The fantastic world of drug discovery

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The $100M Club: Where the Major League Life Sciences Companies Are | Xconomy

Great list by Luke Timmerman. Please do check it out. Pretty impressive growth by the Boston biotech scene, but I’m not sure if they can keep this up for many more years to come.

I hope I am wrong. I will hopefully be graduating in a few years and would like many more options while looking for a job. 

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Drug discovery: Excersized rats live longer and stapled peptides last longer!!

Had a chance to listen to another couple of interesting talks this week.

The first one was by Dr. Konstantin Khrapko from the Harvard medical school, talking about the somatic mutations of mitochondrial DNA. I have to admit that I have almost no experience in his field of mitochondrial DNA research. Apparently, the mitochondrial DNA (mDNA) present in each mitochondria, in each cell, undergoes a number of mutations over our lifetime and they influence a number of physiological functions. The mDNA have almost no DNA repair mechanisms unlike the nuclear genomic DNA. Hence, large number of mutations get accumulated over time and cause age-related diseases. One of the interesting phenomenon that Khrapko and others in the field have observed is that these mutations are identical in all mitochondria in the same cell (or bunch of cells risen from the same mother cell) indicating a common source and a quick spread. They are not sure about how the initial mutation/deletion gets transmitted to the others, but this can be measured pretty accurately now. 

Logic would dictate that mtDNA mutations, when present at levels lower than in phenotypically normal Polgmut/+ mice (dashed green line), are irrelevant for aging. However, in aged human colon, the typical histological pattern of mitochondrial defects (blue crypts in the inset) associated with increased mtDNA mutant fractions in individual crypts suggests otherwise15. Fractions in colon include clonally expanded mutants only. Error bars represent estimated variation of the data. Figure provided by L. Greaves and D. Turnbull (University of Newcastle).(Source: Mitochondrial DNA mutations and aging: a case closed?Konstantin Khrapko & Jan Vijg Nature Genetics 39, 445 - 446 (2007))

So how does this affect the rest of us not working in this field? Well, when they developed a rat model by causing similar mutations/deletions in the mDNA of fertilized eggs, the offsprings grow old and diseased rather quickly!! This rapid aging with features including, muscle loss, har loss, greying of hair, CNS disorders, poor metabolism etc is rather clear from the pictures of these rats. The rather more interesting observation was that when these rats were made to exercise (since birth), they avoided this prognosis completely and were indistinguishable from the regular rats!!

So what does all this mean? Well they are still trying to figure it out. I don’t know about you but In the meantime, I would help myself to a healthy serving of exercise in the hope that it will extend my lifespan!

The second talk was by Dr. Tomi Sawyer from Aileron Therapeutics on the development of stapled peptides and how this work led to a $1.1 billion aggrement with Roche! I am sure most of you readers are familiar with the fact that peptides are an excellent alternative to small-molecule drugs due to their specificity and ‘easy’ development. But, one of the major drawbacks since their develpoment a couple of decades ago has been their poor stability in the gut and in the plasma. One of the novel methods that Aileron have used to stabilize these peptides is by “stapling” these peptides using chemical linkers. This not only improves their stability as a peptide but is also able to hold the peptide in the form of a alpha helix thus enabling their use in protein-protein interaction modulations.

One of the targets they have been working on for Roche is the MDM2 and MDMX dual-targeting alpha-helical peptides as an anti-cancer therapy. These stabilized peptides can interact with both MDM2 and MDMX proteins, with good affinity, and prevent their interaction with p53. This allows p53, a pro-apoptotic protein, to kill the cancerous cells. Although I was familiar with this strategy from the FierceBiotech’s coverage of their recent Phase I trial success, I did not realise that some of these peptides have a plasma half-life of around 24 hours!! This obviously makes it a very interesting drug design strategy to watch out in the near future. 

Filed under stapled peptides mitochondria mDNA drug discovery seminar

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Big pharma at its best and worst!

This week, I had the opportunity to listen to Dr. Doug Johnson, a medicinal chemist from Pfizer in Cambridge, Boston. He spoke about his group’s decade old project of developing FAAH inhibitors and beta-secretase inhibitors using click chemistry to study their interactions with the respective enzymes/proteins.

I happen to work in a lab that also works on developing selective ligands for FAAH and other endocannabinoid targets. It obviously got my interest that they had developed and optimized a drug molecule which is a highly selective FAAH inhibitor. This work could be one of those classic examples of how target-based drug design is such an asset that is used in the industry (and in academia) in drug discovery and yet how lucky you have to be to stumble upon the right bunch of steps (among a myriad of possibilities) to improve the pharmacological profile of the hit.

But the interesting bit (or rather a head-desk moment) of the talk came up during the Q&A session at the end of the talk. He was asked about why this compound was studied in a osteoporosis pain model rather than the more traditional endocannabinoid target models. And if you are familiar with how big pharma works, it would not come as a surprise that this was because of a major reorganization at Pfizer that led to the use of this highly selective FAAH covalent inhibitor for a “wrong” indication rather than in a neuropathic pain or MS model. The “pain group” in the company had apparently turned its focus onto ion channels and away from the endocannabinoid system during the reorganization. The cannabinoid drug obviously failed the Phase II trial and is now sitting in some cupboard waiting for the company to decide on which new (appropriate) indication it should be tested for.

Lets hope they get their act together and push this molecule to the right trial at the earliest.

Filed under Pfizer Drug Design FAAH cannabinoid system drug discovery

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Ligand structure based protein design!

Gone are the days when we just try (and hope) to design/synthesize/discover specific and selective ligands that fit to a protein of interest and elicit the effect that is required to treat/cure diseases. Although this quarter century-old drug discovery approach is the hallmark of most current drug discovery operations around the world, it has not been the most efficient in generating “winning” drug molecules.

Now a couple of groups at UW (Barry Stoddard & David Baker and their colleagueshave tried to reverse this age-old approach and have combined computational prediction models with some heavy biochemistry, to design new protein molecules with binding pockets that would best fit a ligand of interest! They published these results in Nature this week - Computational design of ligand-binding proteins with high affinity and selectivity and is definitely worth a read.

In summary, they developed specific proteins that bind to Digoxigenin (DIG), a steriod molecule. They begin their computational search by using over 400 protein scaffolds from known proteins which are then modified/mutated/refolded to improve the binding affinity with DIG to sub-picomolar levels. Yes, such computational studies have been published in the past and have been partly successful (refer 9-14 of the references in the above paper). But, this study follows up these predictions by actually expressing these novel proteins in-vitro and then studying the effects of mutations in the binding pocket and how it affects the binding affinity of DIG and other steroidal molecules. Remarkably, the results are very convincing and the newly designed proteins exhibit amazing selectivity towards DIG over other ligands.

This is a remarkable achievement and hats off to these guys for this wonderful and comprehensive work. I am looking forward to more from the groups involved in this study, in the near future, with some practical applications of such designed proteins.

Filed under protein protein design drug discovery biotechnology

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Llama-derived single variable domains (Nanobodie... [J Biol Chem. 2013] - PubMed - NCBI

Nanobodies, if you remember, are single-variable domain antibodies generated from llamas, which were used as one of the strategies for the crystallization of a number of GPCRs including the beta-adrenergic receptors and then the CXCR7 receptors. These nanobodies can stabilize a specific conformation of the GPCR and effectively mimic a small molecule or peptide agonist, antagonist or inverse agonist ligand.

It is great to see that apart from those experimental applications, they also have some very interesting clinical applications. This is the first paper with some in-vivo data that I have come across that show some very promising results for these antibodies. I hope to see more in the near future on other receptors as well.

Filed under GPCR Nanobodies science biochemistry drugdiscovery antibodies

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Chaperonin-mediated Protein Folding. [J Biol Chem. 2013] - PubMed - NCBI

Very interesting review of the history of the study of chaperonins by a legend in the field - Dr. Arthur Horwich. Protein folding is without question one of the most interesting topics in the field of molecular and cell biology, yet one of the least well understood.

We are still far far away from efficiently folding a particular amino acid chain into a functional protein by just adding a bunch of chaperonins, other ancillary agents along with the right environmental conditions. Lets hope that this “utopia” is too far away in the future.

Filed under chaperonins proteinfolding proteins biochemistry biologicalchemistry

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Chemical reporters for biological discovery

A very interesting review of some of the amazing bioorthogonal reporter molecules and their chemistry for biochemical discovery with all kinds of biomolecules.

My own experience (although only second hand. They are studied by other grad students in my lab) has been with activity-based protein profiling (ABPP) of serine hydrolase enzymes. . Although ABPP was touched upon briefly, it was not discussed in depth in this review. If interested, you might want to check this paper by Ben Cravatt from Scripps - Activity-based protein profiling for biochemical pathway discovery in cancer.

Filed under ABPP chemical reporters science chemistry

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ASPET 4th GPCR Colloquium roundup

I had the pleasure of attending the last month’s two day GPCR seminar series held in Boston as part of the Experimental Biology 2013 conference. I won’t go into some elaborate description of all the talks or the posters that were presented. But I would like to point out some of the rather extraordinary tit-bits that I have picked up over the two days regarding how GPCR research is being done in some of the leading labs in the world.

  • Atleast 3 biased ligands from Trevena (a spin-off from Bob Leftkowitz’s lab) are in the clinical trials and have shown some very promising results so far! (Yay! first biased ligand on the way people.)
  • Michel Bouvier’s group are trying to apply some of the techniques we have learnt in the past decade of genome sequencing techniques for GPCR ligand screening. They have started screening compounds using a BRET-based ultra-high throughput screening of compounds in relation to over 20 different secondary signaling proteins/parameters in a single plate setup! The mind-blowing pictures of a 1536-well plates with different colored intensities brings back memories of DNA microarrays.
  • Another interesting aspect of converging in-vitro data from these biased ligands to in-vivo mechanisms was covered by Dr. Tobin. One interesting detail about how they started this work was that one of his graduate students went ahead to prove that there is correlation between them, inspite of his previous objections to not waste money on this! Hope all the PIs in the room were listening and another story for the “Hey look, Grad students are right too!!” book that I am writing. (Unfortunately, it is still in its infancy :p)
  • Jeff Conn’s group are trying to improve the effects of current ligands by adding allosteric modulators that are designed to favor one conformation over the other depending on the indication of use. (Nice to finally hear and meet one of the PIs I was looking to work for through grad school!)
  • Jefe Aube’ provided some med chem humor when he showed some data that went against the popular jokes about medicinal chemists - “SAR to biologists usually means methyl, ethyl, propyl, butyl…futile” when talking about how simple SAR changes improved potency and efficacy of their novel scaffolds.
  • Mark von Zastrow went over his recently published work (Comformational biosensors reveals GPCR signaling from endosomes) in Nature, with some extraordinary FRET images and videos that convincingly and (for the first time) directly prove that GPCRs signal even from the endosomes. 
  • Roger Sunahara compiled all the structures of GPCRs obtained so far and a few other studies added to them to predict that G-proteins bind weakly to the ligand-free receptor. Then following ligand binding, they form stronger interactions and also change the extracellular conformation of the receptor preventing the release of the ligand.
  • Another company I have been hearing a lot about over the last few years is Heptares (a spin-off of Christopher Tate’s mutation-based GPCR stabilization work at MRC, Cambridge University). Fiona Marshall showcased some of the details of how they carry out GPCR structural characterization. One of the coolest bits that blew my mind (and I am sure quite a few others) is that they solve a different crystal structure every 2 weeks!! Also that they prepare about 1000 mutations for each receptor to pick out the right mutations that stabilize the receptor for crystallization!! (How exactly are we in academia to compete with this?)

I unfortunately did not get a chance to attend the two Kobilka talks earlier in the week, but made it to the Lefkowitz’s talk on Wednesday. It was very similar to his Nobel talk but one bit that stuck in my head was that how proud he is of Kobilka’s endurance during some tough financial times in his lab. He is certainly an excellent scientist and an even better mentor (if that is even possible).

In all, it was a great couple of days to meet and talk to some of the people in the field of GPCR research. I only managed to take a couple of pictures of Dr. Lefkowtiz from afar and here they are -



Hopefully, I will be back with another post soon. As always, comments, shares and likes are welcome.


Filed under gpcr EB2013 science

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Umbrella project @MIT (at Jack barry field, cambridge MA). I was part of this cool sociology project studying group interaction by Pilobolus who came to MIT over the weekend. Do check this video explaining the concept - 

Umbrella project @MIT (at Jack barry field, cambridge MA). I was part of this cool sociology project studying group interaction by Pilobolus who came to MIT over the weekend. Do check this video explaining the concept -