Bio Screening Industry News

BERKELEY, Calif.–(BUSINESS WIRE)–Plexxikon Inc. today announced the issuance of key composition-of-matter patents covering novel compounds discovered through the company’s Scaffold-Based Drug Discovery™ platform. Plexxikon’s pipeline of preclinical and clinical stage product opportunities currently span potential treatments for cardio-renal disease, CNS disorders, inflammation, metabolic disease and oncology. Two of the three recently issued patents (U.S. patents no. 7,498,342 and no. 7,504,509) cover compounds derived from the company’s discovery efforts to target protein kinases for the treatment of multiple indications including oncology and inflammation. The third patent (U.S. patent no. 7,476,746) covers novel compounds from the company’s PPAR (peroxisome proliferator-activated receptor) program yielding novel therapeutic opportunities for metabolic disorders and other diseases.

“We are pleased to be adding these additional patents to our growing and broad intellectual property portfolio,” stated K. Peter Hirth, Ph.D., chief executive officer of Plexxikon. “Plexxikon’s novel approach to drug discovery has enabled the company to advance multiple first-in-class drug candidates which are covered by strong intellectual property, and as a result, to secure significant pharmaceutical industry interest in our programs.”

In contrast to fragment-based approaches, Plexxikon’s platform has generated multiple product opportunities by mining the relatively unexplored chemical space of scaffold-like cores and by utilizing co-crystallography early in the discovery process to guide chemical optimization of these scaffolds. Further, the company has developed methods to make highly selective kinase inhibitors as yet rarely seen. Plexxikon has demonstrated the ability to develop selectivity between two targets with as little as one amino acid difference in their catalytic domains. This capability has created the opportunity for the development of new targeted drugs not only for oncology, but also for chronic disease indications outside oncology where safety hurdles are even higher. To date, Plexxikon’s platform has led to the development of a targeted medicine for the treatment of melanoma, a drug candidate for polycystic kidney disease (PKD), an oral agent for rheumatoid arthritis and a broad spectrum oral diabetic therapeutic, all representing novel agents addressing significant unmet needs.

Dr. Prabha Ibrahim Promoted to Vice President of Chemistry

In other news, Prabha N. Ibrahim, Ph.D., was promoted to the position of vice president of chemistry, bringing over 15 years of experience to her position. As head of chemistry since 2002, she has played a key role in building the company’s synthetic and medicinal chemistry capabilities leading to the discovery of Plexxikon’s novel drug candidates now in the clinic and in preclinical development. Prior to Plexxikon, Dr. Ibrahim was a senior scientist at CV Therapeutics, where she was responsible for the identification and development of preclinical candidates for cardiovascular indications. She also previously worked at Amgen, where she played an integral role in small molecule drug discovery for inflammation therapeutics. Dr. Ibrahim earned her Ph.D. at the University of Victoria, Canada, and was a Welch Foundation Fellow at Rice University in Houston.

Plexxikon Profile

Plexxikon is a leader in the structure-guided discovery and development of novel small molecule pharmaceuticals to treat human disease. The company’s clinical stage programs include PLX4032 for the treatment of melanoma and colorectal cancer, PLX5568 for the treatment of PKD and PLX204 for the treatment of diabetes. Among the company’s preclinical development programs, candidates are being developed for the treatment of rheumatoid arthritis, multiple sclerosis and other autoimmune diseases.

Plexxikon’s proprietary Scaffold-Based Drug Discovery™ platform is being applied to build a pipeline of product opportunities in multiple therapeutic areas. This discovery process integrates multiple state-of-the-art technologies, including structural screening as one key component that provides a significant competitive advantage over other drug discovery approaches. To date, the company has discovered a portfolio of clinical and preclinical stage compounds in varied disease areas addressing significant unmet needs in each therapeutic category.

Plexxikon is seeking pharmaceutical and biotechnology partners for select collaboration opportunities. For more information, please visit www.plexxikon.com.

ScienceDaily (Mar. 27, 2009) — Metabolites are molecular fingerprints of what your cells are up to and Dr. Arun Sreekumar wants to know the impression made by cancer.

You’ve likely heard about metabolites; your physician probably screens for some known ones such as triglycerides or cholesterol at your annual physical. Scientists suspect we have about 3,000 metabolites that come from our food or are synthesized from different compounds in our bodies.

Dr. Sreekumar, a cancer researcher at the Medical College of Georgia Cancer Center, wants those screens of the blood or urine to also detect early signs of cancers such as leukemia, bladder, kidney and breast when the chance for cure is best.

He’s already begun to identify metabolites that indicate not only the presence of prostate cancer, but its aggressiveness, a tool that could help tailor optimal treatment. The search began in men at risk: those with elevated prostate specific antigen, or PSA, levels. A PSA test along with a digital rectal exam is today’s standard for prostate screening so physicians typically do both in men age 50 and older. But PSA levels are actually better at helping determine if prostate cancer has returned, Dr. Sreekumar says.

Elevated levels of PSA, a protein, are not always predictive of cancer, which means a lot of men get unnecessary biopsies. PSA measurements also can’t distinguish between tumors that have a good outcome versus those with a poor one.

“The physician does not really have the tools in hand to really say that this tumor will spread to other organs or not.” says the Georgia Cancer Coalition Distinguished Cancer Scholar. “We want to find clinical markers that supplement PSA.”

Aggressiveness is a major factor in prostate cancer treatment. In fact some men with slow growing disease likely won’t even need treatment. So he wants to provide a complement of biomarkers that accurately diagnose and categorize the disease then help monitor success of treatment. These early studies indicate a urine test may one day be possible to do just that.

He and colleagues at the University of Michigan reported in the Feb. 12 issue of Nature what appears to be one of the first metabolites implicated in cancer invasion. They looked at 1,126 metabolites in 262 samples taken from men with high PSA levels. They consistently found elevated levels of the amino acid sarcosine in the prostate tissues of men with cancer; levels were highest in what appeared to be the most aggressive tumors.

Sarcosine, a modified form of the amino acid glycine, was a known entity but its function was unclear. Scientists thought it might be a dumping ground for excess methyl groups needed to enable chemical changes of genes, proteins and other body components that can affect what and how much they do.

This process called methylation can be a good thing – like when it’s helping an embryo develop – but when it goes badly, it can cause disease such as cancer. While sarcosine’s dumping role seemed to protect from cancer, the Michigan scientists found its action actually helps induce tumors. In fact, when they added it to prostate cancer cells, the cells became more aggressive. Exactly how that process works is still under study but the findings were pretty consistent.

“When we looked at patients with metastatic disease, sarcosine levels were sky high compared to patients with localized tumors,” says Dr. Sreekumar. “It’s enabling invasion.”

Because cancer and people are both very heterogenous, measures need to be taken in larger population samples, he says. Also, they found a small group of patients with negative biopsies and high sarcosine levels. “We don’t know how many of them have missed cancer,” says Dr. Sreekumar who joined the MCG faculty in February.

These are among the reasons he believes in strength in numbers. “In the real world of biomarkers, you want 100 percent sensitivity. If the patient has cancer, you want to pick it up. We need to have a kind of multiplex test where you can test for say10 different entities and have a greater confidence that what you are stating about the tumor is true. Our goal is to develop such a panel and research on sarcosine is a first step toward achieving this.”

In his new position at MCG, he’s looking to expand the number of metabolites known to be predictive of prostate and other cancers. In prostate cancer, he’s beginning with follow up on other metabolites identified in the Michigan study in which researchers identified a total of six metabolites, including sarcosine, linked to increased tumor progression. A total of 89 metabolites were different in metastatic prostate cancer compared to localized disease.

He’s excited about what metabolites will one day tell cancer physicians and patients but adds that they are just a piece of what our bodies can tell us about a potential cancer growing inside. Scientists also need to continue to look at genes expressed by tumors and the proteins expressed by those genes to get the bigger picture. “It’s basically a systems approach you need to take,” he says.

The young scientist has worked with all those pieces in his relatively short career. He started his postdoctoral fellowship at the University of Michigan in1999, when the ability to look at gene expression was new. With his mentor, Dr. Arul M. Chinnaiyan, director of Michigan Center for Translational Pathology, Pathology Research Informatics and Cancer Bioinformatics at Michigan, he helped develop the next step: the ability to look at expression of hundreds of proteins at a time, instead of a handful, an important advance in light of the fact that there are about 1 million proteins. Recently they were among the first to venture into the world of metabolites, which are made by proteins.

“Previous technology was looking at a cell from a narrow perspective and cells never act in isolation, proteins never act in isolation, they always form complexes, act in pathways,” Dr. Sreekumar says.

His inspiration to follow those pathways is a fellow Ph.D. student who died too young and quickly of an aggressive leukemia and the fact that cancer is a leading cause of death worldwide.

San Diego, CA (OBBeC) – Researchers at the University of California, San Diego, developed a unique computational approach to identify key compounds that could lead to new drugs to combat African sleeping sickness — a disease spread by the biting tsetse fly and caused by the parasite Trypanosoma brucei.

Mathematical modelling in biology is often a problem with interactions estimation between a biomolecular target and small molecule compounds.

Knowledge of this interaction allows the interruption of certain processes in cells, for example it can impede diseases such as cancer.

This is why so many efforts focus on designing better models and algorithms for high-throughput virtual screening techniques.

Otava began developing its own virtual screening system in 2004 to incorporate entropy change that occurs during ligand-receptor binding into virtual screening protocol.

This project was initially restricted to model entropy change in harmonic oscillation approximation.

This model is closely related to quality of potential energy calculations.

Otava’s scientists designed a universal polarisable force field to achieve reasonable entropy change accounting (on the basis of unique empirical charges definition scheme).

Spanning entropies with traditional enthalpy calculations for free energy of binding prediction was inaccurate.

Adding ligands desolvation free energy that was calculated with modified GBSA method (up to 0.95 regression coefficient with experimentally derived data) improved the accuracy.

Further testing of the improved virtual screening system showed its efficiency depended on the nearest environmental water molecules, which are usually ignored in high-throughput virtual screening.

Otava’s scientists proposed a new algorithm of molecular docking code to implement fast and accurate water position finding.

Aarhus Denmark — July 23, 2008 — CLC bio has just released a scientific white paper which confirms, that, in benchmarking tests, CLC bio’s new algorithm for assembly of Next Generation Sequencing data is the fastest one available. Not only is CLC bio’s algorithm considerably faster, but it also provides a better quality of the results, compared to other algorithms benchmarked in the white paper.

Assistant Professor at Rutgers University, Dr. Todd P. Michael, states, ‘The speed of CLC bio’s new algorithm for reference assembly of Next Generation Sequencing data raises the bar to a level currently unmatched by any competitor. When CLC bio continues this impressive rate of development, and eventually also handles SOLiD’s Color Space analysis in the same convincing manner, this could easily become a de facto tool for scientists working with Next Generation Sequencing analysis.’

Instead of using around 3 to 4 hours assembling 8.5 million reads against a whole human genome, CLC bio’s assembly algorithm accomplished the same calculation in little more than half an hour, which means at least 5 times faster than the closest competitor.

For the assembly of large data sets, the increase in speed is even bigger: When assembling 86 million reads against the whole human genome, CLC bio’s assembly algorithm is more than 14 times faster, meaning an assembly normally taking almost 40 hours can be done in less than two! At the same time, CLC bio’s algorithm provides a better quality of the results delivered with more than 85% accuracy, compared to around 83% for the other algorithms in the white paper.

Another highly interesting aspect of this improved assembly algorithm is the modest requirements of physical memory - at no point during the benchmark tests did CLC bio’s algorithm require more than 8GB RAM.

The benchmark tests were conducted by comparing both 8.5 million reads and 86 million reads against a whole human genome, kindly supplied by the Beijing Genomics Institute. The data set for the benchmark tests was sequenced on Illumina’s Solexa platform and each read had a length of 35 nucleotides.

Once the assembly algorithm will be released in August, it will be available both in a command-line version on CLC bio’s Bioinformatics Cell platform and through CLC Genomics Workbench, which offers an intuitive graphical interface for analyzing and visualizing Next Generation Sequencing data. CLC bio’s white paper is free to download for everyone at www.clccell.com/ngs

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

• Development of bioinformatics software and hardware based on the latest scientific findings
• User-friendly, integrated and intuitive cross-platform software solutions
• Continuous focus on customer needs and superior customer service
• Frequent product updates including the latest IT technologies and bioinformatics algorithms
• A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Aarhus, Denmark — June 12, 2008 — Today, CLC bio released their new Next Generation Sequencing (NGS) solution, CLC Genomics Workbench, which incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of a typical NGS workflow.

CLC Genomics Workbench is the first comprehensive analysis package which can analyze and visualize data from all the major NGS platforms, such as SOLiD by Applied Biosystems, 454 GS flx by Roche Applied Science, Solexa by Illumina, and HeliScope by Helicos.

Director of Scientific Solutions at CLC bio, Dr. Roald Forsberg, PhD, states, “We set out to overcome two major challenges when analyzing Next Generation Sequencing data. One was to eliminate the analysis bottleneck by being able to analyze NGS data faster than it is produced. We overcame that by implementing an accelerated assembly algorithm in CLC Genomics Workbench which preliminary benchmark tests confirm is a very fast assembly algorithm. Secondly, we wanted to deliver user-friendly software which makes powerful NGS analysis software available to all biomedical researchers.”

In benchmark tests, CLC bio has assembled half a million 454 reads against the full E.coli reference genome in around 2 minutes on a dual-core computer with 1 gigabyte RAM. This speed-up, based on integrated SIMD high-performance computing technology, increases even more when using a computer with more CPU-cores and RAM. CLC bio expects to release a benchmark white paper in the near future.

CLC Genomics Workbench 1.0 takes full advantage of “paired end” data, and supports a number of features and work-tasks, such as reference assembly of genomes, de novo assembly of genomes, SNP detection using advanced models, multiplexing, and high-throughput trimming.

Having completed the first version of CLC Genomics Workbench, CLC bio is already pursuing an ambitious development roadmap, which will enhance future softwares with features such as Digital Gene Expression, metagenomics, clustering and assembly of EST and cDNA sequences, large amounts of genomics and transcriptomics downstream analyses, and workflow support.

CLC Genomics Workbench has already been chosen as Next Generation Sequencing platform for all Danish universities. To read more about CLC Genomics Workbench go to: www.clcbio.com/genomics

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

• Development of bioinformatics software and hardware based on the latest scientific findings
• User-friendly, integrated and intuitive cross-platform software solutions
• Continuous focus on customer needs and superior customer service
• Frequent product updates including the latest IT technologies and bioinformatics algorithms
• A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Services to accelerate programs from biological target to first-in-man use Idealp-Pharma is launching fully integrated drug discovery and preclinical development services combining medicinal chemistry, cheminformatics,
screening, early ADMET and preclinical development capabilities to speed up
partner’s and client’s small molecules programs from biological target to firstin-
man use.

According to Serge Petit, PhD, President and CEO, “Being a one-stop-shop company adds significant value because the lead optimisation process involves iterative cycles for incremental optimization. The main advantages of our one-stop-shop service are to have access to all the experimental data, to be able to refocus the synthesis program and then to make the best decision for the lead optimisation process in accordance with our customers’ specifications.”

“Idealp-Pharma manages its customers’ hit discovery and validation, hit-to-lead
progression and lead-to-candidate process. Our aim is to deliver chemically and
biologically validated hits, accelerating lead optimization and identying IND candidate for our customers”, said Serge Petit. Idealp-Pharma supports also its client’s drug discovery activities by providing modular and customized services such as medicinal chemistry and cheminformatics studies.

More information about integrated drug discovery services can be found at www.idealp-pharma.com
About Idealp-Pharma

Idealp-Pharma’s aim is to expand partner’s drug pipeline by accelerating drug
discovery process from the biological target to first-in-man use. Idealp-Pharma
provides a range of flexible services: including fully integrated drug discovery and preclinical development, medicinal chemistry and cheminformatics.

Idealp-Pharma’s purpose-built lab covers a total of 2000 square meters. Idealp-Pharma now employs 60 staff. More information about Idealp-Pharma can be found at www.idealp-pharma.com

Aarhus Denmark, July 3rd, 2008 – Beijing Genomics Institute (BGI) has signed a global site license agreement for CLC bio’s Next Generation Sequencing solution, CLC Genomics Workbench. The site license covers all researchers at all BGI sites, both inside and outside of China.

Head of Bioinformatics Division at BGI, Ruiqiang Li states, “We have chosen CLC Genomics Workbench as our platform for analyzing Next Generation Sequencing data after testing several commercial solutions, because it’s simply in a league of its own when it comes to flexibility and the way the Next Generation Sequencing tools can be used together with our own algorithms. In an organization of our size - with seventeen Illumina GA analyzers, as well as two AB/SOLiD and three Roche/454 Next Generation Sequencing machines, all of them running at full capacity - efficient workflows are of critical importance. We can support and expand our workflows by giving our scientists easy access via the Workbench to our own in-house developed algorithms. In no time, CLC Genomics Workbench has proved amazingly popular with our internal researchers, due to the fast, user-friendly and versatile platform it provides.”

Director of Partner Sales at CLC bio, Michael Heltzen states, “We are most thrilled to have agreed on a global site license with one of the best bioinformatics and sequencing facilities in the world, only four weeks after our solution for analyzing and visualizing Next Generation Sequencing data was released. Furthermore, we are honored that the famous bioinformatics researchers from BGI have chosen our Workbench as a working platform for both our and their own algorithms, side by side. CLC Genomics Workbench will help the scientists at BGI with their daily research, including prestigious projects like the Giant Panda Genome Project and the 1000 Genomes Project.”

CLC Genomics Workbench is the first comprehensive analysis package which can analyze and visualize data from all the major NGS platforms, such as Solexa by Illumina, SOLiD by Applied Biosystems, 454 by Roche Applied Science, and HeliScope by Helicos. CLC Genomics Workbench takes full advantage of “paired end” data and supports a number of features and work-tasks, such as reference assembly of genomes, de novo assembly of genomes, SNP detection using advanced models, multiplexing, and high-throughput trimming. Read more about it at: www.clcbio.com/genomics

CLC Genomics Workbench is available for Mac OS X, Windows and Linux.

About Beijing Genomics Institute

Beijing Genomics Institute is one of the leading global Genomics Institutes in the world, established in July 1999. Since then, BGI has grown rapidly and is partner in a number of international consortiums, including partnerships with the Wellcome Trust Sanger Institute, NIH and NHGRI on the 1,000 Genomes Project. BGI now has a number of research locations including major sites in Shenzhen and Beijing.

BGI aims to advance the understanding of biology and medicine through the use of large-scale sequencing and bioinformatics analysis. The institute also offers sequencing services to the international community. BGI promotes the use of genome-scale scientific approaches and strongly supports collaborative efforts in order to achieve this goal.

For further information, please contact:
Jia Ye, Spokesperson
Beijing Genomics Institute, Shenzhen
Tel: +86 755 25273910
Fax: +86 755 25273620
E-mail yejia@genomics.org.cn

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

• Development of bioinformatics software and hardware based on the latest scientific findings
• User-friendly, integrated and intuitive cross-platform software solutions
• Continuous focus on customer needs and superior customer service
• Frequent product updates including the latest IT technologies and bioinformatics algorithms
• A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

Aarhus Denmark — July 10, 2008 — On July 1st, CLC bio moved their Danish headquarters to a newly built office building in the Katrinebjerg area - a fast growing Danish ICT community which also features high-tech companies Google, VMware, and B&O, to name a few - as well as the University of Aarhus and the new interdisciplinary nanoscience center, which is currently under construction.

CEO at CLC bio, Thomas Knudsen, states, “This is yet another big step up for us, having outgrown our previous location at the Science Park. Now we reside in a modern office building, where we occupy the entire top floor with a beautiful view of Aarhus and the bay. This move signifies the growth of the company, going from a startup to being an established company - and we’re not stopping here. Our new office leverages plenty of opportunities to grow in the future and we think the future is looking bright for our company!”

CLC bio was established in January of 2005, and has since grown to close to fifty employees, with offices in Aarhus, Denmark; Boston, USA; Nottingham, UK; Rio de Janeiro, Brazil; New Delhi & Hyderabad, India. Currently, CLC bio is working on establishing another new office in Asia, which is slated to open later this year.

CLC bio’s bioinformatics solutions have proven highly popular in a relatively short time span, with close to one million software downloads and more than 75,000 users in three years, since the first software release.

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

• Development of bioinformatics software and hardware based on the latest scientific findings
• User-friendly, integrated and intuitive cross-platform software solutions
• Continuous focus on customer needs and superior customer service
• Frequent product updates including the latest IT technologies and bioinformatics algorithms
• A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price