UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 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 September 30, 2007

o		TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Transition Period from                      to                     

Lexicon Pharmaceuticals, Inc.

Delaware		76-0474169
(State or Other Jurisdiction of Incorporation or Organization)		(I.R.S. Employer Identification Number)

     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, or a non-accelerated filer. See definition of “accelerated filer and large accelerated filer” in Rule 12b-2 of the Exchange Act. (Check one)

Large accelerated filer o                     Accelerated filer  þ             Non-accelerated filer o          

     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 October 31, 2007, 136,791,735 shares of the registrant’s common stock, par value $0.001 per share, were outstanding.

 

 

Lexicon Pharmaceuticals, Inc.

Table of Contents

		Page
Factors Affecting Forward-Looking Statements			2
Part I – Financial Information
Item 1. Financial Statements
Consolidated Balance Sheets – September 30, 2007 (unaudited) and December 31, 2006			3
Consolidated Statements of Operations (unaudited) – Three and Nine Months Ended September 30, 2007 and 2006			4
Consolidated Statements of Cash Flows (unaudited) – Nine Months Ended September 30, 2007 and 2006			5
Notes to Consolidated Financial Statements (unaudited)			6
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations			12
Item 3. Quantitative and Qualitative Disclosures about Market Risk			23
Item 4. Controls and Procedures			23
Part II – Other Information
Item 1A. Risk Factors			24
Item 4. Submission of Matters to a Vote of Security Holders			26
Item 6. Exhibits			26
Signatures			27
Certification of CEO Pursuant to Section 302
Certification of CFO Pursuant to Section 302
Certification of CEO & CFO Pursuant to Section 906

     LexVision^® and OmniBank^® are registered trademarks and the Lexicon name and logo and Genome5000^™ are trademarks of Lexicon Pharmaceuticals, Inc.

Factors Affecting Forward-Looking Statements

     This quarterly report on Form 10-Q contains forward-looking statements. These statements relate to future events or our future financial performance. We have attempted to identify forward-looking statements by terminology including “anticipate,” “believe,” “can,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “plan,” “potential,” “predict,” “should” or “will” or the negative of these terms or other comparable terminology. These statements are only predictions and involve known and unknown risks, uncertainties and other factors, including the risks outlined under “Part II, Item 1A. – Risk Factors,” that may cause our or our industry’s actual results, levels of activity, performance or achievements to be materially different from any future results, levels or activity, performance or achievements expressed or implied by these forward-looking statements.

     Although we believe that the expectations reflected in the forward-looking statements are reasonable, we cannot guarantee future results, levels of activity, performance or achievements. We are not under any duty to update any of the forward-looking statements after the date of this quarterly report on Form 10-Q to conform these statements to actual results, unless required by law.

Part I – Financial Information

Item 1. Financial Statements

Lexicon Pharmaceuticals, Inc.

Consolidated Balance Sheets
(In thousands, except par value)

		As of September 30,				As of December 31,
		2007				2006
		(unaudited)
Assets
Current assets:
Cash and cash equivalents		$	50,721			$	30,226
Short-term investments, including restricted investments of $430			183,624				49,773
Short-term investments held by Symphony Icon, Inc.			39,570				—
Accounts receivable, net of allowance for doubtful accounts of $35			1,747				1,186
Prepaid expenses and other current assets			3,740				4,367
Total current assets			279,402				85,552
Property and equipment, net of accumulated depreciation and amortization of $63,043 and $56,905, respectively			72,350				78,192
Goodwill			25,798				25,798
Other assets			642				724
Total assets		$	378,192			$	190,266
Liabilities, Noncontrolling Interest and Stockholders’ Equity
Current liabilities:
Accounts payable		$	4,913			$	6,513
Accrued liabilities			8,593				7,325
Current portion of deferred revenue			22,978				31,312
Current portion of long-term debt			861				816
Total current liabilities			37,345				45,966
Deferred revenue, net of current portion			18,001				26,688
Long-term debt			30,723				31,372
Other long-term liabilities			754				739
Total liabilities			86,823				104,765
Noncontrolling interest in Symphony Icon, Inc.			25,980				—
Commitments and contingencies
Stockholders’ equity:
Preferred stock, $.01 par value; 5,000 shares authorized; no shares issued and outstanding			—				—
Common stock, $.001 par value; 300,000 shares authorized; 136,792 and 77,804 shares issued and outstanding			137				78
Additional paid-in capital			663,772				437,180
Accumulated deficit			(398,358	)			(351,741	)
Accumulated other comprehensive loss			(162	)			(16	)
Total stockholders’ equity			265,389				85,501
Total liabilities and stockholders’ equity		$	378,192			$	190,266

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

Lexicon Pharmaceuticals, Inc.

Consolidated Statements of Operations
(In thousands, except per share amounts)
(Unaudited)

		Three Months Ended								Nine Months Ended
		September 30,								September 30,
		2007				2006				2007				2006
Revenues:
Collaborative research		$	9,712			$	18,770			$	34,460			$	53,427
Subscription and license fees			455				843				1,850				3,305
Total revenues			10,167				19,613				36,310				56,732
Operating expenses:
Research and development, including stock-based compensation of $965, $1,101, $3,000 and $3,355, respectively			24,518				27,010				77,402				81,115
General and administrative, including stock-based compensation of $635, $660, $1,830 and $2,011, respectively			5,091				5,309				15,395				16,276
Total operating expenses			29,609				32,319				92,797				97,391
Loss from operations			(19,442	)			(12,706	)			(56,487	)			(40,659	)
Interest income			2,166				774				3,811				2,677
Interest expense			(694	)			(817	)			(2,077	)			(2,437	)
Other expense, net			(8	)			(6	)			(34	)			(69	)
Loss before noncontrolling interest in Symphony Icon, Inc.			(17,978	)			(12,755	)			(54,787	)			(40,488	)
Loss attributable to noncontrolling interest in Symphony Icon, Inc.			3,867				—				8,170				—
Net loss		$	(14,111	)		$	(12,755	)		$	(46,617	)		$	(40,488	)
Net loss per common share, basic and diluted		$	(0.14	)		$	(0.20	)		$	(0.53	)		$	(0.63	)
Shares used in computing net loss per common share, basic and diluted			104,196				64,832				87,331				64,676

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

Lexicon Pharmaceuticals, Inc.

Consolidated Statements of Cash Flows
(In thousands)
(Unaudited)

		Nine Months Ended September 30,
		2007				2006
Cash flows from operating activities:
Net loss		$	(46,617	)		$	(40,488	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation			7,138				7,986
Amortization of intangible assets, other than goodwill			—				640
Loss attributable to noncontrolling interest			(8,170	)			—
Stock-based compensation			4,830				5,368
Loss on disposal of property and equipment			—				35
Changes in operating assets and liabilities:
(Increase) decrease in accounts receivable			(561	)			544
Decrease in prepaid expenses and other current assets			627				394
Decrease in other assets			82				202
Increase (decrease) in accounts payable and other liabilities			(317	)			139
Decrease in deferred revenue			(17,021	)			(21,797	)
Net cash used in operating activities			(60,009	)			(46,977	)
Cash flows from investing activities:
Purchases of property and equipment			(1,297	)			(3,163	)
Proceeds from disposal of property and equipment			1				56
Purchases of investments held by Symphony Icon, Inc.			(44,991	)			—
Maturities of investments held by Symphony Icon, Inc.			5,421				—
Purchases of investments			(192,982	)			(42,716	)
Maturities of investments			58,985				79,584
Net cash provided by (used in) investing activities			(174,863	)			33,761
Cash flows from financing activities:
Proceeds from issuance of common stock to Invus, L. P., net of fees			198,135				—
Proceeds from issuance of common stock to Symphony Holdings, LLC, net of fees			14,238				—
Proceeds from exercise of stock options			884				3,920
Repayment of debt borrowings			(604	)			(556	)
Proceeds from purchase of noncontrolling interest by preferred shareholders of Symphony Icon, Inc., net of fees			42,714				—
Net cash provided by financing activities			255,367				3,364
Net increase (decrease) in cash and cash equivalents			20,495				(9,852	)
Cash and cash equivalents at beginning of period			30,226				21,970
Cash and cash equivalents at end of period		$	50,721			$	12,118
Supplemental disclosure of cash flow information:
Cash paid for interest		$	2,004			$	2,053
Supplemental disclosure of non-cash investing and financing activities:
Common stock issued for purchase option in conjunction with Symphony Icon, Inc. financing		$	8,564			$	—
Unrealized gain (loss) on investments		$	(146	)		$	48
Retirement of property and equipment		$	1,001			$	1,664

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

Lexicon Pharmaceuticals, Inc.

Notes to Consolidated Financial Statements
(Unaudited)

1. Basis of Presentation

     The accompanying unaudited consolidated financial statements of Lexicon Pharmaceuticals, Inc. (“Lexicon” or the “Company”) have been prepared in accordance with generally accepted accounting principles for interim financial information and pursuant to the rules and regulations of the Securities and Exchange Commission (“SEC”). Accordingly, they do not include all of the information and footnotes required by generally accepted accounting principles for complete financial statements.

     In the opinion of management, all adjustments (consisting of normal recurring adjustments) considered necessary for a fair presentation have been included. Operating results for the nine-month period ended September 30, 2007 are not necessarily indicative of the results that may be expected for the year ended December 31, 2007.

     The accompanying consolidated financial statements include the accounts of Lexicon and its wholly-owned subsidiaries, as well as one variable interest entity, Symphony Icon, Inc. (“Symphony Icon”), for which the Company is the primary beneficiary as defined by Financial Accounting Standards Board (“FASB”) Interpretation No. 46 (revised 2003), “Consolidation of Variable Interest Entities” (“FIN 46R”). Intercompany transactions and balances are eliminated in consolidation.

     For further information, refer to the financial statements and footnotes thereto included in Lexicon’s annual report on Form 10-K for the year ended December 31, 2006, as filed with the SEC.

2. Net Loss Per Share

     Net loss per share is computed using the weighted average number of shares of common stock outstanding during the applicable period. Shares associated with stock options and warrants are not included because they are antidilutive. There are no differences between basic and diluted net loss per share for all periods presented.

3. Stock-Based Compensation

     On January 1, 2006, Lexicon adopted Statement of Financial Accounting Standards No. 123 (Revised), “Share-Based Payment” (“SFAS No. 123(R)”). This statement requires companies to recognize compensation expense in the statements of operations for share-based payments, including stock options issued to employees, based on their fair values on the date of the grant, with the compensation expense recognized over the period in which an employee is required to provide service in exchange for the stock award. The Company adopted this statement using the modified prospective transition method, which applies the compensation expense recognition provisions to new awards and to any awards modified, repurchased or canceled after the January 1, 2006 adoption date. Additionally, for any unvested awards outstanding at the adoption date, compensation expense is recognized over the remaining vesting period. Stock-based compensation expense is recognized on a straight-line basis. The Company had stock-based compensation expense under SFAS No. 123(R) of $1.6 million and $1.8 million for the three months ended September 30, 2007 and 2006, respectively, and $4.8 million and $5.4 million for the nine months ended September 30, 2007 and 2006, respectively. Stock-based compensation expense under SFAS No. 123(R) has no impact on cash flows from operating activities or financing activities. As of September 30, 2007, stock-based compensation cost for all outstanding

unvested options was $11.4 million, which is expected to be recognized over a weighted-average period of 1.3 years.

Valuation Assumptions

     The fair value of stock options is estimated at the date of grant using the Black-Scholes method. The Black-Scholes option-pricing model requires the input of subjective assumptions. Because the Company’s 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 do not necessarily provide a reliable single measure of the fair value of its employee stock options. For purposes of determining the fair value of stock options granted subsequent to the adoption of SFAS No. 123(R), the Company segregated its options into two homogeneous groups, based on exercise and post-vesting employment termination behaviors, resulting in a change in the assumptions used for expected option lives and forfeitures. Expected volatility is based on the historical volatility in the Company’s stock price. The following weighted-average assumptions were used for options granted in the nine-month periods ended September 30, 2007 and 2006, respectively:

						Risk-free
		Expected				Interest				Expected				Estimated				Dividend
		Volatility				Rate				Term				Forfeitures				Rate
September 30, 2007:
Employees			67	%			4.5	%			6				21	%			0	%
Officers and non-employee directors			67	%			4.6	%			9				4	%			0	%
September 30, 2006:
Employees			69	%			4.6	%			7				18	%			0	%
Officers and non-employee directors			69	%			4.7	%			9				3	%			0	%

Stock Option Activity

     The following is a summary of option activity under Lexicon’s stock option plans for the first nine months of 2007:

										Weighted
						Weighted				Average
						Average				Remaining
						Exercise				Contractual				Aggregate
		Options				Price				Term				Intrinsic Value
		(in thousands)												(in thousands)
Outstanding at December 31, 2006			15,815			$	5.99
Granted			2,792				3.86
Exercised			(513	)			1.80
Canceled			(1,597	)			6.93
Outstanding at September 30, 2007			16,497				5.67				5.4			$	4,052
Exercisable at September 30, 2007			11,859			$	6.23				4.0			$	4,012

     The weighted-average grant date fair value of options granted during the nine-month periods ended September 30, 2007 and 2006 was $2.74 and $2.99, respectively. The total intrinsic value of options exercised during the nine-month periods ended September 30, 2007 and 2006 was $978,000 and $310,000, respectively. As of September 30, 2007, 990,092 shares of common stock were available for grant under Lexicon’s stock option plans.

Stock Options Outstanding

     The following table summarizes information about stock options outstanding at September 30, 2007:

Options Outstanding																	Options Exercisable
									Weighted Average
					Outstanding as of				Remaining				Weighted								Weighted
Range of					September 30,				Contractual				Average				Exercisable as of				Average
Exercise Price					2007				Life (In Years)				Exercise Price				September 30, 2007				Exercise Price
					(In thousands)												(In thousands)
$	1.67	–	2.50			4,141				1.7			$	2.49				4,141			$	2.49
	3.15	–	4.72			6,029				8.1				3.94				2,102				3.99
	4.76	–	7.12			2,167				6.7				5.75				1,577				5.76
	7.15	–	10.55			2,503				5.0				8.55				2,382				8.60
	10.87	–	14.44			1,207				3.5				12.63				1,207				12.63
	16.63	–	22.06			356				2.5				19.70				356				19.70
	25.25	–	31.63			25				3.1				26.03				25				26.03
	38.00	–	38.50			69				3.0				38.49				69				38.49
						16,497				5.4			$	5.67				11,859			$	6.23

4. Recent Accounting Pronouncements

     On January 1, 2007, Lexicon adopted FASB Interpretation No. 48, “Accounting for Uncertainty in Income Taxes, an interpretation of FASB Statement No. 109” (“FIN 48”). FIN 48 clarifies the accounting for income taxes by prescribing the minimum recognition threshold a tax position is required to meet before being recognized in the financial statements. FIN 48 also provides guidance on derecognition, classification, interest and penalties, accounting in interim periods, disclosure and transition. There was no effect on the Company’s consolidated financial position, results of operations or cash flows as a result of adopting FIN 48. As of January 1, 2007 and September 30, 2007, the Company did not have any unrecognized tax benefits.

     The Company is primarily subject to U.S. federal and New Jersey and Texas state income taxes. The tax years 1995 to current remain open to examination by U.S. federal authorities and 2004 to current remain open to examination by state authorities. The Company’s policy is to recognize interest and penalties related to income tax matters in income tax expense. As of January 1, 2007 and September 30, 2007, the Company had no accruals for interest or penalties related to income tax matters.

     At December 31, 2006, the Company had net operating loss (“NOL”) carryforwards of approximately $267.4 million and research and development (“R&D”) credit carryforwards of approximately $14.4 million expiring beginning in 2011. Utilization of the NOL and R&D credit carryforwards may be subject to a significant annual limitation due to ownership changes that have occurred previously or could occur in the future provided by Section 382 of the Internal Revenue Code. The Company has conducted a limited analysis to determine whether a change in control has occurred since the Company’s formation and does not believe a significant limitation, if any, would be determined upon a detailed analysis. Further, until a Section 382 study is completed and any limitation known, no amounts are being presented as an uncertain tax position under FIN 48. The Company has established a full valuation allowance for its NOL and R&D credit carryforwards.

     In September 2006, the FASB issued Statement of Financial Accounting Standards No. 157, “Fair Value Measurements” (“SFAS No. 157”). The statement defines fair value, establishes a framework for measuring fair value in generally accepted accounting principles, and expands disclosures about fair value measurements. This statement applies under other accounting pronouncements that require or permit fair value measurements, the FASB having previously concluded in those accounting pronouncements that

fair value is the relevant measurement attribute. Accordingly, this statement does not require any new fair value measurements. SFAS No. 157 is effective January 1, 2008. The Company is currently evaluating the effect, if any, of this statement on its financial condition and results of operations.

5. Debt Obligations

     In April 2004, Lexicon obtained a $34.0 million mortgage on its facilities in The Woodlands, Texas. The mortgage loan has a ten-year term with a 20-year amortization and bears interest at a fixed rate of 8.23%.

6. Commitments and Contingencies

     In May 2002, Lexicon’s subsidiary Lexicon Pharmaceuticals (New Jersey), Inc. leased a 76,000 square-foot laboratory and office space in Hopewell, New Jersey under an agreement which expires in June 2013. The lease provides for an escalating yearly rent payment of $1.3 million in the first year, $2.1 million in years two and three, $2.2 million in years four to six, $2.3 million in years seven to nine and $2.4 million in years ten and eleven. Lexicon is the guarantor of the obligations of its subsidiary under the lease. The Company is required to maintain restricted investments to collateralize the Hopewell lease. As of September 30, 2007, the Company had $430,000 in restricted investments to collateralize a standby letter of credit for this lease.

7. Arrangements with Symphony Icon, Inc.

     On June 15, 2007, Lexicon entered into a series of related agreements providing for the financing of the clinical development of LX6171, LX1031 and LX1032, along with any other pharmaceutical compositions modulating the same targets as those drug candidates (the “Programs”). The agreements include a Novated and Restated Technology License Agreement pursuant to which the Company licensed to Symphony Icon, a wholly-owned subsidiary of Symphony Icon Holdings LLC (“Holdings”), the Company’s intellectual property rights related to the Programs. Holdings contributed $45 million to Symphony Icon in order to fund the clinical development of the Programs.

     Under a Share Purchase Agreement, dated June 15, 2007, between the Company and Holdings, the Company issued and sold to Holdings 7,650,622 shares of its common stock on June 15, 2007 in exchange for $15 million and the Purchase Option (as defined below).

     Under a Purchase Option Agreement, dated June 15, 2007, among the Company, Symphony Icon and Holdings, the Company has received from Holdings an exclusive purchase option (the “Purchase Option”) that gives the Company the right to acquire all of the equity of Symphony Icon, thereby allowing the Company to reacquire all of the Programs. The Purchase Option is exercisable by the Company at any time, in its sole discretion, beginning on the one-year anniversary of the Closing Date and ending on the four-year anniversary of the Closing Date (subject to an earlier exercise right in limited circumstances) at an exercise price of (i) $72 million, if the Purchase Option is exercised on or after the one-year anniversary of the Closing Date and before the two-year anniversary of the Closing Date, (ii) $81 million, if the Purchase Option is exercised on or after the two-year anniversary of the Closing Date and before the three-year anniversary of the Closing Date and (iii) $90 million, if the Purchase Option is exercised on or after the three-year anniversary of the Closing Date and before the four-year anniversary of the Closing Date. The Purchase Option exercise price may be paid in cash or a combination of cash and Common Stock, at the Company’s sole discretion, provided that the Common Stock portion may not exceed 40% of the Purchase Option exercise price.

     Under an Amended and Restated Research and Development Agreement, dated June 15, 2007, among the Company, Symphony Icon and Holdings (the “R&D Agreement”), Symphony Icon and the

Company will develop the Programs in accordance with a specified development plan and related development budget. The R&D Agreement provides that the Company will continue to be primarily responsible for the development of the Programs. The Company’s development activities will be supervised by Symphony Icon’s Development Committee, which is comprised of an equal number of representatives from the Company and Symphony Icon. The Development Committee will report to Symphony Icon’s Board of Directors, which is currently comprised of five members, including one member designated by the Company and two independent directors.

     Under a Research Cost Sharing, Payment and Extension Agreement, dated June 15, 2007, among the Company, Symphony Icon and Holdings, upon the recommendation of the Development Committee, Symphony Icon’s Board of Directors may require the Company to pay Symphony Icon up to $15 million for Symphony Icon’s use in the development of the Programs in accordance with the specified development plan and related development budget. The Development Committee’s right to recommend that Symphony Icon’s Board of Directors submit such funding requirement to the Company will terminate on the one-year anniversary of the expiration of the Purchase Option, subject to limited exceptions.

     In accordance with FIN 46R, Lexicon has determined that Symphony Icon is a variable interest entity for which it is the primary beneficiary. As a result, Lexicon has included the financial condition and results of operations of Symphony Icon in its consolidated financial statements. Symphony Icon’s cash and cash equivalents have been recorded on Lexicon’s consolidated financial statements as short-term investments held by Symphony Icon. The noncontrolling interest in Symphony Icon on Lexicon’s consolidated balance sheet initially reflected the $45 million proceeds contributed into Symphony Icon less $2.2 million of structuring and legal fees and the $8.6 million value of the common stock issued by Lexicon to Symphony Holdings for the Purchase Option. As the collaboration progresses, this line item will be reduced by Symphony Icon’s losses, which were $8.2 million in the nine months ended September 30, 2007, until the balance becomes zero. The reductions to the noncontrolling interest in Symphony Icon will be reflected in Lexicon’s consolidated statements of operations using a similar caption and will reduce the amount of Lexicon’s reported net loss.

8. Agreements with Invus, L.P.

     On June 17, 2007, Lexicon entered into a series of agreements with Invus, L.P. (“Invus”) under which Invus made an investment in the Company’s common stock and has certain other rights described below.

     Lexicon entered into a Securities Purchase Agreement (the “Securities Purchase Agreement”) with Invus under which the Company issued and sold to Invus 50,824,986 shares in an initial investment (the “Initial Investment”) and permitted Invus to require, subject to specific conditions, that the Company conduct certain rights offerings (the “Rights Offerings”). In connection with the Securities Purchase Agreement, Lexicon also entered into a Warrant Agreement with Invus under which the Company issued to Invus warrants (the “Warrants”) to purchase 16,498,353 shares of its common stock at an exercise price of $3.0915 per share.

     Initial Investment. In the Initial Investment which closed on August 28, 2007, Invus purchased 50,824,986 shares of Lexicon’s common stock for a total of approximately $205.4 million, resulting in net proceeds of $198.1 million after deducting fees and expenses of approximately $7.3 million. The Warrants automatically terminated upon the closing of the Initial Investment. This purchase resulted in Invus’ ownership of 40% of the post-transaction outstanding shares of Lexicon’s common stock.

     Rights Offerings. For a period of 90 days following November 28, 2009 (the “First Rights Offering Trigger Date”), Invus will have the right to require Lexicon to make a pro rata offering of non-transferable rights to acquire common stock to all of its stockholders (the “First Rights Offering”) in an

aggregate amount to be designated by Invus not to exceed $172.3 million, minus the aggregate net proceeds received in all Qualified Offerings (as defined below), if any, completed prior to the First Rights Offering Trigger Date. The price per share of the First Rights Offering would be designated by Invus in a range between $4.50 and a then-current average market price of the Company’s common stock. The First Rights Offering Trigger Date could be changed to as early as August 28, 2009 with the approval of the members of the Company’s board of directors who are not affiliated with Invus (the “Unaffiliated Board”). All stockholders would have oversubscription rights with respect to the First Rights Offering, and Invus would be required to purchase the entire portion of the First Rights Offering that is not subscribed for by other stockholders.

     For a period of 90 days following the date (the “Second Rights Offering Trigger Date”) which is 12 months after the later of (a) the First Rights Offering Trigger Date or (b) the date on which Invus exercised its right to require Lexicon to conduct the First Rights Offering, Invus would have the right to require the Company to make a pro rata offering of non-transferable rights to acquire common stock to all of its stockholders (the “Second Rights Offering” and, together with the First Rights Offering, the “Rights Offerings”) in an aggregate amount to be designated by Invus not to exceed an amount equal to $344.5 million, minus the amount of the First Rights Offering, minus the aggregate net proceeds received in all Qualified Offerings, if any, completed prior to the Second Rights Offering Trigger Date. The price per share of the Second Rights Offering would be designated by Invus in a range between $4.50 and a then-current average market price of the Company’s common stock. All stockholders would have oversubscription rights with respect to the Second Rights Offering, and Invus would be required to purchase the entire portion of the Second Rights Offering that is not subscribed for by other stockholders.

     A “Qualified Offering” consists of a bona fide financing transaction comprised of Lexicon’s issuance of shares of its common stock at a price greater than $4.50 per share, which transaction is not entered into in connection with the Company’s entry into any other transaction (including, a collaboration or license for the discovery, development or commercialization of pharmaceutical products) involving the purchaser of such common stock. Until the later of the completion of the Second Rights Offering or the expiration of the 90-day period following the Second Rights Offering Trigger Date, Lexicon will not, without Invus’ prior consent, issue any shares of its common stock at a price below $4.50 per share, subject to certain exceptions.

     In connection with the Securities Purchase Agreement, Lexicon entered into a Stockholders’ Agreement with Invus under which Invus (a) has specified rights with respect to designation of directors and to participate in future equity issuances by the Company, (b) is subject to certain standstill restrictions, as well as restrictions on transfer and the voting of the shares of common stock held by it and its affiliates, and (c), as long as Invus holds at least 15% of the total number of outstanding shares of the Company’s common stock, is entitled to certain minority protections.

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

Overview

     We are a biopharmaceutical company focused on the discovery and development of breakthrough treatments for human disease. We use our proprietary gene knockout technology to disrupt, or knock out, the function of genes in mice and then employ an integrated platform of advanced medical technologies to systematically discover the physiological and behavioral functions and pharmaceutical utility of the genes we have knocked out and the potential drug targets encoded by the corresponding human genes. For targets that we believe have high pharmaceutical value, we engage in programs for the discovery and development of potential small molecule, antibody and protein drugs. We have advanced two drug candidates from these programs into human clinical trials, with five additional drug candidates in preclinical development and compounds from a number of additional programs in various stages of preclinical research. We believe that our systematic, target biology-driven approach to drug discovery will enable us to substantially expand our clinical pipeline and we have initiated our 10_TO10 program with the goal of advancing ten drug candidates into human clinical trials by the end of 2010.

     We are working both independently and through strategic collaborations and alliances to capitalize on our technology and drug target discoveries and to develop and commercialize drug candidates emerging from our drug discovery and development programs. We have established alliances with Bristol-Myers Squibb Company to discover and develop novel small molecule drugs in the neuroscience field; with Genentech, Inc. for the discovery of therapeutic proteins and antibody targets and the development of antibody and protein drugs based on those targets; and with N.V. Organon for the discovery of another group of therapeutic proteins and antibody targets and the development and commercialization of antibody and protein drugs based on those targets. In addition, we have established collaborations and license agreements with other leading pharmaceutical and biotechnology companies, research institutes and academic institutions under which we receive fees and, in some cases, are eligible to receive milestone and royalty payments, in return for granting access to some of our technologies and discoveries for use in the other organization’s own drug discovery efforts. Finally, we have established a clinical development financing arrangement with Symphony Icon, Inc. under which we have licensed to Symphony Icon our intellectual property rights to our drug candidates, LX6171, LX1031 and LX1032, subject to our exclusive option to reacquire all rights to those drug candidates. We are consolidating the financial condition and results of operations of Symphony Icon in accordance with FASB Interpretation No. 46, as described under the heading “Critical Accounting Policies.”

     We derive substantially all of our revenues from drug discovery alliances, target validation collaborations for the development and, in some cases, analysis of the physiological effects of genes altered in knockout mice, academic, non-profit and government arrangements, and technology licenses. To date, we have generated a substantial portion of our revenues from a limited number of sources.

     Our operating results and, in particular, our ability to generate additional revenues are dependent on many factors, including our success in establishing collaborations, alliances and technology licenses, expirations of our collaborations and alliances, the success rate of our discovery efforts leading to opportunities for new collaborations, alliances and licenses, as well as milestone payments and royalties, the timing and willingness of collaborators to commercialize products which may result in royalties, and general and industry-specific economic conditions which may affect research and development expenditures. Our future revenues from collaborations, alliances and academic, non-profit and government arrangements are uncertain because our existing agreements have fixed terms or relate to specific projects of limited duration. Our future revenues from technology licenses are uncertain because they depend, in large part, on securing new agreements. Our ability to secure future revenue-generating

agreements will depend upon our ability to address the needs of our potential future collaborators, granting agencies and licensees, and to negotiate agreements that we believe are in our long-term best interests. We may determine that our interests are better served by retaining rights to our discoveries and advancing our therapeutic programs to a later stage, which could limit our near-term revenues. Because of these and other factors, our operating results have fluctuated in the past and are likely to do so in the future, and we do not believe that period-to-period comparisons of our operating results are a good indication of our future performance.

     Since our inception, we have incurred significant losses and, as of September 30, 2007, we had an accumulated deficit of $398.4 million. Our losses have resulted principally from costs incurred in research and development, general and administrative costs associated with our operations, and non-cash stock-based compensation expenses associated with stock options granted to employees and consultants. Research and development expenses consist primarily of salaries and related personnel costs, material costs, facility costs, depreciation on property and equipment, legal expenses resulting from intellectual property prosecution and other expenses related to our drug discovery and development programs, the development and analysis of knockout mice and our other target validation research efforts, and the development of compound libraries. General and administrative expenses consist primarily of salaries and related expenses for executive and administrative personnel, professional fees and other corporate expenses, including information technology, facilities costs and general legal activities. In connection with our ongoing target validation research efforts and the expansion of our drug discovery and development programs, we expect to incur increasing research and development and general and administrative costs. As a result, we will need to generate significantly higher revenues to achieve profitability.

Critical Accounting Policies

Revenue Recognition

     We recognize revenues when persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the price is fixed or determinable, and collectibility is reasonably assured. Payments received in advance under these arrangements are recorded as deferred revenue until earned.

     Upfront fees under our drug discovery alliances are recognized as revenue on a straight-line basis over the estimated period of service, generally the contractual research term, to the extent they are non-refundable. Research funding under these alliances is recognized as services are performed to the extent they are non-refundable, either on a straight-line basis over the estimated service period, generally the contractual research term, or as contract research costs are incurred. Milestone-based fees are recognized upon completion of specified milestones according to contract terms. Payments received under target validation collaborations and government grants and contracts are recognized as revenue as we perform our obligations related to such research to the extent such fees are non-refundable. Non-refundable technology license fees are recognized as revenue upon the grant of the license, when performance is complete and there is no continuing involvement.

     Revenues recognized from multiple element contracts are allocated to each element of the arrangement based on the relative fair value of the elements. The determination of fair value of each element is based on objective evidence. When revenues for an element are specifically tied to a separate earnings process, revenue is recognized when the specific performance obligation associated with the element is completed. When revenues for an element are not specifically tied to a separate earnings process, they are recognized ratably over the term of the agreement.

     A change in our revenue recognition policy or changes in the terms of contracts under which we recognize revenues could have an impact on the amount and timing of our recognition of revenues.

Research and Development Expenses

     Research and development expenses consist of costs incurred for Company-sponsored as well as collaborative research and development activities. These costs include direct and research-related overhead expenses and are expensed as incurred. Patent costs and technology license fees for technologies that are utilized in research and development and have no alternative future use are expensed when incurred.

     We have concluded a Phase 1b clinical trial of our most advanced drug candidate, LX6171, an orally-delivered small molecule compound that we are developing as a potential treatment for disorders characterized by cognitive impairment. We have also recently concluded a Phase 1b clinical trial for another drug candidate, LX1031, an orally-delivered small molecule compound that we are developing as a potential treatment for irritable bowel syndrome. We have advanced five other compounds into preclinical development in preparation for regulatory filings for the commencement of clinical trials. Compounds from a number of additional drug programs are in various stages of preclinical research. The drug development process takes many years to complete. The cost and length of time varies due to many factors, including the type, complexity and intended use of the drug candidate. We estimate that drug development activities are typically completed over the following periods:

Phase		Estimated Completion Period
Preclinical development		1-2 years
Phase 1 clinical trials		1-2 years
Phase 2 clinical trials		1-2 years
Phase 3 clinical trials		2-4 years

     We expect research and development costs to increase in the future as our drug programs advance in preclinical development and clinical trials. Due to the variability in the length of time necessary for drug development, the uncertainties related to the cost of these activities and ultimate ability to obtain governmental approval for commercialization, accurate and meaningful estimates of the ultimate costs to bring our potential drug candidates to market are not available.

     We record our research and development costs by type or category, rather than by project. Significant categories of costs include personnel, facilities and equipment costs, laboratory supplies and third-party and other services. In addition, a significant portion of our research and development expenses is not tracked by project as it benefits multiple projects. Consequently, fully-loaded research and development cost summaries by project are not available.

Consolidation of Variable Interest Entity

     We consolidate the financial condition and results of operations of Symphony Icon in accordance with FASB Interpretation No. 46 (revised 2003), “Consolidation of Variable Interest Entities,” or FIN 46R. While Symphony Icon is defined under FIN46R to be a variable interest entity for which we are the primary beneficiary, Symphony Icon is wholly-owned by the noncontrolling interest holders. Therefore, we deduct the losses attributed to the noncontrolling interest from our net loss in the consolidated statements of operations and we also reduce the noncontrolling interest holders’ ownership interest in the consolidated balance sheets by Symphony Icon’s losses.

Stock-based Compensation Expense

     On January 1, 2006, we adopted Statement of Financial Accounting Standards No. 123 (Revised), “Share-Based Payment,” or SFAS No. 123(R). This statement requires companies to recognize compensation expense in the statements of operations for share-based payments, including stock options issued to employees, based on their fair values on the date of the grant, with the compensation expense recognized over the period in which an employee is required to provide service in exchange for the stock award. We adopted this statement using the modified prospective transition method, which applies the compensation expense recognition provisions to new awards and to any awards modified, repurchased or canceled after the January 1, 2006 adoption date. Additionally, for any unvested awards outstanding at the adoption date, compensation expense is recognized over the remaining vesting period. Stock-based compensation expense is recognized on a straight-line basis. We had stock-based compensation expense under SFAS No. 123(R) of $1.6 million and $1.8 million for the three months ended September 30, 2007 and 2006, respectively, and $4.8 million and $5.4 million for the nine months ended September 30, 2007 and 2006, respectively. Stock-based compensation expense under SFAS No. 123(R) has no impact on cash flows from operating activities or financing activities. As of September 30, 2007, stock-based compensation cost for all outstanding unvested options was $11.4 million, which is expected to be recognized over a weighted-average vesting period of 1.3 years.

     The fair value of stock options is estimated at the date of grant using the Black-Scholes option-pricing model. For purposes of determining the fair value of stock options granted subsequent to the adoption of SFAS No. 123(R), we segregated our options into two homogeneous groups, based on exercise and post-vesting employment termination behaviors, resulting in a change in the assumptions used for expected option lives and forfeitures. Expected volatility is based on the historical volatility in our stock price. The following weighted-average assumptions were used for options granted in the nine-month periods ended September 30, 2007 and 2006, respectively:

						Risk-free
		Expected				Interest				Expected				Estimated				Dividend
		Volatility				Rate				Term				Forfeitures				Rate
September 30, 2007:
Employees			67	%			4.5	%			6				21	%			0	%
Officers and non-employee directors			67	%			4.6	%			9				4	%			0	%
September 30, 2006:
Employees			69	%			4.6	%			7				18	%			0	%
Officers and non-employee directors			69	%			4.7	%			9				3	%			0	%

Goodwill Impairment

     Goodwill is not amortized, but is tested at least annually for impairment at the reporting unit level. We have determined that the reporting unit is the single operating segment disclosed in our current financial statements. Impairment is the condition that exists when the carrying amount of goodwill exceeds its implied fair value. The first step in the impairment process is to determine the fair value of the reporting unit and then compare it to the carrying value, including goodwill. We determined that the market capitalization approach is the most appropriate method of measuring fair value of the reporting unit. Under this approach, fair value is calculated as the average closing price of our common stock for the 30 days preceding the date that the annual impairment test is performed, multiplied by the number of outstanding shares on that date. A control premium, which is representative of premiums paid in the marketplace to acquire a controlling interest in a company, is then added to the market capitalization to determine the fair value of the reporting unit. If the fair value exceeds the carrying value, no further action is required and no impairment loss is recognized. Additional impairment assessments may be

performed on an interim basis if we encounter events or changes in circumstances that would indicate that, more likely than not, the carrying value of goodwill has been impaired.

Recent Accounting Pronouncements

     On January 1, 2007, we adopted Financial Accounting Standards Board, or FASB, Interpretation No. 48, “Accounting for Uncertainty in Income Taxes, an interpretation of FASB Statement No. 109,” or FIN 48. FIN 48 clarifies the accounting for income taxes by prescribing the minimum recognition threshold a tax position is required to meet before being recognized in the financial statements. FIN 48 also provides guidance on derecognition, classification, interest and penalties, accounting in interim periods, disclosure and transition. There was no effect on our consolidated financial position, results of operations or cash flows as a result of adopting FIN 48. As of January 1, 2007 and September 30, 2007, we did not have any unrecognized tax benefits.

     We are primarily subject to U.S. federal and New Jersey and Texas state income taxes. The tax years 1995 to current remain open to examination by U.S. federal authorities and 2004 to current remain open to examination by state authorities. Our policy is to recognize interest and penalties related to income tax matters in income tax expense. As of January 1, 2007 and September 30, 2007, we had no accruals for interest or penalties related to income tax matters.

     At December 31, 2006, we had net operating loss carryforwards of approximately $267.4 million and research and development credit carryforwards of approximately $14.4 million expiring beginning in 2011. Utilization of the net operating loss and research and development credit carryforwards may be subject to a significant annual limitation due to ownership changes that have occurred previously or could occur in the future provided by Section 382 of the Internal Revenue Code. We have conducted a limited analysis to determine whether a change in control has occurred since our formation and do not believe a significant limitation, if any, would be determined upon a detailed analysis. Further, until a Section 382 study is completed and any limitation known, no amounts are being presented as an uncertain tax position under FIN 48. We have established a full valuation allowance for our net operating loss and research and development credit carryforwards.

     In September 2006, the FASB issued Statement of Financial Accounting Standards No. 157, “Fair Value Measurements,” or SFAS No. 157. The statement defines fair value, establishes a framework for measuring fair value in generally accepted accounting principles, and expands disclosures about fair value measurements. This statement applies under other accounting pronouncements that require or permit fair value measurements, the FASB having previously concluded in those accounting pronouncements that fair value is the relevant measurement attribute. Accordingly, this statement does not require any new fair value measurements. SFAS No. 157 is effective January 1, 2008. We are currently evaluating the impact of this statement on our financial condition and results of operations.

Results of Operations

Three Months Ended September 30, 2007 and 2006

Revenues

     Total revenues and dollar and percentage changes as compared to the corresponding period in the prior year are as follows (dollar amounts are presented in millions):

		Three Months Ended September 30,
		2007				2006
Total revenues		$	10.2			$	19.6
Dollar decrease		$	(9.4	)
Percentage decrease			48	%

	•		Collaborative research - Revenue from collaborative research decreased 48% to $9.7 million, primarily due to the recognition of revenue in the previous period under a contract with the National Institutes of Health as well as reduced revenue under Lexicon’s neuroscience alliance with Bristol-Myers Squibb resulting from the conclusion of the revenue recognition period for the upfront payment received under the alliance.
	•		Subscription and license fees - Revenue from subscriptions and license fees decreased 46% to $0.5 million, primarily due to lower royalties received under a technology license agreement with Deltagen, Inc.

     Research and Development Expenses

          Research and development expenses and dollar and percentage changes as compared to the corresponding period in the prior year are as follows (dollar amounts are presented in millions):

		Three Months Ended September 30,
		2007				2006
Total research and development expense		$	24.5			$	27.0
Dollar decrease		$	(2.5	)
Percentage decrease			9	%

          Research and development expenses consist primarily of salaries and other personnel-related expenses, facility and equipment costs, laboratory supplies, third-party and other services and stock-based compensation expenses.

	•		Personnel — Personnel costs decreased 21% to $10.5 million, primarily due to lower salary and benefit costs as a result of a reduction in our personnel in January 2007. Salaries, bonuses, employee benefits, payroll taxes, recruiting and relocation costs are included in personnel costs.
	•		Facilities and equipment — Facilities and equipment costs decreased 11% to $4.8 million, primarily due to a decrease in depreciation expense.
	•		Laboratory supplies — Laboratory supplies expense decreased 20% to $2.8 million, primarily due to a reduction in our personnel in January 2007.
	•		Third-party and other services — Third-party and other services increased 63% to $4.4 million, primarily due to an increase in third-party preclinical and clinical research and development costs.
	•		Stock-based compensation — Stock-based compensation expense decreased 12% to $1.0 million, primarily as a result of forfeitures of unvested stock options.
	•		Other — Other costs increased 4% to $1.2 million.

     General and Administrative Expenses

          General and administrative expenses and dollar and percentage changes as compared to the corresponding period in the prior year are as follows (dollar amounts are presented in millions):

		Three Months Ended September 30,
		2007				2006
Total general and administrative expense		$	5.1			$	5.3
Dollar decrease		$	(0.2	)
Percentage decrease			4	%

          General and administrative expenses consist primarily of personnel costs to support our research activities, facility and equipment costs, professional fees such as legal fees, and stock-based compensation expenses.

	•		Personnel - Personnel costs decreased 15% to $2.5 million, primarily due to lower salary and benefit costs as a result of a reduction in our personnel in January 2007.
	•		Facilities and equipment - Facilities and equipment costs decreased 25% to $0.6 million, primarily due to a decrease in depreciation expense.
	•		Professional fees - Professional fees increased 118% to $0.8 million, primarily due to increased professional, consulting and litigation costs.
	•		Stock-based compensation - Stock-based compensation expense decreased 4% to $0.6 million, primarily as a result of forfeitures of unvested stock options.
	•		Other — Other costs were $0.6 million, consistent with the prior year.

     Interest Income, Interest Expense and Other Expense, Net

          Interest Income. Interest income increased 180% to $2.2 million in the three months ended September 30, 2007 from $0.8 million in the corresponding period in 2006, due to higher average cash balances.

          Interest Expense. Interest expense decreased 15% to $0.7 million in the three months ended September 30, 2007 from $0.8 million in the corresponding period in 2006.

          Other Expense, Net. Other expense, net increased 33% to $8,000.

     Noncontrolling Interest in Symphony Icon, Inc.

          For the three month periods ended September 30, 2007 and 2006, the losses attributed to the noncontrolling interest holders of Symphony Icon were $3.9 million and none, respectively.

     Net Loss and Net Loss per Common Share

          Net Loss and Net Loss per Common Share. Net loss increased to $14.1 million in the three months ended September 30, 2007 from $12.8 million in the corresponding period in 2006. Net loss per common share decreased to $0.14 in the three months ended September 30, 2007 from $0.20 in the corresponding period in 2006.

          Our quarterly operating results have fluctuated in the past and are likely to do so in the future, and we believe that quarter-to-quarter comparisons of our operating results are not a good indication of our future performance.

Nine Months Ended September 30, 2007 and 2006

     Revenues

          Total revenues and dollar and percentage changes as compared to the corresponding period in the prior year are as follows (dollar amounts are presented in millions):

		Nine Months Ended
		September 30,
		2007				2006
Total revenues		$	36.3			$	56.7
Dollar decrease		$	(20.4	)
Percentage decrease			36	%

	•		Collaborative research - Revenue from collaborative research decreased 36% to $34.5 million, primarily due to decreased revenue under our alliance with Bristol-Myers Squibb resulting from the conclusion of the revenue recognition period for the upfront payment we received under the alliance. Additionally, the prior year included the achievement of a performance milestone under our Takeda alliance.
	•		Subscription and license fees - Revenue from subscriptions and license fees decreased 44% to $1.9 million, primarily due to lower royalties received under a technology license with Deltagen.

     Research and Development Expenses

          Research and development expenses and dollar and percentage changes as compared to the corresponding period in the prior year are as follows (dollar amounts are presented in millions):

		Nine Months Ended
		September 30,
		2007				2006
Total research and development expense		$	77.4			$	81.1
Dollar decrease		$	(3.7	)
Percentage decrease			5	%

          Research and development expenses consist primarily of salaries and other personnel-related expenses, facility and equipment costs, laboratory supplies, third-party and other services and stock-based compensation expenses.

	•		Personnel — Personnel costs decreased 13% to $34.1 million, primarily due to lower salary and benefit costs as a result of a reduction in our personnel in January 2007, offset in part by severance payments resulting from such reduction in personnel.
	•		Facilities and equipment — Facilities and equipment costs decreased 5% to $15.3 million, primarily due to a decrease in depreciation expense.
	•		Laboratory supplies — Laboratory supplies expense decreased 21% to $8.8 million, primarily due to a reduction in our personnel in January 2007.
	•		Third-party and other services — Third-party and other services increased 79% to $12.8 million, primarily due to an increase in third-party preclinical and clinical research and development costs.

	•		Stock-based compensation — Stock-based compensation expense decreased 11% to $3.0 million, primarily as a result of forfeitures of unvested stock options.
	•		Other — Other costs decreased by 14% to $3.5 million, primarily due to the amortization of other intangibles in 2006.

     General and Administrative Expenses

          General and administrative expenses and dollar and percentage changes as compared to the corresponding period in the prior year are as follows (dollar amounts are presented in millions):

		Nine Months Ended
		September 30,
		2007				2006
Total general and administrative expense		$	15.4			$	16.3
Dollar decrease		$	(0.9	)
Percentage decrease			5	%

          General and administrative expenses consist primarily of personnel costs to support our research activities, facility and equipment costs, professional fees such as legal fees, and stock-based compensation expenses.

	•		Personnel - Personnel costs decreased 11% to $8.1 million, primarily due to lower salary and benefit costs as a result of a reduction in our personnel in January 2007, offset in part by severance payments resulting from such reduction in personnel.
	•		Facilities and equipment - Facilities and equipment costs decreased 18% to $1.9 million, primarily due to a decrease in depreciation expense.
	•		Professional fees - Professional fees increased 55% to $1.8 million, primarily due to increased litigation, professional and consulting costs.
	•		Stock-based compensation - Stock-based compensation expense decreased 9% to $1.8 million primarily as a result of forfeitures of unvested stock options.
	•		Other — Other costs were $1.7 million, consistent with the prior year.

     Interest Income, Interest Expense and Other Expense, Net

          Interest Income. Interest income increased 42% to $3.8 million in the nine months ended September 30, 2007 from $2.7 million in the corresponding period in 2006, due to higher average cash balances.

          Interest Expense. Interest expense decreased 15% to $2.1 million in the nine months ended September 30, 2007 from $2.4 million in the corresponding period in 2006.

          Other Expense, Net. Other expense, net decreased 51% to $34,000.

     Noncontrolling Interest in Symphony Icon, Inc.

          For the nine month periods ended September 30, 2007 and 2006, the losses attributed to the noncontrolling interest holders of Symphony Icon were $8.2 million and none, respectively.

     Net Loss and Net Loss per Common Share

          Net Loss and Net Loss per Common Share. Net loss increased to $46.6 million in the nine months ended September 30, 2007 from $40.5 million in the corresponding period in 2006. Net loss per common share decreased to $0.53 in the nine months ended September 30, 2007 from $0.63 in the corresponding period in 2006.

Liquidity and Capital Resources

          We have financed our operations from inception primarily through sales of common and preferred stock, contract and milestone payments to us under our drug discovery alliance, target validation, database subscription and license agreements, government grants and contracts, and financing obtained under debt and lease arrangements. We have also financed certain of our research and development activities under our agreements with Symphony Icon. From our inception through September 30, 2007, we had received net proceeds of $550.2 million from issuances of common and preferred stock, including $203.2 million of net proceeds from the initial public offering of our common stock in April 2000, $50.1 million from a July 2003 common stock offering, $37.5 million from an October 2006 common stock offering and $198.1 million from an August 2007 sale of common stock to Invus, L.P. In addition, from our inception through September 30, 2007, we received $416.8 million in cash payments from drug discovery alliances, target validation collaborations, database subscription and technology license fees, sales of compound libraries and reagents, and government grants and contracts, of which $377.9 million had been recognized as revenues through September 30, 2007.

          As of September 30, 2007, we had $234.3 million in cash, cash equivalents and short-term investments and $39.6 million in investments held by Symphony Icon. We had $80.0 million in cash, cash equivalents and short-term investments as of December 31, 2006. We used cash of $60.0 million in operations in the nine months ended September 30, 2007. This consisted primarily of the net loss for the period of $46.6 million offset by non-cash charges of $7.1 million related to depreciation expense and $4.8 million related to stock-based compensation expense; a $17.0 million decrease in deferred revenue; a $8.2 million loss attributable to noncontrolling interest and changes in other operating assets and liabilities of $0.2 million. Investing activities used cash of $174.9 million in the nine months ended September 30, 2007, primarily due to purchases of investments of $193.0 million, purchases of investments held by Symphony Icon of $45.0 million and by purchases of property and equipment of $1.3 million, offset by net maturities of short-term investments of $59.0 million and maturities of investments held by Symphony Icon of $5.4 million. Financing activities provided cash of $255.4 million, primarily due to $198.1 million in proceeds from the issuance of common stock to Invus, L.P., net of fees and expenses, $42.7 million in proceeds from the purchase of noncontrolling interest by preferred shareholders of Symphony Icon, $14.2 million in proceeds from issuance of common stock to Symphony Holdings, LLC, net of fees, and $0.9 million from stock option exercises, offset by principal repayments of $0.6 million on the mortgage loan.

          On June 17, 2007, we entered into a securities purchase agreement with Invus, L.P, pursuant to which Invus purchased 50,824,986 shares of our common stock for approximately $205.4 million on August 28, 2007. This purchase resulted in Invus’ ownership of 40% of the post-transaction outstanding shares of our common stock. Pursuant to the securities purchase agreement, Invus also has the right to require us to initiate up to two pro rata rights offerings to our stockholders, which would provide all stockholders with non-transferable rights to acquire shares of our common stock, in an aggregate amount of up to $344.5 million, less the proceeds of any “qualified offerings” that we may complete in the interim involving the sale of our common stock at prices above $4.50 per share. The first rights offering may be initiated, subject to certain adjustments, beginning on November 28, 2009, and the second rights offering may be initiated beginning on the date that is 12 months after the later of the initiation of the first rights

offering and November 28, 2010 if the first rights offering does not take place. The initial investment and subsequent rights offerings, combined with any qualified offerings, were designed to achieve up to $550 million in proceeds to us. Invus would participate in each rights offering for up to its pro rata portion of the offering, and would commit to purchase the entire portion of the offering not subscribed for by other stockholders.

          In connection with the securities purchase agreement, we entered into a stockholders’ agreement with Invus under which Invus (a) will have specified rights with respect to designation of directors and to participate in future equity issuances by us, (b) will be subject to certain standstill restrictions, as well as restrictions on transfer and the voting of the shares of common stock held by it and its affiliates, and (c), as long as Invus holds at least 15% of the total number of outstanding shares of our common stock, will be entitled to certain minority protections.

          On June 15, 2007, we entered into a series of related agreements providing for the financing of the clinical development of LX6171, LX1031 and LX1032, along with any other pharmaceutical compositions modulating the same targets as those drug candidates. Under the financing arrangement, we licensed to Symphony Icon, a wholly-owned subsidiary of Symphony Icon Holdings LLC, our intellectual property rights related to the programs and Holdings contributed $45 million to Symphony Icon in order to fund the clinical development of the programs. We also entered into a share purchase agreement with Holdings under which we issued and sold to Holdings 7,650,622 shares of our common stock in exchange for $15 million and an exclusive option to acquire all of the equity of Symphony Icon, thereby allowing us to reacquire the programs. The purchase option is exercisable by us at any time, in our sole discretion, beginning on June 15, 2008 and ending on June 15, 2011 (subject to an earlier exercise right in limited circumstances) at an exercise price of (i) $72 million, if the purchase option is exercised on or after June 15, 2008 and before June 15, 2009, (ii) $81 million, if the purchase option is exercised on or after the June 15, 2009 and before the June 15, 2010 and (iii) $90 million, if the purchase option is exercised on or after June 15, 2010 and before June 15, 2011. The purchase option exercise price may be paid in cash or a combination of cash and common stock, at our sole discretion, provided that the common stock portion may not exceed 40% of the purchase option exercise price.

          Upon the recommendation of Symphony Icon’s development committee, which is comprised of an equal number of representatives from us and Symphony Icon, Symphony Icon’s board of directors may require us to pay Symphony Icon up to $15 million for Symphony Icon’s use in the development of the programs in accordance with the specified development plan and related development budget. The development committee’s right to recommend that Symphony Icon’s board of directors submit such funding requirement to us will terminate on the one-year anniversary of the expiration of the purchase option, subject to limited exceptions.

          In April 2004, we obtained a $34.0 million mortgage on our facilities in The Woodlands, Texas. The mortgage loan has a ten-year term with a 20-year amortization and bears interest at a fixed rate of 8.23%. In May 2002, our subsidiary Lexicon Pharmaceuticals (New Jersey), Inc. leased a 76,000 square-foot laboratory and office space in Hopewell, New Jersey under an agreement which expires in June 2013. The lease provides for an escalating yearly base rent payment of $1.3 million in the first year, $2.1 million in years two and three, $2.2 million in years four to six, $2.3 million in years seven to nine and $2.4 million in years ten and eleven. We are the guarantor of the obligations of our subsidiary under the lease.

          Our future capital requirements will be substantial and will depend on many factors, including our ability to obtain alliance, collaboration and technology license agreements, the amount and timing of payments under such agreements, the level and timing of our research and development expenditures, market acceptance of our products, the resources we devote to developing and supporting our products

and other factors. Our capital requirements will also be affected by any expenditures we make in connection with license agreements and acquisitions of and investments in complementary technologies and businesses. We expect to devote substantial capital resources to continue our research and development efforts, to expand our support and product development activities, and for other general corporate activities. We believe that our current unrestricted cash and investment balances and cash and revenues we expect to derive from existing and new drug discovery alliances, target validation collaborations, government grants and contracts, and technology licenses will be sufficient to fund our operations for at least the next twelve months. During or after this period, if cash generated by operations is insufficient to satisfy our liquidity requirements, we will need to sell additional equity or debt securities or obtain additional credit arrangements. Additional financing may not be available on terms acceptable to us or at all. The sale of additional equity or convertible debt securities may result in additional dilution to our stockholders.

Disclosure about Market Risk

          We are exposed to limited market and credit risk on our cash equivalents, which have maturities of three months or less at the time of purchase. We maintain a short-term investment portfolio which consists of U.S. government agency debt obligations, investment grade commercial paper, corporate debt securities and certificates of deposit that mature within twelve months and auction rate securities that mature greater than twelve months from the time of purchase, which we believe are subject to limited market and credit risk. We currently do not hedge interest rate exposure or hold any derivative financial instruments in our investment portfolio.

          We have operated primarily in the United States and substantially all sales to date have been made in U.S. dollars. Accordingly, we have not had any material exposure to foreign currency rate fluctuations.

Item 3. Quantitative and Qualitative Disclosures about Market Risk

          See “Disclosure about Market Risk” under “Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations” for quantitative and qualitative disclosures about market risk.

Item 4. Controls and Procedures

          Our chief executive officer and chief financial officer have concluded that our disclosure controls and procedures (as defined in rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934) are sufficiently effective to ensure that the information required to be disclosed by us in the reports we file under the Securities Exchange Act is gathered, analyzed and disclosed with adequate timeliness, accuracy and completeness, based on an evaluation of such controls and procedures as of the end of the period covered by this report.

          Subsequent to our evaluation, there were no significant changes in internal controls or other factors that could significantly affect internal controls, including any corrective actions with regard to significant deficiencies and material weaknesses.

Part II Other Information

Item 1A. Risk Factors

          The following risks and uncertainties are important factors that could cause actual results or events to differ materially from those indicated by forward-looking statements. The factors described below are not the only ones we face and additional risks and uncertainties not presently known to us or that we currently deem immaterial also may impair our business operations.

Risks Related to Our Need for Additional Financing and Our Financial Results

	•		we will need substantial amounts of additional capital in the future; if it is unavailable, we will be forced to significantly curtail or cease operations and, if it is not available on reasonable terms, we may be forced to obtain funds by entering into financing agreements on unfavorable terms
	•		we have a history of net losses, and we expect to continue to incur net losses and may not achieve or maintain profitability
	•		our operating results have been and likely will continue to fluctuate, and we believe that period-to-period comparisons of our operating results are not a good indication of our future performance

Risks Related to Our Business

	•		we are an early-stage company, and we may not successfully develop or commercialize any therapeutics or drug targets that we have identified
	•		clinical testing of our drug candidates in humans is an inherently risky and time-consuming process that may fail to demonstrate safety and efficacy, which could result in the delay, limitation or prevention of regulatory approval
	•		we are dependent upon our collaborations with major pharmaceutical companies, and if we are unable to achieve milestones under those collaborations or if our collaborators’ efforts fail to yield pharmaceutical products on a timely basis, our business will suffer
	•		conflicts with our collaborators could jeopardize the success of our collaborative agreements and harm our product development efforts
	•		if we are unable to internally establish drug development and commercialization capabilities or arrange for the provision of such functions by third parties, our ability to develop and commercialize pharmaceutical products would be significantly impaired
	•		we lack the capability to manufacture materials for preclinical studies, clinical trials or commercial sales and will rely on third parties to manufacture our potential products, which may harm or delay our product development and commercialization efforts
	•		we face substantial competition in our drug discovery and product development efforts
	•		we may engage in future acquisitions, which may be expensive and time consuming and from which we may not realize anticipated benefits
	•		if we lose our key personnel or are unable to attract and retain additional personnel, we may be unable to successfully develop and commercialize our own products

	•		any contamination among our knockout mouse population could negatively affect the reliability of our scientific research or cause us to incur significant remedial costs
	•		because all of our target validation operations are located at a single facility, the occurrence of a disaster could significantly disrupt our business
	•		we use hazardous chemicals and radioactive and biological materials in our business; any disputes relating to improper handling, storage or disposal of these materials could be time consuming and costly

Risks Related to Our Industry

	•		our ability to patent our inventions is uncertain because patent laws and their interpretation are highly uncertain and subject to change
	•		if we are unable to adequately protect our intellectual property, third parties may be able to use our technology, which could negatively impact our ability to compete in the market
	•		we may be involved in patent litigation and other disputes regarding intellectual property rights and may require licenses from third parties for our discovery and development and planned commercialization activities, and we may not prevail in any such litigation or other dispute or be able to obtain required licenses
	•		we use intellectual property that we license from third parties, and if we do not comply with these licenses, we could lose our rights under them
	•		we have not sought patent protection outside of the United States for some of our inventions, and some of our licensed patents only provide coverage in the United States, and as a result, our international competitors could be granted foreign patent protection with respect to our discoveries
	•		our industry is subject to extensive and uncertain government regulatory requirements, which could significantly hinder our ability, or the ability of our collaborators, to obtain, in a timely manner or at all, regulatory approval of potential therapeutic products, or to commercialize such products
	•		if our potential products receive regulatory approval, we or our collaborators will remain subject to extensive and rigorous ongoing regulation
	•		the uncertainty of pharmaceutical pricing and reimbursement may decrease the commercial potential of any products that we or our collaborators may develop and affect our ability to raise capital
	•		we may be sued for product liability
	•		public perception of ethical and social issues may limit or discourage the use of our technologies, which could reduce our revenues

          For additional discussion of the risks and uncertainties that affect our business, see the section captioned “Risk Factors” included in our Registration Statement on Form S-3 (Registration No. 333-144933), as filed with the Securities and Exchange Commission.

Item 4. Submission of Matters to a Vote of Security Holders

          A special meeting of stockholders was held on August 23, 2007 to consider and vote on the following proposals, each of which were considered and approved, with the following numbers of shares voted for, voted against and abstaining with respect to such matters:

Matter		For				Against				Abstain
Ratification and approval of the Invus transaction, which included, among other things, the issuance by us of 50,824,986 shares of our common stock for approximately $205.4 million and may include the issuance of additional shares of our common stock in up to two rights offerings pursuant to a securities purchase agreement between us and Invus L.P., dated as of June 17, 2007, as it may be amended from time to time			60,177,808				589,610				80,661
Ratification and approval of an amendment to our certificate of incorporation increasing the number of authorized shares of our common stock from 120 million to 300 million			60,122,117				642,301				83,661

There were no broker non-votes with respect to either of the proposals.

Item 6. Exhibits

Exhibit No.		Description
31.1		—		Certification of CEO Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2		—		Certification of CFO Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1		—		Certification of CEO and CFO Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

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.

Index to Exhibits

Exhibit No.		Description
31.1		—		Certification of CEO Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2		—		Certification of CFO Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1		—		Certification of CEO and CFO Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002