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Operator
Good day, ladies and gentlemen, and welcome to the BioCryst third quarter 2012 earnings conference call. At this time all participants are in a listen-only mode. Later we will conduct a question-and-answer session and instructions will be given at that time. (Operator instructions). As a reminder, this conference call is being recorded.
I'd now like to introduce our host for today, Mr. Robert Bennett, Executive Director of Investor Relations and Communications. Sir, please go ahead.
Robert Bennett - Executive Director of IR and Communications
Thanks, Ben, and good morning everyone and welcome to BioCryst's third quarter 2012 quarter update and financial results conference call. At this time all participants are in a listen-only mode. Later we'll open up the call for your questions and instructions for queuing will be provided at that time.
Today's press release and accompanying slides for this call are available on our website at www.biocryst.com. Joining me on the call today are Jon Stonehouse, Chief Executive Officer of BioCryst, Dr. Bill Sheridan, our Chief Medical Officer, and Tom Staab, Chief Financial Officer.
Before we begin, I'll read a portion of the formal statement as shown on slide two regarding the risk factors associated with today's call. Today's conference call will contain forward-looking statements including statements regarding future results, un-audited and forward-looking financial information, and Company performance or achievements. These statements are subject to known and unknown risks and uncertainties, which may cause our actual results, performance, or achievements to be materially different from any future results or performance expressed or implied in this presentation. You should not place undue reliance on the forward-looking statements. For additional information including important risk factors, please refer to BioCryst documents filed with the SEC, which can be found on our Company website.
With that I will turn the call over to Jon.
Jon Stonehouse - President, CEO
Thank you, Rob. Good morning, and thanks to everyone for joining us today. I'll start out today's call with a review of the peramivir interim analysis and then address both the opportunities and challenges that lie ahead for BioCryst.
Obviously we are disappointed with the results of the interim analysis of our peramivir Phase 3 trial in patients hospitalized with serious influenza. The pre-planned interim analysis indicated that the recalculated sample size for the primary efficacy analysis exceeded 320 subjects, the pre-defined futility boundary for the trial. There was only a small difference in time to clinical resolution between the standard of care plus peramivir-treated arm compared to the standard of care plus placebo arm.
After we received notice from the data monitoring committee, or DMC, regarding the result, we promptly shared the outcomes with HHS BARDA. Consistent with the DMC recommendation, BioCryst suspended enrollment in the study. We are now proceeding with a full analysis of the trial. Although we will discuss the findings from the analysis with our partners, the most likely outcome is termination of the program.
This Phase 3 trial in hospitalized influenza patients was unprecedented and challenging due to the general lack of research in this specific area and the novelty of this endpoint in time to clinical resolution. These factors increased clinical risk for the trial. However, we chose to pursue this program based on the high unmet medical need for IV therapy for hospitalized influenza patients and the interest in funding by HHS BARDA.
While we failed to show a large enough difference in this trial with peramivir, it's important to remember that peramivir was successfully approved in Japan and Korea based on a different indication and primary endpoint in clinical trials that supported approval. In January 2010, Shionogi received approval of peramivir for the treatment of outpatient influenza in Japan and launched peramivir under the commercial name Rapiacta.
Going forward we need to focus on the rest of our portfolio. We're fortunate to have other promising assets. Our top priorities include advancing BioCryst pipeline and the Presidio merger to create a company with a two-prong focus on antivirals and orphan disease drugs, initially for HCV and hereditary angioedema.
We also need to carefully manage our cash. To that end, we will evaluate operational changes that would further decrease our cost structure, and we will focus our resources on advancing the pipeline to potential value-creating milestones that can put us back on a path to long-term success and sustainability.
Here are the things we plan to do in the coming months. First, bring the BCX4161 hereditary angioedema program into Phase 1 before yearend. Upon successful completion of Phase 1, we can then move quickly to HAE patients -- patient trials with a modest investment. The key at this stage of the program is to demonstrate we have adequate and consistent oral bioavailability to inhibit kallikrein and ultimately prevent HAE attacks. If we are successful, 4161 could revolutionize the treatment of HAE.
Second, initiate additional preclinical studies for BCX5191 before the end of 2012. If we are successful in demonstrating meaningful preclinical antiviral activity of 5191 in chimpanzees infected with HCV, we will seek to reengage the FDA regarding potential pathways to move the program forward to clinical development.
Third, secure a partner for ulodesine. We are in discussions with potential partners. While it is difficult to predict when the process will conclude, partnering remains a top priority, and we will work to get this done as soon as possible so ulodesine can enter Phase 3.
While these last two weeks have been challenging, we remain committed to honoring our signed merger agreement with Presidio and advancing our assets to the next important milestones between now and the end of next year. With that, I will turn it over to our CFO, Tom Staab, who will discuss our third quarter financial results.
Thomas Staab - SVP, CFO
Thank you, Jon, and good morning everyone. I'm pleased to share with you some details regarding our third quarter 2012 financial results. Throughout 2012 we have consistently achieved the financial goals established for the Company, and the third quarter is further evidence of our accomplishments. We continue to deliver substantially reduced general and administrative expenses in 2012, which are roughly half of 2011 levels. These reductions continue to illustrate our commitment to a key operating principle, which is focusing our cash resources on advancing our development programs while minimizing non-critical and non-project spending. In addition, we are narrowing our development focus and related expenditures to antivirals and hereditary angioedema.
Now I'd like to discuss our third quarter financial results for 2012, which are summarized on slide three. Revenues for the third quarter of 2012 were $5.8 million compared to $5.2 million in the third quarter of 2011. This revenue increase resulted primarily from the recognition of $2.8 million of deferred Rapiacta royalty revenue from Shionogi, which was largely offset by a decrease in collaboration revenue from HHS BARDA.
Our revenue situation in the third quarter of 2012 is unique as we recognize seven quarters of deferred Rapiacta royalty revenue. This recognition occurred in the third quarter of 2012, as we needed two complete and representative flu seasons in Japan to give us reasonable historical experience to record an appropriate amount of Rapiacta royalty revenue in accordance with generally accepted accounting principles. As mentioned in the press release, there is no underlying impact to our cash balance as all royalty payments were directed to pay obligations on our non-recourse notes payable.
Continuing the revenue discussion, the increase in royalty revenue was substantially offset by a decrease in the amount of revenue associated with reimbursement for parameter development. Parameter development activity and related reimbursement under the HHS BARDA contract is below levels in 2011 as 2012 parameter development activity was predominantly focused on the 301 clinical trial for which there was slower enrollment due to mild flu seasons, whereas in 2011 there was more substantial and broader parameter development activity.
Third quarter 2012 R&D expenses were $12.1 million, down from $15.1 million in last years quarter. Our R&D program expense mix has changed as lower development cost associated with the ulodesine and parameter programs was partially offset by higher development costs associated with the BCX5191 and 4161 preclinical programs. We expect our R&D concentration to continue toward our preclinical programs, especially on our BCX4161 drug candidate for hereditary angioedema as we expect it to begin Phase 1 testing before yearend. In addition, the R&D mix will be further impacted by the recent suspension of patient enrollment in our peramivir 301 study and completion of the ulodesine Phase 2 development program.
Third quarter 2012 general and administrative expenses were $1.6 million and reflect a 46% reduction from the $3 million of expense incurred in the third quarter of 2011. This decrease in administrative expenses is even more impressive as 2012 expenses included a portion of Presidio due diligence and merger costs, which when excluded, provide for an over 53% decrease in 2012 administrative expenses. As mentioned earlier, we are extremely pleased with our ability to curtail administrative costs and more fully dedicate resources towards advancing our drug candidate portfolio.
Moving down below the operating line, we incurred $1.2 million of non-cash interest expense and mark-to-market losses of approximately $600,000 in third quarter of both 2012 and 2011. The interest expense and hedge loss for both periods relates to our non-recourse debt and our hedge arrangement enacted in conjunction with the Rapiacta royalty monetization completed in the first quarter of 2011.
Our nine-month financial results for 2012 and 2011 are summarized on slide four. Revenue for the nine months ending September 30, 2012, increased to $22.2 million compared to $14.1 million for the nine months ending September 30, 2011. The increase was primarily due to the recognition of approximately $8 million of previously deferred forodesine-related revenue during the first quarter of 2012 and $2.8 million of Rapiacta revenue recognized during the third quarter.
Revenue from reimbursement on peramivir development for the nine months of 2012 decreased $1.7 million or 14% compared to the same period of 2011. Nine-month 2012 R&D expenses were $40.4 million, down slightly from $43 million in the first nine months of 2011. Lower ulodesine and peramivir development costs were partially offset by higher development costs in 2012 associated with the BCX5191 and 4161 preclinical programs and recognition of $1.9 million of previously deferred forodesine expenses associated with the amendment of our Mundipharma agreement.
General and administrative costs through September 30, 2012, decreased sharply to $4.9 million from $9.9 million in the nine-month period of 2011. The 51% decrease resulted from a significant reduction of non-critical consulting and other administrative expenses as well as one-time expenses incurred in the 2011 relocation of our corporate headquarters.
In the first nine months of 2012 we incurred $3.5 million of interest expense compared to $2.6 million in 2011. The difference resulted from nine month of interest in 2012 versus approximately seven and a half months in 2011. The 2012 period also included a mark-to-market loss of $1.5 million compared to $2.9 million for the same period of 2011, reflecting changes in the US dollar/Japanese yen exchange rate.
Now moving to slide five, I'd like to discuss our cash usage and our 2012 financial outlook. At September 30, 2012, we had cash and investments of $43.8 million compared to $57.7 million at the end of 2011. Our operating cash usage for the third quarter and nine months ended September 30, 2012, was $9.7 million and $29.7 million, respectively. As a reminder, operating cash use excludes any impact of our royalty monetization, hedge collateral posted or returned, sale of stock in the marketplace, and any other non-routine cash inflows.
Considering recent events in our peramivir and BCX5191 programs, we are evaluating operational changes to decrease our cost structure to better position our Company to achieve value-creating milestones and to conserve our cash resources to extend further into the future.
In regards to our outlook for the remainder of 2012, we are reiterating our prior operating cash utilization guidance of $37 million to $43 million and operating expense guidance of $57 million to $69 million as we announced in August. As a reminder, our outlook depends on peramivir-related operating expenses and excludes any consideration of cash inflows derived from out-licensing ulodesine.
That concludes my financial review, and I'd like to turn the call over to Dr. Bill Sheridan. Bill?
Bill Sheridan - SVP, Chief Medical Officer
Thanks, Tom. The medical need for an oral safe prophylactic treatment for hereditary angioedema is high, making HAE a compelling opportunity. Kallikrein inhibition is a well-validated approach, and the development pathway is well understood in this orphan disease. Our HAE program consists of two kallikrein inhibitor projects, the lead compound, BCX4161 poised to enter Phase 1 clinical studies by yearend, and a next-generation research project.
The key goal for the 4161 study is to demonstrate oral bioavailability in humans. We need to see consistent PK with adequate exposure levels that suppress kallikrein. Fortunately, the level of 4161 needed to fully inhibit kallikrein are quite low, less than 100 nanomole. We have learned about PK and PD quickly and anticipate having results in early 2013.
If 4161 passes this test, we should be able to more this project through trials in HAE patients expeditiously. At the same time, our discovery team has been working on new compounds for HAE with a totally different chemical scaffold with the main goal of improving bioavailability. This discovery project is now at the stage of advanced lead optimization and could be ready to move into preclinical development during 2013.
BioCryst's HCV portfolio consists of two NS5B nuc projects, BCX5191 and a next-generation research program. Last week we outlined the next steps for 5191. The key here is to find out whether 5191 achieves substantial antiviral effects in chimpanzees with HCV infection at exposure levels equivalent to or below the [novel] level identified in rats. We are focused on initiating these studies by yearend.
If we are successful in demonstrating meaningful antiviral activity of 5191 in this animal model, we will seek to reengage the FDA regarding potential pathways to move the program forward to clinical development. While this work is progressing, we will continue to develop a set of compounds that may have a superior therapeutic index compared to 5191. This research is at the stage of selecting several compounds to take into screening animal safety experiments, and if successful could provide an optimized lead to advancing to full preclinical development during the first half of 2013.
Today we would like to introduce an additional BioCryst antiviral project, BCX4430, the lead compound in our broad-spectrum antiviral program. It is targeted at pathogens that cause serious life-threatening viral hemorrhagic fevers, or VHS, diseases characterized by both high morbidity and mortality and lack of any approved therapies. The VHS pathogens include filoviruses, such as Marburg virus and Ebola virus, and flaviviruses, such as Yellow Fever virus. These viruses are categorized by government agencies as high-priority pathogens for development of medical countermeasures in order to protect civilian and military populations.
Our lead compound, 4430, has shown a very broad spectrum of antiviral activity in cell culture experiments with inhibitory activity against at least 15 viruses from nine different families and activity in several different animal models. In the next weeks and months, we will be presenting results of testing for 4430 in models of infection for filoviruses and flaviviruses. Next week, studies of 4430 in Yellow Fever virus infection will be presented at the Second Antiviral Congress in Cambridge, Massachusetts, and we look forward to highlighting those results in more detail then.
We plan to apply for federal funding to bring this project forward into full preclinical development and could submit an IND within one year of securing development funding. The path forward for this project is development under the Animal Rule for one or more high-priority biothreats to enable US government stockpiling as a medical countermeasure.
With that, we will now open up the call for your questions.
Operator
(Operator instructions). Our first question today comes from the line of Ed Arce from MLV and Company. Your line is open. Please go ahead. Pardon me, our question comes from Rahul Jasuja from Noble Financial. Your line is now open. Please go ahead.
Rahul Jasuja - Analyst
Hi. Good morning everybody. Thanks for taking my questions. Couple questions. I want to start with the peramivir program. So Jon, just looking at it, so how do I square this? How do we square this regarding the fact that you've got an approved intravenous version of this approved in Japan? I guess it's outpatient as opposed to hospitalized. And then we've got stockpiling about 23 million a few years ago that had patient exposure. There seems to be a need for this. There seems to be efficacy and safety, albeit not in a registration path. How does the government and how does BioCryst look at this asset going forward given what happened today?
Jon Stonehouse - President, CEO
Thanks for your question, Rahul. So you probably touched on the most frustrating part of this, which is we have the experience with the EUA. Our partner Shionogi has gotten the product approved in Japan, clearly in a different indication doing different trials and using a different endpoint. But as I described in my prepared comments, we took a different path for the reasons that I listed, the high unmet medical need and the interest in the funding from HHS BARDA.
And unfortunately with the endpoint that we were pursuing, we were unable to show a difference. So it's very frustrating, but I think what I would say to investors is put peramivir in its proper context in the portfolio of BioCryst. It's been funded by the government and we had always said that what we had hoped for if we were successful was a stockpiling order and it was a source of non-dilutive capital. And unfortunately it appears that that's not going to happen as a result of this Phase 3 result, but in the scheme of the overall portfolio, I think there are a number of attractive assets that we can continue to pursue that have meaningful value creating potential.
Rahul Jasuja - Analyst
And Jon, just a theoretical question. In the event that a flu outbreak happens that is akin to the one in the past, is it still possible that the NIH, the federal agencies could do stockpiling akin to last time and it could be compensation for BioCryst, or that doesn't hold anymore?
Jon Stonehouse - President, CEO
Well, so remember that the original EUA was done before we had even started the Phase 3.
Rahul Jasuja - Analyst
Right.
Jon Stonehouse - President, CEO
So the federal government always has the ability in an emergency to issue an emergency use authorization. We've demonstrated that we can manufacture the drug safe, but that's a decision that the government makes.
Rahul Jasuja - Analyst
Okay. So I want to move on to 5191 if I could, and some of these questions probably are -- I guess this is directed to Bill maybe. So looking at 5191, one of the trends that I've noticed, and do correct me if I'm wrong here, is that you've got the issue with these purine-based nucs and not the [thermodyne] or thymine-based nucs. Methylguanosine clearly was the [sugar] in the case of BMS Inhibitex, methylguanosine in the case of Idenix. And then I think (inaudible) 215A, the one that was halted, was also an adenosine-based purine nuc.
While the uracil-based, the pyrimidine-based nucs, 7977, VX-135, the Vertex compound, and even R718, the cytosine-based have sort of had a path. Bill, could you add some color on that? Am I sort of harping in the wrong direction here? Is there an issue with purines?
Bill Sheridan - SVP, Chief Medical Officer
Thanks for the question. I think each of these molecules have to be independently assessed. They're all different structurally. And I think it's too early to come to conclusions on the basis of purine or pyrimidine or a specific base and whether or not the base is modified and so on. Each of them is different.
There was a paper published in the last year or so that reviewed the nucleosides that are already on the market for HIV and hepatitis B, pointing out that -- and also hematological conditions, pointing out that it's very difficult to predict the safety profile of these compounds. There are some seams, but you can't be confident in assuming class of fix of a particular type of structure.
Rahul Jasuja - Analyst
Okay. And then though going forward, if you're developing sort of a better version of 5191 or another nucleoside of any kind, would an adenosine-based one be the preferred one, or would it not be the preferred one going forward? Again, a theoretical question.
Bill Sheridan - SVP, Chief Medical Officer
I think that's also rather difficult to answer. The immediate task for us is to get the chimp study done that we've discussed. The perspective we have is that safe doses of 5191 will be adequate to treat HCV infection, and that's what we need to show. So that's an important study.
As I mentioned in the remarks, we also have a research program that is attempting to improve the therapeutic index. We'll have to see how that goes, and the next step there is to do screening safety studies in animals. This is a field we have been working on for some time, and we have a portfolio of research molecules, but I think it's premature to get into the details of what they are.
Jon Stonehouse - President, CEO
And Rahul, I would just add to Bill's comments, to start from scratch now is probably a bit challenging given that the speed at which you need to get these things to market. So we've been working on a set of backups for a while, and so those are the ones that we'll focus on in addition to 5191.
Rahul Jasuja - Analyst
Okay. And then one final question. Jon, a little more color on the gout space for 420 -- for ulodesine. Obviously investors are waiting for that and promise (inaudible), but could you just add some more on that? Thanks.
Jon Stonehouse - President, CEO
Sure. So as I said in my prepared comments, we are in discussions. I've been doing deals for a long time and the completion of these are always difficult to predict. But we want to get this Phase 3 started, right? We've completed the Phase 2 program. We're doing some of the work to get ready for the Phase 3, and so the quicker we can get this done the better, so that's a top priority for us.
Rahul Jasuja - Analyst
And you said that you've done some of the work for the Phase 3? That is with no intention of ever pursuing a Phase 3, it's just to sort of round it up. Is that right?
Jon Stonehouse - President, CEO
Yes. It's to be able to hand it over to a partner that can then hit the ground running. It's not to start it up on our own. I think the cost of the trial -- and a strategic view that we've always had is it's important to get this in the hands of somebody that has the capability and the knowledge and the space and that kind of thing to develop this and market this product much more effectively than we could on our own.
Rahul Jasuja - Analyst
Got it. Thanks.
Jon Stonehouse - President, CEO
Yes.
Operator
Thank you. Our next question comes from the line of Heather Behanna from JMP Securities. Your line is open. Please go ahead.
Heather Behanna - Analyst
Hi guys. Good morning. Most of my questions were answered. I just -- so when we think about the backups, your next generation, are these also from the nucleoside class and are you looking for more target in liver exposure, or is your goal still to have something that is readily available in the plasma, sort of in the similar profile as 5191?
Bill Sheridan - SVP, Chief Medical Officer
In general, to answer your question, yes, they're in the nucleoside class in BioCryst's research program. Obviously with a pending merger there are other things that we can work on as well, and we talked about that in a previous call.
But specifically what might be the goal? I think that the likely type of drug there is something that we would be able to measure in the plasma but we have specific targets that I don't want to get into today about liver exposure and the like.
Heather Behanna - Analyst
Okay. Great. And for the chimp study, is there any more color you could give us on timing? I mean, you had said I believe that this would be a seven-day study? So should we expect some sort of readout in the first quarter?
Bill Sheridan - SVP, Chief Medical Officer
No, I think that we are moving forward quickly to get that study up and running. As is always the case, you have to go through contracting and the other steps to get a study moving, but we're confident that we can do that by the end of the year. And this is not a huge undertaking, so we anticipate, as I said in my prepared remarks, that we should be able to do that and get results pretty quickly. I don't want to put a definitive timeline on it.
Heather Behanna - Analyst
Okay. Great. Thank you.
Operator
Thank you. (Operator instructions). Our next question comes from the line of Ed Arce from MLV and Company. Your line is open. Please go ahead.
Ed Arce - Analyst
Hi. Good morning. Thanks for taking my questions. I just wanted to start off with a question about the Presidio acquisition. I realize that you've got a portfolio of next-generation research projects following up behind 5191, but in the event that the 5191 development is terminated, the remaining projects are clearly very early stage. So I'm just wondering, I realize that you've signed a definitive merger agreement, but are there clauses or avenues for Presidio to decide to exit from the deal?
Thomas Staab - SVP, CFO
So thanks for the question, Ed. We believe that the rationale for the deal still makes sense for the reasons that I listed before when talked about 5191. So the first one is HCV is a very attractive area. Second, Presidio has high-quality assets and capability. We always said when we announced the merger that we weren't going to be limited to any one combination, that we'd pursue all types of combinations, both internal molecules and external. And we still think that that makes sense, so whether it's 5191 or other combinations, we think that that still is good strategic rationale.
Then if you look at the balance of the portfolio, right? The HCV compounds and HAE, I think both companies need more assets, and so that I think makes sense from a strategic perspective. And then lastly, as you said, we have a signed merger agreement in place, and we intend to honor it. So we still, like I said before, we still believe that the strategic rationale for this deal makes sense.
Ed Arce - Analyst
Okay. And then moving over to, well I guess this is still 5191. I just was curious on the posters that you will be presenting later this week and in the weekend at AASLB. Could you give us a little bit more clarity on what the focus of those posters will be?
Bill Sheridan - SVP, Chief Medical Officer
The poster is about the preclinical bench characterization of the compound.
Ed Arce - Analyst
Okay. So it will discuss some of the toxicity --?
Bill Sheridan - SVP, Chief Medical Officer
So there will be some -- it's a bench experiment type focus.
Ed Arce - Analyst
Okay. Okay. Thank you very much.
Jon Stonehouse - President, CEO
You're welcome.
Ed Arce - Analyst
Appreciate it.
Operator
Thank you. And I'm showing no further questions. Ladies and gentlemen, this does conclude our program. Thank you for your attendance and have a great rest of the day. You may all now disconnect.