In Silico Methods For Drug Discovery Highlighted

November 3, 2000


San Diego, CALIF. — The trend towards in silico (computer-based) design and selection of new molecules to improve the efficiency and reduce the cost of drug discovery and development will be a major theme at the American Association of Pharmaceutical Scientists (AAPS) meeting in Indianapolis from October 29 – November 2. At the largest annual gathering of pharmaceutical scientists in the world, Trega Biosciences, Inc., an innovator in modeling systems to simulate how drug candidates will be processed in the body, is presenting data on its absorption model, and “sneak previewing” the capability of its second model to predict metabolism. Absorption and metabolism are the first two modules of Trega’s iDEA Predictive ADME (absorption, distribution, metabolism and excretion) Simulation System.

“We are witnessing a paradigm shift in the pharmaceutical industry concerning the process of making smart decisions about which drugs to develop, and more and more software is becoming available to discovery scientists to enable such decisions earlier in the process,” said Patrick Sinko, Ph.D. Dr. Sinko, Trega’s Chief Scientist of Discovery Technologies, and Professor and Chairman, Department of Pharmaceutics, College of Pharmacy, Rutgers University, is a featured speaker at the AAPS Symposium on “Enabling Technologies for Ensuring Developability.”

Dr. Sinko added: “Much of the estimated cost of $650 million to get a drug to market is not for developing the one successful drug, but for the 90+% of drugs that will fail prior to getting to market. Perhaps the most exciting area, therefore, is in ADME simulation, because an understanding of the bioavailability of a drug in humans is so critical to its downstream success in the clinic. The Trega iDEA Simulation System, for example, offers a tremendous amount of leverage because it can be applied so early in the discovery process. Trega’s initial iDEA absorption module is designed to enable a scientist to use in vitro data to predict drug impact in humans.

Dr. Carleton Sage, Senior Computational Scientist, of Trega Biosciences,, will present a poster on “In silico prediction of Caco-2 permeability from molecular structure.” Caco-2 is an established in vitro method for estimating permeability and an input to the iDEA absorption module. Trega set out to show that if Caco-2 permeability could be predicted using molecular structure, then human absorption properties could be incorporated much earlier in the drug discovery process, thereby eliminating wasteful and expensive testing of poorly absorbed compounds. After generating data on 230 drugs, both marketed and failed, Trega constructed a number of models, the best of which accurately predicts Caco-2 permeability based solely on molecular structure as in input. The experiment validates the premise that synthesis or experimentation may not be necessary first steps to understanding absorption characteristics of compounds.

“Currently, Trega is demonstrating the ability to go from structural data to predict the in vitro outcome. Thus, for the first time ever, the next generation of Trega’s absorption model will provide the research scientist with a design continuum that goes directly and reliably from the molecular structure of a drug on the computer screen to a prediction of the bioavailability of that drug on humans,” Dr. Sinko concluded.

Dr. Glen Leesman, Principal Scientist, of Trega will be presenting data that further validates the premise that Trega’s absorption model accurately predicts drug absorption when applied in a “real-world” pharmaceutical research setting. The accuracy of the model had initially been demonstrated using data provided by a consortium of pharmaceutical companies. The rate and extent of absorption of eight additional drugs, provided by F. Hoffmann LaRoche for this experiment, were then evaluated. The selected drugs had diverse chemical and physical properties and were provided for evaluation with molecular weight as the only form of identity. The Trega model accurately predicted the relevant biopharmaceutical outcomes for all eight drugs. Dr. Leesman’s, et. al., poster is entitled, “Assessment of the physiologically-based iDEA predictive model using an external (blinded) data set.”

“Consistent with our modular design strategy, our scientists have developed the next generation model that uses chemical structure to predict Caco-2 permeability. This feature is particularly applicable in early discovery for in silico screening of large numbers of compounds and significantly expands the scope of solutions that can be addressed by predictive modeling,” said Michael G. Grey, Trega’s President and CEO. “Furthermore, external researchers have validated the utility and reliability of the commercially available physiologically-based iDEA absorption model.”

Trega is developing a predictive model to simulate how a compound is metabolized in the human body and plans to preview elements of the model during the conference. The metabolism model is being developed using in vitro data and human pharmacokinetic data to build predictive relationships. The data required for this model includes the output from the iDEA absorption module and data generated by performing an in vitro hepatocyte assay in the laboratory. The model then predicts the amount of drug that passes through the liver unchanged.

“The development of our metabolism model is representative of our strategy of developing each module with collaborators in pharmaceutical companies. As we recently announced, Janssen Research Foundation and The R.W. Johnson Pharmaceutical Research Institute, members of the Johnson & Johnson family of companies, will collaborate with Trega to further enhance the predictive capabilities of iDEA predictive model,” continued Mr. Grey. “We intend to complete development of the metabolism module by the end of this year with the next release of the iDEA Simulation System. Trega plans to enable the comprehensive in silico prediction of bioavailability with a suite of modules to simulate absorption, metabolism, distribution and excretion.”

Trega Biosciences, Inc. is a premier provider of products that accelerate and improve drug discovery through its iDiscovery technologies linking biology and chemistry with information technologies. Trega’s iDEA Predictive ADME Simulation System of information-based models simulate, in silico, how drug candidates will be processed in the body, thereby enabling selection of those with optimal characteristics for clinical development. Together with its iDEA products, Trega’s Chem.Folio libraries of information-enhanced small molecules are designed to facilitate the identification and optimization of drug candidates. For additional information on Trega, please visit our Web site at .


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!

What’s New in Computing vs. COVID-19: Fugaku, Congress, De Novo Design & More

July 2, 2020

Supercomputing, big data and artificial intelligence are crucial tools in the fight against the coronavirus pandemic. Around the world, researchers, corporations and governments are urgently devoting their computing reso Read more…

By Oliver Peckham

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time last year, IBM announced open sourcing its Power instructio Read more…

By John Russell

HPC Career Notes: July 2020 Edition

July 1, 2020

In this monthly feature, we'll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it's a promotion, new company hire, or even an accolade, we've got Read more…

By Mariana Iriarte

Supercomputers Enable Radical, Promising New COVID-19 Drug Development Approach

July 1, 2020

Around the world, innumerable supercomputers are sifting through billions of molecules in a desperate search for a viable therapeutic to treat COVID-19. Those molecules are pulled from enormous databases of known compoun Read more…

By Oliver Peckham

HPC-Powered Simulations Reveal a Looming Climatic Threat to Vital Monsoon Seasons

June 30, 2020

As June draws to a close, eyes are turning to the latter half of the year – and with it, the monsoon and hurricane seasons that can prove vital or devastating for many of the world’s coastal communities. Now, climate Read more…

By Oliver Peckham

AWS Solution Channel

Maxar Builds HPC on AWS to Deliver Forecasts 58% Faster Than Weather Supercomputer

When weather threatens drilling rigs, refineries, and other energy facilities, oil and gas companies want to move fast to protect personnel and equipment. And for firms that trade commodity shares in oil, precious metals, crops, and livestock, the weather can significantly impact their buy-sell decisions. Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This year is no different though the conversion of ISC to a digital Read more…

By John Russell

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time Read more…

By John Russell

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This yea Read more…

By John Russell

Racism and HPC: a Special Podcast

June 29, 2020

Promoting greater diversity in HPC is a much-discussed goal and ostensibly a long-sought goal in HPC. Yet it seems clear HPC is far from achieving this goal. Re Read more…

Top500 Trends: Movement on Top, but Record Low Turnover

June 25, 2020

The 55th installment of the Top500 list saw strong activity in the leadership segment with four new systems in the top ten and a crowning achievement from the f Read more…

By Tiffany Trader

ISC 2020 Keynote: Hope for the Future, Praise for Fugaku and HPC’s Pandemic Response

June 24, 2020

In stark contrast to past years Thomas Sterling’s ISC20 keynote today struck a more somber note with the COVID-19 pandemic as the central character in Sterling’s annual review of worldwide trends in HPC. Better known for his engaging manner and occasional willingness to poke prickly egos, Sterling instead strode through the numbing statistics associated... Read more…

By John Russell

ISC 2020’s Student Cluster Competition Winners Announced

June 24, 2020

Normally, the Student Cluster Competition involves teams of students building real computing clusters on the show floors of major supercomputer conferences and Read more…

By Oliver Peckham

Hoefler’s Whirlwind ISC20 Virtual Tour of ML Trends in 9 Slides

June 23, 2020

The ISC20 experience this year via livestreaming and pre-recordings is interesting and perhaps a bit odd. That said presenters’ efforts to condense their comments makes for economic use of your time. Torsten Hoefler’s whirlwind 12-minute tour of ML is a great example. Hoefler, leader of the planned ISC20 Machine Learning... Read more…

By John Russell

At ISC, the Fight Against COVID-19 Took the Stage – and Yes, Fugaku Was There

June 23, 2020

With over nine million infected and nearly half a million dead, the COVID-19 pandemic has seized the world’s attention for several months. It has also dominat Read more…

By Oliver Peckham

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

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

Global Supercomputing Is Mobilizing Against COVID-19

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled... Read more…

By Oliver Peckham

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

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Steve Scott Lays Out HPE-Cray Blended Product Roadmap

March 11, 2020

Last week, the day before the El Capitan processor disclosures were made at HPE's new headquarters in San Jose, Steve Scott (CTO for HPC & AI at HPE, and former Cray CTO) was on-hand at the Rice Oil & Gas HPC conference in Houston. He was there to discuss the HPE-Cray transition and blended roadmap, as well as his favorite topic, Cray's eighth-gen networking technology, Slingshot. Read more…

By Tiffany Trader

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

Leading Solution Providers


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

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist 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

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

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

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

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