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SDBN October 26th Event Featuring Trius Therapeutics
Posted by Mary Canady October 5th, 2010 .
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Trius Therapeutics is a great local company which recently had an initial public offering (IPO), quite a feat in this economy. What is the secret to their success? They focus on antibacterials for life threatening applications, and have used a creative combination of licensing and funding to build a strong portfolio in that area. Working with bacterial proteins helps Trius to leverage structure-based drug design (SBDD) technologies to efficiently optimize lead compounds. Dr. John Finn, Trius’ Chief Scientific Officer (bio), will present a talk titled “Innovative Antibacterial Drugs by Design; The Trius Therapeutics Story,” and as always you’ll have plenty of time to talk with him and others from Trius. Register here.

Sponsors

Sponsorships are available and affordable, with a speaking option available, contact us!

Event Details

Who: Biotechnology professionals in the greater San Diego area
What: San Diego Biotechnology August Event Featuring Trius Therapeutics
When: Tuesday, October 26th, 5:30-9:00 p.m.
Where: Tango Del Rey, 3567 Del Rey Street, San Diego 92109 (Directions below)
Cost: $25/$20 Academic
Contact: http://sdbn.org/contact
For more information about the event: http://sdbn.org/october

Directions: From the North: South on Interstate 5, Exit Balboa Ave, Straight to 4th Traffic Light then left on Bunker Hill St. Building directly ahead 3 blks. From the South: North on Interstate 5, Exit Grand/ Garnet Ave, Straight to 3rd Traffic Light then right on Bunker Hill St. Building directly ahead 3 blks. Park on the street or in the structure just past (south of) Tango del Rey. DO NOT park in the Science Center lot.

Biotechnology, Drug Discovery, Headline, SDBN Blog, SDBN Events »

September 28th Event Sponsored by Halozyme Therapeutics
Posted by Mary Canady September 6th, 2010 .
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We’re going to try something new for the San Diego Biotechnology Network in September. The folks at Halozyme have offered to start hosting events quarterly at their site in Sorrento Valley, and we’ll kick of the first event learning about their exciting science September 28th. They focus on therapeutics that work subcutaneously by targeting the extracellular matrix (the image is from a mural in their lobby) and have had lots of great news lately, so it will be nice to hear more. As always we’ll have plenty of time for networking in a casual atmosphere, and we’ll provide a light dinner. Hope to see you there, click here to register.

Sponsored by:

Event Details

Who: Biotechnology professionals in the greater San Diego area
What: San Diego Biotechnology August Event Hosted by Halozyme
When: Tuesday, September 28th, 5:30-9:00 p.m.
Where: Halozyme Therapeutics, 11404 Sorrento Valley Road, San Diego, CA 92121 (Map)
Cost: $20/$15 Academic
Contact: http://sdbn.org/contact
For more information about the event: http://sdbn.org/september

Drug Discovery, Headline, SDBN Blog, SDBN Events, Uncategorized »

SDBN August 18th Event: The Human Genome 10 Years Later: What Does it Mean for San Diego Biotech?
Posted by Mary Canady July 23rd, 2010 .
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June 2010 marks the 10th anniversary of the sequencing of the human genome. As Francis Collins has pointed out, “we invariably overestimate the short-term impacts of new technologies and underestimate their longer-term effects.” As a member of the community for 14 years, I can tell you that this is true for San Diego, as the expectations in 2000 were likely too high, but the last ten years have brought unexpected progress in many areas.

San Diego has a great ecosystem to take advantage of these exciting longer-term benefits, ranging from our expertise in creating cutting edge research tools, to ground breaking drug discoveries, to new classes of diagnostics, to the exciting new field of synthetic genomics. Of course, Craig Venter has given us a big vote of confidence by relocating here. Let’s bring together experts in an interactive environment August 18th to discuss how we can take advantage of these exciting opportunities. Register here.

Panelists:

Michael Cooke, Ph.D., Director of Immunology Discovery, Genomics Institute of the Novartis Foundation (GNF) (Bio)
Kelly Frazer, Ph.D., Chief of the Division of Genome Information Sciences for the UCSD Department of Pediatrics (more info)
Tom Novak, Ph.D.,, SVP of Research, of Fate Therapeutics (Bio)
Aristides A. N. Patrinos, Ph.D., President, Synthetic Genomics (more info)
Emily Winn-Deen, Ph.D.,, Vice President, Diagnostics Development at Illumina (Bio)

Moderators:

Scott Markel, Principal Bioinformatics Architect, Accelrys, and Paul Flook, Senior Director, Life Sciences R&D, Accelrys

Here are some seed questions for the discussion, and as always feel free to submit your questions as comments below:

• How will the direct to consumer genomics market impact our economy?
• How is genomics being used in drug discovery, and what therapeutic areas have the most promise for San Diego?
• Will the continuing affordability of sequencing affect the landscape of companies?
• What are the best adaptations we can make to take better advantage of the opportunities?

Sponsors

Event Details

Who: Biotechnology professionals in the greater San Diego area
What: San Diego Biotechnology August Event: The Human Genome 10 Years Later: What Does it Mean for San Diego Biotech?
When: Wednesday, August 18th, 5:30-9:00 p.m.
Where: Tango Del Rey, 3567 Del Rey Street, San Diego 92109 (Directions below)
Cost: $25/$20 Academic
Contact: http://sdbn.org/contact
For more information about the event: http://sdbn.org/august

Directions: From the North: South on Interstate 5, Exit Balboa Ave, Straight to 4th Traffic Light then left on Bunker Hill St. Building directly ahead 3 blks. From the South: North on Interstate 5, Exit Grand/ Garnet Ave, Straight to 3rd Traffic Light then right on Bunker Hill St. Building directly ahead 3 blks. Park on the street or in the structure just past (south of) Tango del Rey. DO NOT park in the Science Center lot.

Drug Discovery, Headline, SDBN Blog, SDBN Events »

SDBN July 21st Speed Networking Event Sponsored by Life Technologies
Posted by Mary Canady July 1st, 2010 .
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Our January Speed Networking event went so well that we promised we’d do it again so that you can meet as many local biotech professionals as possible in one night. How does it work? Check out our report of the last speed networking event for more details, and basically show up with plenty of business cards, something to take notes with, and craft a thirty second ‘elevator speech’ which describes who you are and what you’re looking for professionally. We always have a nice mix of professionals at our events, so it’s a great place if you’re looking for a job, for business partners, or just want to make a lot of new connections.

Our friends at Life Technologies are sponsoring the event, and we’re very excited because you’ve told us you want to learn more about them (2010 Poll). They’ll bring information on the business and open positions. With so much exciting news always coming from them, it will surely be an interesting night!

Sponsor

Event Details

Who: Biotechnology professionals in the greater San Diego area
What: San Diego Biotechnology Speed Networking Event July 21st Sponsored by Life Technologies
When: Wednesday, July 21st, 5:30-9:00 p.m.
Where: Tango Del Rey, 3567 Del Rey Street, San Diego 92109 (Directions below)
Cost: $20/$15 Academic, +$5 at the door (cash/check only)
Contact: http://sdbn.org/contact
For more information about the event: http://sdbn.org/july

Directions: From the North: South on Interstate 5, Exit Balboa Ave, Straight to 4th Traffic Light then left on Bunker Hill St. Building directly ahead 3 blks. From the South: North on Interstate 5, Exit Grand/ Garnet Ave, Straight to 3rd Traffic Light then right on Bunker Hill St. Building directly ahead 3 blks. Park on the street or in the structure just past (south of) Tango del Rey. DO NOT park in the Science Center lot.

To share this post easily, cut and paste: SDBN July 21st Speed Networking Event Sponsored by Life Technologies http://sdbn.org/july

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San Diego Stem Cell Coalition to Fight ALS: CIRM Update
Posted by Mary Canady June 30th, 2010 .
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Rat hippocampal neurons and astrocytes: See photo credits below

The California Institute for Regenerative Medicine (CIRM) granted a local interdisciplinary research team from UCSD, Salk, and Life Technologies $11.5 million for research aimed at finding a cure for amyotrophic lateral sclerosis (ALS), or Lou Gehrig’s disease. On June 23rd, CIRM hosted a public research update which I attended. The project is an excellent example of local research organizations and companies working together towards translating research into real cures, funded by California citizens who realize the promise of stem cell technologies.

The ALS team is led by Lawrence Goldstein, Ph.D., and Don Cleveland, Ph.D., from UCSD, and Samuel Pfaff from The Salk Institute. Drs. Goldstein and Cleveland spoke at the event, along with Life Technologies’ Mark Bonyhadi, Ph.D., UCSD’s Martin Marsala, MD, and Lucie Bruijn, Ph.D, from the ALS Association. Goldstein and Cleveland gave a great introduction to the project and explained that ALS is caused by the death of motor neurons, and that the cells’ environment is very important to their survival. Astrocyte cells have a very intimate relationship with motor neurons, and disease progression is predicted to be slowed if healthy precursors are introduced. As Goldstein and Cleveland explained, the ‘neighborhood’ of motor neurons is very important in determining their well being, and healthy astrocytes are the equivalent of neighbors who don’t have parties and mow your lawn for you. The team plans to create and transplant human astrocyte precursors (hAPs) from human embryonic stem cells (hESCs) into human spines. Begining with rodent models, they predict that the first clinical trials could take place in 2014.

Dr. Mark Bonyhadi from Life Technologies then explained how they will help create and analyze the hAPs and develop the processes to prepare them for FDA submission. Life Tech’s long history with high quality cell media and wide-ranging protein and cell analysis tools makes them a perfect partner. Dr. Martin Marsala described the preclinical animal studies that will be performed, and indicated that they have worked with a company called Neuralstem previously to show that spinal cell transplantations can be successful.

Dr. Lucie Bruijn from the ALS Association talked about the fact that there is only one drug available for the disease, and that other stem cell efforts are underway which will help develop the transplantation methods in parallel (Side note: normally drug discovery research is highly secretive, but do publicly funded efforts benefit from removing this veil?). ALS clinical trials are tracked on their website.

The research presented was inspiring, but the clear highlight of the event for me was to hear from ALS patient Dan Desmond. As a veteran, he is unfortunately part of a group that has a higher prevalence to contract the disease, the cause of which is only 10% genetic in nature. From his wheelchair, Dan told us about the progression of the disease, his carpe diem attitude, and he thanked the researchers for their work. Dan received a well-deserved standing ovation at the end of his courageous speech.

Hearing directly from patients is perhaps an unexpected benefit of moving basic research towards a more translational model, where curing disease is viewed as a near-term goal. As described by Dr. Goldstein, CIRM has challenged researchers to rethink assumptions and timelines to come up with solutions to fast-track therapeutics. CIRM is clearly ‘stepping up to the plate’ (pun intended) to make Prop 71′s goals of making California a leader in stem cell therapies come to light. This exciting project pairing our local institutions is a fantastic example of the synergies. Have you thought about who you could work with locally? (Hint: come to our events for ideas…)
Photo by GEHealthcare on Flickr under a Creative Comments License

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#SBS10 Day 4 Meeting report: Cracking the histone code
Posted by Dr. Gunn April 15th, 2010 .
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Today is the final day of reports from the 2010 meeting of the Society for Biomolecular Science in Phoenix. The meeting organizers have been excellent hosts and I’d like to express my sincerest thanks for their hospitality. After this, I have one last post containing all the interesting little observations and snippets of info that I deserve a mention, but didn’t fit into the larger topical posts. I also had some interesting discussions outside the official event that I’d love to continue online.

This morning’s session was on epigenetics and it probably won’t surprise my academic audience that pharma has, for the most part, passed on debating whether or not there is a histone code and has instead devoted itself to developing tools for writing, reading, and erasing epigenetic modifications. So what are they doing, then? (more…)

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#SBS10 Day 3 – Smart mice and blowing House, M.D.’s mind: Drug discovery in epigenetics
Posted by Dr. Gunn April 14th, 2010 .
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At the afternoon session of the Society for Biomolecular Science in Phoenix, it’s all about epigenetics, the study of heritable changes that don’t involve changes in genetic sequence.  Epigenetics explains why identical twins turn out a little different and even clones won’t be exactly identical.

Manfred Jung from Freiberg kicked off the session giving an overview of recent developments in epigenetics and presented what would become the central theme of the afternoon: Here are some diseases which haven’t received the amount of attention they deserve, here are some enzymes and proteins that cause the diseases when there’s something wrong with them, here’s how to target those enzymes. Go get ‘em, boys! (more…)

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#SBS10 report: iPS disease models coming of age for neurology
Posted by Dr. Gunn April 14th, 2010 .
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I went to a morning session on stem cells on day 2 of the Society for Biomolecular Science meeting in Phoenix, a meeting focused on advancements in drug discovery and screening technology.  After this, it’s all epigenetics.

Stephen Haggarty, Director of the Stanley Center Department of Chemical Neurology spoke on stem cells as genetically accurate disease models. The idea here is that you can take cells from a patient (and relatives) and use the clever trick first reported by Yamanaka et al. to convert skin fibroblast cells into stem cells, called induced pluripotent stem cells, or iPS cells.  What this gets you is a genetically identical population of cells to do experiments or drug screening on. Since they all share the genetic mutation or mutations that are responsible for the disease affecting the patient, they’ll give you an early indication of how the drug would affect the patient. The challenge here is getting a population of cells that actually act in the dish as they would in the patient, and Dr. Haggerty reports progress his group has made in this area.

Ever since Yamanaka’s paper came out, the promise of the technique was to create patient specific stem cells for either rejection-free transplants or drug screening, yet we’re only just starting to see cell lines become available for use in this way.  There are many issues related to the technique of inducing the stemness that causes cells to behave in ways that isn’t true to the disease, and the degree to which one cell within a tissue differs from neighboring cells in the same diseased tissue varies are problems that are only just beginning to be addressed. However, using a heritable and common neurological disorder, Fragile X syndrome,  in which the genes involved are known, he’s derived some patient specific cells which act like the disease cells do in the body.  Using fibroblasts from the Coriell repository, a repository of cells including those from diseased individuals, they derived some iPS cell lines that accurately behave as do cells isolated from a diseased individual and therefore make a good disease model.  This approach could still run into complications from the effects of the stem cell induction process, but it seems fairly promising.

Work on a more complex genetic disorder, Bipolar disorder, is ongoing.

‘Technical note: Lithium for bipolar disorder is an old therapy, but Li also inhibits GSK3beta, activating Wnt and promoting cell division and other stem cell properties, so expect some interesting hits to be found in this area.

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SBS Meeting report shows strong growth of Pubchem database #SBS10
Posted by Dr. Gunn April 14th, 2010 .
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I’m blogging this week from the 2010 Society for Biomolecular Science meeting with my colleague Mary Canady.  I’ll be covering the scientific sessions and sharing interesting developments in drug discovery and screening technologies. You can also follow the #SBS10 hashtag on twitter for updates.

On Tuesday, Steve Bryant from NIH gave a report on the increasing utility of the NIH Pubchem database for pharma drug screening programs.  The Pubchem database, named after Pubmed, the go-to resource for life science research abstracts, is an open repository for structure and activity information about molecules which have drug potential. The database is being developed under the Genbank model, wherein researchers are encouraged to upload the results of screening runs so that this information can be linked to in publications and accessible to others.

As a resource, Pubchem has seen strong adoption by researchers in industry and academia.  To give a quick snapshot, the number of contributing organizations have grown 5-fold over the past 5 years. 60000 users submit data daily, with the number unique substances now numbering around 70 million.  For each of these compounds, information on bioactivity is also being collected. Over 90 million activities are associated with these compounds, and the rate of increase of this bioassay data is on the steep part of the exponential growth curve, meaning that number I just wrote is already wrong. While the bioassay information currently requires direct upload, there are plans to derive additional data from published literature.

Following Steve’s report, Josh Bittker gave a brief summary of how the Broad Institute is using Pubchem. They have a reporting mandate as part of a grant and are developing a pipeline for automatically submitting machine readable assay results to Pubchem.  As part of this automatic reporting, there’s an automatic embargo on the data for 1 year.

Simone Graeber then gave an update on an EU effort along the lines of Pubchem.  They go a little further than just a database, developing their own library of 0.5 million compounds, with a 17000 compound subset derived from this covering much of the “activity space” of the larger set and more usable by smaller groups without the resources to screen the whole larger library.  You may be wondering, as someone in the audience did, why they’re developing their own database instead of submitting to Pubchem. Apparently they included some proprietary compounds in their library and there are legal issues complicating the assay result reporting.

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SBS Day Two: A Holistic Approach To Drug Discovery #sbs10
Posted by Mary Canady April 14th, 2010 .
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I’m blogging from the Society for Biomolecular Sciences conference in Phoenix, the organizers were kind enough to offer two of us complimentary passes. I was surprised that the sessions were separated into disease area, technique, or ‘phenomenon’ (e.g., epigenetics) which seemed a bit curious as well, as I had expected the different types of assay technologies would have been the basis (e.g. HTS, Cell-based). It will be interesting to see how this changes if SBS merges with ALA. Nevertheless, I’ve been spending most of my time in the oncology session, and have been looking for trends to share with you, as that is usually the most valuable thing I take away from conferences.

Over the years, I’ve noticed the evolution of different themes each year at drug discovery conferences. In the kinase area alone, I’ve been going to conferences from before the kinome was sequenced, to the era of differing theories of the efficacy of specific targeting, to today’s somewhat routine screening and questions regarding what will be the ‘next big thing’ (but have we figured them out yet?) I think a major theme of this meeting, and something I’ve seen evolving over the past few years, is the idea that a holistic approach to drug discovery, whereby high-throughput screening is seen as part of the process and not the dominant technology.

Peter Simpson of AstraZeneca talked about the need for quality assays across the spectrum, from eliminating error through acoustic liquid delivery, microfluidic methods, and an standardized ‘uber’ kinase assay to utilizing biophysical and fragment-based technologies to round out the information used for lead discovery and optimization. Indeed, a more holistic approach seems to be the norm, perhaps a response to the tightening of belts we’ve all experienced in this economy.

Part of this holistic approach is the the parallel utilization of cell-based assays, which are becoming an essential and more reliable part of the drug discovery process. Perusing the exhibit floor underlines this theme–I didn’t have to walk far to find many great examples of companies pushing the boundaries to improve cell-based assay technologies. SRU Biosystems launched BIND Scanner, a label-free technology and an instrument/software combination which specializes in analyzing data from samples with low cell numbers, such as primary and stem cells. Perkin Elmer has introduced Operetta, ‘bench-top high content screening.’ Fluxion is a South San Francisco company, has married microfluidics with standard 96-well plates to simulate more physiological conditions for live cell assays. Corning continues to make strides with its Epic label-free system, and has a few interesting posters. On the reagents side, Cellular Dynamics is a Madison, Wisconsin based company based on the research and IP from James Thompson of UW, and they aim to create many types of cells for screening utilizing induced pluripotent stem (iPS). Indeed, the confluence of the increased availability of such reagents and improved instrumentation makes this an exciting time for drug discovery.

As a (former?) scientist, one thing really nags me however. From what I’ve seen, most of the cell-based assays still give a binary answer. In other words, the cell reacts to stimuli or doesn’t, and this is plugged into the ‘old’ HTS-type thinking–hit or no hit (correct me if I’m wrong). I can’t help but think that the next wave, after the growing sophistication of the cell-based technologies, will be another wave of informatics/image analysis, whereby cellular responses are deconvoluted further, yielding more important information from these assays.