Protein Biomarkers part I: Fact versus Fiction

Preface to Biomarkers

Its difficult to know where to begin when discussing the nascent biotechnological sector known as Biomarkers. I think therefore it may be helpful for the uninitiated to give the term some context and definition. In its simplest definition, a biomarker is any substance which is used as an indicator of a biologic, or phenotypic state. Under this definition, biomarkers are used every day when physicians listen to a patient lungs, take blood pressure, perform standard blood titers to measure hematocrit levels or white blood cell counts, during urine tests for drug metabolites or diabetes and so on. Biomarkers can be DNA, such as the gene which signifies Huntington's disease or any other genetic disorder, or RNA in expression profiles. Also of note, the concept of biomarkers is a cornerstone of the larger topics of personalized medicine and preventive medicine.

This being said, the term biomarkers has been expicitly defined by the National Institutes of Health

A characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes or pharmalogical responses to a therapeutic intervention

Therefore the term biomarker can be applied accurately in reference to individual genotypes. The most notable success in this area has been the selection of HER2 positive breast cancer patients during the acceleration of Roche's Herceptin through the clinical trial process. The power of DNA gene profiling, such as is done with microarray chips and/or genomic sequencing projects is enormous and ongoing. However, correlating DNA "biomarkers" (a.k.a. genes) to diseases is nothing particularily new and in this author's opinion is simply a semantic repackaging of efforts that began in the genomics era. In contrast, protein specific biomarker concepts are just now beginning to evolve, are grasped much less readily by the general public and are more easily leveraged with scientific knowledge. Therefore, keeping the broader definition in mind, the rest of the article will focus specifically on protein biomarkers and technologies.

The Promise of Biomarkers
Any scientist worth their salt will quickly find themselves inundated with conditional modifiers when writing about biomarkers. This is because the hype surrounding the field is historically paralleled only by the hype surrounding the sequencing of the human genome. Astute observers will also note that the excitement around biomarkers is justified in many ways by the same arguments used previously for the genomics bubble, which has of yet not exactly lived up to investors' expectations. Therefore it is convenient here to include a section describing what I will euphemize as the promise of biomarkers, in this way I hope to make plain that while scientifically exciting, the biomarker field is very much hypothetical from an investor standpoint.

Organic life, for the most part is comprised entirely of proteins. It is important to remember that in the human organism, roughly 21,000 genes encode at least one million different proteins. Theoretically speaking, every disease state imaginable will be able to be detected by either foreign or aberrant proteins, or abnormal protein levels. (The same can not be said for genes). Identification and characterization of any protein entity which can designate disease activity will result in a "bio"marker. Clinical detection of these protein signals can then in turn be used to monitor and gauge specific aspects of a given disease. Furthermore, any number of effective biomarkers may be used together in a panel to create a diagnostic "fingerprint" of the pathology in a single sample.

Biomarkers are an Intermediary between treatment and disease

These protein indicators have an incredible potential value in the understanding of the mechanism of disease progression. In addition, as more individual patients are screened using biomarker panels, different pathology "fingerprints" will likely divide many of the known disease categories into subtypes, with the result of much more medically descriptive diagnoses. This knowledge, and the ability to select between subtypes, can also allow the healthcare industry to expedite successful therapeutic development by selecting clinical subjects with those subtypes more responsive to a given treatment. At the same time, a decrease in negative incidents in the marketplace will be possible, if prescribing physicians have an analogous yardstick for pathology subtype treatment options. If these reasons aren't enough to get excited about the the prospect of biomarkers, the detection and identification of such proteins can also lead to preventative treatments, potential drug targets, diagnostic tools, and surrogate endpoints for clinical trials.

Protein Biomakers can gauge disease subtype and progression. This will allow therapeutic developers to:

• Diagnose patients earlier and more accurately
  
• Perform more directed clinical trials
• Assess disease state primary endpoints with confidence
• Decrease unresponsive or adversely affected patients in the marketplace
• Potentially discover new therapeutic targets
  

In essence, the nascent field of biomarker discovery can be described as disease pathway research. A validated biomarker is simply an identified protein constituent which is affected in some way by a pathological state. Some might point out that in fact, this has been the modus operandi of great many academic biomedical researchers for decades, and therefore the notion of "biomarkers" is more of a new buzzword than a research concept. This may be true with regards to academia. However insofar as the drug development and pharmaceutical industry is concerned, seeing real value in disease pathway illumination has only recently gained traction.

The Business of Serendipity
Everybody has a pet theory as to the causes of Big Pharma's lack of R&D productivity, and mine goes something like this. Until relatively recently, drug developers' business strategy relied on a blockbuster model as the goal, and academically validated targets as the starting line. They each made huge libraries of small molecule pharmacophores and screened the same targets. Eventually corporate risk aversion manifested itself in me-too therapeutics and huge marketing sales forces. The point here is that it wasn't (and perhaps still isn't) seen as scientifically or financially feasible for these companies to screen for novel effected proteins along distant and undiscovered disease pathway branches.

However, summarizing the recent prevailing expert opinions; so long as the pharmaceutical industry leaves the deepening of disease understanding to academia, the inevitable result will continue to be the same big pharma corporations screening the same published targets with most likely the same pharmacophore libraries (or more recently recombinant protein, or RNA libraries). This lack of scientific competitive advantage is one reason behind the recent trend of niche market focus in the pharmaceutical industry. Moreover, the revelation that disease understanding has intrinsic value via potential biomarker discovery, in addition to proprietary target identification, has cemented this strategy of intellectual capital at least amongst the pundits.

The fact that success in biological discovery most often proceeds by serendipity is probably only surprising to non-scientists. Nevertheless, investors need to weigh risks, and business plans necessarily must project return on investment. Therefore, short of cutting as broad a swath as NIH funding, the pharmaceutical industry needs to increase exposure to proprietary understanding of disease in a way amenable to statistical evaluation. Nothing fits this bill more perfectly than proteomics.

Proteomics
I assume that a number of my readers will be nonplussed to discover that the major thesis laid out at this point is that protein biomarker discovery is tantamount to proteomics. However the major objective in on my part has been to simply to disentangle the fact from the fiction and the jargon from the investment opportunities. To this end, I believe this quote sums up the recent proteomics history fairly well.

The age of proteomics has been announced in the mid 1990’s and since then a tremendous rush of proteome gold miners started grounding the claims. There were people claiming to (i) analyze the whole proteome, (ii) determine the interactome, (iii) determine the global phosphoproteome , (iv) determine the secretome, (v) and many more. Such buzzwords give the impression that with some mass spectrometers, computers, and algorithms we have the Holy Grail in our hand and will soon be able to elucidate the biology.
Now 10 years later, quite a number of studies are published every week dealing with high-throughput proteomics experiments. Very often, in such studies, the technical limitations are addressed or long lists of qualitatively identified proteins are reported, only.

So -- in fact, proteomics as a science and as a sector remains only in its infancy in terms of technological development necessary to elucidate the dazzlingly complex interactions of proteins necessary for biomarker discovery. However due to the somewhat dire situation of the drug discovery industry described above, coupled with the potential of protein biomarkers, there is little doubt that these nascent technologies have recently benefitted, and will continue to receive substantial investments in the coming years.

I'd like to break part I off here and let this article stand as a review to bring the unindoctrinated protein biomarker investor up to speed. In part II I plan to cover the vision of interplay between biomarkers and therapeutics and finally get down to which protein biomarker technologies I see as the most promising areas for investment.

Targanta Therapeutics Part III : To Buy or Not?

Targanta Therapeutics Financials:

IPO Date: 10/9/2007
Raised in IPO: $58million
Lead Underwriter: Credit Suisse
Burn Rate: $52.2million (nine months ended 08/30/07)
Cash: ~$49million (08/30/07)

Targanta expects to file a NDA for oritivancin in the first quarter of 2008. Even still this is cutting it a bit close, as at the current burn rate I would expect them to run out of cash sometime in March. In addition, the press release stated that most of the increase in spending was related to R&D expenditures for their lead candidate. I feel that this burn rate is unacceptable, especially for a therapeutic supposedly to have met phase III primary endpoints 5 years ago. From the prospectus, Targanta has purportedly been rigoriously performing in vitro potency tests, but literature searches don't reveal much in the way of the fruits of these labors. At any rate, it doesn't seem the money is going to executive compensation.

Oritavancin History
Oritavancin was originally discovered in the mid 90s by Eli Lilly research laboratories. In 2001, Lilly licensed the glycopeptide antibiotic to Intermune who subsequently finished the phase III studies, but delayed filing the NDA in 2004 because of adverse side effects including injection site phlebitis. In 2005, Intermune divested itself of oritavancin, citing a business focus on pulmonary and hepatology therapies, by selling the worldwide ownership rights to Targanta.

Targanta has apparently negotiated an undisclosed, but signifigantly lower, royalty rate with Lilly. They have already paid out $1 million and may owe up to $35 million more in regulatory and sales milestones. As of April 15, Targanta had paid $4 million of the $9 million in cash and $17.5 million of the $25 million in convertible debt it owes to InterMune.

Targanta FDA Interactions
From the prospectus:

When we acquired the world-wide rights to oritavancin in 2005, we developed and implemented a comprehensive strategy to gain a better understanding of injection-site phlebitis. We concluded that the risk of phlebitis was no higher with oritavancin than with equally potent doses of vancomycin. We first presented the data from our effort to characterize the risk of phlebitis to the FDA at a meeting on July 20, 2006. At our FDA meeting on January 31, 2007, the FDA agreed to remove the clinical hold on oritavancin.

In addition, the two phase III trials have both been non-inferiority designs compared with vancomycin. Targanta has cited multiple communications in which the FDA has confirmed that this design would be acceptable for the desired cSSSI NDA indication, despite the fact that the required delta (cure rate difference) is now 10% and the 2003 trials were conducted using the previous accepted delta of 15%. Approval of the NDA however is strongly contingent upon information describing the benefits of oritavancin (over vancomycin).

Targanta To Buy or Not?
Theravance has been spotlighted significantly over Targanta mainly because of the upcoming February 27 FDA review concerning the telavancin NDA. In October, Theravance recieved a letter from the FDA requesting additional information prior to approval consideration. As such, investors aren't particularily bullish on THRX and as of writing this article short interest stands around 8%.

Targanta appears to be timing its proceedings around telavancin, which makes sense in one regard as the FDA has been described as fickle with respect to antibiotic approvals, and management is probably waiting to see how telavancin gets treated by the regulatory bodies. On the other hand, its pretty clear that Targanta doesnt have the finances to perform many more clinical trials (or experiments of any kind for that matter) so its unclear which recourse they might take if the FDA comes down hard on glycopeptides.

In evaluating TARG, I think its safe to say that the market timing is very favorable. I have been interested speculative portfolio exposure to infectious disease biotech niche markets, and this fits that bill perfectly. From a scientific perspective, I think that oritavancin, and indeed telavancin are sound, not necessarily groundbreaking new methods of bactericidal activity but improvements on vancomycin without a doubt. That vancomycin retains 80% market share is a testament to the potential utility of antibiotics which are vancomycin 2.0. It is from the management perspective, where I draw some hesitation on Targanta. It is clear from the FDA correspondence that clincal data and supplementary science is going to make or break this NDA, and while I can see the astronomical burn rate what I cant find is the scientific results. Because of this opacity, we need to trust that the money spent in the last five years has gone to building a mountain of evidence to throw at the FDA. I would be suprised to find $100million had been spent elsewhere, nevertheless this remains the weak point in the investor thesis.

I am going to go ahead take a favorable stance on both Targanta and Theravance. This is based on the thesis outlined in both part I and part II. There is a frightening medical need for new antibiotic therapies, and the science of telavancin and oritavancin is very sound (see the chart in part II). I'm not sure what effect approval, or disapproval of telavancin will have on TARG, but if we assume it to be sympathetic, the play would be to wait until the end of next month to move on Targanta. For those in an extremely speculative mood, based on the differential science one could double-dip this market and playing both THRX and TARG immediately. Otherwise, for my father-in-law, or anyone else who would like exposure to stocks benefiting from potential 'superbug' outbreaks, I greatly favor the daptomycin (Cubicin made by CBST) play, proper timing withstanding.

Thanks for reading.
Disclosure Statement: I have no position in any of the stocks mentioned above.

Targanta Therapeutics Part II : Oritavancin

Last time I covered the state of antibiotic resistant microorganisms, namely Staphylococcus aureus and its Methicillin-resistant brethren (MRSA). Hopefully it is now abundantly clear why microbiologists, infectious disease specialists, and even congress are becoming increasingly concerned with the lack of alternative antibiotic options.

Competition in the cSSSI market

Targanta's lead product is Oritavancin, a novel intravenous antibiotic, for the treatment of serious gram-positive bacterial infections, including complicated skin and skin structure infections (cSSSI), and bacteremia. Antibiotics designed to treat serious infections caused by resistant gram-positive bacteria accounted for approximately $945 million in U.S. sales in 2006 (up from $284 million in 2002). The predominant treatment for resistant gram-positive bacteria is vancomycin, which currently accounts for approximately 85% of courses of therapy in the United States for antibiotic-resistant gram-positive pathogens. Two other antibiotics comprise the majority of remaining sales in the resistant gram-positive market: linezolid (Zyvox^®, Pfizer $782 million in 2006) ; and daptomycin (Cubicin^®, Cubist $190 million in 2006).

Importantly, competition for supplemental cSSSI treatments is heating up. Theravance's telavancin NDA is set to be reviewed by the end of next month. Arpida's iclaptrim passed phaseIII trials in july of last year and has already presumably filed the NDA. In addition, J&J, Pfizer and Wyeth, among others, all have next-generation antibiotic candidates still in the clinical trial phase.

Therefore to discern whether oritivancin has any kind of competitive advantage, we are going to have to hit the scientific data pretty hard. Let's get started.

Oritavanicin: Mechanism of Action

Most gram positive bacteria are surrounded by a peptidoglycan layer composed of a cross-linked polymeric network made from a monomeric unit. This cell wall is generally essential to the viability of the microorganism by providing both structure and protection. The glycopeptide class of antibiotics, of which vancomycin and oritavanicin are included, inhibit synthesis of this cell wall effectively by tightly binding to the peptidoglycan monomer and halting the crosslinking process. This in turn leads to the collapse of the cell wall by shifting the dynamic equilibrium towards de-assembly, which precipitates cell lysis and bacterial death.

Specifically, atomic resolution structures have shown that glycopeptide antibiotics bind to the D-Ala-D-Ala fragment of the peptidoglycan monomer. The antibiotic heptapeptide backbone adopts a rigid conformation forming a carboxylate binding pocket to bind the D-amino acids via a series of hydrogen bonds. Different glycopeptides have different affinities based on their structure, and there is also a general trend of dimerization correlation with affinity. Moreover, greater antibacterial activity has been shown for those compounds which are able to anchor to the plasma membrane through the use of a hydrophobic side chain. Oritavancin is a derivative of a strongly dimerized glycopeptide which can also anchor to the plasma membrane via an alkyl side chain.

In enterococci bacterium, the development of vancomycin resistance (VRE) arose as a result of the bacterium reorganizing its peptioglycan precursor compostion to a D-Ala-D-Lac. This alteration requires 5 genes (vanA) and deprives vancomycin of a single hydrogen bond, enough to bestow resistance. The mechanism of community acquired S. aureus resistance is less well understood, but it is believed to result in part from increased cell wall synthesis and overproduction of antibiotic binding proteins, in this manner vancomycin is potentially unable to either diffuse through the thickened wall or inhibit all the available PG precursors, or both. Finally, laboratory findings have discovered the enterococci vanA gene cluster transferred into a clinical isolate of MRSA, giving rise to highly resistant VRSA.

Competition Assessment
Now armed with some mechanism of action, we can compare oritavancin with MRSA and VRSA indicated therapies currently on the market, as well as the other directly competing glycopeptide antibiotics.

Linezolid:
Linezolid (Zyvox^®) is an oxazolidinone compound approved by the FDA in 2000. This antibiotic inhibits bacterial protein synthesis by binding to the 50S ribosomal subunit, and covers all important Gram-positive pathogens. Linezolid can be administered either intravenously or orally with 100% bioavailability, and has been approved to treat community acquired and nosocomial pneumonia, cSSSI, MRSA and VRE. Due its broad coverage of bacterial pathogens, and its availability in oral form, it is not suprising that Linezolid will continue to be a popular treatment in the first line of defense against antibiotic resistant infections. However, as with other antibiotics, popularity is often a curse, and reports as early as 2001 have described resistance to Linezolid amongst MRSA and VRE. In this manner, I would expect future prescription of Linezolid to increase linearly while the corresponding reports of resistance to follow a more exponential curve.

Daptomycin:
Daptomycin (Cubicin^®) is a nonribosomal lipopeptide antibiotic. It's proposed mechanism of action is an intriguing process by which Ca²⁺ dependent conformational changes allow the lipopeptide to insert into the bacterial membrane causing lipid disruptions and membrane leakage, destroying the membrane potential. The FDA approved daptomycin in 2003 for use in patients with cSSSIs, and subsequently approved its use for endocarditis and bacteremia indications in 2006. In vitro, daptomycin is active against S. aureus (including MRSA and VRSA) and VRE. Resistance to daptomycin is rare but has been reported, potentially owing in VRSA to a thickened cell wall which limits the antibiotic's ability to reach the cell membrane. In addition, daptomycin has failed to meet non-inferiority criteria for community acquired pneumonia due to interactions with pulmonary surfactants.

Telavancin:
Telavancin is a glycopeptide derived from vancomycin. As such it also inhibits cell-wall biosynthesis by binding to late-stage cell-wall precursors. However, telavancin contains an additional lipophilic (decylaminoethyl) side chain attached to the vancosamine sugar, as well as a hydrophilic ([phosphonomethyl]aminomethyl) group on the 4′ position of amino acid 7. The addition of the lipophilic decylaminoethyl substituent to the molecule classifies this agent as a lipoglycopeptide, and is speculated to cause the observed effect of disruption of the bacterial membrane functional integrity. The spectrum of activity for telavancin is similar to that of vancomycin, but is characterized by a minimum inhibitory concentration (MIC) that is generally two to eight times lower for most organisms tested including VRSA and VRE.

Enough Space in the Market?
From the above I think that its clear that there is certainly enough difference between linezolid, daptomycin and the glycopeptide class of antibiotics to warrant FDA approval of Theravance's telavancin. This becomes even more of reasonable possiblity when we consider part I, and the shrinking arsenal of available approved treatments in light of new evolving resistant strains. From this standpoint telavancin (and oritavancin) would become updates to the most widely prescribed vancomycin. But is there enough difference between telavancin and oritavancin to make a call on Targanta?

If your still with me this is where we can be glad we did our homework. Oritivancin, because its strongly dimerized, has the edge on organisms with the D-Ala-D-Lac mutation that steals a hydrogen bond from the other glycopeptide antibiotics. This includes vancomycin resistant enterococcus (VRE) and strains of VRSA arising from the vanA gene cluster transfer. This point has been difficult to cite definitively, due to the copious studies both in vitro and in vivo and performed using differing methods which make direct comparison difficult. However, in this article the literature has been distilled into exactly the table we are looking for.

I think it goes without saying that the data is not exactly crystal clear. However, as predicted Oritavancin does have a very favorable profile with regards to the VRE strains. Unfortunately the literature is very imprecise when it comes to direct comparisons of efficacy with regards to VRSA strains. I assume that this is because full-blown VRSA is rare and most strains are in fact stronger or weaker VISA members.

In conclusion, the business of antibiotics must be evaluated on slightly different grounds from other therapeutics. This is because the pathology itself is constantly evolving, giving rise to an unusual situation whereby a therapeutic effectiveness begins to decrease in proportion to its popularity. In this regard, differences in mechanism of action are equally if not more important in an antibiotic's evaluation than the particular in vitro MIC numbers.

Next time, we'll cover the licensing aspects of oritivancin (its passed through a few hands) as well as Targanta's financial situation to hopefully come to some sort of a conclusion.