UNITED
STATES


SECURITIES
AND EXCHANGE COMMISSION


Washington,
D.C.  20549


FORM
10-Q





(Mark
One)





[X]           Quarterly Report Pursuant To
Section 13 Or 15(d) Of The


Securities Exchange Act Of
1934


For the quarterly period ended
September 30, 2009





OR





[   ]          
Transition Report
Pursuant To Section 13 Or 15(d) Of The


Securities Exchange Act Of
1934


For the transition period from
_______________ to _______________








Commission
File Number: 0-23317


ORE
PHARMACEUTICAL HOLDINGS INC.


(Exact
name of registrant as specified in its charter)







Delaware
              27-1088078(State
      or other jurisdiction of
              (I.R.S.
      Employerincorporation
      or organization)
              Identification
      No.)




610
Professional Drive, Suite 101


Gaithersburg,
Maryland 20879


(Address
of principal executive offices)


(240)
361-4400


(Registrant’s
phone number, including area code)







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 xNO o




Indicate
by check mark whether the registrant has submitted electronically and posted on
its corporate Web site, if any, every Interactive Data File required to be
submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding
12 months (or for such shorter period that the registrant was required to submit
and post such files):YESoNO o




Indicate
by check mark whether the Registrant is a large accelerated filer, an
accelerated filer, a non-accelerated filer, or a smaller reporting
company.  See the definitions of “large accelerated filer,”
“accelerated filer” and “smaller reporting company” in Rule 12b-2 of the
Exchange Act.






Large
      accelerated filer o
              Accelerated
      filer o
              Non-accelerated
      filer o
              Smaller
      reporting company x(Do
      not check if a smaller reporting company)




Indicate
by check mark whether the registrant is a shell company (as defined in Rule
12b-2 of the Exchange Act). YESoNO x





The number
of shares outstanding of the Registrant’s Common Stock, $.01 par value, was
5,473,519 as of October 31, 2009.





ORE
PHARMACEUTICAL HOLDINGS INC.






TABLE
      OF CONTENTSPART I
              FINANCIAL INFORMATIONItem 1.
              Financial Statements
              3Consolidated Condensed Balance Sheets at September 30, 2009
      and December 31, 2008
              3Consolidated Condensed Statements of Operations for the Three
      and Nine Months Ended September 30, 2009 and 2008
              4Consolidated Condensed Statements of Cash Flows for the Nine
      Months Ended September 30, 2009 and 2008
              5Notes to Consolidated Condensed Financial
      Statements
              6Item 2.
              Management’s Discussion and Analysis of Financial Condition
      and Results of Operations
              11Item 4T.
              Controls and Procedures
              14PART II
              OTHER INFORMATIONItem 1.
              Legal Proceedings
              15Item 2.
              Unregistered Sales of Equity Securities and Use of
      Proceeds
              15Item 3.
              Defaults Upon Senior Securities
              15Item 4.
              Submission of Matters to a Vote of Security
      Holders
              15Item 5.
              Other Information
              15Item 6.
              Exhibits
              15Signatures
              
              16






Reorganization
of Ore Pharmaceuticals Inc. into a Holding Company Structure




On October
20, 2009, the stockholders of Ore Pharmaceuticals Inc. (“Ore”) adopted the
Agreement and Plan of Reorganization, dated August 14, 2009, by and among Ore,
Ore Pharmaceutical Holdings Inc. (the “Registrant”) and Ore Pharmaceuticals
Merger Sub Inc. (the “Agreement”).  The reorganization contemplated by
the Agreement (the “Reorganization”) was consummated on October 20,
2009.  In accordance with the Agreement, as described in the
Registrant’s Registration Statement on Form S-4, originally filed with the
Securities and Exchange Commission on August 14, 2009, and as amended
thereafter, Ore became a wholly owned subsidiary of the Registrant and each
share of Common Stock of Ore was exchanged for one share of Common Stock of the
Registrant.  The Common Stock of the Registrant is listed for trading on
The NASDAQ Capital Market under the symbol “ORXE,” the same symbol under which
Ore’s Common Stock traded before the Reorganization.  As a result of
the Reorganization, the Common Stock of Ore has ceased to trade on The NASDAQ
Capital Market.  As a result of the Reorganization, the Registrant is
the successor issuer to Ore pursuant to Rule 12g-3 under the Securities Exchange
Act of 1934, as amended (the “Exchange Act”).  Pursuant to paragraph
(a) of Rule 12g-3, the Registrant’s Common Stock is deemed registered under
Section 12(g) of the Exchange Act and the Registrant has succeeded to Ore’s
reporting obligations under Sections 13(a) and 15(d) of the Exchange
Act.  References to Ore, the Registrant or the Company for the period
prior to October 20, 2009 refer to Ore Pharmaceuticals Inc. and for the period
following October 20, 2009 refer to Ore Pharmaceutical Holdings
Inc.





Because
the Reorganization occurred subsequent to the quarterly reporting period ended
September 30, 2009, the Consolidated Condensed Financial Statements consist of
the accounts of Ore Pharmaceuticals Inc. (see Note 7 of the consolidated
condensed financial statements included in Part 1 of this report).






2.





PART
I                               FINANCIAL
INFORMATION





Item
1.              Financial
Statements





ORE
PHARMACEUTICALS INC.





CONSOLIDATED
CONDENSED BALANCE SHEETS


(in
thousands, except share data)




September
      30,
              
              
              December
      31,2009
              
              
              2008(unaudited)ASSETSCurrent
      assets:Cash
      and cash equivalents
              
              $
              6,957
              
              
              $
              10,784Marketable
      securities available-for-sale
              
              
              68
              
              
              
              -Prepaid
      expenses
              
              
              229
              
              
              
              200Notes
      receivable, net
              
              
              790
              
              
              
              3,252Other
      current assets
              
              
              37
              
              
              
              70Total
      current assets
              
              
              8,081
              
              
              
              14,306Property
      and equipment, net
              
              
              36
              
              
              
              483Other
      intangibles, net
              
              
              694
              
              
              
              573Note
      receivable, net
              
              
              -
              
              
              
              338Other
      assets
              
              
              25
              
              
              
              -Total
      assets
              
              $
              8,836
              
              
              $
              15,700LIABILITIES
      AND STOCKHOLDERS' EQUITYCurrent
      liabilities:Accounts
      payable
              
              $
              758
              
              
              $
              623Accrued
      compensation and employee benefits
              
              
              144
              
              
              
              1,185Other
      accrued expenses
              
              
              1,434
              
              
              
              1,267Current
      portion of long-term debt
              
              
              450
              
              
              
              477Total
      current liabilities
              
              
              2,786
              
              
              
              3,552Deferred
      rent
              
              
              24
              
              
              
              -Total
      liabilities
              
              
              2,810
              
              
              
              3,552Commitments
      and contingencies
              
              
              -
              
              
              
              -Stockholders'
      equity:Preferred
      stock, $.01 par value; 10,000,000 shares authorized; and no shares issued
      andoutstanding
      as of September 30, 2009 and December 31, 2008
              
              
              -
              
              
              
              -Common
      stock, $.01 par value; 60,000,000 shares authorized;  5,473,519
      and 5,483,519 sharesissued
      and outstanding as of September 30, 2009 and December 31, 2008,
      respectively
              
              
              55
              
              
              
              55Additional
      paid-in-capital
              
              
              385,019
              
              
              
              384,922Accumulated
      other comprehensive income
              
              
              68
              
              
              
              -Accumulated
      deficit
              
              
              (379,116
              )
              
              
              (372,829
              )Total
      stockholders' equity
              
              
              6,026
              
              
              
              12,148Total
      liabilities and stockholders' equity
              
              $
              8,836
              
              
              $
              15,700




See accompanying
notes.






3.




ORE
PHARMACEUTICALS INC.





CONSOLIDATED CONDENSED STATEMENTS OF OPERATIONS


(in
thousands, except per share data)


(unaudited)




Three
      Months Ended
              
              
              Nine
      Months EndedSeptember
      30,
              
              
              September
      30,2009
              
              
              2008
              
              
              2009
              
              
              2008Services
      revenue
              
              $
              -
              
              
              $
              200
              
              
              $
              25
              
              
              $
              1,950Expenses:Research
      and development
              
              
              501
              
              
              
              2,342
              
              
              
              2,080
              
              
              
              8,547Selling,
      general and administrative
              
              
              986
              
              
              
              2,632
              
              
              
              5,292
              
              
              
              10,302Total
      expenses
              
              
              1,487
              
              
              
              4,974
              
              
              
              7,372
              
              
              
              18,849Loss
      from operations
              
              
              (1,487
              )
              
              
              (4,774
              )
              
              
              (7,347
              )
              
              
              (16,899
              )Interest
      (income), net
              
              
              (335
              )
              
              
              (146
              )
              
              
              (502
              )
              
              
              (648
              )(Income)/loss
      on equity investments
              
              
              (558
              )
              
              
              2,964
              
              
              
              (558
              )
              
              
              2,964Gain
      on sale of DioGenix Inc.
              
              
              -
              
              
              
              (146
              )
              
              
              -
              
              
              
              (146
              )Net
      loss
              
              $
              (594
              )
              
              $
              (7,446
              )
              
              $
              (6,287
              )
              
              $
              (19,069
              )Basic
      and diluted net loss per share
              
              $
              (0.11
              )
              
              $
              (1.36
              )
              
              $
              (1.15
              )
              
              $
              (3.33
              )Shares
      used in computing basic and dilutednet
      loss per share
              
              
              5,474
              
              
              
              5,477
              
              
              
              5,474
              
              
              
              5,719




See
accompanying notes.






4.





ORE
PHARMACEUTICALS INC.





CONSOLIDATED CONDENSED STATEMENTS OF CASH FLOWS


(in
thousands)


(unaudited)








Nine
      Months EndedSeptember
      30,2009
              
              
              2008Cash
      flows from operating activities:Loss
      from operations
              
              $
              (6,287
              )
              
              $
              (19,069
              )Adjustments
      to reconcile loss from operations to net cash flowsfrom
      operating activities:Depreciation and amortization
              
              
              102
              
              
              
              847Non-cash stock-based compensation expense
              
              
              97
              
              
              
              130Write-down of equity investment
              
              
              -
              
              
              
              2,964Gain on sale of equity investment
              
              
              (558
              )
              
              
              -Gain on sale of DioGenix Inc.
              
              
              -
              
              
              
              (146
              )Other non-cash items
              
              
              141
              
              
              
              22Changes
      in operating assets and liabilities:Prepaids and other assets
              
              
              (21
              )
              
              
              2,437Accounts payable
              
              
              135
              
              
              
              (244
              )Accrued expenses
              
              
              (850
              )
              
              
              (1,688
              )Deferred revenue
              
              
              -
              
              
              
              (1,500
              )Net cash flows from operating activities
              
              
              (7,241
              )
              
              
              (16,247
              )Cash
      flows from investing activities:Purchases of property and equipment
              
              
              (20
              )
              
              
              (171
              )Proceeds from sale of property and equipment
              
              
              70
              
              
              
              -Purchases of licenses and patent costs
              
              
              (167
              )
              
              
              (383
              )Proceeds from sale of marketable securities
    available-for-sale
              
              
              -
              
              
              
              10,527Purchase of marketable securities available-for-sale
              
              
              -
              
              
              
              (4,501
              )Proceeds received from notes receivables
              
              
              3,000
              
              
              
              -Proceeds from sale of equity investment
              
              
              558
              
              
              
              -Net proceeds received from sale of Genomics Assets
              
              
              -
              
              
              
              412Net proceeds received from sale of Preclinical Division
              
              
              -
              
              
              
              272Net proceeds received from sale of DioGenix Inc.
              
              
              -
              
              
              
              500Net cash flows from investing activities
              
              
              3,441
              
              
              
              6,656Cash
      flows from financing activities:Purchase of common stock
              
              
              -
              
              
              
              (2,991
              )Repayments of an equipment loan
              
              
              (27
              )
              
              
              (38
              )Net cash flows from financing activities
              
              
              (27
              )
              
              
              (3,029
              )Net
      decrease in cash and cash equivalents
              
              
              (3,827
              )
              
              
              (12,620
              )Cash
      and cash equivalents, beginning of period
              
              
              10,784
              
              
              
              26,323Cash
      and cash equivalents, end of period
              
              $
              6,957
              
              
              $
              13,703Supplemental
      disclosure:Interest paid
              
              $
              -
              
              
              $
              4Non-cash
      investing transactions:Fair value of promissiory note received in connection with the sale of
      DioGenix Inc.
              
              $
              -
              
              
              $
              673




See
accompanying notes.






5.




ORE
PHARMACEUTICALS INC.





Notes to Consolidated Condensed Financial Statements


September
30, 2009


(in
thousands, except share and per share data)


(unaudited)





Note
1 — Organization and summary of significant accounting policies





Description
of Business





Ore
Pharmaceuticals Inc. (the “Company”) is a pharmaceutical asset management
company.  The Company acquires interests in pharmaceutical assets
whose value, it believes, it can significantly enhance through targeted
development, with the goal of then monetizing these assets through sales or
out-licensing transactions.  The Company currently is focusing on
developing and monetizing its current portfolio, which includes four
clinical-stage compounds in-licensed from major pharmaceutical
companies.  The four compounds in the Company’s development portfolio
are: ORE1001, its lead compound, ORE10002, ORE5002 (tiapamil) and ORE5007
(romazarit).





On October
20, 2009, the Company completed a reorganization that was undertaken primarily
in order to better protect the value of the Company’s approximately $324,000 in
gross net operating and capital loss carryforwards that can be used to reduce
the amount of income tax the Company could be required to pay on future earnings
from its business.  As a result of this reorganization, the Company
became a wholly owned subsidiary of a new company, Ore Pharmaceutical Holdings
Inc., as of October 20, 2009 (see Note 7).





Basis
of Presentation





The
accompanying unaudited consolidated condensed financial statements have been
prepared in accordance with United States Generally Accepted Accounting
Principles (“GAAP”) for interim financial information and the instructions to
Form 10-Q and Article 8-03 of Regulation S-X.  The consolidated
condensed balance sheet as of September 30, 2009, consolidated condensed
statements of operations for the three and nine months ended September 30, 2009
and 2008 and the consolidated condensed statements of cash flows for the nine
months ended September 30, 2009 and 2008 are unaudited, but include all
adjustments (consisting of normal recurring adjustments) that the Company
considers necessary for a fair presentation of the financial position, operating
results and cash flows, respectively, for the periods
presented.  Although the Company believes that the disclosures in
these financial statements are adequate to make the information presented not
misleading, certain information and footnote information normally included in
financial statements prepared in accordance with GAAP have been condensed or
omitted pursuant to the rules and regulations of the United States Securities
and Exchange Commission (“SEC”).  All material intercompany accounts
and transactions have been eliminated in consolidation.





In 2008,
the Company sold its wholly owned subsidiary, DioGenix Inc., which was its
molecular diagnostics business.  The results of operations for the
Company’s molecular diagnostic business were not considered material and,
therefore, have not been classified as a discontinued
operation.  There was no revenue from the Company’s molecular
diagnostics business.





Results
for any interim period are not necessarily indicative of results for any future
interim period or for the entire year.  The accompanying unaudited
consolidated condensed financial statements should be read in conjunction with
the consolidated financial statements and notes thereto included in the
Company’s Annual Report on Form 10-K for the year ended December 31,
2008.





Use
of Estimates





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






6.




Fair
Value Measurements





The
Company adopted Accounting Standards Codification (“ASC”) Topic 820 (“ASC 820”),
previously referred to as Statement of Financial Accounting Standards (“SFAS”)
No. 157 “Fair Value Measurements” for financial assets and liabilities on
January 1, 2008.  The Company adopted ASC 820 for non-financial assets
and liabilities on January 1, 2009.





ASC 820
discusses valuation techniques, such as the market approach (comparable market
prices), the income approach (present value of future income or cash flow) and
the cost approach (cost to replace the service capacity of an asset or
replacement cost).  The statement utilizes a fair value hierarchy that
prioritizes the inputs to valuation techniques used to measure fair value into
three broad levels.  The following is a brief description of those
three levels:





·
            Level
      1:  Observable inputs such as quoted prices (unadjusted) in
      active markets for identical assets or
  liabilities.




·
            Level
      2:  Inputs other than quoted prices that are observable for the
      asset or liability, either directly or indirectly.  These
      include quoted prices for similar assets or liabilities in active markets
      and quoted prices for identical or similar assets or liabilities in
      markets that are not active.




·
            Level
      3:  Unobservable inputs that reflect the reporting entity’s own
      assumptions.




The
Company’s recurring financial assets and liabilities subject to fair value
measurements and the necessary disclosures are as follows:






Fair
      Valueas
      of
              
              
              Fair
      Value Measurements at September 30, 2009September
      30,
              
              
              Using
      Fair Value Hierarchy2009
              
              
              Level
      1
              
              
              Level
      2
              
              
              Level
      3Cash
      and cash equivalents
              
              $
              6,957
              
              
              $
              6,957
              
              
              $
              -
              
              
              $
              -Marketable
      securities available-for-sale
              
              
              68
              
              
              
              68
              
              
              
              -
              
              
              
              -Total
              
              $
              7,025
              
              
              $
              7,025
              
              
              $
              -
              
              
              $
              -




Marketable
securities available-for-sale includes an equity investment in a publicly-traded
company and is carried at market value based on quoted market
prices.  Unrealized gains and losses for this investment are reported
as a separate component of stockholders’ equity until realized.





The
amounts in the Company’s Consolidated Condensed Balance Sheets for notes
receivable, accounts payable and long-term debt approximate fair value due to
their short-term nature.





There were
no required fair value measurements for non-financial assets and liabilities in
the third quarter of 2009.





Comprehensive
Loss





The
Company accounts for comprehensive loss as prescribed by ASC 220, previously
referred to as SFAS No. 130, “Reporting Comprehensive
Income.”  Comprehensive income (loss) is the total net income (loss)
plus all changes in equity during the period except those changes resulting from
investment by and distribution to owners.  Total comprehensive loss
was $526 and $7,446 for the three months ended September 30, 2009 and 2008,
respectively, and $6,219 and $19,023 for the nine months ended September 30,
2009 and 2008, respectively.





New
Accounting Pronouncements





In June
2009, the Financial Accounting Standards Board (“FASB”) issued an accounting
pronouncement found under ASC 105, previously referred to as SFAS No. 168, “The
FASB Accounting Standards Codification and the Hierarchy of Generally Accepted
Accounting Principles, a replacement of FASB Statement No. 162”, which
establishes the FASB Accounting Standards Codification as the source of
authoritative accounting principles recognized by the FASB to be applied in the
preparation of financial statements in conformity with GAAP.  ASC 105
explicitly recognizes rules and interpretive releases of the SEC under federal
securities laws as authoritative GAAP for SEC registrants.  ASC 105
was effective for financial statements issued for interim and annual reporting
periods ending after September 15, 2009 (the quarter ended September 30, 2009
for the Company) and did not have an impact on the Company's final position or
results of operations.





In May
2009, the FASB issued an accounting pronouncement found under ASC 855-10,
previously referred to as SFAS No. 165, “Subsequent Events”, which establishes
general standards of accounting for and disclosure of events that occur after
the balance sheet date, but before financial statements are issued or are
available to be issued.  ASC 855-10 is effective for financial
statements issued for interim and annual reporting periods ending after June 15,
2009 (the quarter ended June 30, 2009 for the Company).  The adoption
of ASC 855-10 did not have an impact on the Company's financial position or
results of operations.






7.




In April
2009, the FASB issued an accounting pronouncement under ASC 825-10-50 extending
the disclosure requirements for financial instruments, previously referred to as
FASB Staff Position (“FSP”) No. 107-1 and Accounting Principles Board Opinion
No. 28-1, “Interim Disclosures about Fair Value of Financial
Instruments”.  ASC 825-10-50 requires disclosures in interim reporting
periods and in financial statements for annual reporting periods regarding the
fair value of all financial instruments for which it is practicable to estimate
that value, whether recognized or not on the company's balance
sheet.  ASC 825-10-50 requires entities to disclose the methods and
significant assumptions used to estimate the fair value of financial instruments
and describe changes in methods and significant assumptions, in both interim and
annual financial statements.  ASC 825-10-50 is effective for interim
reporting periods ending after June 15, 2009 (the quarter ended June 30, 2009
for the Company).  While the adoption of ASC 825-10-50 impacts the
Company's disclosures, it did not have an impact on the Company's financial
position or results of operations.





In April
2009, the FASB issued an accounting pronouncement found under ASC 320-10-65,
previously referred to as FSP SFAS 115-2 and SFAS 124-2, “Recognition and
Presentation of Other-Than-Temporary Impairments,” which modifies the
recognition requirements for other-than-temporary impairments of debt securities
and enhances existing disclosures with respect to other-than-temporary
impairments of debt and equity securities.  ASC 320-10-65 is effective
for interim and annual reporting periods ending after June 15, 2009 (the quarter
ended June 30, 2009 for the Company).  The adoption of ASC 320-10-65
had no impact on the Company’s financial position or results of
operations.
 
 In
February 2008, the FASB issued a one-year deferral for non-financial assets and
liabilities to comply with ASC 820, previously referred to as
SFAS No. 157.  The Company adopted ASC 820 for financial
assets and liabilities effective January 1, 2008 (see Note 1, Fair Value
Measurements).  The Company adopted ASC 820 as it pertains to
non-financial assets and liabilities effective January 1, 2009 and the adoption
had no impact on the Company’s financial position or results of
operations.


In
December 2007, the FASB issued an accounting pronouncement found under ASC 805,
previously referred to as SFAS No. 141 Revised, “Business
Combinations”.  ASC 805 requires an acquirer to determine the fair
value of the consideration exchanged as of the acquisition date (i.e. the date
the acquirer obtains control).  Previously, an acquisition was valued
as of the date the parties agreed upon the terms of the
transaction.  ASC 805 also modifies, among other things, the
accounting for direct costs associated with an acquisition, contingencies
acquired and contingent consideration.  The Company adopted ASC 805
effective January 1, 2009 for business combinations occurring after the
effective date.





In
December 2007, the FASB ratified an accounting pronouncement found under
ASC 808-10-15, previously referred to as Emerging Issues Task Force
No. 07-1, “Accounting for Collaborative Agreements”.  ASC
808-10-15 provides guidance regarding financial statement presentation and
disclosure of collaborative arrangements, as defined therein.  The
Company adopted ASC 808-10-15 effective January 1, 2009 and the adoption had no
impact on the Company’s financial position or results of
operations.





Note
2 – Liquidity and management’s plans





Since
inception, the Company has incurred, and continues to incur, significant losses
from operations.  At September 30, 2009, the Company had $7,025 in
cash and cash equivalents and marketable securities
available-for-sale.  The Company has realigned its corporate resources
and as a result significantly reduced its workforce from 71 employees on
December 31, 2007 to 6 employees as of September 30, 2009.  In
addition, the Company assigned its original Cambridge, Massachusetts lease and
leased new space in Cambridge, Massachusetts at a lower cost.  The
Company believes that its existing cash and cash equivalents and marketable
securities available-for-sale, continuing cash savings resulting from its
ongoing cash conservation efforts and proceeds from the collection of its
remaining outstanding note receivable, will be sufficient to allow the Company
to operate into the first quarter of 2011, including the costs of initiating and
completing the Phase Ib/IIa clinical trial for ORE1001, which is expected to be
completed in the third quarter of 2010.  However, there can be no
assurance that the Company will be successful in its continuing cash
conservation efforts, the collection of its remaining outstanding note
receivable or, if necessary, attracting additional
financing.  Furthermore, there is no assurance if the Company
completes its Phase Ib/IIa clinical trial of ORE1001 that the results will be
satisfactory or will enable the Company to successfully out-license
ORE1001.  If the Company is not successful in achieving its
objectives, it might be necessary to discontinue operations and liquidate the
Company in late 2010.  The balance sheet at September 30, 2009 does
not include any adjustments relating to recoverability and classification of
recorded asset amounts or the amounts and classifications of liabilities that
might be necessary in the event of such liquidation.





Note
3 — Stock-based compensation





At
September 30, 2009, the Company has the following stock-based compensation
plans: the 1997 Equity Incentive Plan (the “Stock Plan”) and the 1997
Non-Employee Directors’ Stock Option Plan (the “Directors’ Plan”) (see Note
7).





The
Company recorded stock-based compensation expense (benefit) of $40 and ($99) for
the three months ended September 30, 2009 and 2008, respectively, and $97 and
$130 for the nine months ended September 30, 2009 and 2008,
respectively.  During the three months ended September 30, 2008, the
stock-based compensation benefit of ($99) was due to the reversal of previously
recognized expense for restricted stock awards that were forfeited, or that the
Company had determined were not probable to vest.







8.




Stock
Option Awards





The
Company determined the fair value of each option grant on the date of grant
using the Black-Scholes option pricing model for the indicated periods, with the
following assumptions:




Three
      Months Ended
              
              Nine
      Months EndedSeptember
      30,
              
              September
      30,2009
              
              2008
      (1)
              
              2009
              
              2008Weighted
      average fair value of grants
              $0.32
              
              -
              
              $0.26
              
              $0.97Expected
      volatility
              69%
              
              -
              
              69%
      to 79%
              
              61%
      to 65%Risk-free
      interest rate
              2.75%
              
              -
              
              1.31%
      to 2.75%
              
              2.53%
      to 3.04%Expected
      lives
              5
      years
              
              -
              
              5
      years
              
              3
      yearsDividend
      rate
              0%
              
              -
              
              0%
              
              0%(1)
      No stock option awards were granted during the three months ended
      September 30, 2008.




The
following is a summary of option activity for the nine months ended September
30, 2009:




Per
      ShareWeighted-
              
              
              AggregateNumber
      of
              
              
              Average
              
              
              IntrinsicShares
              
              
              Exercise
      Price
              
              
              ValueOutstanding
      at January 1, 2009
              
              
              683,847
              
              
              $
              24.10Options
      granted
              
              
              1,036,100
              
              
              $
              0.47Options
      exercised
              
              
              -
              
              
              $
              -Options
      cancelled
              
              
              (394,008
              )
              
              $
              18.24Outstanding
      at September 30, 2009
              
              
              1,325,939
              
              
              $
              7.37
              
              
              $
              201Exercisable
      at September 30, 2009
              
              
              350,348
              
              
              $
              26.18
              
              
              $
              23






The
aggregate intrinsic value in the table above represents the total intrinsic
value (the excess of the Company’s closing stock price on the last trading day
of September 2009 over the exercise price, multiplied by the number of
in-the-money options) that would have been received by the option holders had
all option holders exercised their options on September 30,
2009.  This amount is subject to change based on changes to the fair
market value of the Company’s Common Stock.




As of
September 30, 2009, $270 of total unrecognized compensation cost related to
stock option awards is expected to be recognized over a weighted-average period
of 1.8 years.  This estimate does not include the impact of other
possible stock-based awards that may be made during future periods.





Restricted
Stock Awards





The
Compensation Committee of the Board of Directors of the Company had previously
approved grants for shares of restricted stock under the Stock Plan subject to
certain performance- or time-based vesting conditions which, if not met, would
result in forfeiture of the shares and the reversal of any previously recognized
related stock-based compensation expense.





The
following is a summary of restricted stock awards activity for the nine months
ended September 30, 2009:




Per
      ShareWeighted-AverageNumber
      of
              
              
              Grant-DateShares
              
              
              Fair
      ValueOutstanding
      at January 1, 2009
              
              
              10,000
              
              
              $
              6.15Restricted
      stock granted
              
              
              -
              
              
              $
              -Restricted
      stock vested
              
              
              -
              
              
              $
              -Restricted
      stock forfeited
              
              
              (10,000
              )
              
              $
              6.15Outstanding
      at September 30, 2009
              
              
              -
              
              
              $
              -





Performance-based
non-vested restricted stock awards are recognized as compensation expense over
the expected vesting period based on the fair value at the date of grant and the
number of shares ultimately expected to vest.






9.




Note
4 — Loan and grant agreements with the State of Maryland





During the
second quarter of 2009, the Company received a notice requiring repayment of all
amounts potentially due under a loan and a grant agreement with the State of
Maryland that total $715 at September 30, 2009.  The Company has
recorded the amounts due under the loan and grant agreements within the current
portion of long-term debt and other accrued expenses.  The Company is
in discussions with the State of Maryland concerning the terms of potential
repayment of these amounts.





Note
5 — Ocimum Biosolutions Inc. promissory note and related agreements





In
connection with the sale of the Company’s Genomics business pursuant to a
certain Asset Purchase Agreement with Ocimum Biosolutions Limited, as parent,
and Ocimum Biosolutions Inc., a Delaware corporation (“Ocimum”), as Purchaser,
which was completed on December 14, 2007, the Company had received as partial
payment for the sales price, a $3,000 secured promissory note from Ocimum and
Ocimum Biosolutions Limited, guaranteed by Coramandel Prestcrete Private
Limited, a company incorporated in the Republic of India.  The
promissory note, secured by a security agreement between Ocimum and the Company,
was due and payable on June 15, 2009.





In June
2009, the Company entered into a superseding $3,000 secured promissory note
(“Note”) with Ocimum and its affiliate, Ocimum Biosolutions India Limited, a
company incorporated in the Republic of India, which was secured pursuant to a
superseding security agreement (“Security Agreement”) with Ocimum and repayment
of which was guaranteed by a guaranty agreement with Coramandel Infrastructure
Private Limited, a company incorporated in the Republic of India, in favor of
the Company.  The superseding agreements were effective as of June 15,
2009, and the original promissory note, security agreement and related guarantee
agreement were cancelled and terminated.





In
connection with the sale of the Genomics business, the Company had assigned its
related real estate lease, but had remained primarily liable through January
2011 in the event Ocimum failed to perform its obligations under the
lease.  An escrow account served partially to secure Ocimum’s
performance.  In July 2009, the landlord agreed to release the Company
from liability under the lease, and the escrow agreement between Ocimum and the
Company was terminated.





During the
third quarter of 2009, the Company collected the outstanding principal of the
Note plus additional amounts relating to principal adjustments and
interest.





Note
6 — Lease abandonment





In the
second quarter of 2009, the Company vacated substantially all of its
Gaithersburg, Maryland facility and recorded a non-cash accelerated lease
expense and write-down of leasehold improvements and other related assets of
$749, which is included in Selling, General and Administrative expenses in the
Company’s Consolidated Condensed Statements of Operations for the nine months
ended September 30, 2009.





Note
7 — Subsequent events





On October
20, 2009, the Company’s stockholders approved, and the Company completed, a
reorganization of the Company that was undertaken primarily in order to better
protect the value of the Company’s approximately $324,000 in gross net operating
and capital loss carryforwards (collectively, the “NOLs”) that can be used to
reduce the amount of income tax the Company could be required to pay on future
earnings from its business.  As a result of this reorganization, Ore
Pharmaceuticals Inc. became a wholly owned subsidiary of a new company, Ore
Pharmaceutical Holdings Inc. (“Ore Holdings”).  All the outstanding
shares of Ore Pharmaceuticals Inc. were converted into shares of Ore Holdings
and Ore Holdings then became the publicly traded, NASDAQ listed
company.  In addition, on October 20, 2009, the Company’s stockholders
approved the adoption of a new stock-based compensation plan, which replaced the
Company’s Stock Plan and Directors’ Plan.





The
Company evaluated all events or transactions that occurred after
September 30, 2009 and through November 13, 2009, the date these financial
statements were filed with the SEC.






10.




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





This
Quarterly Report on Form 10-Q (“Form 10-Q”) contains forward-looking statements
regarding future events and the future results of Ore Pharmaceutical Holdings
Inc. (“Ore Holdings”) that are based on current expectations, estimates,
forecasts and projections about the industries in which Ore Holdings and its
subsidiaries operate and the beliefs and assumptions of the management of Ore
Holdings. Words such as “expects,” “anticipates,” “targets,” “goals,”
“projects,” “intends,” “plans,” “believes,” “seeks,” “estimates,” variations of
such words, and similar expressions are intended to identify such
forward-looking statements. These forward-looking statements are only
predictions and are subject to risks, uncertainties and assumptions. Therefore,
actual results may differ materially and adversely from those expressed in any
forward-looking statements. Factors that might cause or contribute to such
differences include those discussed in our Annual Report on Form 10-K for the
year ended December 31, 2008 under the section entitled “Risk Factors” and in
our subsequent filings with the United States Securities and Exchange Commission
(“SEC”). Ore Holdings undertakes no obligation to revise or update publicly any
forward-looking statements to reflect any change in management’s expectations
with regard thereto or any change in events, conditions, or circumstances on
which any such statements are based.





Unless the
context otherwise requires, references in this Form 10-Q to “Ore,” “Ore
Pharmaceuticals,” “Ore Holdings,” “DioGenix,” the “Company,” “we,” “us,” and
“our” refer to Ore Pharmaceutical Holdings Inc., its wholly owned subsidiary,
Ore Pharmaceuticals Inc., and its formerly wholly owned subsidiary, DioGenix
Inc.





Overview





Ore
Pharmaceutical Holdings Inc. is a pharmaceutical asset management
company.  We acquire interests in pharmaceutical assets whose value,
we believe, we can significantly enhance through targeted development, with the
goal of then monetizing these assets through sales or out-licensing
transactions.  In order to fund these activities, we intend to source
third-party financing using alternative investment vehicles designed to align
the investment profile of each program with the interests of its direct
investors, as well as our stockholders.  We anticipate that designing,
raising and investing these alternative vehicles will be a regular part of our
ongoing activities as a company.  We believe this model of drug
development offers enhanced capital efficiency, shorter development timelines
and better alignment of the risks and rewards of drug development for different
groups of investors compared to traditional methods.





We are
establishing a business model under which we anticipate that Ore will earn
program management advisory fees for acquiring, developing through proof of
concept and then monetizing pharmaceutical assets, as well as retain substantial
economic interests in successful programs.  Our goal is to create an
investment-driven, investor returns-focused organization with the appropriate
corporate structure and skill sets to execute on our strategy.  To
this end, we have assembled a management team with three key areas of expertise
required to implement this model: clinical development, public- and
private-market healthcare finance and pharmaceutical business
development.





Following
our reorganization described below, we will focus on developing and monetizing
our current portfolio, which includes four clinical-stage compounds in-licensed
from major pharmaceutical companies.  Each of these compounds has been
observed to be well-tolerated in human clinical trials to date.  We
are evaluating our lead compound, ORE1001, as a potential treatment for
Inflammatory Bowel Disease (IBD).  IBD is a severe gastrointestinal
condition that is estimated to affect as many as one million people in the
United States alone.  We expect to initiate a Phase Ib/IIa clinical
trial in patients with ulcerative colitis – one of the two main disorders
comprising IBD – in the fourth quarter of 2009.





In
September 2009, we received notice from The NASDAQ Stock Market that our stock
would be subject to delisting if we did not regain compliance by having a
closing bid price equal to or above $1.00 per share for a minimum of 10
consecutive trading days prior to March 15, 2010.  While we will
attempt to regain compliance, there can be no assurance that the bid price of
our stock will close at or above $1.00 per share for the required time during
the grace period or that on March 15, 2010, we will meet all applicable
standards for initial listing (except the bid price requirement) on The NASDAQ
Capital Market in order to be eligible for an additional 180 calendar day
compliance period.





On October
20, 2009, we completed a reorganization of the Company that was undertaken
primarily in order to better protect the value of our approximately $324 million
in gross net operating and capital loss carryforwards (collectively, the “NOLs”)
that can be used to reduce the amount of income tax we could be required to pay
on future earnings from our business.  As a result of this
reorganization, Ore Pharmaceuticals Inc. became a wholly owned subsidiary of a
new company, Ore Pharmaceutical Holdings Inc. (“Ore Holdings”).  All
the outstanding shares of Ore Pharmaceuticals Inc. were converted into shares of
Ore Holdings and Ore Holdings then became the publicly traded, NASDAQ listed
company that we now refer to as “Ore”.





We have
incurred net losses in each year since our inception, including losses of $22.5
million in 2008 and $34.7 million in 2007.  At September 30, 2009, we
had an accumulated deficit of $379.1 million.  Our losses have
resulted principally from costs incurred by our ongoing business, as well as
businesses we have sold.  We expect to incur additional losses in the
future.






11.




Results
of Operations





Three
Months Ended September 30, 2009 and 2008





Revenue.  We had no
revenue for the three months ended September 30, 2009 compared to $0.2 million
for the three months ended September 30, 2008.  During the three
months ended September 30, 2008, our revenue resulted primarily from the
achievement of a milestone unrelated to our pharmaceutical asset management
business.





Research and Development
Expense. Research and development expenses, which now consist almost
entirely of costs associated with the clinical development of ORE1001, decreased
to $0.5 million for the three months ended September 30, 2009 from $2.3 million
for the same period in 2008.  The decrease is primarily a result of
lower employee and facility-related costs due to our significant workforce
reductions.  For the remainder of 2009, we expect the significant
decrease in research and development expenses over 2008 to continue, primarily
as a result of workforce reductions.





Selling, General and Administrative
Expense. Selling, general and administrative expenses, which now consist
primarily of accounting, legal, human resources and other general corporate
expenses, decreased to $1.0 million for the three months ended September 30,
2009 from $2.6 million for the same period in 2008 primarily as a result of
lower employee costs due to our significant workforce reductions and reduced
professional fees relating to strategic planning.  For the remainder
of 2009, we expect the significant decrease in selling, general and
administrative expenses over 2008 to continue, primarily as a result of
workforce reductions and reduced professional fees relating to strategic
planning.





Net Interest Income. Net
interest income increased to $0.3 million for the three months ended September
30, 2009 from $0.1 million for the same period in 2008, due to principal
adjustments, which were recorded as interest income, and interest related to the
superseding secured promissory note from Ocimum Biosolutions Inc. (“Ocimum”),
partially offset by the decline in the balance of our cash and cash equivalents
and marketable securities available-for-sale and a decrease in our rates of
return on investments.





(Income)/Loss on Equity Investments.During the three months ended September 30, 2009, we recorded other
income of $0.6 million related to the sale of a portion of our investment in
Neuralstem, Inc. (“Neuralstem”). During the three months
ended September 30, 2008, we recorded a $3.0 million write-down of the remaining
book value of our investment in Xceed Molecular Inc. (“Xceed”, formerly
MetriGenix Corporation), due to an other-than-temporary decline in its estimated
fair value.





Nine
Months Ended September 30, 2009 and 2008





Revenue.  We had
less than $0.1 million of revenue for the nine months ended September 30, 2009
compared to $2.0 million for the nine months ended September 30,
2008.  During the nine months ended September 30, 2008, our revenue
resulted primarily from a licensing agreement for certain technology unrelated
to our pharmaceutical asset management business.





Research and Development
Expense. Research and development expenses decreased to $2.1 million for
the nine months ended September 30, 2009 from $8.5 million for the same period
in 2008.  The decrease is primarily a result of lower employee and
facility-related costs due to our significant workforce reductions.





Selling, General and Administrative
Expense. Selling, general and administrative expenses decreased to $5.3
million for the nine months ended September 30, 2009 from $10.3 million for the
same period in 2008 primarily as a result of lower employee costs due to our
significant workforce reductions, reduced professional fees relating to
strategic planning and the absence of $0.4 million of expense related to the
purchase of shares from a former director that occurred in 2008, partially
offset by $0.3 million in net facility-related lease abandonment costs in
2009.





Net Interest Income. Net
interest income decreased to $0.5 million for the nine months ended September
30, 2009 from $0.6 million for the same period in 2008, due to the decline in
the balance of our cash and cash equivalents and marketable securities
available-for-sale and a decrease in our rates of return on investments,
partially offset by principal adjustments, which were recorded as interest
income, and interest related to the superseding secured promissory note from
Ocimum.





(Income)/Loss on Equity Investments.During the nine months ended September 30, 2009, we recorded other income
of $0.6 million related to the sale of a portion of our investment in
Neuralstem. During the nine months
ended September 30, 2008, we recorded a $3.0 million write-down of the remaining
book value of our investment in Xceed, due to an other-than-temporary decline in
its estimated fair value.





Liquidity
and Capital Resources





Historically,
we have financed our operations through the issuance and sale of equity
securities, payments from customers and sales of parts of our business and
assets from time to time.  As of September 30, 2009, we had
approximately $7.0 million in cash and cash equivalents and marketable
securities available-for-sale, compared to $10.8 million as of December 31,
2008.






12.




Net cash
used in operating activities decreased to a negative $7.2 million for the nine
months ended September 30, 2009 from a negative $16.2 million for the same
period in 2008, primarily due to our reduced net loss for the nine months ended
September 30, 2009.





For the
nine months ended September 30, 2009, our investing activities consisted
primarily of the collection of the $3 million interest bearing promissory note
in connection with the 2007 sale of our Genomics business to Ocimum and $0.6
million in proceeds from the sale of an equity investment.





In
connection with the 2008 sale of DioGenix Inc. to Nerveda, Inc. (“Nerveda”), the
balance of the purchase price is due pursuant to a $0.8 million interest bearing
promissory note, with receipt of two principal payments of $0.4 million plus
interest due December 2009 and June 2010, subject to acceleration in certain
events.





In 2008,
we assigned our lease in Cambridge, Massachusetts, but remain liable under the
lease in the event of the assignee’s default.  The lease expires in
August 2013 and at September 30, 2009, the total remaining amounts due under the
lease for the balance of the term is $4.5 million.





In
connection with the 2006 sale of our Preclinical Division to Bridge
Pharmaceuticals, Inc. (“Bridge”), less than $0.1 million of the sales price
remains in escrow pending resolution between the parties.  We continue
to guarantee two leases now held by Bridge.  The leases expire in
February 2011 and December 2013 and at September 30, 2009, the total remaining
amounts due under the leases for the balance of the terms is $0.8 million and
$3.0 million, respectively.





Our
financing activities for the nine months ended September 30, 2008 primarily
consisted of the purchase of shares from a former director for $3.0
million.





In the
second quarter of 2009, we received a notice requiring repayment of all amounts
potentially due under a loan and a grant agreement with the State of Maryland
that total $0.7 million.  We have recorded the amounts due under the
loan and grant agreement within current portion of long-term debt and other
accrued expenses.  We are in discussions with the State of Maryland
concerning the terms of potential repayment of this amount.





We believe
that existing cash and cash equivalents and marketable securities
available-for-sale, the anticipated receipt of $0.8 million relating to the
promissory note from Nerveda and our ongoing cash conservation efforts, will
enable us to support our operations into the first quarter of 2011, including
the costs of initiating and completing the Phase Ib/IIa clinical trial for
ORE1001, which is expected to be completed in the third quarter of
2010.  However, there can be no assurance that we will be successful
in our continuing cash conservation efforts, the full collection of our
outstanding note receivable or, if necessary, attracting additional
financing.  Furthermore, there is no assurance if we complete our
clinical trial, that the results will be satisfactory or will enable us to
successfully out-license ORE1001.  If we are not successful in
achieving our objectives, it might be necessary to discontinue our operations
and liquidate the Company in late 2010.  We currently expect long-term
support of our operations to come from possible future financings and payments
from commercial arrangements from our portfolio of drug
candidates.  These estimates are forward-looking statements that
involve risks and uncertainties.  Our actual future capital
requirements and the adequacy of our available funds will depend on those
factors discussed above and in the Company’s Annual Report on Form 10-K for the
year ended December 31, 2008 under the section entitled “Risk Factors” and in
our subsequent filings with the SEC.





Recently
Issued Accounting Pronouncements





In June
2009, the Financial Accounting Standards Board (“FASB”) issued an accounting
pronouncement found under Accounting Standards Codification (“ASC”) 105,
previously referred to as SFAS No. 168, “The FASB Accounting Standards
Codification and the Hierarchy of Generally Accepted Accounting Principles, a
replacement of FASB Statement No. 162”, which establishes the FASB Accounting
Standards Codification as the source of authoritative accounting principles
recognized by the FASB to be applied in the preparation of financial statements
in conformity with GAAP.  ASC 105 explicitly recognizes rules and
interpretive releases of the SEC under federal securities laws as authoritative
GAAP for SEC registrants.  ASC 105 was effective for financial
statements issued for interim and annual reporting periods ending after
September 15, 2009 (our quarter ended September 30, 2009) and did not have an
impact on the our final position or results of operations.





In May
2009, the FASB issued an accounting pronouncement found under ASC 855-10,
previously referred to as SFAS No. 165, “Subsequent Events”, which establishes
general standards of accounting for and disclosure of events that occur after
the balance sheet date, but before financial statements are issued or are
available to be issued.  ASC 855-10 is effective for financial
statements issued for interim and annual reporting periods ending after June 15,
2009 (our quarter ended June 30, 2009).  The adoption of ASC 855-10
did not have an impact on our financial position or results of
operations.





In April
2009, the FASB issued an accounting pronouncement found under ASC 825-10-50
extending the disclosure requirements for financial instruments, previously
referred to as FASB Staff Position (“FSP”) No. 107-1 and Accounting Principles
Board Opinion No. 28-1, “Interim Disclosures about Fair Value of Financial
Instruments”.  ASC 825-10-50 requires disclosures in interim reporting
periods and in financial statements for annual reporting periods regarding the
fair value of all financial instruments for which it is practicable to estimate
that value, whether recognized or not on the company's balance
sheet.  ASC 825-10-50 requires entities to disclose the methods and
significant assumptions used to estimate the fair value of financial instruments
and describe changes in methods and significant assumptions, in both interim and
annual financial statements.  ASC 825-10-50 is effective for interim
reporting periods ending after June 15, 2009 (our quarter ended June 30,
2009).  While the adoption of ASC 825-10-50 impacts our disclosures,
it did not have an impact on our financial position or results of
operations.






13.




In April
2009, the FASB issued and accounting pronouncement found under ASC 320-10-65,
previously referred to as FSP SFAS 115-2 and SFAS 124-2, “Recognition and
Presentation of Other-Than-Temporary Impairments,” which modifies the
recognition requirements for other-than-temporary impairments of debt securities
and enhances existing disclosures with respect to other-than-temporary
impairments of debt and equity securities.  ASC 320-10-65 is effective
for interim and annual reporting periods ending after June 15, 2009 (our quarter
ended June 30, 2009).  The adoption of ASC 320-10-65 had no impact on
our financial position or results of operations.


In
February 2008, the FASB issued a one-year deferral for non-financial assets and
liabilities to comply with ASC 820, previously referred to as
SFAS No. 157.  We adopted ASC 820 for financial assets and
liabilities effective January 1, 2008 (see Note 1, Fair Value
Measurements).  We adopted ASC 820 as it pertains to
non-financial assets and liabilities effective January 1, 2009 and the adoption
had no impact on our financial position or results of operations.


In
December 2007, the FASB issued an accounting pronouncement found under ASC 805,
previously referred to as SFAS No. 141 Revised, “Business
Combinations”.  ASC 805 requires an acquirer to determine the fair
value of the consideration exchanged as of the acquisition date (i.e. the date
the acquirer obtains control).  Previously, an acquisition was valued
as of the date the parties agreed upon the terms of the
transaction.  ASC 805 also modifies, among other things, the
accounting for direct costs associated with an acquisition, contingencies
acquired and contingent consideration.  We adopted ASC 805 effective
January 1, 2009 for business combinations occurring after the effective
date.





In
December 2007, the FASB ratified accounting pronouncement found under ASC
808-10-15, previously referred to as Emerging Issues Task Force No. 07-1,
“Accounting for Collaborative Agreements.”  ASC 808-10-15 provides
guidance regarding financial statement presentation and disclosure of
collaborative arrangements, as defined therein.  We adopted ASC
808-10-15 effective January 1, 2009 and the adoption had no impact on our
financial position or results of operations.





Item4T.                      Controls
and Procedures





Evaluation
of Disclosure Controls and Procedures





Our
principal executive officer and principal financial officer, after evaluating
the effectiveness of our disclosure controls and procedures (as defined in
Exchange Act Rules 13a-15(e) and 15d-15(e)) as of the end of the period covered
by this Quarterly Report on Form 10-Q, have concluded that, based on such
evaluation, our disclosure controls and procedures were effective to ensure that
information required to be disclosed by us in the reports that we file or submit
under the Exchange Act is recorded, processed, summarized and reported, within
the time periods specified in the SEC’s rules and forms, and is accumulated and
communicated to our management, including our principal executive and principal
financial officers, or persons performing similar functions, as appropriate to
allow timely decisions regarding required disclosure.





Our
management, including the principal executive and principal financial officers,
does not expect that our disclosure controls or our internal control over
financial reporting will prevent or detect all errors and all instances of
fraud.  A control system, no matter how well designed and operated,
can provide only reasonable, not absolute, assurance that the control system’s
objectives will be met.  The design of a control system must reflect
the fact that there are resource constraints, and the benefits of controls must
be considered relative to their costs.  Further, because of the
inherent limitations in all control systems, no evaluation of controls can
provide absolute assurance that misstatements due to error or fraud will not
occur or that all control issues and instances of fraud, if any, within the
Company have been detected.  These inherent limitations include the
realities that judgments in decision-making can be faulty and that breakdowns
can occur because of simple error or mistake.  Controls can also be
circumvented by the individual acts of some persons, by collusion of two or more
people, or by management override of the controls.  The design of any
system of controls is based, in part, on certain assumptions about the
likelihood of future events and there can be no assurance that any design will
succeed in achieving its stated goals under all potential future
conditions.  Projections of any evaluation of the effectiveness of
controls to future periods are subject to risks.  Over time, controls
may become inadequate because of changes in conditions or deterioration in the
degree of compliance with policies or procedures.





Changes
in Internal Control Over Financial Reporting





There were
no changes in our internal controls over financial reporting during the third
quarter of 2009 that materially affected or are reasonably likely to materially
affect our internal controls over financial reporting.






14.




PART
II                                OTHER
INFORMATION





Item
1.              Legal
Proceedings





We are not
currently a party to any material legal proceedings.





Item
2.              Unregistered
Sales of Equity Securities and Use of Proceeds





None.





Item
3.              Defaults
Upon Senior Securities





None.





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





None.





Item
5.              Other
Information





On October
20, 2009, at the annual meeting of stockholders (“Annual Meeting”), the
stockholders approved the 2009 Omnibus Equity Incentive Plan (“2009 Plan”),
under which 2,224,092 shares of Common Stock have been reserved for issuance,
including 700,000 shares newly authorized at the Annual Meeting and 1,524,092
shares related to the 1997 Equity Incentive Plan and 1997 Non-Employee
Directors’ Plan (the “Prior Plans”).  The 2009 Plan replaces the Prior
Plans, which were terminated upon the stockholders approval of the 2009
Plan.





Item
6.              Exhibits




3.1
              Certificate
      of Incorporation of Ore Pharmaceutical Holdings Inc.3.2
              Bylaws
      of Ore Pharmaceutical Holdings Inc. (1)*10.92c
              2009
      Performance Year Incentive Compensation Plan.*10.114
              Letter
      Agreement, dated July 15, 2009, from Ore Pharmaceuticals Inc. to Benjamin
      L. Palleiko. (2)10.115
              Release
      of Further Performance Under Lease, effective July 31, 2009, between 50
      West Watkins Mill Road, LLC and Ore Pharmaceuticals Inc.
    (3)*10.118
              Consulting
      Agreement between Ore Pharmaceuticals Inc. and Mark D. Gessler, effective
      July 23, 2009.31
              Certifications
      pursuant to Rule 13a-14(a)/15d-14(a) promulgated under the Securities
      Exchange Act of 1934, as amended.32
              Certifications
      pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of
      the Sarbanes-Oxley Act of
2002.








*
indicates management compensatory plan, contract or arrangement.


(1)
            Filed
      as Appendix C to the Registrant’s Registration Statement on Form S-4/A,
      filed on September 2, 2009 (Registration No. 333-161363), and incorporated
      herein by reference.


(2)
            Filed
      as Exhibit 10.114 to Ore Pharmaceuticals Inc.’s Current Report on Form
      8-K, filed on July 21, 2009 (File No. 0-23317), and incorporated herein by
      reference.


(3)
            Filed
      as Exhibit 10.115 to Ore Pharmaceuticals Inc.’s Current Report on Form
      8-K, filed on August 6, 2009 (File No. 0-23317), and incorporated herein
      by reference.





15.





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.









ORE
      PHARMACEUTICAL HOLDINGS INC.Date:   
       November 13, 2009
              
              By:
              /s/ Benjamin L. PalleikoBenjamin
      L. PalleikoSenior
      Vice President and Chief Financial Officer(Principal
      Financial and Accounting Officer)






16.