October 10, 2012
Nobel prize for GPCRs!
Congratulations to Brian Kobilka and Jeff Lefkowitz for the 2012 Chemistry Nobel Prize !
Now the world will need to learn how to say 'G-protein coupled receptors'.
C O N G R A T U L A T I O N S ! ! ! !
Emerald Insights Blog: Opinion
December 30, 2010
Pocket Guide to GPCR Structures Still Valid
The 2008 'pocket guide to GPCRs' - structure determination of GPCRs that is, - still serves well. Just after the Adenosine A2A receptor structure was published in October 2008, this featured article in Nature Structural Biology Knowledgebase laid out the following strategy for successful determination of crystallographic GPCR structures:
- Increase compactness & stability: shorten third cytoplasmic loop; identify stabilizing mutations, such as C-terminal deletion
- Adjust purification regime: add cholesterol hemisuccinate throughout purification
- Increase crystallizability: replace long loop section of third intracellular loop by T4 lysozyme fusion
- Stabilize protein during crystallization: employ LCP crystallization methodology use monoolein with added cholesterol; co-crystallize with ligand
In 2008 this was a just a trend (N=3), now at the end of 2010 with 2 more GPCR structures in our pocket, both of which follow these guidelines, this pocket guide is starting to look like a rule book.
All the best,
Peter
Reference: Hodges, M. (2008). A pocket guide to GPCRs PSI Structural Genomics Knowledgebase DOI: 10.1038/fa_psisgkb.2008.16
December 24, 2010
Most Popular GPCR Blog Posts in 2010
What are readers of this GPCR blog most interested in? Below is the list of the top 10 blog posts that were requested often during this year. If this is close to what you’re interested in, you may want to subscribe via RSS.
So, here are the top ten blog posts:
- GPCRs of known structure
- New GPCR structure: CXCR4 Chemokine Receptor (HIV and cancer target)
- GPCR crystallization conditions
- Upcoming GPCR structure conferences
- Top 10 GPCR Structure Papers (from F1000)
- Next GPCR structures in the pipeline
- NIH funded ‘GPCR structure’-related projects
- New GPCR Structure: Dopamine D3 Receptor
- Keep ‘em coming: 3 more GPCR structures
- GPCR-related Press Releases of the first half of 2010
No surprise in the choice of topic: structure, structure, structure.
This should set the theme for 2011,
Peter
December 18, 2010
3 New GPCR Structures Expected for 2011 (Maybe)
This year we’ve seen 2 new X-ray GPCR structures published, and the PDB now shows 27 entries (list here).
Let’s put this progress into a historical perspective: The first protein structure was published in 1960 (Kendrew et al.), the first membrane protein structure in 1985 (Deisenhofer, et.al) and the first GPCR structure appeared in the PDB in 2000 (Palczewski et al.). As of today the Protein Data Bank lists a staggering 69,967 entries (soluble and membrane protein structures, with a variety to techniques used), of these about 719 are membrane protein structures, of which 262 are unique.
What does that tell us for GPCR structures in 2011? One could reasonably expect to see two or three new unique GPCR structures in 2011 and maybe an additional 10 GPCR structures that are related to already determined ‘base structures’ (for instance the advertised antagonist bound b2AR structure). This estimate is a continuation of a trend that was first described by Richard Dickerson in 1978 for soluble proteins and then applied to membrane proteins by Stephen White (see here for Stephen’s fantastic Membrane Proteins of known 3D Structure site).
Figure: Progress of structure determination as tracked by the PDB and Stephen White’s site.
The numbers to extend this Dickerson-White law to GPCRs by fitting m = exp(by) are still somewhat shaky for GPCRs, but if the exponential trend holds true we could reasonably expect more than 2 and less than 3 unique GPCR structures in 2011 (one of them: S1P receptor). Another way to look at GPCR structural biology is that, compared to soluble proteins, GPCR structure determination is back in the mid nineteen seventies.
We’ve got a long way to go,
Peter
References
First Protein Structure:
KENDREW JC, DICKERSON RE, STRANDBERG BE, HART RG, DAVIES DR, PHILLIPS DC, & SHORE VC (1960). Structure of myoglobin: A three-dimensional Fourier synthesis at 2 A. resolution. Nature, 185 (4711), 422-7 PMID: 18990802
First Membrane Protein Structure:
Deisenhofer J., Epp O., Miki K., Huber R., and Michel H. 1985. Structure of the protein subunits in the photosynthetic reaction centre of Rhodospeudomonas viridis at 3 Å resolution. Nature 318:618-624.
First X-ray crystallographic structure of a G-protein coupled receptor:
Palczewski, K. (2000). Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor Science, 289 (5480), 739-745 DOI: 10.1126/science.289.5480.739
December 11, 2010
What’s the Most Important GPCR Structure?
I was recently asked "which of the published GPCR structures…are most relevant to drug discovery?"
Like many simple sounding questions there's no way to give a straight answer. Why is that? I think that the relevance of a particular GPCR structure is in the eye of the beholder. Let's look at the GPCR structures out there now and start with the seemingly simplest one to give a poor ranking: rhodopsin. One could say that the relevance of this structure has decreased for those molecular modelers that require starting coordinates to build accurate GPCR models of other receptors. The non-rhodopsin structures should serve as better starting points. On the other hand, since there is structural data available for rhodopsin in different conformational substates (photoactivated and ground states, with and without retinal ligand, nicely defined water molecules) there is currently no other GPCR that's better understood in terms of detailed function. The latter is supported by a wealth of spectroscopic and biochemical work that paints the most detailed picture (movie!) of receptor function.
What about Dopamine D3, beta 1 / 2 Adrenergic receptors and the Adenosine receptor? Here one could argue that for those researchers who want to discover new drugs, the structures of these receptors may not be that helpful since there's ample evidence (i.e. drugs out in the marketplace) that it is fundamentally possible to develop compounds that interact with these receptors in desired ways. Hence no need for structural insight. I'm playing devils advocate here, because having access to accurate structural models and a structure-producing method does increase the efficiency for structure guided drug discovery efforts a lot. And it may even provide fundamentally new starting points, for instance by applying fragment-based crystallographic screening.
What about the CXCR4 receptor then? Certainly a highly relevant target (HIV) - and my personal favorite; however, if you want to make an impact on as many peoples' health as possible, you may want to focus on cardiovascular diseases and neurological disorders instead.
So, if you have a research agenda, you better know which GPCR structure is closest to you. For those asking which GPCR structure is the most relevant to drug discovery I say 'those ones we haven't see yet'.
Does that make sense?
Peter
November 18, 2010
How to Tell Your Parents About Those GPCRs
A lot of GPCR researchers over here in the US are preparing for next weeks' trip back to their family to celebrate Thanksgiving. At one point the topic of discussion will inevitably come to "what's going on in your field?" - the dreaded potential conversation stopper. For those of you who have had difficulties answering this question in plain language without getting caught up in jargon, you may want to check out this neat write-up in NATURE CHEMICAL BIOLOGY about the progress that has been achieved during the 'naughties' in the field of - what some people prefer to call - 'chemical biology' (why not stick with the old-fashioned term 'biochemistry'?):
Bucci M, Goodman C, & Sheppard TL (2010). A decade of chemical biology. Nature Chemical Biology, 6 (12), 847-854 PMID: 21079586
Of course GPCRs and their structure are a big deal for all of us who are working on them. So I was glad to see the structure of the beta2-adrenergic receptor listed as a 2007 milestone. This feature in Nat. Chem. Biol. also contains a separate box, explaining the actual finding and the relevance of this GPCR structure in clear language.
Definitely worth printing out and bringing along as 'supporting materials'. Just imagine: GPCRs could be a conversation starter this year.
Happy T-day,
Peter
November 6, 2010
The GPCR Dimer Opportunity
Starting out as a GPCR dimer skeptic I have been 'converted' over the course of the past several years. For instance, one of the most impressive demonstrations of GPCR dimers in vivo I saw presented during this year's Keystone meeting on GPCRs by Nigel Birdsall: He has used single molecule imaging TIRF microscopy to monitor - beyond doubt - the formation and dissociation of muscarinic receptors in CHO cells. His movies of single receptors forming dimers are very convincing. Nigel's group can track individual receptors over time, their mobility, clustering and follow the receptor dimerization kinetics. This is a fantastic body of work.
A study by Albizu et al. then added another 'beyond doubt' qualifier: assymetric activation of Oxytocin receptors as shown with time-resolved FRET between ligands. BTW, the power of the fluorescence probes toolset that was developed and employed for this study is amazing in itself. The significance of this work though, lies in the fact that dimers were shown to exist not only in transfected cell lines, but in native tissue: Oxytocin receptor oligomers in mammary gland tissue.
So, since at least some GPCR dimers/oligomers are for real, they form new points of attack for the development of compounds that interfere with the dimerization/oligomerization processes. Developing ligands that disrupt interfaces is a particularly difficult exercise and I have not seen many success stories for supposedly simpler soluble proteins. The nicely formed ligand binding pockets in the GPCR structures that we have seen so far, are highly attractive starting points for computational-based drug discovery. But the interfaces may proof much more productive in yielding new classes of ligands.
Cheers,
Peter
October 16, 2010
GPCR Crystallization as Stepping Stones for R&D
There's a nice write-up in GEN on the progress in the field of GPCR crystallization / structural biology and the impact this has on R&D efforts. I couldn't agree more with what Mike Hanson from Receptos says about the utility of lipidic cubic phases for the crystallization of G protein coupled receptor molecules. The List of "GPCRs of known structure" speaks for itself as it shows that the majority of the all crystal structures are based on crystals that have been grown within lipidic cubic phases.
Here at Emerald we have developed several relevant patented technologies ourselves and hold exclusive licenses to technologies that are indispensible for the practical aspects that are involved in GPCR crystallization. Some of these technologies are distributed as products via Emerald BioSystems. For instance, there is the 'Cubic LCP Cubic Kit' and the 'Cubic™ Screen', crystallization tools that are specifically designed for lipidic cubic phase - based membrane protein crystallization. These products aid researchers to set up crystallization trials with their own GPCR preparations.
Over here, at Emerald BioStructures we offer research services that apply these membrane protein crystallization technologies and tools within contract research projects. In fact, we have all the components in place to go from gene to membrane protein structure to provide our clients with unique insight into their drug targets (download a description of our membrane protein structure determination services here). At the heart of the matter, we feel that the field of membrane protein crystallography has now matured to a state where it can be applied within drug discovery projects and make a significant impact to lead optimization and to the discovery of new compounds, for instance with crystallographic fragment screening.
Soluble protein structure based drug discovery has an impressive track record of giving researchers a key advantage in their drug discvoery efforts. Demonstrating the value of crystallography for membrane proteins such as GPCRs is the logical next step.
This brings me to my shameless plug: Should you be interested in Emerald BioStructures' membrane protein structural biology services, please contact us here - or send me an email directly, I'd be happy to discuss specifics.
All the best,
Peter
September 30, 2010
GPCRs Leading in Poll for 2010 Nobel Target Class
64% of the GPCR blog readers think that GPCRs are worthy a Nobel Prize. See the box on the right. Check out the timer that shows how many days and hours we're away from the announcement of the 2010 Nobel for Chemistry (the 2010 Nobel to Medicine went to Robert G. Edwards for his work on in-vitro fertilization). To spice this up a little I've set up a poll over at Emerald BioSystems. Cast your vote here on the protein target areas and find out what everybody else thinks.
All the best,
Peter
September 2, 2010
How Many More GPCR Structures to Go? (280)
Here is a semi-serious attempt to estimate the number of GPCR structures that would be 'nice to see' from a drug discovery standpoint. Let's look at the fundamental numbers, starting out with Vassilatis et al., (PNAS (2003) . vol. 100. no. 8. 4903–4908) who say that a total of 367 GPCRs constitute the complete repertoire of GPCRs for endogenous ligands in the human genome. This provides a good upper estimate.
For many of these targets drugs have already been developed - in the absence of target GPCR structure information, mind you. How many? Overington et al. (Nature Reviews Drug Discovery 5, 993-996 (2006)) address this by asking the fundamental question: "How many drug targets are there?" and lay out the numbers. They then go on to compile the gene family of Rhodopsin-like GPCRs, constituting for 26.8% of all FDA-approved drugs.
Taking this fraction and applying it to the total 'consensus number of 324 drug targets for all classes of approved therapeutic drugs' yields a total of ca. 87 different, already 'drugged' GPCR targets. This is close to the 81 GPCRs listed in the Molecular Pharmacopoeia Poster.
From a structure based drug discovery perspective however, you could say that the GPCRs that have already been drugged are of somewhat less importance. This is of course debatable, but for simplicity sake, let's take the stance that only the not-yet-drugged GPCRs fall into the 'interesting' category. The simple math would then work out like this:
367 GPCRs with endogenous ligands -
87 human GPCRs that are drugged already
= 280 desirable GPCR structures.
Of course this is only an estimate. Potentially a gross underestimate: In a perfect world scenario you'd want to see the structures of several conformational substates to guide medicinal chemistry efforts. On the other hand, given the similarity in overall architecture we may need a lot fewer than all 280 GPCR structures to make good, computationally supported, guesses to support new ligand discovery and optimization. However, we're not even coming close to this point yet, given the poor performance of the 'community-wide assessment of GPCR structure modelling and ligand docking' project (where computational groups were asked to model the structure of the A(2A) Adenosine receptor bound to ZM241385 prior to its publication).
For all the GPCR structural biologists amongst us this bodes well: there's a lot to do.
Cheers,
Peter