Archive for the ‘ChemInformatics’ Category

Plexxikon Receives Key Patents on Novel Compounds for Multiple Programs

Last Updated on Friday, 27 March 2009 10:00 Written by admin Friday, 27 March 2009 10:00

BERKELEY, Calif.–(BUSINESS WIRE)–Plexxikon Inc. today announced the issuance of key composition-of-matter patents covering novel compounds discovered through the companyâ€™s Scaffold-Based Drug Discoveryâ„¢ platform. Plexxikonâ€™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 companyâ€™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 companyâ€™s PPAR (peroxisome proliferator-activated receptor) program yielding novel therapeutic opportunities for metabolic disorders and other diseases.

â€œWe are pleased to be adding these additional patents to our growing and broad intellectual property portfolio,â€ stated K. Peter Hirth, Ph.D., chief executive officer of Plexxikon. â€œPlexxikonâ€™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.â€

In contrast to fragment-based approaches, Plexxikonâ€™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, Plexxikonâ€™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 companyâ€™s synthetic and medicinal chemistry capabilities leading to the discovery of Plexxikonâ€™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 companyâ€™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 companyâ€™s preclinical development programs, candidates are being developed for the treatment of rheumatoid arthritis, multiple sclerosis and other autoimmune diseases.

Plexxikonâ€™s proprietary Scaffold-Based Drug Discoveryâ„¢ 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.

Posted under ChemInformatics, Clinical Trials, Compound Libraries, Discoveries, Innovations and Patents, Drug-Like Compounds, North America, Press Releases, Targeted Libraries | No Comments

Molecular Fingerprints Point The Way To Earlier Cancer Diagnosis And More Targeted Treatment

Last Updated on Friday, 27 March 2009 09:52 Written by admin Friday, 27 March 2009 09:52

ScienceDaily (Mar. 27, 2009) â€” 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 â€“ like when it’s helping an embryo develop â€“ 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.

Posted under Cancer Research, ChemInformatics, North America, Proteomics | No Comments

ZINC Database – emolecule repository

Last Updated on Monday, 12 January 2009 03:52 Written by Editor Monday, 12 January 2009 03:52

What is ZINC? It is a free database of millions of commercially-available compounds for virtual screening in ready-to-dock format.

Why is it needed? Compounds that are available today can become unavailable in six months because of unavailability of the underlying reagents. For most vendors, the list of available compounds is significantly smaller than the list of compounds they have made in the past. If you are doing virtual HTS you are probably interested in a quick verification of predicted hits. So, it makes sense to know which compounds can be ordered quickly i.e turn-around time of 30 days or less.

Why is this a difficult task? Typically, this means maintaining databases of compounds and updating them on regular basis. In my experience, I have received updates from vendors as frequently as a dozen times an year to none at all. Staying up-to-date with chemical vendor catalogs can quickly become a daunting challenge for small labs and organizations who donâ€™t have dedicated people for this purpose.

How does ZINC help? They stay up-to-date with vendors. At any time, you can download the original 2D vendor catalog from ZINC. They have grown significantly in size and use in the last 5 years. More consumers typically means lesser bugs and better updated catalogs.

Of course, ZINC allows you to download the 3D formats as well. I have not found any documentation on their 2D to 3D pipeline. It may be available upon request. Going from 2D to 3D is a whole bag of tricks. One could potentially glue together applications provided by software vendors such as Open Eye or Molecular Networks to create a 2D to 3D pipeline. While it is great to have your own pipeline as it enables greater control on bugs and issues, it is significant amount of algorithmic work. Therefore, for some organizations, having a ready to dock 3D format is a considerable time saving.

Any Gotchas? I have not found any useful information or discussion at the ZINC forums. Ideally, it would be good to know the quality of vendors. Are these vendor lists as up-to-date as they claim to be? What is the typical ordering time? Quality of drug like compounds is also an issue.

In ZINCâ€™s 3D formatted database,Â the compounds are renamed using ZINC ID and any information about the original vendor catalog ID is lost. This can be tricky when ordering compounds from vendors. The vendor catalog ID can be retrieved by going to the original vendor catalog and matching the compound but this translates to extra algorithmic work.

Nutshell? Nevertheless this is the best free resource on the web that allows user to download latest vendor compounds for virtual screening. The closest competition, emolecules charges upwards of $20K for doing the same.

Source: biotechnorati.wordpress.com
Other online searchable by structure databases:

Bioscreening Compounds

Compounds and Compound Libraries from TimTec

Posted under ChemInformatics, Compound Libraries, Drug-Like Compounds, New Products, North America, Press Releases | No Comments

Virtual Screening Gives Drug Design a Boost

Last Updated on Wednesday, 19 November 2008 05:07 Written by Editor Wednesday, 19 November 2008 05:07

San Diego, CA (OBBeC) â€“ 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.

Around 150,000 people per year get African sleeping sickness. Unless treated, the illness is invariably fatal and with limited treatment available. The commonly used medicines to treat the disease are either difficult to administer, expensive, or toxic. For example, the widely used drug melarsoprol is essentially arsenic dissolved in antifreeze. Only one new drug to treat African sleeping sickness has appeared in the past 50 years. “The biomedical significance of new drugs to treat trypanosomal diseases, which occur mainly in developing countries, would be huge,” says Peter Preusch, of the National Institute of General Medical Sciences (NIGMS).

The research team led by computational biologist J. Andrew McCammon, have identified five compounds that could provide the solution for this problem. The compounds block the activity of the trypanosomal REL1 enzyme, which the parasite needs in order to survive. According to the press report, REL1 has a unique role in the trypanosome’s mitochondria, the organelles that provide the parasite with energy. The enzyme joins mitochondrial messenger RNA fragments, making them whole and functional. These messages are the blueprints for making the proteins that power the mitochondria. Without REL1, some of these mitochondrial proteins are missing, which slows energy production and kills the parasite.

The results appeared online this week in the Proceedings of the National Academy of Sciences.

New Computational Approach
The approach developed by McCammon’s group uses a combination of several computational tools. It starts with a detailed model of the biological target –REL1 in this case — derived from X-ray crystallography. It then uses biophysical principles to find all the ways in which the protein can twist, turn, and wiggle.

“We know that proteins aren’t static,” said Dr. Rommie Amaro, the lead author of the study. “They’re dynamic moving machines. The unique thing about this approach is that it allows full protein flexibility.”

Though, predicting the countless shapes that a large, complex molecule like a protein can adopt requires enormous computer power. A REL1 analysis done on a regular desktop could take years while those on supercomputers take a few days. The computers used in this study, explains Amaro, are among the most powerful in the country.

Once they know the dynamics, the researchers carry out a virtual screen of hundreds of compounds, testing their ability to stick to a key part of REL1. Compounds that stick tightly have a good chance of inhibiting the enzyme’s activity and killing the parasite.

“It’s rather like a child’s puzzle where one must put the cow-shaped piece into the cow shaped hole in the barnyard scene,” explains Preusch, who oversees computational biology grants at NIGMS, which partially funded the work. But like real cows, he added, molecules are in constant motion. “McCammon has developed methods that take these motions into account, as well as the changes in a protein’s shape that can occur upon binding.”

The virtual screen predicted that about a dozen compounds would bind tightly to REL1′s hot spot. Knowing that a slightly different version of one of these might stick even more tightly, the researchers searched a large database of existing compounds for structurally similar molecules.

When they tested their best candidates experimentally, five inhibited REL1. These five molecules, which block the activity of a crucial trypanosomal enzyme, can now serve as the basis for future drug design and discovery efforts.

Future Outlook
McCammon’s computational method has already proven its utility for designing other important drugs. His group used it to develop a model for a new class of drugs to treat AIDS that led to raltegravir, which the Food and Drug Administration approved in 2007. McCammon’s team also used the method to identify promising drug candidates for treating H5N1 avian flu.

McCammon’s team is now focusing on designing even better inhibitors of trypanosomal REL1. The goal is to tweak the inhibitors’ structures, making them bind even more tightly to REL1 and less tightly to related human enzymes. Binding to human enzymes makes an inhibitor less attractive as a drug candidate because the interactions could cause undesired side effects.

This work, says McCammon, “tells a story that may be of wide interest.” The computational approach not only could lead to improved drugs for treating African sleeping sickness, but it could be used to develop compounds for use against other illnesses for which we need better medications.

Posted under BioInformatics, ChemInformatics, Compound Screening, Drug-Like Compounds, HIV Research, North America, Press Releases, Targeted Libraries | No Comments

Otava develops virtual screening system

Last Updated on Tuesday, 11 November 2008 03:01 Written by admin Tuesday, 11 November 2008 03:01

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.

Posted under BioInformatics, ChemInformatics, Europe, Press Releases | No Comments

CLC bio release white paper on the world’s fastest Next Generation Sequencing assembly algorithm

Last Updated on Monday, 28 July 2008 07:03 Written by admin Monday, 28 July 2008 07:03

Aarhus Denmark — July 23, 2008 — CLC bio has just released a scientific white paper which confirms, that, in benchmarking tests, CLC bioâ€™s new algorithm for assembly of Next Generation Sequencing data is the fastest one available. Not only is CLC bioâ€™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, â€˜The speed of CLC bioâ€™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 SOLiDâ€™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.â€™

Instead of using around 3 to 4 hours assembling 8.5 million reads against a whole human genome, CLC bioâ€™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 bioâ€™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 bioâ€™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 bioâ€™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 Illuminaâ€™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 bioâ€™s Bioinformatics Cell platform and through CLC Genomics Workbench, which offers an intuitive graphical interface for analyzing and visualizing Next Generation Sequencing data. CLC bioâ€™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 bioâ€™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

Posted under BioInformatics, ChemInformatics, Discoveries, Innovations and Patents, Europe, Genomics & Pharmacogenomics, Press Releases | No Comments

CLC Genomics Workbench – CLC bio releases Next Generation Sequencing data analysis solution

Last Updated on Friday, 18 July 2008 07:00 Written by admin Friday, 18 July 2008 07:00

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, â€œWe 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.â€

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 â€œpaired endâ€ 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 bioâ€™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

Posted under BioInformatics, ChemInformatics, Europe, Genomics & Pharmacogenomics, New Products, Press Releases | No Comments

Idealp-Pharma launches Â« hit-to-candidate Â» services

Last Updated on Friday, 18 July 2008 06:36 Written by admin Friday, 18 July 2008 06:36

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
partnerâ€™s and clientâ€™s small molecules programs from biological target to firstin-
man use.

According to Serge Petit, PhD, President and CEO, â€œBeing 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.â€

â€œIdealp-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 customersâ€, said Serge Petit. Idealp-Pharma supports also its clientâ€™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-Pharmaâ€™s aim is to expand partnerâ€™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-Pharmaâ€™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

Posted under ChemInformatics, Drug-Like Compounds, Europe, HT Screening, Medicinal Chemistry, Press Releases | No Comments

Beijing Genomics Institute signs global site license with CLC bio for Next Generation Sequencing software platform

Last Updated on Friday, 18 July 2008 05:34 Written by admin Friday, 18 July 2008 05:34

Aarhus Denmark, July 3rd, 2008 â€“ 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, â€œWe have chosen CLC Genomics Workbench as our platform for analyzing Next Generation Sequencing data after testing several commercial solutions, because itâ€™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.â€

Director of Partner Sales at CLC bio, Michael Heltzen states, â€œWe 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.â€

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 bioâ€™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

Posted under Asia, BioInformatics, ChemInformatics, Collaborations, Genomics & Pharmacogenomics, North America, Press Releases | No Comments

CLC bio moves to new Headquarters in Denmark

Last Updated on Tuesday, 15 July 2008 07:18 Written by admin Tuesday, 15 July 2008 07:18

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, â€œThis 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!â€

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 bioâ€™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 bioâ€™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

Posted under BioInformatics, ChemInformatics, Europe, Press Releases | No Comments

CLC bio to collaborate with Microsoft on integrating life science technology

Last Updated on Wednesday, 30 April 2008 05:02 Written by admin Wednesday, 30 April 2008 05:02

Boston, USA — April 29, 2008 — Today at the Bio-IT World Conference & Expo in Boston, USA, CLC bio announced collaboration with Microsoft Corp. on integrating CLC bio’s extensive bioinformatics solutions with Microsoft’s software platform, for the benefit of companies, corporations, and institutions in the biotech, pharmaceutical, and life science sectors. CLC bio has already added support for Microsoft SQL Server in its database solution, CLC Bioinformatics Database, as well as support for Microsoftâ€™s high-performance computing solutions, Windows Compute Cluster Server 2003 and Windows HPC Server 2008.

Dr. Rudy Potenzone, worldwide pharmaceutical industry technology strategist at Microsoft Corp. and director of the Bio IT Alliance, states,
‘We are delighted to work together with CLC bio, a member of the Bio IT Alliance and one of the world’s leading bioinformatics solution providers. This collaboration will ultimately help life sciences firms transition to the Microsoft platform throughout their research and development departments. CLC bioâ€™s tools, fully integrated with the Microsoft Office System, increase ease of use and expand the number of potential users, while reducing administrative overhead and creating a lean workflow. Furthermore, CLC bio’s internationally renowned experts are available for consulting and customized development.’

Jan Lomholdt, Vice President at CLC bio, continues,
‘With our support for Microsoftâ€™s server solutions, the first step in the process has already been taken. The second step is to further advance our collaboration in areas such as Next Generation Sequencing and high-performance computing, which ultimately can help realize the potential of personalized medicine. As a former member of Microsoft’s World Wide Advisory Council, I have first hand experience of the strength and potential Microsoft brings to the table with a collaboration like this, which of course is interesting for a company like ours.’

Windows HPC Server 2008, the successor to Windows Compute Cluster Server 2003, includes a common set of High Performance Computing productivity tools that reaches across desktop and clusters, including a new Parallel Computing Initiative for multicore development. CLC bio’s high-performance computing solution for servers and clusters, CLC Bioinformatics Cell, supports Microsoft’s Message Passing Interface (MPI) in order to run bioinformatics algorithms such as HMMER, ClustalW, and Smith-Waterman on Windows HPC Server 2008 installations.

All CLC bio’s solutions are cross-platform, running on Windows 2000, Windows XP, Windows Vista, as well as Mac OS X and Linux

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 bioâ€™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

Posted under BioInformatics, ChemInformatics, Collaborations, North America, Press Releases | No Comments

Evotec Expands Collaboration with InterMune

Last Updated on Thursday, 6 March 2008 12:32 Written by admin Thursday, 6 March 2008 12:32

Hamburg, Germany | Oxford, UK- Evotec AG (Frankfurt Stock Exchange: EVT) today announced that InterMune, Inc., has signed a second drug discovery contract with Evotec.

Evotec will support InterMune’s research efforts using their medicinal chemistry know-how. In addition, they will utilize their expertise and technologies in computational chemistry, protein production, X-Ray crystallography and ADMET to further characterize active compounds and optimize their potency and selectivity to generate lead molecules for subsequent progression into clinical trials.

This contract expands Evotec’s existing collaboration with InterMune which was initiated in early 2007. This collaboration applies Evotec’s fragment-based drug discovery platform, EVOlutionTM, in combination with their ultra-high-throughput screening (uHTS) technologies to InterMune’s targets.Â To date new lead series have been identified for further optimization. Evotec also provides medicinal chemistry, secondary screening, protein production, X-ray crystallography and ADMET. The financial terms include a technology access fee for access to Evotec’s fragment-based drug discovery platform, EVOlutionTM, plus ongoing research funding.

“With the support of Evotec, InterMune has made considerable progress in their Hepatitis C drug discovery and development program. We are pleased that InterMune saw the value in our proprietary fragment-based drug discovery technology and that it has contributed to the success to their research efforts,” said Dr Mark Ashton, Executive Vice President Business Development Services at Evotec.

Posted under ChemInformatics, Collaborations, Europe, Hepatitis Research, Medicinal Chemistry, Press Releases | No Comments

CLC bio provides bioinformatics solution for vaccine target development to ACE BioSciences

Last Updated on Wednesday, 19 December 2007 08:01 Written by admin Wednesday, 19 December 2007 08:01

Odense & Aarhus, Denmark — December 18, 2007 — ACE BioSciences, an emerging pharmaceutical company focused on developing novel protein-based vaccines and antibodies to address infectious diseases, and CLC bio, the world’s leading bioinformatics solutions provider, today announced a collaborative bioinformatics agreement.

Dr. Ingelise Saunders, Chief Executive Officer at ACE BioSciences said,
‘At ACE BioSciences we place considerable emphasis on selecting partners based on their scientific know-how – and in that regard we recognize CLC bio as the leading company within bioinformatics, with a global reputation and internationally renowned experts. We see this collaboration as a significant opportunity to augment and expand our bioinformatics platform to increase efficiency, enhance our analyses, and accelerate our research.’

Dr. Jannick D. Bendtsen, project manager and Senior Scientific Officer at CLC bio commented,
‘We are looking forward to this collaboration, which is scientifically interesting and challenging. The implementation of our customized software will streamline and fast-track analysis and further increase statistical confidence in the selection of novel candidates for inclusion in the ACE BioSciencesâ€™ development portfolio. Implementation of automated target validation protocols will increase efficiency and the rate of data throughput, improve quality assurance and enhance data security.’

Under the terms of the agreement, CLC bio will upgrade and expand ACE BioSciences’ existing bioinformatics platform to ensure the company is taking advantage of the most up-to-date, relevant, and innovative software, including state-of-the-art protein vaccine target characterization. In addition, CLC bio will provide greater integration and cross-referencing capabilities, securing for ACE BioSciences the ability to apply more extensive statistical analyses to its databases and laboratory information. CLC bio’s customized solution will strengthen ACE BioSciences’ ability to compare, rank, and prioritize potential vaccine targets.

The solution provided to ACE BioSciences consists of a number of CLC workbenches for DNA, RNA, and protein sequence analysis, supplemented with customized bioinformatics modules that are proprietary for ACE BioSciences

Read more about CLC bioâ€™s customized software solutions on:
www.clcbioconsulting.com

About ACE BioSciences

ACE BioSciences is an emerging pharmaceutical company focused on developing novel protein-based vaccines and antibodies to address infectious diseases. It has unique expertise in the extraction and analysis of the cell surface proteins used by pathogens (eg bacteria, viruses and fungi) to interact with and infect human host cells.

The company’s lead product, ACE393, is an injectable vaccine that is on track to become the world’s first commercial vaccine for Travellers’ Diarrhoea caused by Campylobacter infection, having successfully completed Phase I clinical trials in March 2007.

Campylobacter is one of the greatest causes of gastroenteritis in the developed world as well as a significant contributor to travellers’ diarrhoea. The annual global commercial market for a Campylobacter vaccine is estimated to be worth â‚¬ 350 million.

ACE BioSciences aims to develop a portfolio of products independently and in collaboration with other companies and as part of that strategy the company signed a collaborative development agreement with the US Naval Medical Research Center (NMRC) to progress ACE393 through Phase II clinical trials. In addition to ACE393, the company is working on ACE537, an oral, Phase I, Enterotoxigenic E Coli (ETEC) vaccine which has the potential to be the first to market in the US and EU and which combats the single biggest cause of travelers diarrhoea. It is also working on a vaccine for Streptococcus pneumoniae, the bacterium responsible for Pneumococcal disease.The market for a Streptococcus product would be multibillion and ACE BioSciences aims to partner the project.

About CLC bio

CLC bioâ€™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

Posted under BioInformatics, ChemInformatics, Europe, Press Releases | No Comments

CLC bio helps increase productivity with new integrable database solution

Last Updated on Friday, 30 November 2007 06:27 Written by admin Friday, 30 November 2007 06:27

Aarhus, Denmark — November 29th, 2007 — CLC bio, the worldâ€™s leading bioinformatics solution provider, today announced the release of CLC Bioinformatics Database. This powerful and versatile database solution enables research organizations, from small university departments and clinical labs to large biotech and pharmaceutical companies, to maximize their potential, through increased productivity. An increase in productivity will help increase the number of drug candidates, by empowering scientists to do more with their research. In turn this gives companies a more efficient use of R&D budgets.

Dr. Darrol Baker, Sales Manager at CLC bio states,
CLC Bioinformatics Database raises the bar for what can be expected from a database solution! Our development team has focused on eliminating classic obstacles such as different operating systems, limited support for database formats, or limited access to a central storage facility. The security and management facilities in CLC bio’s Bioinformatics Database can potentially help organizations stop misuse or loss of data, as well as help protect their intellectual property rights.

For organizations already having an existing relational database in use for sharing DNA, RNA, and protein sequence data, the CLC Bioinformatics Database interface can be customized to store and retrieve data directly from that database. The result is a solution that enables all users of CLC bio’s software to work directly on – and fully integrated with – the organization’s existing database. This ensures the same data sharing, data searching and data security characteristics as if the database had been a stand alone database – except for the fact that the CLC bio data is now fully integrated with all other sequence data in the organization. The design, API-customization, implementation, and data migration can be carried out by the customer or by CLC bio’s consultants.

As with all other of CLC bio’s solutions, CLC Bioinformatics Database is cross-platform, running on Mac OS X, Windows, and Linux. Additionally, this solution will enable users across various workgroups to work on data in a central, shared, and secure relational database. CLC Bioinformatics Database integrates and runs smoothly with several types of databases, including Oracle, PostgreSQL, and MySQL.

For more information on CLC Bioinformatics Database, go to:
www.clcbio.com/database

About CLC bio

CLC bioâ€™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

Posted under BioInformatics, ChemInformatics, Europe, Press Releases | No Comments

New Database Screening Criteria Improves Identification Of Anticancer Drugs

Last Updated on Tuesday, 20 November 2007 02:41 Written by Fred Tuesday, 20 November 2007 02:41

Scientists in Indiana and Michigan have developed a better way of mining a vast computerized database for chemical nuggets that could become tomorrow’s cancer medications.

The new “data mining” method pinpoints chemical structures with drug-like activity. It could speed the identification and development of new, more effective drugs against breast, prostate, lung and other cancers.

Computers have become a mainstay in the drug discovery process and have led to the identification of dozens of promising anticancer drugs. However, as the amount and complexity of information increases, new analysis methods need to keep pace.

In the new report, David J. Wild and colleagues analyzed data from the National Cancer Institute Developmental Therapeutics Program, a database of 40,000 compounds that have been tested against 60 tumor cell lines. The researchers identified a set of common structural features that can be used to more accurately predict which compounds are most active against cancer cells.

In a series of experiments, they showed that applying these new criteria significantly increased the accuracy rate of identifying drug-like molecules in comparison to standard screening methods.

The journal article”Chemical Data Mining of the NCI Human Tumor Cell Line Database” is scheduled for publication in the Nov./Dec. issue of ACS’ Journal of Chemical Information and Modeling.

Posted under ChemInformatics, Discoveries, Innovations and Patents, North America, Press Releases | No Comments

Upstream Biosciences Launches Chemoinformatics Program to Extend Its Drug Discovery Capabilities

Last Updated on Monday, 12 November 2007 03:53 Written by Fred Monday, 12 November 2007 03:53

Upstream Biosciences Inc. (OTCBB: UPBS) today announced it is establishing a Chemoinformatics Program to extend its drug discovery efforts into additional disease areas. Upstream’s Chemoinformatics Program combines artificial intelligence, advanced computational methods and chemical diversity techniques that will be applied to the company’s proprietary drug scaffolds and compound library. This effort will initially build on Upstream’s recently acquired novel compounds that in laboratory studies demonstrate both human and veterinary potential against major tropical parasitic diseases, including trypanosomiasis and leishmaniasis. Separately, Upstream also announced that it has filed a provisional United States patent on methods for incorporating data on genetic variations it will generate in its biomarker discovery efforts as well as those in the public domain into the Chemoinformatics program.

Upstream obtained exclusive worldwide rights to its existing library of novel compounds and potential drug scaffolds through the company’s acquisition of Pacific Pharma Technologies. Upstream intends to combine its state-of-the-art computational approaches with advanced chemistries to produce novel compounds with enhanced efficacy and reduced toxicity for conditions such as infectious diseases and cancer. The proprietary scaffolds acquired by Upstream will also be used to develop additional compound libraries.

Upstream also intends to use relevant genetic variations it will identify in its biomarker discovery program as well as genetic variations in the public domain as inputs into the Chemoinformatics Program. These genetic variations may include differences that impact drug metabolism, treatment efficacy or susceptibility to drug toxicity or to the development of drug resistance. In some cases researchers may “design around” a variation to minimize its impact, or conversely, data on the variation could be used by researchers to help achieve specific drug attributes.

“Our Chemoinformatics Program will focus on optimizing our proprietary compound library and enhancing our ability to use it to discover additional novel drugs,” said Joel L. Bellenson, Chief Executive Officer of Upstream. “The innovative drug discovery approach we are developing complements the core competencies we are applying in our biomarker discovery programs and potentially positions us to expand into additional therapeutic areas. The provisional patent filing we announced today brings together these two programs, covering methods for applying data on genetic variations that we will generate in the biomarker program to our computational drug discovery activities.”

Mr. Bellenson and Upstream President Dexster Smith bring considerable expertise to these computational programs, having pioneered some of the first computer-based systems for managing combinatorial chemistry and pathogen screening data as co-founders of Pangea Systems/Doubletwist, which made history in 1999 by providing computational tools for annotating the first draft of the human genome.

The provisional United States patent filing is titled, “Method for combining 3D quantitative chemical structure activity relationships (QSAR) of compounds with genetic variation of drug targets and metabolic enzymes to optimize efficacy, provide predictive toxicology, and address drug resistant microorganisms.”

About Upstream Biosciences Inc.

Founded in 2004, Upstream Biosciences is an emerging leader in the discovery and development of novel drugs for tropical parasitic diseases and in the development of genetic diagnostics for cancer susceptibility and drug response. Upstream’s innovative approach to drug discovery and its proprietary data mining pipeline enable it to apply advanced computational approaches to generating novel drug candidates and to locating and analyzing the genetic variations important to disease progression and drug response. For more information visit www.upstreambio.com.

Notice Regarding Forward-Looking Statements: This news release contains “forward-looking statements”, as that term is defined in Section 27A of the United States Securities Act of 1933, as amended, and Section 21E of the United States Securities Exchange Act of 1934, as amended. Statements in this press release which are not purely historical are forward-looking statements and include any statements regarding beliefs, plans, expectations or intentions regarding the future. Such forward-looking statements include, among others, the expectation and/or claim, as applicable, that: (i) the Company intends to combine its state-of-the-art computational approaches with advanced chemistries to produce novel compounds with enhanced efficacy and reduced toxicity for conditions such as infectious diseases and cancer; (ii) the intent to use relevant genetic variations it will identify in its biomarker discovery program as well as genetic variations in the public domain as inputs into the Chemoinformatics Program; (iii) genetic variations may include differences that impact drug metabolism, treatment efficacy or susceptibility to drug toxicity or to the development of drug resistance; and (iv) the Company’s drug discovery approach complements the core competencies it is applying in its biomarker discovery programs and potentially positions the Company to expand into additional therapeutic areas. Actual results could differ from those projected in any forward-looking statements due to numerous factors. Such factors include, among others:

(i) the risk that the Company does not execute its business plan; (ii) the inability of the Company to keep pace with technological advancements in the field of genetic diagnostics and the treatment of tropical parasitic diseases; (iii) the Company’s inability to adequately protect its intellectual property or the Company’s inadvertent infringement of third party intellectual property; (iv) the Company not being able to retain key employees; (v) competitors providing better or cheaper products and technologies; (vi) markets for the Company’s products not developing as expected; (vii) the Company’s inability to finance its operations or growth; (viii) inability to obtain all necessary government and regulatory approvals; (ix) the inability to effectively market and commercialize the Company’s technologies, including the establishment of viable relationships with third parties; and (x) the conference not proceeding as planned for any reason. These forward-looking statements are made as of the date of this news release and the Company assumes no obligation to update the forward-looking statements, or to update the reasons why actual results could differ from those projected in the forward-looking statements. Although the Company believes that the beliefs, plans, expectations and intentions contained in this press release are reasonable, there can be no assurance those beliefs, plans, expectations, or intentions will prove to be accurate. Investors should consider all of the information set forth herein and should also refer to the risk factors disclosed in the Company’s periodic reports filed from time-to-time with the Securities and Exchange Commission and available at www.sec.gov.

Posted under Business and Investment, ChemInformatics, North America, Press Releases, USA and Canada | No Comments

Reducing the ‘what ifs’ in drug discovery

Last Updated on Thursday, 25 October 2007 12:47 Written by Fred Thursday, 25 October 2007 12:47

With emergence of specialised software applications, drug discovery has become a highly cost-competitive area for Indian pharma companies. Nagesh Joshi examines the use of specialised software applications in drug discovery

Drug discovery was the main aim of any pharma company, prior to the advent of the doctrine that companies could have a profitable business model without selling a drug they actually ‘invented’. A pharma company could just make changes in the ‘process’ and have a ‘generic’ version of a drug. This doctrine was supported by most of the developing economies in order to protect their populations from the over-pricing of the patented ‘original’ versions of various life saving drugs.

After the advent of WTO norms, which have been accepted by almost all nations now, product patents on original drugs have become recognisable even in developing nations. Companies have been forced to wait until the patents lapse to market generic versions.

The drug discovery process has become more and more complex, time consuming and very expensive, causing a many-fold increase in the R&D budgets of pharma companies. It still remains the best chance to make money for a pharma company, but has become unaffordable for all except the so-called ‘big pharma’. However, the other leaner business models are emerging. One case-in-point being the recent new drug development agreement between Nicholas Piramal India Limited (NPIL) and Eli Lilly, wherein NPIL will develop, and in certain regions, commercialise a select group of Lilly’s pre-clinical drug candidates.

Biopharmaceutical companies are also coming up with cheaper, faster and more efficient ways of getting to new chemical entities. The advent of in-silico technologies for optimising the R&D pipeline from basic biology phase to chemistry phase, to lead optimisation and so on up to clinical trials has also led to considerable improvements in efficiency.

“Another business model, especially important to India, is to spin off R&D as a separate business entity to raise resources, as well as reduce risk. Variants of this strategy have been followed by Ranbaxy, Dr Reddy’s Laboratories, NPILâ€”the three largest pharma companies of Indiaâ€”for high-rewards in the area of research and development,” says Dr Vijay Chandru, Chairman, Co-Founder & Chief Executive Officer, Strand Life Sciences.

An important trend here is the rising investment in health care related expenses on IT by many developing nations, including India, that are opening new doors.

Need for computing software

The traditional method of drug discovery, as known to all pharma companies and research scientists, is a highly serendipitous process. Therefore, the cost of developing a successful new molecule also reflects the expense of failed molecules. Thus, the scientists/researchers are always looking for ways to avoid failures and to improve their chances of success.

Therefore, certain technologies, which facilitate the enhancement of predictability, for example, computer aided drug design (CADD) or molecular modelling, are finding increased acceptance in the process of drug discovery. Most innovation driven research companies are utilising CADD as a fundamental step in optimising their research activities and finding ways to arrest the failures earlier. There are computing softwares which help knowledgeable scientists in the ‘what-if analysis’ by studying various molecule-protein interaction scenarios, comprehensive exploration of the chemical and biological space without actually making them, design better leads, detect problems at molecular level at an early stage so that time and effort in the essential experimental work in the laboratory is optimised, thus improving overall research productivity.

There are two main challenges that the drug discovery domain is facing presently:

1. The rising cost of the process of drug discovery itself, with scarce talented resources and rising input costs affects the efficiency of the process

2. The intellectual property rights (IPR) protection issues arising because different countries follow different norms affects the effectiveness of the process

Apart from these two, there are other nagging issues such as, the limited success pharma and biotech companies have achieved in terms of reducing the development time period, in spite of the availability of several reliable in-silico methods and technologies.

The rising number of generic companies as well as ‘one product’ or ‘one technology’ companies are reducing the market share enjoyed earlier by the major pharma companies, putting pressure on their bottom lines ,as well as top lines.

The present scenario

While the technologies have not matured to the extent that their output is always right, technology products, as a tool in the hands of a knowledgeable scientist, is a significant contributor towards improving research productivity. Therefore, the expectations from technology are increasing day by day.

“Amongst the few technology providers in CADD and molecular modelling domain, companies which are innovative and are keeping pace with the evolving science are likely to survive and grow rapidly. On the other hand, significant opportunities for students are emerging in the CADD area, as it is increasingly adopted as a fundamental activity in most drug discovery programs globally,” says Atul Aslekar, Chief Executive Officer, VLife Sciences.

“A typical research program consists of two distinct phasesâ€”discovery and development. In the first phase, CADD is increasingly used as a starting point”, says Dr Sudhir Kulkarni, Principle Scientist at VLife Sciences.

CADD provides a strong tool to scientists, which enables them to custom design a new molecule, keeping in mind the specific requirements of protein causing disease condition. It also helps scientists to try out various ideas in a short time, as compared to conventional methods. In-silico technologies like CADD enhance the exploration space for a new molecule. Novel virtual screening technologies are enabling scanning of the chemical possibilities on variety of criteria such as ligand binding, absorption, distribution, metabolism, and excretion (ADME) properties, etc. CADD technologies are helping in understanding drug-target interactions at a molecular level, which helps in designing better drug candidates. In the hands of an able scientist, CADD can not only significantly save the invested time, but can also lead to higher quality of pre-clinical candidates with higher probability of success, in later investigations.

Different research organisations, trade magazines and industrial bodies have put the research expenses going into drug discovery anywhere between $500 million-1.2 billion. However, an expenditure of about $900 million-1 billion may be considered as a reliable estimate from the amount of R&D expenses disclosed by all the big pharma companies, and the number of new drugs they have been able to discover over the last decade.

Anu Acharya, Chief Executive Officer, Ocimum BioSolutions, places the potential size of the drug discovery software market as $2 billion. According to her, “The drug discovery software market in India is at a nascent to mid-maturity stage.”

An estimate of the failure rate could be had from the reality, that of the approximately 5,000 compounds that enter the medicinal chemistry and drug metabolism and pharmaco-kinetics (DMPK) evaluation phases of drug discovery, only one succeeds and becomes a drug.

“There are several pain points that specialised software tools can help relieve for scientists working on drug discovery. Specialised software can either be used to manage data and analyse it or to generate very large amounts of data by carrying out experiments on a scale hitherto impossible,” informs Dr Chandru of Strand Life Sciences.

The software applications used for generation of data are usually in the preliminary stages of the drug discovery process. These stages involve basic biological and chemistry research for identifying targets, biomarkers, genes responsible for the disease etc. on the biology side. On the chemistry side, it involves a lot of high throughput screening processes to quickly and cheaply eliminate potentially less useful hits. Software tools used during this stage run specialised algorithms and applications for identifying patterns, outliers and specific features in data points generated through experiments. Some applications, such as the embedded software in various gene expression analysis equipment, help in generation of such data points.

In the later stages of the process, data management and analysis for better and more efficient decision support become more important. The software applications used here are focused more on statistical data analysis and modelling ,using various machine learning-based techniques.

The main steps in which software applications prove helpful are QSAR modeling, computational chemistry modelling for early ADME-Tox and DMPK predictions. Recently, data at the stage of clinical trials has also been put to statistical tests using high-end statistical analysis software tools.

Areas where molecular modelling may prove helpful

Quality of the software suite

Reliability and predictability of performance, consistent delivery and accuracy of output, equal ease-of-use for beginner, moderate and advance skilled users, and flexibility of analysis/performance options for users are few important qualities of good software. A vendor should ideally, have high quality resources for developing the software with rich experience in having actually done the laboratory experimentation that the software is going to aid in, have quality development, data security and testing processes in place, rapid and end-to-end customer support capabilities in case of queries and/or failures of any scale and type.

Phases in drug discovery that can use software:

The following stages require software applications to support efficient decision making at each of these stages. They are arranged in the order of appearance in the drug discovery pipeline:

1. Systems biology modelling
2. SNP & gene expression analysis
3. Biomarkers
4. Pathway analysis
5. Molecular profiling
6. Computational chemistry
7. Focused libraries
8. QSAR modeling
9. Lead optimization
10. ADME-Tox

Software implementation checklist

Product pricing

The software products used in drug discovery domain are priced differentially. Pricing is highly flexible as the deliverables are quite readily customisable. Most vendors prefer enterprise-wide licensing deals with annual maintenance contracts, since they usually have lock in periods (commonly three years).

The more advanced or specialised products are still sold on outright purchase basis. These are typically for very specialised and/or limited access use. Drug development agreements are on the rise and industry analysts predict many more pharma companies will follow the model set by the NPIL-Lilly deal. The GVK BIO Wyeth Hyderabad Chemistry Center, a built-to-suit research centre for Wyeth Pharmaceuticals located in Hyderabad, is another example.

In conclusion, though the market for drug discovery/development software products is still at a fairly nascent phase in India, it seems set to grow as Indian pharma companies position themselves as partners in drug discovery and developers. Companies like Strand Lifesciences, Ocimum BioSolutions, VLife Sciences and the likes will reap the benefits of being the early birds in a sunrise industry.

Posted under Asia, ChemInformatics, Drug-Like Compounds, Press Releases | No Comments

BIO-Europe 2007 to Offer Free Access to DMS Biotech Industry Database

Last Updated on Tuesday, 16 October 2007 06:45 Written by admin Tuesday, 16 October 2007 06:45

Carlsbad, CA, and Washington D.C., Sept. 27, 2007 â€“ EBD Group and the Biotechnology Industry Organization (BIO) today announced a collaboration with DMS Data Systems, a provider of online life sciences industry data, to provide BIO-Europe 2007 attendees with access to the DMS Data Center, which contains information on specific diseases, technologies and other market-specific data. The DMS Data Center is now accessible at http://www.dmsdatacenters.com/beddc/

The BIO-Europe 2007 International Partnering Conference will be November 12-14, 2007 in Hamburg, Germany at the Congress Center Hamburg.

â€œWe are pleased to further enhance the BIO-Europe partnering experience by offering delegates access to comprehensive, current and in-depth industry information. DMS Data Center provides yet another dimension of information to consider when evaluating specific partnering opportunities and developing successful partnering strategies,â€ said Carola Schropp, Managing Partner, EBD Group.

â€œDMS is a perfect complement to the partnering opportunities offered by the BIO-Europe conferences,â€ said Richard Franklin, chairman of DMS Data Systems. â€œDMS Data Center gives BIO-Europe delegates the in-depth and comprehensive industry data they need to make educated decisions about the deals they consider and pursue.â€

About BIO-Europe 2007

BIO-Europe 2007 is the largest stand-alone partnering conference for the global biotech industry. Delegates from all parts of the biotechnology value-chain come to BIO-Europe to efficiently identify, engage and enter into the strategic relationships that drive their business successfully forward. It is anticipated that this yearâ€™s BIO-Europe partnering event will draw 2,000 industry attendees from almost 40 countries, representing more than 1,100 companies for three days of high-level networking. BIO-Europe features the industryâ€™s most advanced web-based partnering system that delegates will use to generate in excess of 7,000 partnering meetings. BIO-Europe features an exceptional international exhibition where companies, organizations and biotech regions can showcase their offerings. Additional networking opportunities will abound at evening and special events. BIO-Europe is co-organized by EBD Group and Biotechnology Industry Organization, in partnership with European Biopharmaceutical Enterprises.

About DMS

DMS Data Systems designs, develops, and sells on-line, searchable, industry-specific databases, with a focus on the Biomedical industries, including the pharmaceutical, biotechnology, bioinformatics, diagnostics, medical device, equipment, drug delivery, and contract research and manufacturing sectors.

Its products, including the NewsAnalyzer, the IndustryAnalyzer, Clinical Trials Plus, and the DMS Data Center, are valuable tools for business development, clinical development, competitive intelligence, strategic planning, and due diligence.

These products are used by biomedical companies, licensing and competitive intelligence professionals, investment banks, venture capital companies, contract research organizations, and University technology transfer offices, as well as executive search firms, publishing companies, public relations and advertising companies, and consulting and law firms.

About EBD Group

EBD Group International, LLC is the leading partnering firm for the global biotechnology industry. Since 1993, firms in the life sciences have leveraged EBD Groupâ€™s partnering conferences, technology and services to identify business opportunities and develop strategic relationships that drive their business. EBD Groupâ€™s conferences (run in collaboration with leading industry partners and international trade associations such as the Biotechnology Industry Organization (BIO)Â include BIO-Europe (co-organized with BIO), the preeminent stand-alone or ex-U.S. partnering conference for the biotechnology industry; BIO-Europe Spring; the investor conference, BioEquity Europe (co-organized with BioCentury Publications and BIO); and the convergent medical technology partnering conference, BioDevice Partnering. EBDâ€™s novel, web-based, partnering software system is also used at numerous third-party events around the world. Outside of the conference format, EBD Groupâ€™s consultants can provide hands-on assistance for firms seeking to in- or out-license products and technologies. EBD Group has offices in San Diego, Munich and London. For more information visit www.ebdgroup.com.

About BIO

BIO represents more than 1,100 biotechnology companies, academic institutions, state biotechnology centers and related organizations across the United States and 31 other nations. BIO members are involved in the research and development of healthcare, agricultural, industrial and environmental biotechnology products. BIO also produces the annual BIO International Convention, the global event for biotechnology. www.bio.org

Posted under ChemInformatics, Europe, North America, Press Releases | No Comments

CLC bio solves bioinformatics data management challenges with release of database solution

Last Updated on Sunday, 14 October 2007 07:27 Written by admin Sunday, 14 October 2007 07:27

Aarhus, Denmark — October 12th, 2007 — CLC bio, the world’s leading bioinformatics solution provider, today announced a November release of CLC Bioinformatics Database. This powerful and versatile database solution – currently in beta-testing – enables users of CLC bio’s DNA, RNA, and protein sequence analysis software to store and work on their sequence data in a central, shared, and secure relational database.

CLC bio’s new database solution is scalable and fully customizable, making it an ideal choice for many research organizations, from small university departments and clinical labs to large biotech and pharmaceutical companies. The solution is aimed at organizations wishing to profit from the considerable business value of selecting a modern and flexible bioinformatics platform.

Mr. Jan Lomholdt, Vice President of Global Sales at CLC bio states
With this powerful and highly customizable solution for data sharing and efficient workflow support, CLC bio is leaping forward. Many academic and industrial customers have asked for a solution to share, manage and secure their valuable bioinformatics data, and we are proud to announce that we – as always – have developed what our customers ask for.

CLC Bioinformatics Database raises the bar for what users can expect from a database solution, as the development team has focused heavily on eliminating classic obstacles such as different operating systems, limited support for database formats, or limited access to a central storage facility. As with all other of CLC bio’s solutions, CLC Bioinformatics Database is cross-platform, running on Mac OS X, Windows, and Linux. Additionally, this solution will enable users across various workgroups to work on data in a central, shared, and secure relational database.

For the benefit of the diverse base of more than 50,000 existing users of CLC bio’s solutions, CLC Bioinformatics Database integrates and runs smoothly with several types of databases, including Oracle, PostgreSQL, and MySQL. Furthermore it is the customer’s choice whether the solution should run as a stand-alone database, or if it should be fully customized and integrated with the customer’s existing database or even multiple databases.

For more information on CLC Bioinformatics Database, go to:
www.clcbio.com/database

CLC bioâ€™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

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Spellex releases Spellex Biotech v.2007, the newest upgrade of the worldâ€™s first Bioscience spell checking software.

Last Updated on Monday, 13 August 2007 01:06 Written by Fred Monday, 13 August 2007 01:06

TAMPA, FL — Spellex Corporation announces the new release of the 2007 version of their popular bioscience spelling software for Microsoft and other programs. The new release includes more than 200,000 specialty words from the bioscience industry and new spelling engine enhancements.

Benefits:Â Â The Spellex Biotech spelling dictionary allows users to save time and increase their accuracy. By adding Spellex Biotech to your Microsoft or WordPerfect program, your spell checker will provide correct spelling choices for incorrectly spelled bioscience terminology.Â The spell checker also allows users to look up unsure spelling of bioscience words by phonetic or typographical search without leaving their document. The regular Microsoft or WordPerfect spelling dictionary and the Spellex dictionary are spell checked simultaneously with one mouse click.

Spellex Corporation has added more than 20 Customer-Driven enhancements to their Spellex Biotech 2007 spell check program, including upgrades and updates to the biotech dictionary, spelling engine, registration program, and installation program.

Features: Â Spellex Biotech is a comprehensive spelling dictionary reference that adds more than 200,000 bioscience terms to the userâ€™s spell checker for specialties ranging from Agronomy to Zygote research.Â Spellex Biotech covers more than 70 different bioscience fields including agronomy, biochemistry, bioinformatics, biomedical engineering, biophysics, ecology, molecular and genetic biology, microbiology, organic chemistry, taxonomy, toxicology, and pharmacology, to name only a few. Â Spellex Biotech includes thousands of abbreviations and acronyms encompassing scientific product names and devices, as well as medically and biotechnologically relevant organisms.

Users can also correctly spell newly introduced bioscience terminology by subscribing to the Spell-X-BioPlus^TM software subscription service.Â This quarterly software subscription service updates the Spellex dictionaries with new biotechnology terms, new pharmaceutical terms, and more.Â

Spellex dictionaries are compatible with Microsoft, most Windows programs, developer tools, custom applications, Web browsers, and are available in US English or UK English.

To request product information or to place an order, contact Spellex Corporation at 800-442-WORD (9673) or 813-792-7000.Â You can also visit www.spellex.com/products/biotech.htm.

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Spellex releases Spellex Biotech v.2007, the newest upgrade of the worldâ€™s first Bioscience spell checking software.

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