UNITED STATES SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, DC 20549
FORM 10-Q
(Mark One)
     
þ   Quarterly Report Pursuant to Section 13 or 15 (d) of the Securities Exchange Act of 1934
For the quarterly period ended June 30, 2008.
OR
     
o   Transition Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934
For the transition period from                      to                     .
Commission file number 001-32629
AVALON PHARMACEUTICALS, INC.
(Exact Name of Registrant as Specified in Its Charter)
     
Delaware   52-2209310
(State or Other Jurisdiction of   (I.R.S. Employer Identification No.)
Incorporation or Organization)    
     
20358 Seneca Meadows Parkway    
Germantown, Maryland   20876
(Address of Principal Executive Offices)   (Zip Code)
Registrant’s Telephone Number, Including Area Code: (301) 556-9900
     Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes þ No o
     Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):
             
Large accelerated filer o   Accelerated filer o   Non-accelerated filer o   Smaller reporting company þ
        (Do not check if a smaller reporting company)    
     Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes o No þ
     As of July 31, 2008, 17,033,441 shares of Avalon Pharmaceuticals, Inc. common stock, par value $.01 per share, were outstanding.
 
 

 


 

AVALON PHARMACEUTICALS, INC.
         
    Page
PART I. FINANCIAL INFORMATION
       
 
       
Item 1. Financial Statements
    4  
 
       
Balance Sheets as of June 30, 2008 (unaudited) and December 31, 2007
    4  
 
       
Statements of Operations for the three and six months ended June 30, 2008 and 2007 (unaudited)
    5  
 
       
Statements of Cash Flows for the six months ended June 30, 2008 and 2007 (unaudited)
    6  
 
       
Notes to Financial Statements (unaudited)
    7  
 
       
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations
    12  
 
       
Item 3. Quantitative and Qualitative Disclosures About Market Risk
    16  
 
       
Item 4T. Controls and Procedures
    16  
 
       
PART II. OTHER INFORMATION
       
 
       
Item 4. Submission of Matters to a Vote of Security Holders
    16  
 
       
Item 6. Exhibits
    17  
 
       
SIGNATURES
    18  

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FORWARD-LOOKING STATEMENTS
      From time to time in this interim quarterly report we may make statements that reflect our current expectations regarding our future results of operations, economic performance, and financial condition, as well as other matters that may affect our business. In general, we try to identify these forward-looking statements by using words such as “anticipate,” “believe,” “expect,” “estimate,” and similar expressions.
      All of these items involve significant risks and uncertainties. These and any of the other statements we make in this quarterly report that are forward-looking are made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. We caution you that our actual results may differ significantly from the results we discuss in the forward-looking statements.
      We discuss some factors that could cause or contribute to such differences in the “Risk Factors” section of our Annual Report on Form 10-K for the fiscal year ended December 31, 2007. In addition, any forward-looking statements we make in this document speak only as of the date of this document, and we do not intend to update any such forward-looking statements to reflect events or circumstances that occur after that date.

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PART I. FINANCIAL INFORMATION
Item 1. Financial Statements
AVALON PHARMACEUTICALS, INC.
BALANCE SHEETS
(in thousands, except share amounts)
                 
    June 30,     December 31,  
    2008     2007  
    (Unaudited)          
ASSETS
               
Current assets:
               
Cash and cash equivalents
  $ 4,806     $ 6,276  
Short-term marketable securities
    6,855       15,558  
Accounts receivable
    19       200  
Interest receivable
    90       190  
Prepaid expenses
    889       743  
Deposits
          102  
 
           
Total current assets
    12,659       23,069  
Restricted cash and marketable securities
    4,458       5,275  
Property and equipment, net
    6,657       7,325  
Long-term marketable securities
    535       1,416  
Deferred financing costs, net
    265       220  
 
           
Total assets
  $ 24,574     $ 37,305  
 
           
 
               
LIABILITIES AND STOCKHOLDERS’ EQUITY
               
Current liabilities:
               
Accounts payable
  $ 1,932     $ 1,063  
Accrued expenses and other current liabilities
    698       1,207  
Deferred revenue and customer advances
    1,017       1,204  
Current portion of long-term debt
    1,200       1,211  
 
           
Total current liabilities
    4,847       4,685  
Deferred rent
    428       446  
Long-term debt, net of current portion
    4,800       6,000  
Stockholders’ equity:
               
Series C Junior Participating Preferred stock, $0.01 par value, 300,000 shares authorized, no shares issued and outstanding
           
Common stock, $0.01 par value; 60,000,000 shares authorized; 17,033,441 and 17,026,462 shares issued and outstanding at June 30, 2008 and December 31, 2007, respectively
    170       170  
Additional capital
    150,528       150,331  
Other comprehensive income
    6       50  
Accumulated deficit
    (136,205 )     (124,377 )
 
           
Total stockholders’ equity
    14,499       26,174  
 
           
Total liabilities and stockholders’ equity
  $ 24,574     $ 37,305  
 
           
See accompanying notes.

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AVALON PHARMACEUTICALS, INC.
STATEMENTS OF OPERATIONS
(in thousands, except share and per share amounts)
(Unaudited)
                                 
    Three Months Ended     Six Months Ended  
    June 30,     June 30,  
    2008     2007     2008     2007  
Revenues
  $ 137     $ 78     $ 187     $ 809  
   
Costs and expenses:
                               
Research and development
    4,509       4,066       8,869       8,178  
General and administrative
    1,281       2,043       3,413       4,271  
 
                       
Total costs and expenses
    5,790       6,109       12,282       12,449  
 
                       
Loss from operations
    (5,653 )     (6,031 )     (12,095 )     (11,640 )
Other income (expense):
                               
Interest income
    153       378       460       717  
Interest expense
    (92 )     (158 )     (208 )     (330 )
Other
    14       2       16       99  
 
                       
Total other income (expense), net
    75       222       268       486  
Net loss
  $ (5,578 )   $ (5,809 )   $ (11,827 )   $ (11,154 )
 
                       
 
                               
Net loss per share — basic and diluted
  $ (0.33 )   $ (0.40 )   $ (0.69 )   $ (0.82 )
 
                       
 
                               
Weighted average number of shares — basic and diluted
    17,033,042       14,672,577       17,031,620       13,547,779  
See accompanying notes.

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AVALON PHARMACEUTICALS, INC.
STATEMENTS OF CASH FLOWS
(in thousands)
(Unaudited)
                 
    Six Months Ended  
    June 30,  
    2008     2007  
Operating activities
               
Net loss
  $ (11,827 )   $ (11,154 )
   
Adjustments to reconcile net loss to net cash used in operating activities:
               
Depreciation
    874       1,061  
Non-cash interest expense
    106       108  
Amortization of premium on investments
    (151 )     (244 )
Stock based compensation
    196       1,002  
Changes in operating assets and liabilities:
               
Prepaid expenses
    (146 )     31  
Accounts receivable and other assets
    383       215  
Accounts payable
    869       (537 )
Accrued expenses and other current liabilities
    (509 )     (40 )
Deferred revenue and customer advances
    (187 )     340  
Deferred rent
    (18 )     (10 )
 
           
Net cash used in operating activities
    (10,410 )     (9,228 )
Investing activities
               
Proceeds from the sale and maturities of marketable securities
    16,718       15,640  
Purchases of marketable securities
    (6,210 )     (25,317 )
Purchases of property and equipment
    (206 )     (309 )
 
           
Net cash provided by (used in) investing activities
    10,302       (9,986 )
Financing activities
               
Principal payments on debt
    (1,200 )     (1,450 )
Proceeds from issuance of common stock
          28,320  
Deferred financing costs
    (162 )     (148 )
 
           
Net cash provided by (used in) financing activities
    (1,362 )     26,722  
 
           
Net (decrease) increase in cash and cash equivalents
    (1,470 )     7,508  
Cash and cash equivalents at beginning of period
    6,276       3,099  
 
           
Cash and cash equivalents at end of period
  $ 4,806     $ 10,607  
 
           
See accompanying notes.

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AVALON PHARMACEUTICALS, INC.
NOTES TO FINANCIAL STATEMENTS
JUNE 30, 2008
(UNAUDITED)
1. Basis of Presentation
     The financial statements included in this report have been prepared, without audit, pursuant to the rules and regulations of the Securities and Exchange Commission. Certain information and footnote disclosures, normally included in financial statements prepared in accordance with U.S. generally accepted accounting principles, have been condensed or omitted pursuant to such rules and regulations. These financial statements should be read in conjunction with the audited financial statements and the related notes included in our Annual Report on Form 10-K for the fiscal year ended December 31, 2007.
     In the opinion of our management, any adjustments contained in the accompanying unaudited financial statements as of and for the three and six months ended June 30, 2008 and 2007 are of a normal recurring nature and are necessary to present fairly our financial position, results of operations and cash flows. Interim results are not necessarily indicative of results for the full fiscal year.
2. Liquidity Risks and Management’s Plans
     The accompanying financial statements have been prepared on a going-concern basis, which contemplates the realization of assets and satisfaction of liabilities in the normal course of business. Since inception, the Company has incurred, and continues to incur, significant losses from operations. On August 13, 2008 the Company announced that it was restructuring its operations. As a result, the Company reduced its workforce by approximately one third. The Company expects to incur restructuring charges related to this action of $0.9 million to $1.1 million. These charges will be included in the Company’s statement of operations principally in the third quarter of 2008. Company management estimates that its current capital resources will not be sufficient to fund the Company’s restructured operations significantly beyond December 31, 2008 without an additional curtailment of operating and capital expenditures, additional partnership revenues, or new equity or debt financing.
     The Company’s ability to continue as a going concern is dependent on its success at raising additional capital sufficient to meet its obligations on a timely basis, and to ultimately attain profitability. Management is active in discussions to raise the necessary funds for the Company’s growth and development activities. However, there is no assurance that the Company will raise capital sufficient to enable the Company to continue its restructured operations significantly beyond December 31, 2008.
     In the event the Company is unable to successfully raise additional capital, it is unlikely that the Company will have sufficient cash flows and liquidity to finance its business operations as currently contemplated. Accordingly, in the event new financing is not obtained, the Company will likely reduce general and administrative expenses and delay research and development projects as well as further acquisition of scientific equipment and supplies until it is able to obtain sufficient financing to do so.
     These factors could significantly limit the Company’s ability to continue as a going concern. The balance sheets do not include any adjustments relating to recoverability and classification of recorded asset amounts or the amounts and classification of liabilities that might be necessary should the Company be unable to continue in existence.
3. Organization
     Avalon Pharmaceuticals, Inc. (“Avalon,” or the “Company”), was incorporated on November 10, 1999, under the laws of the state of Delaware. Avalon is a biopharmaceutical company using proprietary technology, AvalonRx ® , to discover and develop novel therapeutics.
4. Recent Accounting Pronouncements
     In September 2006, the FASB issued SFAS No. 157, Fair Value Measurements (“SFAS 157”). SFAS 157 provides guidance for using fair value to measure assets and liabilities. It also responds to investors’ requests for expanded information about the extent to which companies measure assets and liabilities at fair value, the information used to measure fair value and the effect of fair value measurements on earnings. SFAS 157 applies whenever other standards require (or permit) assets or liabilities to be measured at fair value, and does not expand the use of fair value in any new circumstances. SFAS 157 is effective for financial statements issued for fiscal years beginning after November 15, 2007. The Company has adopted the provisions of SFAS 157 as of January 1, 2008, for financial instruments. Although the adoption of SFAS 157 did not materially impact its financial condition, results of operations or cash flow, the Company is now required to provide additional disclosures as part of its financial statements. SFAS 157 establishes a three-tier fair value hierarchy, which prioritizes the inputs used in measuring fair value. These tiers include:
    Level 1, defined as observable inputs such as quoted prices in active markets for identical assets;
 
    Level 2, defined as observable inputs other than level 1 prices such as quoted prices for similar assets; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities; and
 
    Level 3, defined as unobservable inputs in which little or no market data exists, therefore requiring an entity to develop its own assumptions.

7


 

     The Company’s cash equivalents, short-term, long-term and restricted marketable securities are subject to fair value measurements. The inputs used in measuring the fair value of these instruments are considered to be level 1 in accordance with the SFAS 157 hierarchy.
     In February 2007, the FASB issued SFAS No. 159, The Fair Value Option for Financial Assets and Financial Liabilities — Including an amendment of FASB Statement No. 115 (“SFAS 159”). SFAS 159 expands the use of fair value accounting but does not affect existing standards that require assets or liabilities to be carried at fair value. Under SFAS 159, a company may elect to use fair value to measure accounts and loans receivable, available-for-sale and held-to-maturity securities, equity method investments, accounts payable, guarantees and issued debt. Other eligible items include firm commitments for financial instruments that otherwise would not be recognized at inception and non-cash warranty obligations where a warrantor is permitted to pay a third party to provide the warranty goods or services. If the use of fair value is elected, any upfront costs and fees related to the item must be recognized in earnings and cannot be deferred, such as debt issuance costs. The fair value election is irrevocable and generally made on an instrument-by-instrument basis, even if a company has similar instruments that it elects not to measure based on fair value. At the adoption date, unrealized gains and losses on existing items for which fair value has been elected are reported as a cumulative adjustment to beginning retained earnings. Subsequent to the adoption of SFAS 159, changes in fair value are recognized in earnings. SFAS 159 is effective for financial statements issued for fiscal years beginning after November 15, 2007. The adoption of SFAS No. 159 did not have a material impact on our financial position or results of operations.
     In June 2007, the FASB ratified EITF 07-03, Accounting for Nonrefundable Advance Payments for Goods or Services Received for Use in Future Research and Development Activities (“EITF 07-03”). EITF 07-03 requires that nonrefundable advance payments for goods or services that will be used or rendered for future research and development activities be deferred and capitalized and recognized as an expense as the goods are delivered or the related services are performed. EITF 07-03 is effective, on a prospective basis, for financial statements issued for fiscal years beginning after December 15, 2007. The adoption of EITF 07-03 did not have a material impact on our financial statements.
5. Summary of Significant Accounting Policies
Use of Estimates
     The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates.
Reclassification
     Certain reclassifications of prior period amounts have been made to conform with the current year presentation.
Cash and Cash Equivalents
     The Company considers all highly liquid investments with a maturity of three months or less when purchased to be cash equivalents. Cash equivalents consist primarily of money market funds and commercial paper. The Company maintains cash balances with financial institutions in excess of insured limits. The Company does not anticipate any losses with such cash balances.
Marketable Securities
     Marketable securities consist primarily of U.S. Treasury, agency and corporate debt securities with various maturities. Management classifies the Company’s marketable securities as available-for-sale. Such securities are stated at market value, with the unrealized gains and losses included as accumulated other comprehensive income (loss). Realized gains and losses and declines in value judged to be other-than-temporary on securities available for sale, if any, are included in operations. A decline in the market value of any available-for-sale security below cost that is deemed to be other-than-temporary results in a reduction in fair value. The impairment is charged to earnings, and a new cost basis for the security is established. Dividend and interest income are recognized when earned. The cost of securities sold is calculated using the specific identification method.
Revenue Recognition
     Revenue is recognized when there is persuasive evidence that an agreement exists, delivery has occurred, the price is fixed and determinable, and collection is reasonably assured. Payments received in advance of work performed are recorded as deferred revenue and recognized ratably over the performance period. Milestone payments are recognized as revenue when milestones, as defined in the contract, are achieved. During the first six months of 2008, the Company recognized revenue from work performed on its collaboration agreement with Novartis, and recognized no revenue from its other collaboration agreements.

8


 

Research and Development Costs
     Expenditures, other than advance payments for research and development, subject to the provisions of EITF 07-03, are expensed as incurred.
Restricted Cash and Investments
     In accordance with the terms of a financing arrangement with the Maryland Industrial Development Financing Authority (MIDFA) and Manufacturers and Traders Trust Company (M&T Bank), in order to finance the build out of the Company’s corporate headquarters and research facility located in Germantown, Maryland, the Company established an investment account which is pledged as collateral for a letter of credit. The issuer of the letter of credit, M&T Bank, maintains the investment account. M&T Bank’s security interest in the account cannot exceed the minimum required cash collateral amount, which as of June 30, 2008 was defined as an adjusted market value of $4.3 million. This collateral agreement defines adjusted market value as the product of the fair market value of each permitted investment by a defined percentage ranging from 60% to 100%, depending on the nature of the permitted investment. The minimum cash collateral amount automatically decreases each April 1, as specified in the collateral agreement.
Comprehensive Income
     SFAS No. 130, Reporting Comprehensive Income, requires the presentation of comprehensive income or loss and its components as part of the financial statements. For the six months ended June 30, 2008 and 2007, the Company’s net loss plus its unrealized gains (losses) on available-for-sale securities reflects comprehensive income (loss).
Stock-Based Compensation
     The Company accounts for share-based payments in accordance with the provisions of FASB Statement No. 123(R), Share-Based Payment .
     The fair value of each option grant is estimated on the date of grant using the Black-Scholes option-pricing fair value model and recognized as compensation expense over the vesting period of the award using the accelerated attribution method. The following weighted-average assumptions were used for options granted during the three months ended June 30, 2008 and 2007, and a discussion of our methodology for developing each of the assumptions used in the valuation model follows:
                 
    Three Months   Three Months
    Ended   Ended
    June 30, 2008   June 30, 2007
Dividend yield
    0.00 %     0.00 %
Expected volatility
    72.8 %     67.0 %
Risk-free interest rate
    3.27 %     4.83 %
Expected life of the option term (in years)
    5.3       6.0  
Forfeiture rate
    4.2 %     4.2 %
Dividend Yield— The Company has never declared or paid dividends and has no plans to do so in the foreseeable future.
Expected Volatility— Volatility is a measure of the amount by which a financial variable such as a share price has fluctuated (historical volatility) or is expected to fluctuate (expected volatility) during a period. Due to the Company’s limited trading history, there had been inadequate data to calculate historical volatility of our stock. Prior to June 30, 2007, the Company used an average volatility of similar companies in the pharmaceutical industry. Since June 30, 2007, the Company uses an average of the volatility of its own stock and the average volatility of similar companies in the pharmaceutical industry.
Risk-Free Interest Rate— This is the U.S. Treasury rate for the week of each option grant during the quarter having a term that most closely resembles the expected life of the option term.
Expected Life of the Option Term— This is the period of time that the options granted are expected to remain unexercised. The expected term is based upon management’s consideration of the historical life of options, the vesting period of the option granted and the contractual period of the option granted.
Forfeiture Rate— This is the estimated number of stock options granted that are expected to be forfeited or cancelled on an annual basis before becoming fully vested. The Company estimates the forfeiture rate based on past turnover data.

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Stock Compensation Plans
     The Company adopted the Avalon Pharmaceuticals, Inc. 1999 Stock Incentive Plan (the “1999 Plan”) to provide for the granting of stock awards, such as stock options, restricted common stock, and stock appreciation rights to employees, directors and other individuals as determined by the Board of Directors. The Company terminated the 1999 Plan as to future awards effective upon the closing of the Company’s initial public offering in October 2005. As of June 30, 2008, the Company had reserved 449,964 shares of common stock to accommodate the exercise of outstanding options granted under the 1999 Plan.
     Effective upon the closing of the Company’s initial public offering in October 2005, the Company adopted the Avalon Pharmaceuticals, Inc. 2005 Omnibus Long-Term Incentive Plan (the “2005 Plan”) to provide for the granting of stock awards, such as stock options, restricted common stock, stock units, dividend equivalent rights, stock appreciation rights and unrestricted common stock, and other performance and annual incentive awards to employees, directors and other individuals as determined by the Board of Directors. At the inception of the 2005 Plan, 989,738 shares were reserved for issuance under the 2005 Plan. The number of shares available for issuance under the 2005 Plan was increased from 989,738 shares to 1,581,582 shares in June 2006 and from 1,581,582 shares to 2,381,582 shares in June 2007. Additionally, shares that become available due to forfeiture of outstanding awards under the 1999 Plan are available for awards under the 2005 Plan. As of June 30, 2008, the Company had reserved 2,820,874 shares of common stock to accommodate the exercise of outstanding option grants under the 1999 Plan and 2005 Plan and for future grants under the 1999 Plan and 2005 Plan.
     Generally, stock options are granted with an exercise price that equals the fair market value of the Company’s common stock on the grant date. Options typically have a life of ten years and vest over periods ranging from six months to five years. Options generally expire 90 days after an employee terminates employment with the Company.
     Shares of common stock issued to non-employee directors as part of their annual director compensation for the three and six month periods ended June 30, 2008 were 3,528 and 6,979 shares, respectively. The fair market value of these shares, on the date of grant, was approximately $8,750 and $20,208, respectively.
     The weighted-average grant-date fair value of equity awards granted during the three and six month periods ended June 30, 2008 was $1.06 and $1.51, respectively. The total fair value of stock options which vested during the three and six month periods ended June 30, 2008 was approximately $334,000 and $607,000, respectively. There were 1,636,718 fully vested stock options outstanding at June 30, 2008. These stock options had a weighted average remaining life of 6.66 years.
                                 
                    Weighted-        
            Weighted-     Average        
            Average     Remaining     Aggregate  
            Exercise     Contractual     Intrinsic Value  
    Shares     Price     Term     (in thousands)  
Outstanding at March 31, 2008
    2,182,121     $ 4.04                  
Granted
    19,200       1.68                  
Exercised
                           
Forfeited or expired
    80,838       3.81                  
 
                             
Outstanding at June 30, 2008
    2,120,483       4.02                  
 
                             
Vested and expected to vest at June 30, 2008
    1,567,976     $ 4.18       6.66     $  
Exercisable at June 30, 2008
    1,636,718     $ 4.18       6.66     $  
     No stock options were exercised during the six months ended June 30, 2008. Due to the valuation allowance on all deferred tax assets, the Company recorded no tax benefit for stock compensation expense recognized during the three months ended June 30, 2008. As of June 30, 2008, unamortized stock-based compensation expenses of approximately $567,000 remains to be recognized over a weighted average period of 2.4 years.
Basic and Diluted Net Loss Attributable to Common Stockholders Per Common Share
     Basic net loss attributable to common stockholders per common share excludes dilution for potential common stock issuances and is computed by dividing net loss by the weighted-average number of common shares outstanding for the period. Diluted net loss per common share reflects the potential dilution that could occur if securities or other contracts to issue common stock were exercised or converted into common stock. Stock options and warrants were not considered in the computation of diluted net loss per common share for the periods presented, as their effect is antidilutive.
6. Debt
     In February 2008, the Company entered into an amendment to the letter of credit with M&T Bank and the Maryland Industrial Development Financing Authority to extend the expiry of the letter of credit agreement to April 8, 2013. In addition, the amendment removes the Company’s financial covenant obligations under the letter of credit regarding the maintenance of (i) a minimum ratio of current assets to current liabilities and (ii) a minimum tangible net worth.

10


 

7. Stockholders Equity
Preferred Stock
     In April 2007, the Company entered into a Rights Agreement (the “Rights Agreement”) between the Company and American Stock Transfer & Trust Company, as Rights Agent. In connection with the adoption of the Rights Agreement, the Board of Directors of the Company declared a dividend distribution of one right (“Right”) for each outstanding share of common stock, par value $0.01 per share of the Company, payable to stockholders of record on May 10, 2007. Each Right, when exercisable, entitles the registered holder to purchase from the Company one one-thousandth of one share of Series C Junior Participating Preferred Stock at a price of $60.00 per one one-thousandth share, subject to adjustment. The description and terms of the Rights are set forth in the Rights Agreement.
     Initially, the Rights will be attached to all certificates representing shares of common stock then outstanding, and no separate certificates evidencing the Rights will be distributed. The Rights will separate from the common stock and a distribution of Rights Certificates will occur upon the earlier to occur of (i) 10 days following a public announcement that a person or group of affiliated or associated persons has acquired beneficial ownership of 20% or more of the outstanding shares of common stock or (ii) 10 business days following the commencement of, or the first public announcement of the intention to commence, a tender offer or exchange offer the consummation of which would result in the beneficial ownership by a person of 20% or more of the outstanding shares of common stock. (the earlier of such dates being called the “Distribution Date”).
     Until the Distribution Date, (i) the Rights will be evidenced by the common stock certificates, and will be transferred with and only with the common stock certificates, (ii) new common stock certificates issued after May 10, 2007 upon transfer or new issuance of the common stock will contain a notation incorporating the Rights Agreement by reference, and (iii) the surrender for transfer of any certificates for common stock outstanding will also constitute the transfer of the Rights associated with the common stock represented by such certificate.
     The Rights are not exercisable until the Distribution Date and will expire at the close of business on May 10, 2017, unless such date is extended, the Rights Agreement is terminated, or the Rights are earlier redeemed or exchanged by the Company as described below. The Rights will not be exercisable by a holder in any jurisdiction where the requisite qualification to the issuance to such holder, or the exercise by such holder, of the Rights has not been obtained or is not obtainable.
     As soon as practicable following the Distribution Date, separate certificates evidencing the Rights will be mailed to holders of record of the common stock as of the close of business on the Distribution Date and, thereafter, the separate Rights Certificates alone will evidence the Rights. Except as otherwise determined by the Board of Directors of the Company, only shares of common stock issued prior to the Distribution Date will be issued with Rights.
     In the event that a person becomes the beneficial owner of 20% or more of the then outstanding shares of common stock, except pursuant to an offer for all outstanding shares of common stock which the Directors determine to be fair to and otherwise in the best interests of the Company and its stockholders, each holder of a Right will have the right to exercise the Right by purchasing, for an amount equal to the Purchase Price, common stock (or, in certain circumstances, cash, property or other securities of the Company) having a value equal to two times such amount. Notwithstanding any of the foregoing, following the occurrence of the events set forth in this paragraph, all Rights that are beneficially owned by any acquiring person will be null and void.
7. Related Party Transactions
     The Company paid one member of the board of directors consulting fees totaling $27,000 for the six months ended June 30, 2008.
8. Income Taxes
     For the six month periods ended June 30, 2008, and 2007, there is no current provision for income taxes and the deferred tax benefit has been entirely offset by valuation allowances. The difference between the amounts of income tax benefit that would result from applying domestic federal statutory income tax rates to the net loss and the net deferred tax assets is related to certain nondeductible expenses, state income taxes, and the change in the valuation allowance.

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations
      The following discussion and analysis of our results of operations, financial condition and liquidity and capital resources should be read in conjunction with our unaudited consolidated financial statements and related notes contained in this Quarterly Report on Form 10-Q , as well as the audited financial statements and related notes for the fiscal year ended December 31, 2007 and “Management’s Discussion and Analysis of Financial Condition and Results of Operations,” contained in our Annual Report on Form 10-K , for the fiscal year ended December 31, 2007.
Overview
     We are a biopharmaceutical company focused on the discovery, development and commercialization of first-in-class cancer therapeutics. We use AvalonRx®, our proprietary platform, which is based on large-scale biomarker identification and monitoring, to discover and develop therapeutics for pathways that have historically been characterized as “undruggable.”
     Since our inception, our operations have consisted primarily of developing AvalonRx®, utilizing our technology to seek to discover and develop novel cancer therapeutics, and the in-license and development of AVN944. During that period, we have generated limited revenue from collaborative partners, and have had no revenue from product sales. Our operations have been funded principally through the offering of equity securities and debt financings.
     We have never been profitable and, as of June 30, 2008, we had an accumulated deficit of $136.2 million. We had net losses of $11.8 million for the six months ended June 30, 2008 and net losses of $21.7 million for the year ended December 31, 2007. We expect to incur significant operating losses for the foreseeable future as we advance our drug candidates from discovery through preclinical testing and clinical trials and seek regulatory approval and eventual commercialization. We will need to generate significant revenues to achieve profitability, and we may never do so.
     As of June 30, 2008, we had cash, cash equivalents and marketable securities of approximately $16.7 million. Of this amount, $4.5 million is currently held in a restricted account to serve as collateral for our long-term debt. We estimate that our existing capital resources will not be sufficient to fund our planned operations significantly beyond December 31, 2008. Management continues to pursue additional funding sources; however, there is no assurance that we will raise capital sufficient to enable us to continue our operations past December 31, 2008. A failure to raise additional funds in the near term will require us to reduce our operating and capital expenditures, scale back or eliminate some or all of our research and development programs or license to third parties products or technologies that we would otherwise seek to develop ourselves. There is no assurance that we could continue as a going concern if this were the case.
Recent Developments
     On August 13, 2008 the Company announced that it was restructuring its operations to focus on the pre-clinical and clinical development of its Beta-catenin inhibitor program and on its existing collaborations, such as with Merck. The Company is curtailing its other development programs and is seeking a partner for its AVN944 development program. In connection with the restructuring of its operations, the Company is reducing its workforce by approximately one third. The Company expects to report restructuring charges related to these actions of $0.9 million to $1.1 million for severance and related costs.
     On June 13, 2008, the United States Patent Office granted a notice of allowance of claims to Vertex Pharmaceuticals, Inc. for certain revised claims filed by Vertex on its United States patent that covers AVN944. The revised claims correct a defect in the original claims filed by Vertex to include AVN944 within the claims covered by the patent. AVN944 was in-licensed by us from Vertex in February 2005.
Financial Operations Overview
Revenue
     We have not generated any revenue from sales of commercial products and do not expect to generate any product revenue for the foreseeable future. To date, our revenue has consisted of collaboration revenue.
      Collaboration Revenue. Since inception, we have generated revenue solely in connection with our collaboration and pilot study agreements. Our collaborations with Merck, AstraZeneca and Novartis include upfront payments, research funding, and/or payments for the achievement of certain discovery and development related milestones. During the first half of 2008, we recognized revenue from work performed under our collaboration with Novartis and recognized no revenue from our other collaborations.
Research and Development Expense
     Research and development expense consists of expenses incurred in connection with developing and advancing our drug discovery technology and identifying and developing our drug candidates and supporting our collaborative relationships. These expenses consist primarily of salaries and related expenses, the purchase of laboratory supplies, access to data sources, facility costs, costs for preclinical development and expenses related to our in-license and clinical trials of AVN944. Other than for advance payments for research and development costs, subject to the provisions of EITF 07-03, we charge all research and development expenses to operations as incurred.

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     We expect our research and development costs to be substantial as we advance AVN944 through clinical trials and move other drug candidates into preclinical testing and clinical trials. Based on the results of our preclinical studies, we expect to selectively advance some drug candidates into clinical trials. We anticipate that we will select drug candidates and research projects for further development on an ongoing basis in response to their preclinical and clinical success and commercial potential. In July 2007, we initiated U.S. Phase II clinical trials of AVN944 in patients diagnosed with pancreatic cancer. We are currently conducting Phase I clinical trials for AVN944 in patients with hematological cancer and Phase II clinical trials for patients with pancreatic cancer.
General and Administrative
     General and administrative expense consists primarily of salaries and related expenses for personnel in administrative, finance, business development and human resource functions. Other costs include legal costs of pursuing patent protection of our intellectual property and other fees for legal services.
Critical Accounting Policies and Significant Judgments and Estimates
Stock-Based Compensation
     We account for share-based payments in accordance with the provisions of FASB Statement No. 123(R), Share-Based Payment . For the six months ended June 30, 2008, we recorded approximately $176,000 of stock-based compensation expenses, of which $57,000 was included in research and development expense and $119,000 was included in general and administrative expense. Since we continue to operate in a net loss, stock-based compensation expense had no impact for tax-related effects on cash flow from operations and cash flow from financing activities for the six months ended June 30, 2008. As of June 30, 2008, unamortized stock-based compensation expenses of approximately $567,000 remains to be recognized over a weighted-average period of approximately 2.4 years. We amortize stock-based compensation expenses on an accelerated basis over the vesting period.
     We estimated the fair value of stock options granted during the three months ended June 30, 2008 using the Black-Scholes option pricing model. The assumptions used under this model are as follows: (i) expected term of 5.3 years based upon management’s consideration of the historical life of options, the vesting period of the option granted and the contractual period of the option granted; (ii) expected volatility of 72.8% based on historical and peer volatility data; (iii) weighted average risk-free interest rate of 3.27% based on the U.S. Treasury yield curve in effect at the time of grant for periods corresponding with the expected term of the option; and (iv) expected dividend yield of zero percent. In addition, under SFAS 123(R), the fair value of stock options granted is recognized as expense over the service period, net of estimated forfeitures. Based on historical data, we calculated a 4.20% annual forfeiture rate, which we believe is a reasonable assumption. However, the estimation of forfeitures requires judgment, and to the extent actual results or updated estimates differ from our current estimates, such amounts will be recorded as a cumulative adjustment in the period estimates are revised.
     The Black-Scholes option pricing model requires the input of highly subjective assumptions. Because our employee stock options have characteristics significantly different from those of traded options, and because changes in the subjective input assumptions can materially affect the fair value estimate, in management’s opinion, the existing models may not provide a reliable single measure of the fair value of our employee stock. In addition, management will continue to assess the assumptions and methodologies used to calculate estimated fair value of share-based compensation. Circumstances may change and additional data may become available over time, which result in changes to these assumptions and methodologies, and which could materially impact our fair value determination.
Results of Operations
Three Months Ended June 30, 2008 and 2007
      Revenue. Total revenues for the three months ended June 30, 2008 were $137,000, an increase of $59,000 from the same period in the prior year. All 2007 and 2008 revenues were attributable to our collaboration agreement with Novartis.
      Research and Development. Research and development expenses increased by $442,000, or 11%, to $4.5 million for the three months ended June 30, 2008 from $4.1 million for the same period in 2007. The increase in research and development expenses was primarily attributable to increases in clinical trial and product costs related to our AVN944 drug candidate.
     Research and development expenses consist of direct costs which include salaries and related costs of research and development personnel, and the costs of consultants, materials and supplies associated with research and development projects. Indirect research and development costs include facilities, depreciation, patents and other indirect overhead costs.
      General and Administrative. General and administrative expenses decreased by $761,000 or 37%, to $1.3 million for the three months ended June 30, 2008, compared to $2.0 million for the three months ended June 30, 2007. The decrease is primarily attributable to a decrease in compensation expense related to stock options and reduction in costs related to personnel and consultants.
      Interest Income. Interest income decreased by $225,000 or 60%, to $153,000 for the three months ended June 30, 2008, compared to $378,000 for the three months ended June 30, 2007. The decrease in interest income is primarily due to lower balances of cash and investments and lower average interest rates.

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      Interest Expense. Interest expense decreased by $65,000, or 41%, to $92,000 for the three months ended June 30, 2008, compared to $158,000 for the three months ended June 30, 2007. The decrease in interest expense was primarily related to lower debt balances and lower average interest rates on debt.
      Other Income. Other income was $14,000 for the three months ended June 30, 2008, compared to $2,000 for the three months ended June 30, 2007. The increase in other income was primarily related to income from subletting part of our facility and the provision of shared services to subtenants.
Six Months Ended June 30, 2008 and 2007
      Revenue. Total revenues for the six months ended June 30, 2008 were $187,000, a decrease of $662,000 from the same period in the prior year. All 2007 and 2008 revenues were attributable to our collaboration agreement with Novartis.
      Research and Development. Research and development expenses increased by $691,000, or 8%, to $8.9 million for the six months ended June 30, 2008 from $8.2 million for the same period in 2007. The increase in research and development expenses was primarily attributable to increases in clinical trial and product costs related to our AVN944 drug candidate.
      General and Administrative. General and administrative expenses decreased by $857,000 or 20%, to $3.4 million for the six months ended June 30, 2008, compared to $4.3 million for the six months ended June 30, 2007. The decrease is primarily attributable to a decrease in compensation expense related to stock options and a reduction in consulting costs.
      Interest Income. Interest income decreased by $257,000 or 36%, to $460,000 for the six months ended June 30, 2008, compared to $717,000 for the six months ended June 30, 2007. The decrease in interest income is primarily due to lower balances of cash and investments and lower average interest rates.
      Interest Expense. Interest expense decreased by $122,000, or 37%, to $208,000 for the six months ended June 30, 2008, compared to $330,000 for the six months ended June 30, 2007. The decrease in interest expense was primarily related to lower debt balances and lower average interest rates on debt.
      Other Income. Other income was $16,000 for the six months ended June 30, 2008, compared to $99,000 for the six months ended June 30, 2007. The decrease in other income was primarily related to a reduction of income from subletting part of our facility and the provision of shared services to subtenants.
Liquidity and Capital Resources
     Our primary cash requirements are to:
    fund our research and development and clinical programs;
 
    obtain regulatory approvals;
 
    prosecute, defend and enforce any patent claims and other intellectual property rights;
 
    fund general corporate overhead; and
 
    support our debt service requirements and contractual obligations.
     Our cash requirements could change materially as a result of the progress of our research and development and clinical programs, licensing activities, acquisitions, divestitures or other corporate developments.
     We have incurred operating losses since our inception and historically have financed our operations principally through public stock offerings, debt financings, private placements of equity securities, strategic collaborative agreements that include research and development funding and development milestones, and investment income.
     In evaluating alternative sources of financing we consider, among other things, the dilutive impact, if any, on our stockholders, the ability to leverage stockholder returns through debt financing, the particular terms and conditions of each alternative financing arrangement and our ability to service our obligations under such financing arrangements.
     As of June 30, 2008, we had cash, cash equivalents and marketable securities of approximately $16.7 million. Of this amount, $4.5 million is currently held in a restricted account to serve as collateral for our long-term debt. Our funds are currently invested in investment grade commercial paper and United States government securities. We estimate that our existing capital resources will not be sufficient to fund our planned operations significantly beyond December 31, 2008. Management continues to pursue additional funding sources; however, there is no assurance that we will raise capital sufficient to enable us to continue our operations past year end. A failure to raise additional funds in the near term will require us to reduce our operating and capital expenditures, scale back or eliminate some or all of our research and development programs or license to third parties products or technologies that we would otherwise seek to develop ourselves. There is no assurance that we could continue as a going concern if this were the case.

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Sources and Uses of Cash
      Operating Activities. Net cash used in operating activities for the six months ended June 30, 2008 was $10.4 million, compared to $9.2 million for the same period in fiscal 2007. During the first six months of fiscal year 2008, our net loss of $11.8 million was reduced by non-cash charges of $1.0 million, primarily for stock compensation, depreciation and amortization, offset by changes in our net operating assets and liabilities.
      Investing Activities. Net cash provided by investing activities for the six months ended June 30, 2008 was $10.3 million, compared to net cash used in investing activities of $10.0 million for the same period in 2007. Proceeds from the sale and maturity of marketable securities were the primary source of cash from investing activities, providing $16.7 million in the first six months of 2008 and $15.6 million in the comparable period of 2007. Cash used in investing activities principally represents the amount used to purchase marketable securities, net of proceeds from the sale and maturity of marketable securities.
      Financing Activities. Net cash used by financing activities for the six months ended June 30, 2008 was $1.4 million, compared to $26.7 million of net cash provided by financing activities for the same period in 2007. Aggregate proceeds of $28.2 million from the issuance of common stock in two private placements was the principal source of net cash provided by financing activities during the first six months of 2007.
Credit Arrangements
     In April 2003, we entered into a series of agreements with the Maryland Industrial Development Financing Authority, or MIDFA, and Manufacturers and Traders Trust Company, or M&T Bank, in order to finance improvements to our corporate office and research facility located in Germantown, Maryland. MIDFA sold development bonds in the amount of $12.0 million. The proceeds of the bond sale were put in trust to reimburse us for the costs we incurred for improvements to our facility. We are required to repay the trust $1.2 million annually, on the first day of April, for these borrowings. The borrowing bears interest at a variable rate and matures on April 8, 2013. The weighted-average interest rate during the six months ended June 30, 2008 and 2007 was 3.09% and 5.36% respectively
     In connection with the development bond financing, we entered into an agreement with M&T Bank to issue the trustee an irrevocable letter of credit to provide payment of the principal and interest of the bonds. The amount of the letter of credit changes annually, as principal payments are made. As of June 30, 2008, that amount is $6,098,630, consisting of $6.0 million of principal and $98,630 in interest, computed at 50 days at an assumed maximum rate of interest of 12% per annum. The letter of credit expires the earlier of April 8, 2013, or the date the bonds have been paid in full. In consideration of the letter of credit, we have granted M&T Bank a security interest in certain facility improvements, equipment and cash collateral held as restricted cash.
Operating Capital and Capital Expenditure Requirements
     Our future funding requirements will depend on many factors, including but not limited to:
    the size and complexity of our research and development programs;
 
    the scope and results of our preclinical testing and clinical trials;
 
    continued scientific progress in our research and development programs;
 
    the time and expense involved in seeking regulatory approvals;
 
    competing technological and market developments;
 
    acquisition, licensing and protection of intellectual property rights; and
 
    the cost of establishing manufacturing capabilities and conducting commercialization activities.
     Until we can generate a sufficient amount of product revenue to finance our cash requirements, which we may never do, we expect to finance future cash needs primarily through public or private equity offerings, debt financings or strategic collaborations. If we are successful in raising additional funds through the issuance of equity securities, investors likely will experience dilution, or the equity securities may have rights, preferences or privileges senior to those of the holders of our common stock. If we raise funds through the issuance of debt securities, those securities would have rights, preferences and privileges senior to those of our common stock. We do not know whether additional funding will be available on acceptable terms, or at all. If we are not able to secure additional funding in the near term, we will have to significantly reduce our operating and capital expenditures and delay, reduce the scope of, or eliminate one or more of our clinical trials or research and development programs. In addition, we may have to partner one or more of our drug candidate programs at an earlier stage of development, which would lower the economic value of those programs to our Company. We may not be able to continue as a going concern if this were to be the case.

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Item 3. Quantitative and Qualitative Disclosures About Market Risk
     Not applicable pursuant to the rules of the Securities and Exchange Commission relating to the disclosure requirements for a “smaller reporting company.”
Item 4T. Controls and Procedures
      Disclosure Controls and Procedures: Under the supervision and with the participation of our management, including our Chief Executive Officer and our Chief Financial Officer, we have evaluated the effectiveness of our disclosure controls and procedures, as of June 30, 2008 (the “Evaluation Date”). Based on that evaluation, our Chief Executive Officer and Chief Financial Officer have concluded that, as of the Evaluation Date, our disclosure controls and procedures were effective.
      Changes in Internal Control over Financial Reporting: There have been no changes in our internal control over financial reporting during the quarter ended on the Evaluation Date that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.
PART II. OTHER INFORMATION
Item 4. Submission of Matters to a Vote of Security Holders
Our stockholders voted on two items at the Annual Meeting of Stockholders held on June 4, 2008:
  1.   To elect six directors to serve on our Board of Directors for a term of one year and until their successors are elected and qualified:
 
  2.   To ratify the appointment of Ernst & Young LLP as our independent public accounting firm for the fiscal year ending December 31, 2008.
The nominees for director were elected based on the following votes:
                         
Directors   Votes For   Votes Withheld   % Votes For
Kenneth C. Carter, Ph.D.
    11,245,350       917,975       66.02  
Philip Frost, M.D., Ph.D.
    11,986,603       176,722       70.37  
David S. Kabakoff, Ph.D.
    11,244,900       918,425       66.02  
Michael R. Kurman, M.D.
    11,245,850       917.475       66.02  
Bradley G. Lorimier
    11,242,600       920,725       66.00  
William H. Washecka
    11,241,800       921,525       66.00  
The proposal to ratify the appointment of Ernst & Young, LLP as our independent registered public accounting firm for the fiscal year ending December 31, 2008 received the following votes:
    12,146,157 votes for approval;
 
    10,917 votes against;
 
    6,251 abstentions.
There were zero (0) broker non-votes for this item.

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Item 6. Exhibits
     
Exhibit No.   Description
   
31.1
  Certification of Chief Executive Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934 as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
 
   
31.2
  Certification of Chief Financial Officer pursuant to Rule 13a-14(a) under the Securities Exchange Act of 1934 as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
 
   
32.1
  Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C. Section 1350 as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

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SIGNATURES
     Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.
         
 
AVALON PHARMACEUTICALS, INC.
 
 
Date: August 14, 2008  By:   /s/ Kenneth C. Carter  
    Kenneth C. Carter, Ph.D.    
    President, Chief Executive Officer and Director
(Principal Executive Officer) 
 
 
     
Date: August 14, 2008  By:   /s/ C. Eric Winzer  
    C. Eric Winzer    
    Executive Vice President and Chief Financial Officer
(Principal Financial Officer and Principal Accounting Officer) 
 

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