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FINAL TRANSCRIPT

Conference Call Transcript

AMLN - Amylin Pharmaceuticals, Inc. at Cowen and Company Healthcare Conference

Safe Harbor Statement

This presentation contains forward-looking statements about Amylin. Our actual results could differ materially from those discussed due to a number of factors, including: BYETTA and/or SYMLIN may be affected by competition, safety or other issues; clinical trials not being completed in a timely manner or achieving the intended clinical endpoints; NDAs or sNDAs not being submitted in a timely manner or receiving regulatory approval; expense reductions not being as large as we expect; our label update not being finalized in a timely manner; or manufacturing and supply issues. The pace of market acceptance and rate of patient adherence may also affect the potential for BYETTA and/or SYMLIN. These and other risks and uncertainties are described more fully in Amylin’s most recently filed Form 10-K. Amylin disclaims any obligation to update these forward-looking statements.

ADDITIONAL INFORMATION AND WHERE TO FIND IT

This release may be deemed to be solicitation material in respect of the matters to be considered at the 2009 annual meeting of shareholders. Amylin will be filing a proxy statement with the Securities and Exchange Commission (“SEC”). INVESTORS AND SECURITYHOLDERS ARE URGED TO READ THE PROXY STATEMENT AND ANY OTHER RELEVANT DOCUMENTS FILED OR THAT WILL BE FILED WITH THE SEC WHEN THEY BECOME AVAILABLE BECAUSE THEY WILL CONTAIN IMPORTANT INFORMATION. Investors and securityholders will be able to receive the proxy statement and other relevant documents free of charge at the SEC’s web site, www.sec.gov or from Amylin Investor Relations at 9360 Towne Centre Drive, San Diego, California 92121.

PARTICIPANTS IN SOLICITATION

Amylin and its directors and executive officers and other members of management and employees may be deemed to be participants in the solicitation of proxies in respect of the matters to be considered at the 2009 annual meeting of shareholders. Information regarding the interests of Amylin’s directors and executive officers in the proxy contest will be included in Amylin’s definitive proxy statement.

Mar 17, 2009 / 8:00AM ET, AMLN - Amylin Pharmaceuticals, Inc. at Cowen and Company Healthcare Conference

EVENT DATE/TIME: MAR 17, 2009 / 8:00AM ET

CORPORATE PARTICIPANTS

Dan Bradbury

Amylin Pharmaceuticals, Inc. - President & CEO

CONFERENCE CALL PARTICIPANTS

Phil Nadeau

Cowen and Company - Analyst

PRESENTATION

Phil Nadeau - Cowen and Company - Analyst

Good morning and welcome once again to Cowen and Company’s 29th Annual Healthcare Conference. I’m Phil Nadeau, a biotech analyst here at Cowen, and it’s my pleasure to introduce the first presenting company this morning, Amylin Pharmaceuticals.

These are exciting times for Amylin with two drugs on the market and LAR on the cusp of being filed with the FDA. CEO, Dan Bradbury, will give about a 20- to 25-minute talk in this room. There may be questions here — time for questions here and, if not, there is a breakout immediately following in the Tufts Room, which is right around the corner. Dan?

Dan Bradbury - Amylin Pharmaceuticals, Inc. - President & CEO

Thanks, Phil. Good morning and top of the morning to you. Happy St. Patrick’s Day here in Boston and may the luck of the Irish be with you in the markets today.

So before I start just a reminder that most of the comments that I will be making will be about future plans for our organization and I intend to make a number of forward-looking statements, so please consult your SEC filings for a full description of our risks.

2009 is a year in which we are confident of our five-point plan that we have put in place to create value. That plan revolves around BYETTA, exenatide once weekly, SYMLIN, our obesity franchise, and improving our operating results.

With BYETTA we have the opportunity to leverage the inclusion at the end of last year of BYETTA in the ADA/EASD treatment guidelines and capitalize on the shifting patterns of treatment in the diabetes marketplace. We also had the opportunity to gain the approval for a new indication for BYETTA for monotherapy and at the same time get the label update as well to reflect new safety information.

Our number development goal in 2009 is to submit exenatide once weekly. In doing so, we will be leveraging the experience that we have had over the last four years with BYETTA. Accompanying that we will be executing the DURATION studies. These are studies designed to demonstrate that exenatide once weekly is superior to most other treatments for the treatment of diabetes, and indeed will enable us to position exenatide once weekly for a successful launch.

SYMLIN in 2008 grew by more than 30% and we intend to continue that growth rate in 2009.

With our obesity franchise we have two major clinical studies that are being completed. The first of those will complete in the third quarter, the second in the fourth quarter. At that time we will finalize our development strategy at the same time as finalizing a funding strategy for late-stage development in obesity.

And as we progress towards our corporate goal of being cash flow positive by the end — operating cash flow positive by the end of 2010, we will be focused on reducing our expenses and overall improving our operating results.

These five areas of focus in 2009 will provide us the opportunity to create significant value for patients, physicians, payers, and our shareholders.

Let me start off by talking about BYETTA. BYETTA is the first and only FDA-approved GLP-1 agonist and the only medicine today that addresses the significant unmet medical needs in type 2 diabetes by providing powerful sustained A1C control with weight loss. This is supported by a low risk of hypoglycemia. It’s in its fourth year in the market with over one million patients being treated. As I mentioned earlier, it was recently included in the American Diabetes Association treatment guidelines.

We are working to better understand the relationship between BYETTA and pancreatitis reported in some spontaneously reported cases. In keeping with our focus on patient safety, we have continued to pursue drug safety program that includes thorough investigation of individual spontaneous events along with clinical and epidemiological studies.

Now within the detection limits of an initial epidemiology study we have not observed an increased incidence of pancreatitis associated with BYETTA compared to other treatments for diabetes, thus a definitive causal relationship between BYETTA and pancreatitis has not been proven. This initial epidemiology study has just been published in the clinical medical research outcomes journal* last week.

The FDA is continuing with its review of the regulatory application for monotherapy and several other prescribing information updates, including revision of safety language. It is likely that this review will not be complete in this quarter. However, we remain confident that it will happen in the near future and continue to be encouraged with our interactions with the FDA and with their review of the data that we have provided.

We continue to work with our collaborator, Eli Lilly and Company, to improve the effectiveness and the efficiency of our collaboration together.

Now I spoke to you about the positive attributes of BYETTA, powerful glucose control with weight loss, and let me tell you why that is important. 80% of people with type 2 diabetes are overweight, obesity increases the risks of cardiovascular disease 44% in people with type 2 diabetes, and cardiovascular death accounts for at least 75% of all deaths among people with diabetes.

In fact, last October a study published in the Diabetologia , the journal for the European Association for the Study of Diabetes, encompassing over 60,000 patients found that the risk of coronary heart disease and death are significantly increased in the overweight and to an even greater extent in obese patients with type 2 diabetes compared with those who just have type 2 diabetes and are non-obese. In fact, their risk of death increases 71% over a six-year period.

These results provide prospective evidence demonstrating that weight gain is associated with increased cardiovascular risk in type 2 diabetes and therefore weight effects are critical consideration when selecting treatment for type 2 diabetes. Now this Diabetologia paper came out last year after the publication of a number of landmark studies at the American Diabetes Association meeting last June.

At that meeting the UKPDS 10-year follow-up, the ACCORD study, the ADVANCE study, and the VADT study were reported. These studies showed that treating patients earlier and lowering blood glucose without weight gain was critical to improved outcomes. In fact, the ADA and the EASD are considering these data as well and in fact that led to the change in the EASD/ADA guidelines, which included the inclusion of BYETTA in those guidelines.

I will point out that BYETTA was actually the only new medication added to the ADA/EASD guidelines in 2008. Indeed BYETTA was noted as the treatment of choice for patients for whom weight management and hypoglycemia are a concern. Now that represents somewhere around 80% to 90% of patients with type 2 diabetes, so both Amylin’s products, BYETTA and SYMLIN, are unique in that they provide powerful glucose control and weight loss. This positions them well in a market which is currently growing at epidemic proportions — is at epidemic proportions and is growing dramatically.

Moving on to exenatide once weekly. Once approved, exenatide once weekly could be the first once weekly therapy to treat type 2 diabetes with unprecedented efficacy and curable glucose control, sustained weight loss, and improved tolerability relative to BYETTA. Exenatide once weekly has a unique and compelling value proposition. It offers patients, payers, and physicians the long-term adherence solution needed to ensure improved health outcome for this disease.

As you can see in this slide, the A1C decline of 2% that we saw in the pivotal DURATION-1 study is unprecedented for this type of study. 74% of all patients achieved the ADA guideline endpoint of 7% or less. Average weight loss over 30 weeks was 9.5 pounds and there were improvements in CV events — sorry, CV risk factors including blood pressure, cholesterol, and triglycerides. There was no increase in

* Journal title is Current Medical Research and Opinion

hypoglycemia when exenatide once weekly was used with metformin or a thiazolidinediones and overall tolerability is improved compared with BYETTA. In market research studies it isn’t surprising to find that doctors are excited by these results and are eager to bring this — to have this therapy as an option. Bringing exenatide once weekly to the market is our number one development priority.

I talked to you about the reasons why exenatide once weekly is so important, now I will update you on the status of the NDA filing. We had a pre-NDA meeting with the FDA in the second quarter of 2008. As a result of that meeting, we believe that the DURATION-1 study alone provides the necessary pivotal safety and efficacy data for the submission. We confirmed with the FDA at that meeting that we would be referencing the entire exenatide safety database as part of the application.

FDA feedback received in the fourth quarter last year on the DURATION-1 extension study is appropriate as the basis for demonstrating comparability between development scale material and commercial scale material manufactured at our new manufacturing facility in Ohio means that we will have extension data to demonstrate this comparability by the end of this quarter. I should say at the end of this month.

Additionally, the FDA published in December guidance on requirements for all IND holders of anti-diabetic therapies to show that their compounds do not increase the risk of cardiovascular events. We received feedback from the FDA regarding this latest guidance on assessing the risk of cardiovascular risk for exenatide and we were told to proceed with the meta analysis of the controlled clinical trials in the exenatide safety database to evaluate the cardiovascular risk for exenatide once weekly.

We will be providing specific details regarding this analysis in the coming weeks, but just to say at this point the preliminary analysis of this database, which includes several thousand patients, has already been completed and indicates that there is no increased risk of cardiovascular events associated with exenatide treatment. We are in the process of finalizing this analysis and the comparability data and remain on track to submit the exenatide NDA — exenatide once weekly NDA by the end of the second quarter of 2009.

Now I will share with you the progress on the head-to-head exenatide development program to drive rapid adoption at launch. This development program, if you think of it in terms of the context of the environment into which exenatide once weekly will be launching or is prescient, think about all that you have read recently about the need for clinical, comparative data. This program compares exenatide once weekly against alternative therapeutic choices, employing study designs to demonstrate superiority.

The objective is to launch and demonstrate the transformational nature of exenatide once weekly. These trials are on track. DURATION-2 is a head-to-head study of exenatide once weekly against a thiazolidinedione, or DPP-4 inhibitor, on a background of metformin therapy. Results from this study will report in the second quarter of this year.

DURATION-3 is a head-to-head study of exenatide once weekly against insulin glargine on a background of oral agent therapy and the results are expected in the third quarter. The DURATION-4 is a head-to-head study of stand-alone therapies — exenatide once weekly against either metformin, a thiazolidinedione, or a DPP-4 inhibitor. It was initiated last quarter and is expected to be completed next year.

Now also on this slide, please note a very important study is also planned to initiate this year; that is the CV outcomes study. We have seen very positive effects on cardiovascular surrogate outcomes with exenatide; that is blood pressure, triglycerides, and lipids. We have engaged a steering committee composed of outside experts to assist us in designing a robust cardiovascular outcomes study.

The study will give us the opportunity to demonstrate the effects of exenatide once weekly on cardiovascular outcomes as well as other endpoints of interest to our stakeholders. The design will be reviewed with the FDA with plans to initiate patient enrollment in the second half of this year with interim data in 2012 and final data in 2016.

As you can see by looking at this cadre of studies, we are positioning exenatide once weekly for near- and long-term success by addressing the possible entrants of competitors. We believe that these studies will enable exenatide once weekly to dominate the diabetes marketplace in the future.

In summary, exenatide once weekly is a product that we believe will transform diabetes therapy. It will be the first once weekly therapy for diabetes ever. It has transformational efficacy supported by the BYETTA safety profile. The FDA path for regulatory submission is established. We have a manufacturing facility that is operational. We have an aggressive clinical plan to ensure rapid adoption and we believe exenatide once weekly offers a truly unique value proposition for patients, physicians, and for payers. And as I mentioned earlier, we remain on track for submission by the end of the first half of this year.

Now I would like to move on to talk to you about SYMLIN, our other product for use in people with type 1 or type 2 diabetes who use mealtime insulin. SYMLIN is a synthetic analogue of human amylin, a naturally occurring hormone that is made in the beta cells of the pancreas, the same cells that make insulin. SYMLIN is the first and only FDA approved amylin mimic and has been on the market for nearly 4 years. It addresses key unmet needs of insulin therapy by reducing blood glucose fluctuations, improving glucose control, and reducing body weight for people with type 1 and type 2 diabetes who use insulin, mealtime insulin.

SYMLIN had revenue of $86.8 million in 2008, which represented a 33% growth rate over 2007. We expect to see similar growth in 2009 as a result of our very focused physician targeting and patient selection, as well as managing expectations and supporting patients to increased persistence through a high-touch, high-support marketing strategy.

Another area for value creation in Amylin is our obesity program. Our obesity program leverages our experience with diabetes and peptide and protein science, and as a result we are able to develop product candidates utilizing a risk advantaged development strategy that focuses on peptide and protein mimics of human hormones. Overall, our pipeline is built on combining multiple hormones with additive/synergistic effects to produce an integrated neurohormonal therapy for obesity, something we call it INTO, optimizing native hormones through peptide engineering to generate analogues with superior biological and pharmaceutical attributes and incorporating sustained-release or alternative delivery technologies to enhance patient convenience and adherence. Together these approaches offer the potential for safe and effective weight loss, approaching or exceeding double-digit percentage and significant improvements in ancillary medical conditions.

Now to focus on our most advanced opportunity, obesity — that is an obesity combination of analogues of the human hormones amylin and leptin. In our proof-of-concept study, Phase II proof-of-concept study we showed that when we used the amylin and leptin analogues, that is pramlintide and metreleptin, that after 24 weeks there was 12.7% body weight reduction.

In the third quarter of this year we will report out a fully-enrolled study, Phase IIb study which has over 600 patients in it and is a multi-arm study which is looking at different dosing combinations of pramlintide and metreleptin. This study has the promise to meet the unmet needs of safe and highly effective weight loss therapy, and we are looking forward and excited to seeing the results of this study in the third quarter.

Our other opportunity is in our pipeline, is our second-generation amylin mimic called davalintide. This is an amylin mimic which has been optimized for weight loss. This product is in Phase II and the Phase II study will report out in the fourth quarter of this year.

Now I would emphasize that we are keeping close control on all our costs when it comes to our obesity pipeline and are actively managing our R&D expenses. Additionally, we are pursuing options to offset R&D expenses with our obesity and early-stage programs through potential partnerships or project financings. We anticipate having more information to report to you about our obesity strategy by the end of this year.

Now moving onto our fifth and final area of value creation, I will highlight our progress towards improving our operating results. Our key objective as a company is to be cash flow positive from operations by the end of 2010. In 2008 our total revenues were $840 million with product revenues — net product revenues of $765 million and we had a non-GAAP operating loss of approximately $120 million.

For 2009 our goal is to reduce that non-GAAP operating loss to between $75 million and $100 million. We will achieve that by continuing to focus on reducing our overall operating expense. Our GAAP operating expense is estimated to be reduced over 2008 by over $100 million. And we expect to finish 2009 with a cash balance of approximately $600 million, down a couple of hundred million from the end of 2008 where it was $817 million. Additionally, I would point out that we continue to have access to a loan from Eli Lilly and Company of $165 million.

As you can see, we are continuing to be very focused on managing our expenses and indeed focused on managing our cash flow from operations. And we are well capitalized and continue to take deliberate action to manage expense.

On this slide you can see that we have before us a number of regulatory and development milestones representing key near-term value creation opportunities that will position us for long-term success. The FDA is continuing to review the regulatory application for monotherapy for BYETTA and several other prescribing information updates. That includes the revision of the safety language.

As I mentioned, it is likely that that will not be complete in the first quarter. However, we remain confident that it will happen in the near future and we continue to be encouraged by our interactions with the agency and their review of the data that we have provided.

In the second quarter we will report the DURATION-2 study and the DURATION-3 study will be available the following quarter. Also in the third quarter will be the results of the pramlintide/metreleptin study, Phase IIb study, and then we expect the results from the Phase II davalintide

study in the fourth quarter. Finally, we will finalize our obesity funding and development strategy which includes assessing partnership opportunities to offset the cost of advancing these compounds into Phase III by the end of the year.

This is an action-packed year for Amylin with numerous events that we believe will create significant value for shareholders. So to finalize, in 2009 we are confident in our five-point plan for value creation and remain focused on execution. Growing BYETTA, gaining approval of the monotherapy label, submitting exenatide once weekly, continuing to grow SYMLIN, completing the clinical work in our obesity franchise, and focusing intently on managing our operating expense to improve our operating costs are our five goals for 2009.

These five areas we believe will provide significant opportunity to create value for patients, for physicians, for payers, and our shareholders. Thank you for your attention this morning. I very much appreciate it.

Phil, do we have some time for questions? Okay, absolutely. Okay, Phil?

QUESTION AND ANSWER

Phil Nadeau - Cowen and Company - Analyst

(inaudible question - microphone inaccessible) completed within the next few weeks. What is the (inaudible) strategy (inaudible) and if so what type of data will you announce? And maybe give us an idea of how to interpret that?

Dan Bradbury - Amylin Pharmaceuticals, Inc. - President & CEO

I think the key thing will be our internal assessment of whether or not that comparability data meets the requirements as laid out to us in correspondence from the FDA. And I think you can be confident if we are also — continue to announce that we are planning to submit the NDA that we believe that it will have met the end point. Sir?