GLYCOGENESYS INC - 10-Q Quarterly Report

Indicate by check mark whether the Registrant (1) has filed all reports required to be filed by the 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 x No ¨

Indicate by checkmark whether the Registrant is an accelerated filer (as defined in Rule 12b-2 of the Exchange Act). Yes ¨ No x

The number of shares outstanding of the Registrant’s common stock, $.01 par value per share, at November 16, 2004 was 60,504,577 shares.

The accompanying notes are an integral part of these consolidated financial statements.

The accompanying unaudited consolidated financial statements of GlycoGenesys, Inc. (together with its subsidiaries, the “Company”), have been prepared by the Company in accordance with accounting principles generally accepted in the United States of America applicable to interim periods, and with the rules and regulations of the Securities and Exchange Commission. In the opinion of management, such financial statements reflect all adjustments, consisting of only normal recurring adjustments, which are necessary for a fair presentation of the results of the interim periods presented. The results of operations for the interim periods shown in this report are not necessarily indicative of results expected for the full year. These financial statements do not include disclosures associated with the annual financial statements and, accordingly, should be read in conjunction with the Management’s Discussion and Analysis of Financial Condition and Results of Operations and the financial statements and footnotes for the year ended December 31, 2003, included in the Company’s Annual Report on Form 10-K.

The preparation of financial statements in conformity with generally accepted accounting principles requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of operating expenses during the period. Actual results could differ from those estimates.

As of September 30, 2004, the Company had an accumulated deficit of $92,370,520. Despite this accumulated deficit, the Company had a net working capital position (current assets less current liabilities) of $2,926,136 at September 30, 2004. The Company believes that its existing funds and commitments will be sufficient to fund its operating expenses and capital requirements into the first quarter of 2005, allowing the Company to continue its current Phase I dose escalation trial and to initiate its Phase I/II multiple myeloma trial. The Company intends to raise additional capital through equity financings to support its current and planned clinical trials and continued operations. To the extent the Company is unable to raise sufficient funding for its clinical trial program, it will need to accelerate its efforts to repartnering with a large biotechnology or pharmaceutical company. Since inception, the Company has funded its operations primarily through the proceeds from the sale of equity securities. From the inception of the Company through September 30, 2004, the Company has been successful in raising $76.7 million from the sales of equity securities.

In July 2004, the Company completed a financing in which it raised $5.0 million in gross proceeds from the sale of equity securities.

The Company’s future is dependent upon its ability to obtain financing to fund its operations. As of November 16, 2004, the Company has not obtained commitments from existing or potential investors to provide additional financing. The Company will need to raise significant additional funding. The Company expects to incur substantial additional operating costs, including costs related to ongoing research and development activities, preclinical studies and clinical trials. To the extent that the Company is unable to raise additional capital on a timely basis, management plans to slow down research activity to conserve cash. In the event additional financing is not obtained, the Company may be required to significantly reduce or curtail operations.

In June 2004, the Company sold its agricultural product line, Elexa^® for consideration of $50,000 in cash with future royalty and licensing fees payable to the Company.

In its Annual Report on Form 10-K for the year ended December 31, 2003, the Company reported that there is substantial doubt that the Company will have the ability to continue as a going concern and, therefore, may be unable to realize its assets and discharge its liabilities in the normal course of business. The accompanying financial statements do not include any adjustments relating to the recoverability and classification of recorded asset amounts or to amounts and classification of liabilities that may be necessary should the Company be unable to continue as a going concern.

Principal risks to the Company include the need to obtain adequate financing to fund future operations, the successful development and marketing of pharmaceutical products, dependence on collaborative partners, United States Food and Drug Administration approval, dependence on key individuals and competition from similar products and larger companies.

Basic loss per share is computed using the weighted-average number of common shares outstanding. The dilutive effect of the potential common shares consisting of outstanding stock options and warrants is determined using the treasury stock method. Diluted weighted average shares outstanding for the three month and nine month periods ended September 30, 2004 and 2003 excluded the potential common shares from convertible preferred stock, warrants and stock options because their inclusion would be anti-dilutive. At September 30, 2004 and 2003, there were 21,571,386 and 12,927,028 warrants outstanding, respectively, and 1,849,500 and 1,639,833 stock options outstanding, respectively, which were omitted from the net loss per common stock calculations, and 10,189,764 and 11,041,813 shares, respectively, issuable upon conversion of outstanding shares of preferred stock which were also omitted.

In the nine months ended September 30, 2004, the Company issued 154,591 shares of common stock in connection with the exercise of warrants for consideration of $6,046. The Company issued no shares of common stock in connection with the exercise of warrants in the three months ended September 30, 2004.

In the three months ended September 30, 2004, the Company issued 10,000,000 shares of common stock in connection with a private placement of securities for gross consideration of $5 million.

In the nine months ended September 30, 2004, the Company issued (i) 13,450,000 shares of common stock in connection with private placements for gross consideration of $9,312,500, (ii) 1,100 shares of common stock in connection with an option exercised for $296 and (iii) 1,116,790 shares of common stock in connection with the conversion of Series C preferred stock.

The Company has authorized 5,000,000 shares of preferred stock, $0.01 par value. Such preferred stock consists of:

The Company has entered into agreements with various employees and consultants for the grant of stock options and shares of common stock at prices determined by the Compensation Committee of the Company’s Board of Directors. No shares of common stock were issued as compensation for services rendered or for licensing fees during the nine months ended September 30, 2004 and 2003.

During the three months ended September 30, 2004 and 2003, the Company granted options to purchase 9,000 and 10,300 shares of common stock, respectively, at a weighted average exercise price of $0.45 and $1.01, respectively, per share to employees and others. Options to purchase 3,183 shares of common stock were exercised during the three months ended September 30, 2003. No options were exercised during the three months ended September 30, 2004. Options to purchase 9,000 and 78,399 shares of common stock at a weighted average exercise price of $0.45 and $4.67 expired and were cancelled during the three months ended September 30, 2004 and 2003, respectively.

During the nine months ended September 30, 2004 and 2003, the Company granted options to purchase 354,000 and 354,300 shares of common stock, respectively, at a weighted average exercise price of $1.25 and $0.31, respectively, per share to employees and others. Options to purchase 1,100 and 3,183 shares of common stock were exercised during the nine months ended September 30, 2004 and 2003, respectively, at a weighted average exercise price of $0.27 and $0.27, respectively, per share. Options to purchase 29,000 and 128,399 shares of common stock at a weighted average exercise price of $0.85 and $3.60 expired and were cancelled during the nine months ended September 30, 2004 and 2003.

During the three months ended September 30, 2004 and 2003, the Company issued warrants to purchase 8,366,000 and 2,344,148 shares of common stock at a weighted average exercise price of $1.00 and $0.86, respectively. No warrants to purchase common stock expired during the three months ended September 30, 2004 or 2003. No warrants to purchase common stock were exercised during the three months ended September 30, 2004. Warrants to purchase 209,577 shares of common stock at a weighted average price of $0.73 were exercised during the three months ended September 30, 2003.

During the nine months ended September 30, 2004 and 2003, the Company issued warrants to purchase 11,048,500 and 2,344,148 shares of common stock at a weighted average exercise price of $1.19 and $0.86, respectively. Warrants to purchase 154,591 and 639,144 shares were exercised at a price of $0.04 and $0.24 per share during the nine months ended September 30, 2004 and 2003, respectively. Warrants to purchase 1,720,000 shares of common stock expired during the nine months ended September 30, 2004. No warrants to purchase common stock expired during the nine months ended September 30, 2003.

Total non-cash expense related to stock, stock option and warrant grants recorded in the accompanying consolidated statements of operations for the nine months ended September 30, 2004 and 2003 amounted to $17,753 and $0, respectively, and $6,683 and 0 for the three month periods, respectively.

The Company has stock-based employee compensation plans that are described more fully in Note 5 to the Company’s consolidated financial statements included in its Annual Report on Form 10-K for the year ended December 31, 2003. The Company accounts for these plans under the recognition and measurement principles of APB Opinion No. 25, “Accounting for Stock Issued to Employees”, and related interpretations. No stock-based employee compensation cost is reflected in the Consolidated Statements of Operations, as all options granted under these plans had an exercise price equal to or greater than the market value of the underlying common stock on the dates of grant. The following table illustrates the effect on net loss and net loss per common share if the Company had applied the fair value recognition provisions of SFAS No. 123, “Accounting for Stock-Based Compensation” to stock-based employee compensation.

Had the compensation cost for the plans been determined based on the fair value at the grant dates for awards under the plans consistent with the method described in SFAS No. 123, the Company’s net loss and basic and diluted net loss per common share on a pro forma basis would have been:

The preceding pro forma results were calculated using the Black-Scholes option-pricing model. The following assumptions were used for options granted during the three months ended September 30, 2004 and 2003, respectively: (1) risk-free interest rates of 4.3% and 4.2%, respectively; (2) dividend yields of 0.0%; (3) expected lives of 10 years; and (4) volatility of 76.0% and 160.1%, respectively. The weighted average fair value of options granted during the three months ended September 30, 2004 and 2003 was $0.45 and $1.01, respectively.

Stock or other equity-based compensation for non-employees is accounted for under the fair value-based method as required by SFAS No. 123 and Emerging Issues Task Force (“EITF”) Issue No. 96-18, “Accounting for Equity Instruments That Are Issued to Other Than Employees for Acquiring, or in Conjunction with Selling, Goods or Services” and other related interpretations. Under this method, the equity-based instrument is valued at either the fair value of the consideration received or the equity instrument issued on the date of grant. The resulting compensation cost is recognized and charged to operations over the service period, which is usually the vesting period.

Platt License—On January 13, 2004, the Company notified David Platt of its intention to seek arbitration regarding his alleged breaches of the Company’s license agreement with him dated January 7, 1994, as amended (the “License Agreement”). In particular, the Company sought to enforce its rights under the License Agreement to control the prosecution of the patent applications subject to the License Agreement. On February 18, 2004, the Company received a letter from David Platt alleging breaches of its obligations under the License Agreement, specifically failure to: (i) take necessary steps to perfect U.S. Patent Application Serial No. 08/024,487 (the “‘487 Application”), (ii) use its best efforts to commercialize the ‘487 Application and (iii) provide royalty reports. The letter further notified the Company of his intention to terminate the License Agreement if such alleged breaches were not cured within 60 days from the date of the letter.

On November 11, 2004, the arbitrator issued a decision which found that Platt had breached the License Agreement by filing a patent application which was a continuation-in-part of the ‘487 Application without having informed the Company and affirmed the Company’s position that Platt’s subsequent patent application is also covered by the License Agreement. The arbitrator rejected Platt’s contention that the Company had breached the License Agreement and refused to terminate the License Agreement, as Platt had requested. Instead, the arbitrator found that the Company retained its exclusive rights to the technology in question. The arbitrator allowed Platt to continue prosecuting the patent applications, including the ‘487 Application, in which he is listed as inventor, finding that Platt had not relinquished an investor’s right to control prosecution of his applications under the License Agreement. Prosecution of the applications is for the benefit of the Company, which retains exclusive rights to develop and commercialize them.

Platt Litigation—On January 29, 2004, David Platt commenced suit against the Company and certain current and former directors of the Company in the Massachusetts Superior Court, Suffolk County. In his Complaint, Platt seeks damages for alleged breach of his severance agreement with the Company, including the failure to pay approximately $180,000 in severance benefits and alleged breaches in connection with maintenance by the Company of certain restrictions on Platt’s sale of stock. The Complaint further asserts claims against certain current and former directors of the Company for alleged breaches of fiduciary duty in failing to assist in the removal of restrictive legends on David Platt’s shares. Platt also purports to state claims for double or treble damages, as well as attorney fees, under General Laws Chapter 93A, Section 11, the Massachusetts Unfair Trade Practice Act. The case has been assigned under case number 04-0398 and will be heard in the Business Litigation Session of the Suffolk County Superior Court. The Company believes these claims are without merit.

On February 23, 2004, the Company filed its answer and counterclaimed against David Platt for breach of his severance agreement, against Pro-Pharmaceuticals, Inc. for tortious interference with the severance agreement, and against Platt and Pro-Pharmaceuticals, Inc. for misappropriation of proprietary rights and for unfair and deceptive acts. The Company seeks monetary damages and injunctive relief to prevent David Platt and Pro-Pharmaceuticals from engaging in certain competitive activities relating to the use of polysaccharides to treat cancer and further seeks the assignment by David Platt and Pro-Pharmaceuticals of certain intellectual property, including Davanat^®, to the Company. Under the counterclaim for unfair and deceptive acts, the Company is seeking treble damages as well as attorneys’ fees.

On June 21, 2004, the Company added a supplemental counterclaim against David Platt and Pro-Pharmaceuticals for injurious falsehood, unfair competition and unfair and deceptive acts relating to statements made by Pro-Pharmaceutical regarding certain patent applications the Company discontinued prosecuting and contractually returned to David Platt. The Company seeks injunctive relief and monetary damages.

Discovery is proceeding in this matter. A trial is not expected until mid-2005 at the earliest.

While the Company believes that the ultimate outcome of these proceedings will not have a material adverse effect on our financial position, results of operations, or cash flows, legal proceedings are subject to inherent uncertainty. An adverse resolution of the above proceedings could have a material impact on our financial position, results of operations or cash flows. Legal proceedings consume both cash and management attention.

ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

The following discussion should be read in conjunction with the consolidated financial statements and the notes thereto.

The following contains certain forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended, which are intended to be covered by the safe harbors created thereby. All forward-looking statements involve risks and uncertainty. Although we believe that the assumptions underlying the forward-looking statements contained herein are reasonable, any of the assumptions could be inaccurate, and therefore, there can be no assurance that the forward-looking statements included in this report will prove to be accurate. Our actual results may differ materially from the results anticipated in the forward-looking statements. Any statements contained in this Quarterly Report on Form 10-Q that relate to future plans, events or performance are forward-looking statements that involve risks and uncertainties, including but not limited to, risks of product development (such as failure to demonstrate efficacy or safety), risk related to FDA and other regulatory procedures, market acceptance risks, the impact of competitive products and pricing, the results of current and future licensing, joint ventures and other collaborative relationships, the results of financing efforts, litigation risks, developments regarding intellectual property rights and litigation, and other risks identified in the section titled “Quantitative and Qualitative Disclosures about Market Risk—Certain Factors that May Affect Future Results” included herein which discuss factors that could contribute to such material differences. In light of the significant uncertainties inherent in the forward-looking statements included herein, the inclusion of such information should not be regarded as a representation by the Company or any other person that the objectives and plans of the Company will be achieved. We undertake no obligation to publicly release the results of any revisions to these forward-looking statements that may be made to reflect events or circumstances after the date hereof or to reflect the occurrence of unanticipated events.

GlycoGenesys, Inc. (together with its subsidiaries, as the context requires, the “Company”) is a biotechnology company developing novel drug candidates primarily based on carbohydrate compounds and related technologies. The Company’s lead drug candidate GCS-100^®, a potential treatment for multiple forms of solid tumors and bloodborne cancers, completed Phase II(a) clinical trials at low dose levels for pancreatic cancer and for colorectal cancer the results of which were announced in October 2002 and March 2001, respectively. We announced the results of a Phase I dose escalation trial in October 2003, dosing in patients at levels up to 80 mg/m2. In April 2004, the Company initiated a Phase I dose escalation trial to evaluate higher dose levels of GCS-100LE, a low ethanol formulation of GCS-100. The Company plans to initiate a Phase I/II dose escalation trial in multiple myeloma in late 2004/early 2005 at the Dana Farber Cancer Institute. We plan to request Fast Track designation in early 2005.

The Company’s near-term objectives are to continue to proceed through the various phases of United States Food and Drug Administration (“FDA”) clinical trials for GCS-100LE, and to secure the necessary financial resources to conduct such trials, either through repartnering with a large biotechnology or pharmaceutical company or raising funds in the capital market or a combination of both. In March 2004, we opened a laboratory in Cambridge, Massachusetts. In addition, the Company sold its Elexa^® agricultural product line in June 2004 and has divested its other agricultural product line.

The Company’s business was founded in 1992 as IGG International, Inc. to pursue carbohydrate-based pharmaceutical research for cancer therapeutics. In 1995, the Company merged with Alvarada Inc., a publicly-traded corporation having no active operations. In 1998 the Company changed its name to SafeScience, Inc. and in October 2001 the Company changed its name to GlycoGenesys, Inc. The Company’s principal executive offices are located at 31 St. James Avenue, 8th Floor, Boston, MA 02116 and the telephone number is (617) 422-0674. The Company’s home page is located on the worldwide web at http://www.glycogenesys.com.

GlycoGenesys has three wholly-owned subsidiaries, International Gene Group, Inc. (“IGG”), and SafeScience Products, Inc. (“SafeScience Products”) and SafeScience Newco, Ltd. (“SafeScience Newco”). These subsidiaries are currently non-operating subsidiaries.

GlycoGenesys develops human therapeutics, primarily GCS-100, which it exclusively licenses from Dr. David Platt and Wayne State University and the Barbara Ann Karmanos Cancer Institute. Historically, SafeScience Products, Inc. developed agriculture products and developed, marketed, and distributed chemically-safe consumer and commercial products.

Our significant accounting policies are described in the Notes to the Consolidated Financial Statements included in our Annual Report on Form 10-K for the year ended December 31, 2003. The accounting policies used in preparing our interim consolidated financial statements for the nine months ended September 30, 2004 are the same as those described in our Annual Report on Form 10-K.

The Company’s critical accounting policies are those that are important to the portrayal of the Company’s financial condition and operating results and require management’s most difficult, subjective or complex judgments, often as a result of the need to make estimates about the effect of matters that are inherently uncertain. The Company believes that its most critical accounting policy relates to the accounting for its accrued liabilities, specifically clinical research organization costs. While the Company bases its judgments and estimates on historical experience and other assumptions that management believes are appropriate and reasonable under current circumstances, actual results may differ from those estimates.

Accrued liabilities, specifically clinical research organization costs — The preparation of financial statements requires management to make estimates and assumptions that affect the reported amount of assets and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of expenses during the reported period. Specifically, management must make estimates of costs incurred to date but not yet invoiced in relation to external clinical research organization, or CRO, costs. Management analyzes the progress of clinical trials, invoices received and budgeted costs when evaluating the adequacy of the accrued liability. Significant management judgments and estimates must be made and used in connection with the accrued balance in any accounting period. Material differences may result in the amount and timing of the accrued balance for any period if management made different judgments or utilized different estimates.

Results of Operations: Three Months Ended September 30, 2004 versus September 30, 2003

We had a net loss of $2,684,555 for the three months ended September 30, 2004 versus $1,829,957 for the three months ended September 30, 2003.

Research and Development Expenses — Developing carbohydrate-based therapeutic compounds is our primary business focus, which is in the research and development phase. To a lesser extent, we have developed nontoxic agricultural products. We sold our Elexa agricultural product line in June 2004 and have divested our other agricultural product line. Explanations of the changes in both areas from quarter-to-quarter are described in this section.

Our research and development expenses for the three months ended September 30, 2004 and 2003 were:

Total research and development expenses of $1,360,047 for the three months ended September 30, 2004 increased $395,437, or 41%, from $964,610 of expenses for the three months ended September 30, 2003.

Total GCS-100 development expenses of $1,349,002 for the three months ended September 30, 2004 increased $410,098, or 44%, from $938,904 of expenses for the three months ended September 30, 2003. This increase is primarily due to increases in expenses of approximately (i) $375,000 in clinical trial costs, (ii) $75,000 in staffing-related costs, (iii) $74,000 for laboratory costs, (iv) $24,000 for royalties and (v) $11,000 in consulting fees. These increases were partially offset by decreases in GCS-100 production costs of $100,000 and $34,000 in regulatory costs.

Research and development expenses for Elexa-4 and Bb-447, our agricultural compounds, which consisted primarily of wages, consulting, registration and license fees, decreased approximately $15,000, or 57%, to approximately $11,000 for the three months ended September 30, 2004 from approximately $26,000 for the three months ended September 30, 2003. The decrease reflects decreased payroll, consulting and licensing expenses. We sold our Elexa product line in June 2004 and plan to divest our Bb447 product line.

We may seek to expand our drug compound pipeline under development. Any new product candidates will either be developed jointly or licensed by us. The cost related to the development of new product candidates is projected to be in the range of $100,000-$300,000 during the next twelve months, but could vary significantly based on the actual product candidates.

General and administrative expenses increased to $1,337,566 for the three months ended September 30, 2004 from $869,983 for the three months ended September 30, 2003, an increase of $467,583, or 54%. This increase is primarily attributable to increases of approximately (i) $353,000 in legal fees, (ii) $192,000 in consulting expenses and (iii) $37,000 in investor relation expenses. These increases were partially offset by reductions of $50,000 in payroll, $40,000 in rent and $21,000 of insurance expenses.

Interest income increased to $12,967 for the three months ended September 30, 2004 from $4,038 for the three months ended September 30, 2003, an increase of $8,929, or 221%. This increase is attributable to an increase in cash available for investment and higher rates of return on those investments.

Results of Operations: Nine Months Ended September 30, 2004 versus September 30, 2003

We had a net loss of $7,945,561 for the nine months ended September 30, 2004 versus $5,189,244 for the nine months ended September 30, 2003.

Our research and development expenses for the nine months ended September 30, 2004 and 2003 were:

Total research and development expenses of $3,956,740 for the nine months ended September 30, 2004 increased $1,494,846, or 61%, from $2,461,894 of expenses for the nine months ended September 30, 2003.

Total GCS-100 development expenses of $3,903,156 for the nine months ended September 30, 2004 increased $1,592,358, or 69%, from $2,310,798 of expenses for the nine months ended September 30, 2003. This increase is primarily due to increases in expenses of approximately (i) $753,000 in GCS-100 production and development costs, (ii) $249,000 in clinical trial costs, (iii) $196,000 for laboratory costs, (iv) $134,000 for consulting, (v) $132,000 for payroll related costs, (vi) $84,000 in license fees paid to Wayne State University and the Barbara Ann Karmanos Cancer Institute and (vii) $62,000 for pre-clinical studies.

Research and development expenses for Elexa-4 and Bb-447, our agricultural compounds, which consisted primarily of wages, consulting, registration and license fees, decreased approximately $98,000, or 65%, to approximately $54,000 for the nine months ended September 30, 2004 from approximately $151,000 for the nine months ended September 30, 2003. The decrease reflects reduced payroll, licensing and consulting expense. We sold our Elexa product line in June 2004 and plan to divest our Bb447 product line.

General and administrative expenses increased to $4,073,008 for the nine months ended September 30, 2004 from $2,750,902 for the nine months ended September 30, 2003, an increase of $1,322,106, or 48%. This increase is primarily attributable to increases of approximately (i) $780,000 in legal fees, (ii) $337,000 in consulting expenses, (iii) $135,000 in investor relations expenses, (iv) $80,000 in payroll-related costs and (v) $28,000 in travel expenses partially offset by a decrease in depreciation of $33,000 and $37,000 in rent.

Interest income increased to $26,677 for the nine months ended September 30, 2004 from $20,211 for the nine months ended September 30, 2003, an increase of $6,466, or 32%. This increase is attributable to an increase in cash available for investment and higher rates of return on those investments.

For the nine months ended September 30, 2004, our operations utilized cash of $7,241,309 primarily to fund our operating loss, partially offset by an increase in accounts payable. We also invested $173,689 in purchases of property and equipment. In July 2004 we raised $5,000,000 in gross proceeds from the sale of common stock and warrants to purchase common stock. We intend to raise additional funds through sales of our securities and possibly through partnering arrangements with pharmaceutical or mature biotechnology companies.

As of September 30, 2004, our accumulated deficit was $92,370,520 and as of November 16, 2004, our cash balances were $3,314,593. We believe that our existing funds and commitments will be sufficient to fund our operating expenses and capital into the first quarter of 2005, allowing us to continue our current Phase I dose escalation solid tumor monotherapy trial and to initiate our Phase I/II multiple myeloma trial. We intend to raise additional capital through equity financings to support our planned clinical trials and continued operations. To the extent we are unable to raise sufficient funding for clinical trials, we will need to accelerate our efforts to repartner with a large biotechnology or pharmaceutical company. Since inception, we have funded our operations primarily through the proceeds from the sale of equity securities; however, there can be no assurance that additional equity financing will be available.

Our future is dependent upon our ability to obtain financing to fund our operations. As of November 16, 2004, we have not obtained commitments from existing or potential investors to provide additional financing. We will need to raise significant additional funding. We expect to incur substantial additional operating costs, including costs related to ongoing research and development activities, preclinical studies and clinical trials. To the extent that we are unable to raise additional capital on a timely basis, management plans to prioritize research activities to conserve cash. In the event additional financing is not obtained, we may be required to significantly reduce, curtail or cease operations.

During the three months ended September 30, 2004, the only significant change in our reported payments due under contractual obligations at December 31, 2003 relates to our entering into a lease extension for our offices at 31 St. James Avenue in Boston, Massachusetts during the quarter. As a result of the lease extension, our lease payment obligations, including those obligations under our lease of laboratory space at One Kendall Square in Cambridge, Massachusetts, as of September 30, 2004 are approximately: $103,000, $412,000, $412,000, $281,000, $281,000 and $164,000 for 2004, 2005, 2006, 2007, 2008 and thereafter, respectively.

We are not exposed to significant market risk related to changes in currency exchange rates as measured against the U.S. dollar. As of September 30, 2004, we have evaluated our risk and determined that any exposure to currency exchange is not significant to our overall consolidated financial results. There can be no assurance that our exposure will remain at these levels, especially in the event of significant and sudden fluctuations in the value of local currencies. We do not use derivative financial instruments for speculative or trading purposes.

We maintain short-term investments in an overnight money market account comprised of U.S. treasury bills. If market interest rates were to increase immediately and uniformly by 10% from levels that existed at September 30, 2004, the fair value of the portfolio would change by an immaterial amount.

You should carefully consider the risks described below before making an investment decision. If any of the following risks actually occur, our business, financial condition or results of operations could be materially and adversely affected. In such case, the trading price of our common stock could decline, and you may lose all or part of your investment.

WE HAVE EXPERIENCED SIGNIFICANT LOSSES THROUGHOUT OUR HISTORY, WE EXPECT THESE LOSSES TO CONTINUE AND WE MAY NOT ACHIEVE PROFITABILITY IN THE FUTURE.

We began operations in 1993 and have not generated revenue from human therapeutic products. We do not expect to generate product revenue for several years, if at all. We will not generate significant funds unless we receive payments in connection with any potential licensing, marketing or other partnering arrangement with other pharmaceutical or biotechnology companies, or we bring pharmaceutical products to market. Excluding dividends accreted to preferred stock, we have incurred approximately $92.4 million of losses since our inception, including approximately $7.6 million for the year ended December 31, 2003 and $7.9 million in the first nine months of 2004. Extensive losses can be expected to continue for the foreseeable future.

We also expect to continue to incur significant operating expenses and capital expenditures and anticipate that our expenses will increase substantially in the foreseeable future as we:

WE MAY NOT BE ABLE TO OBTAIN ADDITIONAL FUNDING, WHICH COULD REDUCE OUR ABILITY TO FUND, EXPAND OR CONTINUE OPERATIONS.

We believe that our existing funds will be sufficient to fund our operating expenses and capital requirements into the first quarter of 2005, allowing us to continue the current Phase I dose escalation solid tumor monotherapy trial and initiate a Phase I/II trial in multiple myeloma with GCS-100LE, a low ethanol formulation of GCS-100. We intend to raise additional capital through the sale of equity securities to support our additional planned clinical trials and continued operations. To the extent we are unable to raise sufficient funding for the additional clinical trials in the capital markets, we will need to accelerate our efforts to repartner with a large biotechnology or pharmaceutical company and/or curtail our development efforts.

Our future is dependent on our ability to obtain additional financing to fund our operations. We expect to incur substantial additional operating costs, including costs related to ongoing research and development activities, manufacturing, preclinical studies and clinical trials. Additional equity financing may result in dilution to our stockholders. At our current stock price or if the market price of our common stock declines, some potential investors may either refuse to offer us any financing or will offer financing at unacceptable rates or on unfavorable terms. If we are unable to obtain financing necessary to fund our operations, we may have to sell or liquidate GlycoGenesys or significantly reduce, curtail or cease our operations.

Our consolidated financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2003 have been prepared on the assumption that we will continue as a going concern. Deloitte & Touche LLP issued a report dated March 26, 2004 that includes an explanatory paragraph stating that our recurring losses from operations, accumulated deficit of $84.4 million as of December 31, 2003, and our expectation that we will incur substantial additional operating costs, including costs related to ongoing research and development activities, preclinical studies and clinical trials, among other things, raise substantial doubt about our ability to continue as a going concern.

OUR FUTURE PROSPECTS ARE HEAVILY DEPENDENT ON THE RESULTS OF GCS-100 AND IF WE ARE UNSUCCESSFUL IN DEVELOPING GCS-100, WE DO NOT HAVE OTHER PRODUCTS WHICH ARE AS ADVANCED IN DEVELOPMENT AS GCS-100.

While we seek to increase our portfolio of potential products, currently we are not developing a wide array of products. Nearly all of our attention and resources are directed to the development of GCS-100. If GCS-100 is ultimately ineffective in treating cancer, does not receive the necessary regulatory approvals or does not obtain commercial acceptance, we will be materially harmed.

WE ARE DEPENDENT ON THE SUCCESSFUL OUTCOME OF CLINICAL TRIALS FOR GCS-100 AND WILL NOT BE ABLE TO SUCCESSFULLY DEVELOP AND COMMERCIALIZE GCS-100 IF CLINICAL TRIALS ARE NOT SUCCESSFUL.

GCS-100 is not currently approved for sale by the FDA or by any other regulatory agency in the world, and GCS-100 may never receive approval for sale or become commercially viable. Before obtaining regulatory approval for sale, GCS-100 or another product candidate will be subjected to extensive preclinical and clinical testing to demonstrate safety and efficacy for a particular indication for humans in addition to meeting other regulatory standards. Our success will depend on the successful outcome of our clinical trials with GCS-100.

There are a number of difficulties and risks associated with clinical trials. The possibility exists that:

Given the uncertainty surrounding the regulatory and clinical trial process, we may not be able to develop safety, efficacy or manufacturing data necessary for approval of GCS-100 or another product candidate. In addition, even if we receive approval, such approval may be limited in scope and hurt the commercial viability of such product. If we are unable to successfully obtain approval of and commercialize any product candidate, this would materially harm our business, impair our ability to generate revenues and adversely impact our stock price.

OUR ABILITY TO DEVELOP GCS-100 MAY BE HARMED IF WE ARE UNABLE TO FIND A DEVELOPMENT PARTNER.

On December 18, 2002, we and Elan International Services, Ltd. (“EIS”) mutually terminated our joint venture and we acquired all of the outstanding capital stock of SafeScience Newco. SafeScience Newco received a total of approximately $7.3 million of research funds over the course of our joint venture with EIS for the development of GCS-100. We must either fund the development of GCS-100 ourselves or with a new development partner. If we are unable to find a development partner, our ability to develop and commercialize GCS-100, and our prospects as a whole, could be materially harmed.

OUR FAILURE TO PROTECT OUR INTELLECTUAL PROPERTY OR OUR INFRINGEMENT ON THE PROPERTY RIGHTS OF OTHERS MAY IMPEDE OUR ABILITY TO OPERATE FREELY

We rely significantly upon proprietary technology and protect our intellectual property through patents, copyrights, trademarks and contractual agreements as appropriate. We own or exclusively license eight issued U.S. patents having expiration dates ranging from 2013 to 2022. Five of these eight issued patents relate to GCS-100. We own or exclusively license five foreign patents having expiration dates ranging from 2015 to 2017. Four of these five foreign patents relate to GCS-100. We own or exclusively license 12 pending U.S. patent applications, all of which relate to GCS-100 and 49 pending foreign patent applications, of which 40 relate to GCS-100. As we develop GCS-100, we may discover more about its characteristics and manufacturing which will require additional patent prosecution. Thus, we continually evaluate our technology to determine whether to make further patent filings.

To the extent aspects of our technology may be unpatentable, we may decide to maintain such technology as trade secrets or we may protect such unpatented technology by contractual agreements. Our unpatented technology or similar technology could be independently developed by others. In addition, the contractual agreements by which we protect our unpatented technology and trade secrets may be breached. If technology similar to ours is independently developed or our contractual agreements are breached, our technology will be less valuable and our business will be harmed.

There is always a risk that issued patents may be subsequently invalidated, either in whole or in part, and this could diminish or extinguish our patent protection for key elements of our technology. We are not involved in any such litigation or proceedings, nor are we aware of any basis for such litigation or proceedings. We cannot be certain as to the scope of patent protection, if any, which may be granted on our patent applications.

A patent we exclusively license from Wayne State University and the Barbara Ann Karmanos Cancer Institute and patent applications we exclusively license from David Platt could become subject to a proceeding at the U.S. Patent and Trademark Office to determine priority between them. The U.S. Patent and Trademark Office is considering whether such a proceeding is appropriate. Under our license with David Platt, he has the right to prosecute the patent applications covered by the license and therefore we do not have ultimate control over the scope of claims that may issue.

Our potential products or business activities could be determined to infringe intellectual rights of third parties despite our issued patents. Any claims against us or any purchaser or user of our potential products, including GCS-100, asserting that such product or process infringes intellectual property rights of third parties, if determined adversely to us, could have a material effect on our business, financial condition or future operations. Any asserted claims of infringement, with or without merit, could be time consuming, result in costly litigation, divert the efforts of our technical and management personnel, or require us to enter into royalty or licensing agreements, any of which could materially adversely affect our operating results. Such royalty or licensing agreements, if required, may not be available on terms acceptable to us, if at all. In the event a claim is successful against us and we cannot obtain a license to the relevant technology on acceptable terms, license a substitute technology or redesign our products to avoid infringement, our business, financial condition and operating results would be materially adversely affected.

WE DEPEND ON TECHNOLOGY LICENSED TO US BY THIRD PARTIES AND IF WE ARE UNABLE TO CONTINUE LICENSING THIS TECHNOLOGY OUR FUTURE PROSPECTS MAY BE MATERIALLY ADVERSELY AFFECTED.

We license technology, including technology related to GCS-100, from third parties. We anticipate that we will continue to license technology from third parties in the future. To maintain our license with David Platt we must pay an annual license fee equal to the greater of $50,000 or 2% of product sales. To maintain our license with Wayne State University and the Barbara Ann Karmanos Cancer Institute we must, among other things, pay Wayne State University and the Barbara Ann Karmanos Cancer Institute up to $3 million in milestone payments, $10,000 per month until FDA approval (which payments are offset against future royalties), 2% royalties on product sales and receive FDA or equivalent agency approval to sell GCS-100 by January 1, 2008.

The technology we license from third parties would be difficult to replace. The loss of any of these technology licenses would result in delays in the development of our products until equivalent technology, if available, is identified, licensed and integrated and could materially adversely affect our future prospects. The use of replacement technology from other third parties would require us to enter into license agreements with these third parties, which could result in higher royalty payments and a loss of product differentiation, or alternatively may not be available.

WE ARE ENGAGED IN LITIGATION WITH DAVID PLATT AND PRO-PHARMACEUTICALS, INC. AND IF WE ARE UNSUCCESSFUL, WE MAY BE HARMED.

On January 29, 2004, David Platt commenced suit against us and certain of our current and former directors in the Massachusetts Superior Court. In his Complaint, Platt seeks damages for alleged breach of his severance agreement with us, including the failure to pay approximately $180,000 in monthly severance benefits and alleged breaches in connection with the maintenance by us of certain restrictions on Platt’s sale of stock. The Complaint further asserts claims against some of our current and former directors for alleged breaches of fiduciary duty in failing to assist in the removal of restrictive legends on David Platt’s shares. David Platt also purports to state claims for double or treble damages, as well as attorney fees, under the Massachusetts Unfair Trade Practice Act.

On February 23, 2004, we filed our Answer and counterclaimed against David Platt for breach of his severance agreement, against Pro-Pharmaceuticals, Inc. for tortious interference with the severance agreement, and against David Platt and Pro-Pharmaceuticals for misappropriation of proprietary rights and for unfair and deceptive acts. We are seeking monetary damages and injunctive relief to prevent David Platt and Pro-Pharmaceuticals from engaging in certain competitive activities relating to the use of polysaccharides to treat cancer and we are further seeking the assignment by David Platt and Pro-Pharmaceuticals of certain intellectual property to us. Under the counterclaim for unfair and deceptive acts, we are seeking treble damages as well as attorney fees.

On June 21, 2004, the Company added a supplemental counterclaim against David Platt and Pro-Pharmaceuticals for injurious falsehood, unfair competition and unfair and deceptive acts relating to statements made by Pro-Pharmaceuticals regarding certain patent applications the Company discontinued prosecuting and contractually returned to David Platt. The Company seeks injunctive relief and monetary damages.

If we are unsuccessful in defending David Platt’s claims or in our counterclaims, we could be materially adversely affected.

WE EXPECT TO REMAIN DEPENDENT ON THIRD PARTIES FOR RESEARCH AND DEVELOPMENT ACTIVITIES NECESSARY TO COMMERCIALIZE OUR PRODUCTS.

In addition, we utilize the services of several scientific and technical consultants to oversee various aspects of our protocol design, clinical trial oversight and other research and development functions. However, we contract out most of our research and development operations for GCS-100,

utilizing third-party contract manufacturers such as Hollister-Stier Laboratories LLC and Sigma-Aldrich, Inc. to manufacture GCS-100, Incell Corporation, LLC, Cambrex BioScience Walkersville, Inc. and PPD Development, LP for assay and other development work and third-party contract research organizations, such as Glenmere Clinical Research and Medidata Solutions, Inc. in connection with pre-clinical and/or clinical studies in accordance with our designed protocols, as well as conducting research at medical and academic centers, such as the University of Arizona, St. Bartholomew’s and the Royal London School of Medicine, Northeastern University, and the Dana Farber Cancer Institute.

Because we rely on third parties for much of our research and development work, we have less direct control over our research and development. We face risks that these third parties may not be appropriately responsive to our timeframes and development needs and could devote resources to other customers. In addition, certain of these third parties may have to comply with FDA regulations or other regulatory requirements in the conduct of this research and development work, which they may fail to do.

IF THE THIRD PARTIES WE RELY ON FOR MANUFACTURING ARE UNABLE TO PRODUCE THE NECESSARY AMOUNTS OF GCS-100, DO NOT MEET OUR QUALITY NEEDS OR TERMINATE THEIR RELATIONSHIPS WITH US, OUR BUSINESS WILL SUFFER.

We do not presently have our own manufacturing operations, nor do we intend to establish any unless and until, in the opinion of management, the size and scope of our business so warrants. While we have established a manufacturing relationship with Hollister-Stier Laboratories LLC and Sigma-Aldrich, Inc. to provide us with GCS-100 that we believe will provide the capability to meet our anticipated requirements for the foreseeable future, we have not entered into any long-term arrangements for manufacturing and such arrangements may not be obtained on desirable terms. For the foreseeable future, we will be dependent upon third parties to manufacture GCS-100.

Our reliance on independent manufacturers involves a number of risks, including the absence of adequate capacity, the unavailability of, or interruptions in, access to necessary manufacturing processes and reduced control over delivery schedules. Because our manufacturing process is still in a development stage, any changes made to a final commercial manufacturing process may present technical problems to an independent manufacturer. Third-party manufacturers may not comply with FDA regulations, or other regulatory requirements relating to the manufacturing of GCS-100, including compliance with good manufacturing practice, or GMP. We do not have control over, other than through contract, third-party manufacturers’ compliance with these regulations and standards. If our manufacturers are unable or unwilling to continue manufacturing GCS-100 in required volumes, we will have to identify acceptable alternative manufacturers. If we need to change manufacturers, the FDA and corresponding foreign regulatory agencies must have approved these manufacturers. The use of a new manufacturer may cause significant expense and interruptions in supply if the new manufacturer has difficulty manufacturing GCS-100 to our specifications. Further, the introduction of a new manufacturer may increase the variation in the quality of GCS-100.

MANY OF OUR COMPETITORS HAVE SUBSTANTIALLY GREATER RESOURCES THAN WE DO AND MAY BE ABLE TO DEVELOP AND COMMERCIALIZE PRODUCTS THAT MAKE OUR POTENTIAL PRODUCTS NON-COMPETITIVE.

We face significant competition from firms currently engaged in the pharmaceutical and biotechnology industries. GCS-100, our lead drug candidate, being developed for the treatment of various forms of cancer, addresses large markets, which are already populated with several biotechnology and large pharmaceutical companies. These companies utilize different drug discovery platforms, including but not limited to small molecules, protein-based drugs, liposome technology, and genomics. The drug development industry is intensely competitive. According to industry surveys, there are approximately over 400 new drug candidates in development to treat various types of cancer, many of them for multiple indications. According to the PhRMA, approximately 170 pharmaceutical and biotechnology companies and the National Cancer Institute are conducting these efforts. It is estimated that 100 biotechnology companies have more than 100 drug candidates in later stages of clinical development than GCS-100 for acute, life threatening disease, and late stage disease, and that over forty percent of these drug candidates are being developed to treat various types of cancer. Many of our actual or potential competitors have significantly greater financial resources and/or drug development experience than we have. There is no assurance that other carbohydrate-based or non-carbohydrate-based drugs with similar clinical effects to GCS-100 may not already be in development by other companies or that other companies may not successfully develop such drugs in the future.

A biotechnology company such as ours must keep pace with rapid technological change and faces intense competition. We compete with biotechnology and pharmaceutical companies for funding, access to new technology, research personnel and in product research and development. Many of these companies have greater financial resources and more experience than we do in developing drugs, obtaining regulatory approvals, manufacturing and marketing. We also face competition from academic and research institutions and government agencies pursuing alternatives to our products and technologies. We expect that GCS-100 and other product candidates will face intense competition from existing or future drugs. In addition, our product candidates may face increasing competition from generic formulations or existing drugs whose active components are no longer covered by patents. These generic formulations or drugs would present lower-priced competition.

In the two cancer types in which we have conducted Phase II(a) clinical trials, pancreatic and colorectal, there are many drugs being developed. We believe, based on industry studies there are, including GCS-100, approximately 7 drugs in Phase I, 15 drugs in Phase II, 6 drugs in Phase III or pre-registration for treatment of pancreatic cancer. In addition, GCS-100, if it receives FDA approval for pancreatic cancer, will face competition from existing drugs approved or used to treat pancreatic cancer. These drugs are fluorouracil (5-FU), Eli Lilly’s gemcitabine (Gemzar) and Supergens’ Mitozytrex. Combination studies utilizing new drug candidates and Gemzar are ongoing and combination therapies of new drug candidates and Gemzar may present future competition. Aphton’s G17DT is currently being evaluated in combination with Gemzar in a double blinded Phase III clinical trial.

We believe, based on industry studies, there are, including GCS-100, approximately 12 drugs in Phase I, 24 drugs in Phase II, and 10 drugs in Phase III or in pre-registration for treatment of colorectal cancer. In addition, GCS-100, if it receives FDA approval for colorectal cancer, will face competition from existing drugs approved or used to treat colorectal cancer. These drugs include Genenetech’s Avastin, Roche Pharmaceuticals’ capecitabine (Xeloda), fluorouracil (Adrucil or 5-FU), leucovorin in combination with 5-FU, Janssen’s levamisole (Ergamisol) in combination with 5-FU, Pharmacia’s irinotecan (Camptosar) and Imclone’s Erbitux.

We plan to initiate a Phase I/II trial in multiple myeloma late in 2004. We believe, based on industry studies, there are, including GCS-100, approximately five drugs in Phase I, nine in Phase II and five in Phase III or in pre-registration for the treatment of multiple myeloma. In addition, GCS-100, if it receives FDA approval for treatment of multiple myeloma, will face competition from existing drugs approved or used to treat multiple myeloma. These drugs include vincristine, dexamethasone, prednisone, doxorubicin (Adriamycin), melphalan, etoposide, cytarabine, cisplatin, carmustine, cyclophosphamide, Celgene’s Thalomid and Millennium’s Velcade. The majority of the drugs are used in combination therapy in a variety of regiments.

The success of our competitors in any of these efforts would adversely affect our ability to develop, commercialize and market our product candidates.

OUR BUSINESSES ARE SUBJECT TO SIGNIFICANT GOVERNMENT REGULATION AND FAILURE TO ACHIEVE REGULATORY APPROVAL OF OUR DRUG CANDIDATES WOULD SEVERELY HARM OUR BUSINESS.

The FDA regulates the development, testing, manufacture, distribution, labeling and promotion of pharmaceutical products in the United States pursuant to the Federal Food, Drug, and Cosmetic Act and related regulations. We must receive pre-market approval by the FDA prior to any commercial sale of GCS-100 or any other drug candidate. Before receiving such approval we must provide pre-clinical data and proof in human clinical trials of the safety and efficacy of GCS-100 or any other drug candidates, which trials can take several years. In addition, we must show that we can produce GCS-100 or any other drug candidates consistently at quality levels sufficient for administration in humans. Pre-market approval is a lengthy and expensive process. We may not be able to obtain FDA approval for any commercial sale of any drug candidate. By statute and regulation, the FDA has 180 days to review an application for approval to market a drug candidate; however, the FDA frequently exceeds the 180-day time period, at times taking up to 18 months. In addition, based on its review, the FDA may determine that additional clinical trials or pre-clinical data are required. Except for any potential licensing or marketing arrangements with other pharmaceutical or biotechnology companies, we will not generate any revenues in connection with GCS-100 or any other drug candidates unless and until we obtain FDA approval to sell such products in commercial quantities for human application.

REIMBURSEMENT PROCEDURES AND FUTURE HEALTHCARE REFORM MEASURES ARE UNCERTAIN AND MAY ADVERSELY IMPACT OUR ABILITY TO SUCCESSFULLY SELL OR LICENSE ANY PHARMACEUTICAL PRODUCT.

Our ability to successfully sell or license any pharmaceutical product will depend in part on the extent to which government health administration authorities, private health insurers and other organizations will reimburse patients or providers for the costs of our future pharmaceutical products and related treatments. In the United States, government and other third-party payers have sought to contain healthcare costs by limiting both coverage

and the level of reimbursement for new pharmaceutical products approved for marketing by the FDA. In some cases, these payers may refuse to provide any coverage for uses of approved products to treat medical conditions even though the FDA has granted marketing approval. Healthcare reform may increase these cost containment efforts. We believe that managed care organizations and government health insurance programs may seek to restrict the use of new products, delay authorization to use new products or limit coverage and the level of reimbursement for new products. For example, the Medicare Prescription Drug Improvement and Modernization Act of 2003 together with rule making by the Center for Medicare and Medicaid Services could affect drug coverage and payments by Medicare. Internationally, where national healthcare systems are prevalent, little if any funding may be available for new products, and cost containment and cost reduction efforts can be more pronounced than in the United States.

IF WE ARE UNABLE TO ENTER INTO AGREEMENTS WITH THIRD PARTIES TO PROVIDE SALES, MARKETING AND DISTRIBUTION CAPABILITIES, OR TO CREATE THESE FUNCTIONS OURSELVES, WE WILL NOT BE ABLE TO COMMERCIALIZE GCS-100 OR ANY OTHER PRODUCT CANDIDATES.

We do not have any sales, marketing or distribution capabilities. In order to commercialize GCS-100 or other product candidates, if any are approved, we must either make arrangements with third parties to provide sales, marketing and distribution capabilities or acquire or internally develop these functions ourselves. If we obtain FDA approval for GCS-100 or any other product candidate, we intend to rely on relationships with one or more pharmaceutical or biotechnology companies or other third parties with established distribution systems and direct sales forces to market GCS-100 or any other product candidate. If we decide to market any of our product candidates directly, we must either acquire or internally develop a marketing and sales force with technical expertise and with supporting distribution capabilities. The acquisition or development of a sales and distribution infrastructure would require substantial resources, which may divert the attention of our management and key personnel, and negatively impact our product development efforts. Moreover, we may not be able to establish in-house sales and distribution capabilities or relationships with third parties. To the extent we enter into co-promotion or other licensing agreements, our product revenues are likely to be lower than if we directly marketed and sold our product candidates, and any revenue we receive will depend upon the efforts of third parties, which may not be successful.

OUR GROWTH MAY BE LIMITED IF WE ARE UNABLE TO RETAIN AND HIRE ADDITIONAL QUALIFIED PERSONNEL AS NECESSARY.

Our success will depend on our ability to retain key employees and our continuing ability to attract and retain highly qualified scientific, technical and managerial personnel. Under our current clinical trial and business plan, we may add over 12 employees during the course of the next two years, primarily technical or scientific personnel, as needs develop. Competition for such personnel is intense and we may not be able to retain existing personnel or attract qualified employees in the future. Our current financial position, limited drug pipeline and small size make it more difficult to compete for such personnel against larger, more diversified companies. At present, we employ 16 full-time employees and one part-time worker. We depend upon the personal efforts and abilities of our officers and directors, including Bradley J Carver, our President, CEO and Interim Chairman of the Board and John W. Burns, our Senior Vice President, Chief Financial Officer and a director and would be materially adversely affected if their services ceased to be available for any reason and comparable replacement personnel were not employed.

THE BIOTECHNOLOGY BUSINESS HAS A RISK OF PRODUCT LIABILITY, AND IN THE EVENT OF A SUIT AGAINST US, OUR BUSINESS COULD BE SEVERELY HARMED.

The testing, marketing and sale of biotechnology products entails a risk of product liability claims by patients and others. While we currently maintain product liability insurance, such insurance may not be available at reasonable cost and in the event of a significant adverse event with a patient such insurance would likely be insufficient to cover the full amount of the liability incurred. In the event of a successful suit against us, payments and damage to our reputation could have a material adverse effect on our business and financial condition. Even if such a suit is unsuccessful, our reputation could be damaged and litigation costs and expenditures of management time on such matters could adversely affect our business and financial condition.

WE ARE CONTRACTUALLY OBLIGATED TO ISSUE SHARES IN THE FUTURE, INCLUDING SHARES TO BE ISSUED UPON THE CONVERSION OF OUTSTANDING PREFERRED STOCK AND WARRANTS HELD BY EIS, WHICH WILL CAUSE SUBSTANTIAL DILUTION OF YOUR INTEREST IN US.

As of November 16, 2004, there were outstanding options to purchase 1,849,500 shares of common stock, at a weighted average exercise price of $1.96 per share and warrants to purchase 21,571,326 shares of common stock at a weighted average exercise price of $1.67 per share. Moreover, we may in the future issue additional shares to raise capital, acquire other companies or technologies, to pay for services, or for other corporate purposes. Any such issuances will have the effect of further diluting the interest of shareholders.

EIS owns 6,153.51 shares of our Series A preferred stock and 3,471.15 shares of our Series B preferred stock. Each share of our Series A preferred stock and Series B preferred stock is convertible into 1,000 shares of our common stock, subject to anti-dilution adjustments, except 1,209.07 shares of Series A preferred stock which are convertible after December 18, 2004. The Series B preferred stock bears a 7% dividend payable in Series B preferred stock, which compounds annually. Any accrued but unissued Series B preferred stock dividends would be converted into common stock upon conversion of the Series B preferred stock. Accordingly, EIS could acquire upon exercise of warrants held by it and the conversion into common stock of all shares of Series A and Series B preferred stock held by it, including accrued dividends as of September 30, 2004 on the Series B preferred stock but no future dividends, a total of 10,189,764 shares of common stock. This amount of shares represents 16.8% of our common stock outstanding as of November 16, 2004. Pursuant to provisions in our agreement with EIS, if the exercise or conversion of any of our securities held by EIS would result in EIS owning more than 9.9% of our common stock at any time, EIS may opt to receive non-voting securities instead of common stock.

WE MUST COMPLY WITH THE LISTING REQUIREMENTS OF THE NASDAQ SMALLCAP MARKET OR OUR COMMON STOCK MAY DECLINE AND THE LIQUIDITY OF AN INVESTMENT IN OUR SECURITIES WOULD DECREASE.

Our common stock could be delisted from The Nasdaq SmallCap Market for the following reasons, among others:

There are other quantitative and qualitative criteria of the Nasdaq SmallCap Market which if violated could lead to delisting of our common stock.

We may not be able to maintain our compliance with Nasdaq continued listing requirements in the future. We received a letter from Nasdaq on August 8, 2003 that the bid price of our common stock had been below $1.00 for 30 consecutive business days and that we had a 180-day grace period, until February 4, 2004, to achieve a bid price of at least $1.00 for a period of at least 10 consecutive business days or face delisting. In September 2003, we received a letter from Nasdaq that we complied with the minimum bid price requirement. We have on several previous occasions received notice from Nasdaq that we failed to meet certain of its listing requirements. We have been successful in regaining compliance on those occasions. On May 17, 2004, we received a letter from Nasdaq that the bid price of our common stock had been below $1.00 for 30 consecutive business days and that we had a 180-day grace period, until November 15, 2004 to achieve a bid price of at least $1.00 for a period of at least 10 consecutive business days or face delisting. We did not achieve a bid price of at least $1.00 during the 180-day grace period and received a Nasdaq Staff Determination on November 16, 2004 that our securities are subject to delisting. We will request a hearing before a Nasdaq Listing Qualifications Panel to appeal the Nasdaq Staff Determination. The appeal will stay the delisting of the Company’s common stock pending the decision of a Nasdaq Listing Qualifications Panel, which is expected to hear the appeal within 45 days of our request. We cannot state whether the Listing Qualifications Panel will grant our request for continued listing. Our stockholders’ equity was approximately $3.5 million as of September 30, 2004. Our market capitalization was $27.2 million on September 30, 2004 and was $26.0 million on November 16, 2004.

If Nasdaq delisted our common stock, we would likely seek to list our common stock for quotation on a regional stock exchange. However, if we were unable to obtain listing or quotation on such market or exchange, trading of our common stock would occur in the over-the-counter market on an electronic bulletin board for unlisted securities or in what are commonly known as the “pink sheet.” In addition, delisting from Nasdaq and failure to obtain listing or quotation on such market or exchange would subject our common stock to so-called “penny stock” rules. These rules impose additional sales practice and market making requirements on broker-dealers who sell and/or make a market in such securities, such as disclosing offer and bid prices and compensation received from a trade to a purchaser and sending monthly account statements to purchasers. Consequently, broker-dealers may be less willing or able to sell and/or make a market in our common stock. These rules also require that purchasers be accredited investors, which would reduce the number of investors who could purchase our shares. Additionally, an investor would find it more difficult to dispose of, or to obtain accurate quotations for the price of, our common stock. As a result of delisting, it may become more difficult for us to raise funds through the sale of our securities.

BECAUSE THE CURRENT AND POTENTIAL MEMBERS OF OUR BOARD OF DIRECTORS COULD CONTROL A SIGNIFICANT PERCENTAGE OF OUR COMMON STOCK, THEY COULD EXERCISE SUBSTANTIAL CONTROL OVER US.

The holders of the common stock do not have cumulative voting rights. Our directors, two of whom are executive officers of GlycoGenesys, own approximately 4.4% collectively of our common stock outstanding as of November 16, 2004. One of the conditions of the transactions between us, Elan and EIS required that we expand our board of directors at our 2002 annual stockholder’s meeting at which time EIS could appoint one director. EIS decided not to appoint a director at our 2002 annual stockholders’ meeting but may choose to do so in the future as long as they own at least 10%

of our common stock (assuming exercise or conversion of convertible or exercisable securities held by EIS). If EIS appoints a director, members of the board of directors and their affiliates would own approximately 6.3% of our common stock outstanding as of November 16, 2004, assuming EIS has not converted or exercised any of our securities held by it, and the same number of shares are outstanding at such time as are currently outstanding. If EIS and our directors were to have converted or exercised all of our securities held by them, the members of our board of directors and their affiliates would own approximately 21.6% of the common stock outstanding as of November 16, 2004, assuming the number of shares outstanding at such time equals the number of shares currently outstanding plus the number of shares issued on exercise or conversion of securities held by EIS and our directors. This concentration of ownership would allow these stockholders to substantially influence all matters requiring stockholder approval and could have the effect of delaying or preventing a change in control or otherwise discouraging a potential acquirer from attempting to obtain control of us, which in turn could materially adversely affect our stock price.

OUR STOCK PRICE COULD DECLINE IF A SIGNIFICANT NUMBER OF SHARES BECOME AVAILABLE FOR SALE.

As of November 16, 2004, approximately 15,685,148 shares of common stock presently issued and outstanding are “Restricted Securities” as that term is defined in Rule 144 promulgated under the Act. In general, a person (or persons whose shares are aggregated) who has satisfied a one year holding period may sell, within any three month period, an amount of restricted securities which does not exceed the greater of 1% of the then outstanding shares of common stock or the average weekly trading volume during the four calendar weeks prior to such sale. Restricted securities can be sold, under certain circumstances, without any quantity limitation, by persons who are not affiliates of GlycoGenesys and who have beneficially owned the shares for a minimum period of two years. The sale of these restricted shares as well as the shares registered under our nine effective registration statements, shall increase the number of free-trading shares and may have a depressive effect on the price of our securities. Moreover, such sales, if substantial, might also adversely affect our ability to raise additional equity capital.

THE PRICE OF OUR COMMON STOCK HAS BEEN VOLATILE, WHICH COULD RESULT IN SUBSTANTIAL LOSSES BY YOU.

The market price of our common stock, which is traded on the National Association of Securities Dealers Automated Quotation system (Nasdaq—Small Cap) has been, and may continue to be, highly volatile. During the twelve months ending October 31, 2004, our common stock has traded at prices ranging from $0.37 to $2.10 per share. Factors such as announcements of clinical trial results, financings, legal proceedings, technological innovations or new products, either by us or by our competitors or third parties, as well as market conditions within the biotechnology and pharmaceutical industries, may have a significant impact on the market price of our common stock.

In addition, the stock market has from time to time, and especially in the last few years, experienced extreme price and volume fluctuations, particularly in the biotechnology sector, which have often been unrelated to the operating performance of particular companies. Current market conditions are particularly unstable and there is a large degree of uncertainty at this time. In general, biotechnology stocks tend to be volatile even during periods of relative market stability because of the high rates of failure and substantial funding requirements associated with biotechnology companies. Market conditions and conditions of the biotechnology sector could negatively impact the price of our common stock.

Our Chief Executive Officer and Chief Financial Officer have concluded, based on their evaluation as of the end of the period covered by this Form 10-Q that the Company’s “disclosure controls and procedures” (as defined in the Securities Exchange Act of 1934 Rules 13a-15(e) and 15d-15(e)) are effective to ensure that information required to be disclosed in the report that the Company files or submits under the Securities Exchange Act is recorded, processed, summarized and reported within the time periods specified in the Securities and Exchange Commission’s rules and forms.

The Company and certain of its directors are engaged in a lawsuit with David Platt, its former CEO and Chairman, which is described in the Company’s Annual Report on Form 10-K for the year ending December 31, 2003 and Quarterly Reports on Form 10-Q for the quarters ended March 31, and June 30, 2004.

The Company was engaged in an arbitration with David Platt regarding a license agreement between the Company and Platt which the Company initiated in January 2004 and which is described in the Company’s Annual Report on Form 10-K for the year ending December 31, 2003 and Quarterly Reports on Form 10-Q for the quarters ended March 31 and June 30, 2004. On November 11, 2004, the arbitrator issued a decision which found that Platt had breached the License Agreement by filing a patent application which was a continuation-in-part of the ‘487 Application without having informed the Company and affirmed the Company’s position that Platt’s subsequent patent application is also covered by the License Agreement. The arbitrator rejected Platt’s contention that the Company had breached the License Agreement and refused to terminate the License Agreement, as Platt had requested. Instead, the arbitrator found that the Company retained its exclusive rights to the technology in question. The arbitrator allowed Platt to continue prosecuting the patent applications, including the ‘487 Application, in which he is listed as inventor, finding that Platt had not relinquished an investor’s right to control prosecution of his applications under the License Agreement. Prosecution of the applications is for the benefit of the Company, which retains exclusive rights to develop and commercialize them.

(a) Set forth below is information regarding the sale of unregistered shares of equity securities sold by the Company during the three months ended September 30, 2004.

These securities were issued in reliance upon the exemption from registration pursuant to Section 4(2) under the Securities Act of 1933, as amended.

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.

/s/ Bradley J Carver

Bradley J Carver, Chief Executive Officer President and Treasurer

/s/ John W. Burns

John W. Burns, Senior Vice President,

Chief Financial Officer and Secretary

/s/ Patrick J. Joyce

Patrick J. Joyce, Principal Accounting

Officer


			Page
Part I— Financial Information
	Item 1. Financial Statements (Unaudited)
		Consolidated Balance Sheets as of September 30, 2004 and December 31, 2003	3-4
		Consolidated Statements of Operations for the Three and Nine Months Ended September 30, 2004 and 2003	5
		Consolidated Statements of Cash Flows for the Nine Months Ended September 30, 2004 and 2003	6
		Notes to Unaudited Consolidated Financial Statements	7-11
	Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations		12-15
	Item 3. Quantitative and Qualitative Disclosures About Market Risk		15-23
	Item 4. Controls and Procedures		23
Part II— Other Information
	Item 1. Legal Proceedings		23-24
	Item 2. Unregistered Sales of Equity Securities and Use of Proceeds		24
	Item 6. Exhibits		24
Signatures			25


	September 30, 2004			December 31, 2003
Current assets:
Cash and cash equivalents	$	4,586,265		$	3,193,575
Prepaid expenses and other current assets		229,779			301,657

Total current assets		4,816,044			3,495,232

Property and equipment, at cost:
Computer, office and laboratory equipment		857,664			683,975
Furniture and fixtures		294,291			294,291
Motor vehicles		—			25,026

		1,151,955			1,003,292
Less accumulated depreciation		(757,704	)		(693,569	)

Property and equipment, net		394,251			309,723

Other assets:
Restricted cash		148,128			148,128
Other		11,670			11,670

Total other assets		159,798			159,798

Total assets	$	5,370,093		$	3,964,753


	September 30, 2004			December 31, 2003
Current liabilities:
Accounts payable	$	1,462,111		$	813,032
Accrued liabilities		427,797			493,717
Net liabilities of discontinued operations		—			57,698

Total current liabilities		1,889,908			1,364,447

Commitments and contingencies
Stockholders’ equity:
Preferred stock, $0.01 par value (liquidation value $21,814,660 and $21,472,096 as of September 30, 2004 and December 31, 2003, respectively)		96			108
Common stock, $0.01 par value; Authorized – 200,000,000 shares; Issued and outstanding – 60,504,577 and 46,032,096 shares at September 30, 2004 and December 31, 2003, respectively		605,046			460,321
Additional paid-in capital		95,254,604			89,254,349
Note receivable from former officer		—			(2,675,000	)
Deferred compensation		(9,041	)		(14,513	)

Accumulated deficit		(92,370,520	)		(84,424,959	)

Total stockholders’ equity		3,480,185			2,600,306

Total liabilities and stockholders’ equity	$	5,370,093		$	3,964,753


	Three Months Ended September 30,						Nine Months Ended September 30,
	2004			2003			2004			2003
Operating expenses:
Research and development	$	1,360,047		$	964,610		$	3,956,740		$	2,461,894
General and administrative		1,337,566			869,983			4,073,008			2,750,902

Total operating expenses		2,697,613			1,834,593			8,029,748			5,212,796

Operating loss		(2,697,613	)		(1,834,593	)		(8,029,748	)		(5,212,796	)

Other income:
Interest income		12,967			4,038			26,677			20,211
Other income		91			598			57,510			3,341

Total other income		13,058			4,636			84,187			23,552

Net loss		(2,684,555	)		(1,829,957	)		(7,945,561	)		(5,189,244	)
Accretion of preferred stock dividends		(115,021	)		(104,562	)		(342,564	)		(310,277	)

Net loss applicable to common stock	$	(2,799,576	)	$	(1,934,519	)	$	(8,288,125	)	$	(5,499,521	)

Basic and diluted net loss per common stock	$	(0.05	)	$	(0.05	)	$	(0.15	)	$	(0.14	)

Weighted average number of common shares outstanding		60,504,577			42,861,720			53,604,195			39,210,161


	Nine Months Ended September 30,
	2004			2003
Cash flows from operating activities:
Net loss	$	(7,945,561	)	$	(5,189,244	)
Adjustments to reconcile net loss to net cash used in operating and discontinued activities:
Amortization of value of options issued for compensation		17,753			—
Depreciation and amortization		89,161			111,356
Changes in assets and liabilities:
Prepaid expenses and other current assets		71,878			(31,474	)
Accounts payable		649,079			(165,609	)
Accrued liabilities		(65,920	)		(6,131	)
Net liabilities of discontinued operations		(57,698	)		(66,686	)

Net cash used in operating and discontinued activities		(7,241,308	)		(5,347,788	)

Cash flows from investing activities:
Purchase of property and equipment		(173,689	)		(149,802	)
Other		—			175

Net cash used in investing activities		(173,689	)		(149,627	)

Cash flows from financing activities:
Proceeds from sale of common stock, net of issuance costs		8,801,345			3,777,740
Proceeds from exercise of warrants and stock options		6,342			157,251

Net cash provided by financing activities		8,807,687			3,934,991

Net increase (decrease) in cash and cash equivalents		1,392,690			(1,562,424	)
Cash and cash equivalents, beginning balance		3,193,575			6,299,006

Cash and cash equivalents, ending balance	$	4,586,265		$	4,736,582

Supplemental disclosure of non-cash financing activities:
Conversion Series C preferred stock to common stock	$	1,463,000			—

Dividends accreted on Series B preferred stock	$	342,564		$	310,277

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	Three Months Ended September 30,						Nine Months Ended September 30,
	2004			2003			2004			2003
Net loss applicable to common stock, as reported	$	(2,799,576	)	$	(1,934,519	)	$	(8,288,125	)	$	(5,499,521	)

Add: stock-based compensation expense reported in net loss applicable to common stock		6,683			—			17,753			—
Less: stock-based employee compensation expense determined under fair value based method for all awards		(115,740	)		(92,755	)		(431,401	)		(374,743	)

Pro forma net loss applicable to common stock	$	(2,908,633	)	$	(2,027,274	)	$	(8,701,773	)	$	(5,874,264	)

Basic and diluted net loss per common stock, as reported	$	(0.05	)	$	(0.05	)	$	(0.15	)	$	(0.14	)

Pro forma basic and diluted net loss per common stock	$	(0.05	)	$	(0.05	)	$	(0.16	)	$	(0.15	)


10.1		Lease dated April 22, 1999 by and between OMV Associates Limited Partnership and GlycoGenesys, Inc., as amended by (i) the First Amendment to Lease dated February 29, 2000, (ii) the Second Amendment to Lease dated June 1, 2000, and (iii) the Third Amendment to Lease dated August 19, 2004.

31.1		Certification of Chief Executive Officer Pursuant to Section 302 of the Sarbanes Oxley Act of 2003.

31.2		Certification of Chief Financial Officer Pursuant to Section 302 of the Sarbanes Oxley Act of 2003.

32.1		Certification of Chief Executive Officer and Chief Financial Officer Pursuant to Section 906 of the Sarbanes Oxley Act of 2003.