Commercial fragments?

A friend recently asked if I knew of any commercial fragment collections. She knows someone in academia who is interested in exploring fragment-based ligand discovery, and would like to get started with a well-curated library.

At Sunesis, we used custom-built, disulfide-containing fragments for Tethering, but of course most techniques aren't limited to disulfides.

So everyone, does your company sell fragments? Now is your chance to get some free advertising!

Or have you purchased fragment libraries? Did you like them? If not, now is your chance to get some free complaining!

Whatcha Listening To?

I have the bad habit of going up to people and grabbing their IPOD to find out what they are listening to. Tell's a lot about who they are. Sometimes it's embarrassing (Celine Dion!) and sometimes it leads you to new music.
For some Friday fun here are the last five songs on my IPOD:
Miss Freelove '69 by the Hoodoo Gurus
Don't Feel Like Dancing by Scissor Sisters
Loving You by Paolo Nutini
Cursum Perficio by Enya
Rollin' by Limp Bizkit

OK, I admit, I am nothing if not eclectic.

What are you listening to?

What is the Value of the (Technologist) Man?

Protagoras said

"Man is the measure of all things: of things which are, that they are, and of
things which are not, that they are not"

which the first part is the part most of us know.

It is clear that FBDD is "HOT", and I have been struck by how many companies are doing or want to do NMR as part of their FBDD. This is surprising considering that many pharmaceutical companies have been through the ebb and flow of the 3 stages of NMR disease: 1) structure will revolutionize drug discovery (1992-1996), 2) NMR screening will solve the HTS problem (1996-2004), and 3) we have SO learned from out mistakes, trust us THIS time (2004-). As James Bond said, "Once is happenstance, twice coincidence, and three times is enemy action."
I lived through stage 2 and the resultant NMR-ectomy at a Big Pharma. The driver for the round-filing of our group was "business decision", in other words "we have no idea what value you add and sheesh, those silver cans are expensive to upkeep." Obviously, the value of technologists, especially at big companies, is tough to quantify. It is even harder if you don't fully understand the technology or how it is applied. I asked one of our senior management how do you quantitate the contribution of technologists (Computational, Structural Biology, etc.) to a project. His answer was wholly unsatisfying, and state of the art: "We will see over time [thinking to myself at the time, what sort of timeframe?] that projects you are involved with are more successful."
Very Protagoran, don't you think?? But not very satisfying to the technologist.

So, with an increasing level of technology commensurate with an increasing level of FBDD in industry at both the Big and Small pharma level, I pose the question: "What is the value of the technologist?"

Synergy

One advantage of fragment-linking is the potential for synergy: the binding energy of the linked molecule is greater than the sum of the binding energies of the fragments, largely because entropic costs are greater for two molecules than for one. Homodimeric molecules represent a particularly clear case, and in the most recent issue of Bioorg. Med. Chem. Lett., researchers at F. Hoffmann-La Roche provide a nice example of this phenomenon.

A high-throughput screen against the diabetic drug target fructose-1,6-bisphosphatase (FBPase) identified a small thiol with a low micromolar IC₅₀. FBPase is a homo-tetramer, and when the crystal structure of the HTS hit bound to the protein was solved, the researchers found that the thiols had oxidized to form disulfides: two dimers bound to each tetramer, with one phenyl sulfonylurea bound in each of four binding sites. Subsequent analysis of the screening hit revealed it to be contaminated with about 5% of the disulfide, which had presumably formed by air oxidation; this was the source of the inhibition in the HTS assay. In other words, the screen had identified linked fragments.

With this structure in hand, the researchers synthesized a series of dimeric molecules connected by various linkers; they also replaced the aniline with meta-substituted phenyl moieties. Clear linker-length dependence was observed, with the shortest linkers showing no activity, while the molecule with the six-carbon linker shown has an IC₅₀ of 17 nM. Crystallography revealed that this molecule binds in a similar manner as the disulfide, although the linker itself showed some disorder. Gratifyingly, when the molecule was cut in half, the resulting monomer was found to bind much less tightly, with lower ligand efficiency. The dimeric molecule binds with a free energy of 10.6 kcal/mol, almost 2 kcal/mol more than would be predicted by simply adding the binding energies of the monomers.

Of course, the molecule is far from a drug (although it does show an impressive 100% oral bioavailability in mice). Nonetheless, it illustrates one of the key advantages of fragment-based ligand discovery. Fragments linked together can really be more than the sum of their parts.

Upcoming FBDD Conference

In just under three weeks, the XXth ISMC-EFMC Conference will be occuring in lovely Vienna.

There will be many interesting talks given on FBDD.
In Session 1 (Novel Lead Finding Approaches) two of three talks will be on FBDD (SGX and Roderick Hubbard from York/Astex)>
Session 2 (Chemistry Strategies in Reducing Attrition in Drug Discovery) will have a talk from Astex
Session 7 (FBDD, presented jointly by ACS) has three outstanding speakers and should be very interesting. If you haven't caught Alex Alex's paper on the history of FBDD, go and find it in Current Topics in Medicinal Chemistry.

Additionally, there will be a forum entitled : "How to close the gap between academic training in medicinal chemistry and industrial reality?" I think this is a particularly relevent topic for any field and not just medicinal chemistry.


Coming up in 4-5March2009 is Fragments 2009. This is a call for abstracts and to make the general populace aware of the meeting. And of course, what an excellent chance to meet Associate Editor Vicki Nienaber.

We will be post further meeting/symposia notices as we get them.

Pharmacopeia to lay off 40% of workforce

According to MarketWatch, Pharmacopeia announced yesterday (Tuesday) that it "plans to lay off approximately 40% of its workforce through termination of positions. The move adds to a reduction of about 15% of employees at the Princeton, N.J., biotech firm in May, made through both attrition and terminations. The firm said it expects a $3 million charge in the third quarter related to serverance payments. As a result of its reductions in operating expenditures, Pharmacopeia said it expects cash burn for the quarter ending Dec. 31 to be approximately $10 million, excluding severance-related costs."

As the money markets dry up, more companies will seek to cut their running costs, to make their cash reserves last that bit longer. Biotech companies (few of whom post profits) will be particularly at risk from the "credit crunch". Products, early revenues and profits are now the order of the day. In our sector, early licencing candidates will be key, and companies such as Vitae, Astex, Incyte, Onyx and OSI, with optimized candidates in hand, will be the ones to watch.

From Fragment to Clinic: AT7519

A clear, thorough account of fragment-based drug discovery has just appeared in J. Med. Chem. In it, researchers at Astex Therapeutics describe the use of fragment-based X-ray crystallography to identify AT7519, an inhibitor of the kinases CDK 1, 2, 4, and 5. The drug is currently in Phase II clinical trials for cancer.

Starting with just 500 fragments, crystallography allowed the researchers to identify more than 30 fragments that bound in the ATP-binding site, all of which made at least one hydrogen bond to the so-called “hinge region” of the protein. Three of these fragments were optimized using structure-based design and medicinal chemistry, with the most successful yielding AT7519.

The figure shows the progression of the series, starting from the initial fragment, along with the IC50s and the ligand efficiencies of key milestones. Some notable decisions included replacing the indazole moiety with a pyrazole, which resulted in a 30-fold drop in biochemical potency but did not notably reduce the ligand efficiency, and the replacement of a fluorobenzene moiety with a piperidine, which led to a loss in biochemical potency but an improvement in solubility and cell potency. AT7519 showed 86% tumor growth inhibition in an ovarian mouse xenograft model when dosed IP at 7.5 mg/kg. The full paper is well-written and provides an elegant example of taking a fragment all the way to a clinical compound.

Fragment References

Hello again,
The editors of practical fragments have decided that we will do a weekly update of the Fragment literature. We may make it a book club type of thing also where there is a precis of the paper and some discussion around it.
We are also keeping an ongoing Endnote file for FBDD references. This is generated in EndNote X1, and unfortunately we are finding out that X1 doesn't translate well (for example into EndNote 6). So we are posting the library as a .enl file and as an .xml. We can also do .txt, so we hope that this helps.
Of course, after saying all of this, I can't figure out how to add a non-video/audio file to blogger. Any help would be appreciated. Until then, people can email me and I will send it on to them.

Births and Deaths

Everyone knows that Roche made an offer to buy Genentech. What is not as widely know is that, if the deal goes through, Roche will shut down its Palo Alto site, which employs about 1000 people, according to Palo Alto Online.

How does this affect fragments? Hoffmann-LaRoche in Switzerland published an early example of fragment work on DNA gyrase way back in the year 2000 (using a technique called needle screening), and recently Roche Palo Alto has published some very useful guidance on how to identify - and avoid - screening artifacts in SPR (see glossary, 28 July). Practical Fragments wishes the Palo Alto folk the best of luck, and hope they put their considerable skills to good use wherever they land.

On a happier note, the same week the Roche-Genentech deal was announced, newborn Zenobia Therapeutics announced that it had commenced operations. Founded by Vicki Nienaber, who published what I believe is the first demonstration of crystallography-based fragment lead discovery while at Abbott (also in 2000), the company plans to pursue partnerships as well as its own work on neurological and muscular degenerative diseases. The company's motto is "fighting to cure disease, one fragment at a time," and we look forward to watching them grow.

Glossary v1.0

There has been some requests for a glossary/thesaurus especially for the newbies.

I promise you this is not a complete list, nor will it be necessarily alphabetical.

Abbott: Pharmaceutical company considered to be the pioneers of Fragment-based Drug Discovery
CADD: Computer-aided Drug Design. This is a "design" vs. a "discovery" method.
FBDD: Fragment-based Drug Discovery. An ExecDir I knew preferred Discovery over Design for odd reasons, which in typical fashion I forget here.
FBLD: Fragment-based Ligand Discovery. This actually makes more sense, because we are looking for ligands to targets, which eventually will be turned into to drugs. This is to create more of a contrast to standard HTS (see below) which screens for drugs.
Fragment: A chemical structure smaller than the final drug.
IP: Intellectual Property, as in there is none for fragments (That's for you David.)
ITC: Isothermal Calorimetry. Proof that you really needed to take that thermodynamics course in college, and you probably should have taken one in grad school.
Ligand: Chemical moiety that binds (or mostly doesn't bind to target).
NMR: Nuclear Magnetic Resonance Spectroscopy Method which uses the quantum nature of nuclear spins to generate data on the binding and structure of ligands and target.
SBDD: Structure-based Drug Design. I think this is more acceptable to say "drug design" because of inherent use of CADD. There have been more Nobel Prizes for NMR than X-ray.
SPR: Surface Plasmon Resonance, a.k.a BiaCore. Although this is more Xerox than anything else. The method is SPR, the maker of the machines is BiaCore, now a wholly owned subsidiary of GE Healthcare. Of course, just like Xerox and copy machines, there are other manufacturers of SPR equipment.
Target: That to which one wishes to bind a ligand to modulate some biochemical activity in order to achieve a pharmaceutical effect, hopefully with clearly defined IP. Targets can be proteins, nucleic acids, or any other biological entity.
X-ray Crystallography: Method which uses the wave-particle duality of atoms to generate data on the binding and structure of ligands.

Request for Help: Seminal Papers in FBDD

Daniela, Sandra and Antonella from Menarini are writing a book chapter on FBDD. They would like to insert a timeline showing the seminal papers in FBDD that established the scientific bona fides for the use of FBDD.So, this is your chance people, send in the papers you think are crucial to the scientific validation of FBDD. Please include complete citation and what the paper establishes and why it is important.



Two easy ones:

Shuker, S. B., Hajduk, P. J., Meadows, R. P., and Fesik, S. W. (1996) Discovering High-Affinity Ligands for Proteins: SAR by NMR, Science 274, 1531-1534.
This demonstrates a start to finish process for prosecuting fragments. It is especially important in that it also establishes the primacy of having binding information to help drive medchem decisions.

Hajduk, P. J., and Greer, J. (2007) A decade of fragment-based drug design: strategic advances and lessons learned, Nature Reviews Drug Discovery 6, 211-219.
This paper compares and contrasts FBDD vs. more traditional lead-like, HTS screening. It clearly demonstrates the advantages of FBDD in generating high quality hits with a better chance of progressing.



Now you all...

C&EN Cover Story on Fragments

Hi all,

I thought I’d highlight an excellent article on fragment-based lead discovery that appeared as the cover story of C&EN this week.

The story discusses the background of the field, current practice, and very recent industry developments (and I’m not biased for being quoted!).

Also, anyone want to go on record as to when we can expect the first fragment-derived drug to reach market?

Dan

The Future of Fragment Blogging

Or should I say Fragging? Frogging? I will leave Fragonomics as my contribution to the scientific literature.
After some discussion, we have settled on how we are going to utilize this blog. First off, we are going to focus on fragments. PERIOD. We are working with the Structure-based Drug Design blog to have some synergies and limit overlap. As other blogs, forums, etc. come on line we will link to them.

So what about the format for this blog? Some ground rules first:
1. Assume anything you say here is disclosed. There is no confidentiality.
2. As my Latin teacher used to say, "The only stupid questions is the one you never ask."
3. As travel is being restricted across the board, virtual discussions will be the primary way to speak with colleagues. Utilize the tool.
4. This is non-commercial; blatant advertising will get you banned. Companies are of course allowed to share discoveries, as is anyone else.
5. This list is subject to change at any time.


As to format and content, we are planning on having a few "associate editors" who will post entries. Each associate editor will be a subject matter expert in a given general area. They will not necessarily be writing our content; our plan is for you the readers of the blog to write it. If you have a question, write it up and submit it. There will be links to the side to do this.

Appropriate content will be:
Questions of specific and general interest?
Opinion pieces
Invited pieces
Other things I haven't thought of.

Questions of content that need to be discussed are:
Changes in company strategy (this site is closing, or that company is axing this group, etc.)
Job openings or positions wanted.
Any others?


In order for this lively experiment to work, we need it to have engaged, interested readers. Please, let me and the other editors know what else we can do to make this work for you.

If you are interested in being an associate editor, we still have a few openings. Just let me know.

Primary Screening

What are people thoughts about primary screen methodology?

NMR, X-ray, Biochemical, MS, SPR, etc.