC to Work for the World

Researchers from the Center for Digital Health at the Berlin Institute of Health (BIH) are using science to understand the pathophysiology of COVID-19, which can help to inform the development of targeted treatments. Read more…

Legacy HPC System Seeds Supercomputing Excellence at UT Dallas

September 16, 2020

What happens to supercomputers after their productive life at an academic research center ends? The question often arises when people hear that the average age of a top supercomputer at retirement is about five years. Rest assured — systems aren’t simply scrapped. Instead, they’re donated to organizations and institutions that can make... Read more…

By Aaron Dubrow

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

Future of Fintech on Display at HPC + AI Wall Street

September 17, 2020

Those who tuned in for Tuesday's HPC + AI Wall Street event got a peak at the future of fintech and lively discussion of topics like blockchain, AI for risk man Read more…

By Alex Woodie,Tiffany Trader and Todd R. Weiss

IBM’s Quantum Race to One Million Qubits

September 15, 2020

IBM today outlined its ambitious quantum computing technology roadmap at its virtual Quantum Summit. The eye-popping million qubit number is still far out, agrees IBM, but perhaps not that far out. Just as eye-popping is IBM’s nearer-term plan for a 1,000-plus qubit system named Condor... Read more…

By John Russell

Nvidia Commits to Buy Arm for $40B

September 14, 2020

Nvidia is acquiring semiconductor design company Arm Ltd. for $40 billion from SoftBank in a blockbuster deal that catapults the GPU chipmaker to a dominant position in the datacenter while helping troubled SoftBank reverse its financial woes. The deal, which has been rumored for... Read more…

By Todd R. Weiss and George Leopold

AMD’s Massive COVID-19 HPC Fund Adds 18 Institutions, 5 Petaflops of Power

September 14, 2020

Almost exactly five months ago, AMD announced its COVID-19 HPC Fund, an ongoing flow of resources and equipment to research institutions studying COVID-19 that began with an initial donation of $15 million. In June, AMD announced major equipment donations to several major institutions. Now, AMD is making its third major COVID-19 HPC Fund... Read more…

By Oliver Peckham

HPC Strategist Dave Turek Joins DNA Storage (and Computing) Company Catalog

September 11, 2020

You've heard the saying "flash is the new disk and disk is the new tape," which traces its origins back to Jim Gray*. But what if DNA-based data storage could o Read more…

By Tiffany Trader

Google’s Quantum Chemistry Simulation Suggests Promising Path Forward

September 9, 2020

A much-anticipated prize in quantum computing is the ability to more accurately model chemical bonding behavior. Doing so should lead to better chemical synthes Read more…

By John Russell

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what Read more…

By Oliver Peckham

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th Read more…

By Tiffany Trader

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

Leading Solution Providers

Contributors

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

Oracle Cloud Infrastructure Powers Fugaku’s Storage, Scores IO500 Win

August 28, 2020

In June, RIKEN shook the supercomputing world with its Arm-based, Fujitsu-built juggernaut: Fugaku. The system, which weighs in at 415.5 Linpack petaflops, topp Read more…

By Oliver Peckham

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

DOD Orders Two AI-Focused Supercomputers from Liqid

August 24, 2020

The U.S. Department of Defense is making a big investment in data analytics and AI computing with the procurement of two HPC systems that will provide the High Read more…

By Tiffany Trader

Joliot-Curie Supercomputer Used to Build First Full, High-Fidelity Aircraft Engine Simulation

July 14, 2020

When industrial designers plan the design of a new element of a vehicle’s propulsion or exterior, they typically use fluid dynamics to optimize airflow and in Read more…

By Oliver Peckham

Microsoft Azure Adds A100 GPU Instances for ‘Supercomputer-Class AI’ in the Cloud

August 19, 2020

Microsoft Azure continues to infuse its cloud platform with HPC- and AI-directed technologies. Today the cloud services purveyor announced a new virtual machine Read more…

By Tiffany Trader

Japan’s Fugaku Tops Global Supercomputing Rankings

June 22, 2020

A new Top500 champ was unveiled today. Supercomputer Fugaku, the pride of Japan and the namesake of Mount Fuji, vaulted to the top of the 55th edition of the To Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This