Stock SEC Filing: Learn Why Pillar Pharmaceuticals I Lp Just Purchased Idera Pharmaceuticals, Inc Stake?

Stock SEC Filing: Learn Why Pillar Pharmaceuticals I Lp Just Purchased Idera Pharmaceuticals, Inc Stake?

The New Pillar Pharmaceuticals I Lp Holding in Idera Pharmaceuticals, Inc

Pillar Pharmaceuticals I Lp filed with the SEC SC 13D/A form for Idera Pharmaceuticals, Inc. The form can be accessed here: 000119312516738792. As reported in Pillar Pharmaceuticals I Lp’s form, the filler as of late owns 19.9% or 29,253,114 shares of the Health Care–company.

Idera Pharmaceuticals, Inc stake is a new one for the and it was filed because of activity on October13, 2016. We feel this shows Pillar Pharmaceuticals I Lp’s positive view for the stock.

Reasons Why Pillar Pharmaceuticals I Lp Bought – Idera Pharmaceuticals, Inc Stock

Purpose of Transaction

Series D Financing

Convertible Preferred Stock and Warrant Purchase Agreement

On November4, 2011, Pillar and the Issuer entered into a Convertible Preferred Stock and Warrant Purchase Agreement (the “SeriesD PurchaseAgreement”) pursuant to which Pillar agreed to acquire from the Issuer (i)1,124,260 shares of Series D Preferred Stock and (ii)Series D Warrants to purchase 2,810,650 shares of Common Stock, for an aggregate purchase price of$9,499,997. The transaction closed on November4, 2011 (the “Series D Closing Date”). The source of funds for the purchase was the working capital of Pillar.

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Limitations on Conversion and Exercise

The terms of the Series D Preferred Stock and the Series D Warrants provide that the Issuer shall not effect (i)any conversion of Series D PreferredStock or (ii)any exercise of Series D Warrants, for a number of shares of Common Stock in excess of that number of shares of Common Stock which, upon giving effect to such conversion or exercise, as the case may be, would cause (A)theaggregate number of shares of Common Stock beneficially owned by Pillar and its affiliates to exceed 19.99% of the total number of issued and outstanding shares of Common Stock of the Issuer as of the Series D Closing Date, or (B)the combinedvoting power of the securities of the Issuer beneficially owned by Pillar and its affiliates to exceed 19.99% of the combined voting power of all of the securities of the Issuer outstanding as of the Series D Closing Date. As described below, thelimitation on the exercise of the Series D Warrants was amended pursuant to the Warrant Amendment. As of the date of this filing, the Series D Preferred Stock has been converted to Common Stock of the Issuer.

Standstill

The Series D Purchase Agreement providesthat, for so long as the total number of shares of Common Stock beneficially owned by Pillar and its affiliates exceeds 15% of the then outstanding shares of Common Stock, neither Pillar nor its affiliates will, directly or indirectly (unlessspecifically invited in writing by the Issuer to do so):

(a) effect or seek, initiate, offer or propose (whether publicly or otherwise) or participate in,any acquisition of any securities (or beneficial ownership thereof) or assets of the Issuer; any tender or exchange offer, merger, consolidation or other business combination involving the Issuer; any recapitalization, restructuring, liquidation,dissolution or other extraordinary transaction with respect to the Issuer; or any “solicitation” of “proxies” or consents to vote any voting securities of the Issuer; provided, that this clause (a)shall not restrict theability of any director of the Issuer that is affiliated with Pillar to (i)acquire, exercise or dispose of any stock options or other equity securities of the Issuer received as compensation for serving as a director or (ii)perform hisor her duties as a director of the Issuer;

(b)form, join or in any way participate in a “group” with respect to any securities of the Issuer;

(c)otherwise act, alone or in concert with others, to seek to control or influence the management, the Company’s Board of Directors (the “Board”) or policies of the Issuer;

(d) take any action which could reasonably be expected to force the Issuer to make a public announcement regarding any of the types of matters set forth inclause (a), (b)or (c)above; or

(e)enter into any agreements, discussions or arrangements with any third party with respect to any of the foregoing.

This standstill provision shall not restrict Pillar’s ability to exercise its preemptive rights as more fully described below under the heading“Preemptive Rights”.

Voting

On any matterpresented to the stockholders of the Issuer for their action or consideration at any meeting of stockholders of the Corporation, each holder of outstanding shares of Series D Preferred Stock shall be entitled to cast a number of votes equal to thenumber of whole shares of Common Stock into which the shares of Series D Preferred Stock held by such holder are convertible as of the record date for determining stockholders entitled to vote on such matter.

The Series D Purchase Agreement provides that, for so long as the total number of shares of Common Stock beneficially owned by Pillar and its affiliatesexceeds 15% of the then outstanding shares of Common Stock, in any election of directors and in any other vote to be taken by the stockholders of the Issuer (whether taken at an annual or special meeting of stockholders or by written action), Pillarand its affiliates will vote such number of shares of Common Stock beneficially owned by Pillar and its affiliates in excess of 15% in the same manner as, and in the same proportion to, the votes cast by the other holders of the Company’sCommon Stock or other voting securities. As described below, this voting limitation was amended pursuant to the Purchase Agreement Amendment.

Preemptive Rights

The Series D Purchase Agreementprovides that, in the event the Issuer on or prior to the earlier of (i)November4, 2014 and (ii)the day that Pillar holds a number of shares of Series D Preferred Stock (including shares of Common Stock issued upon conversion ofthe Series D Preferred Stock) which is less than 50% of the number of shares of Series D Preferred Stock purchased by Pillar, proposes to:

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(a) privately sell and issue securities of the Issuer, Pillar shall have the option to purchase, on the sameterms and conditions offered by the Issuer to the other purchasers of such securities in such additional financing, up to that percentage of the securities sold in such additional financing equal to (A)the number of shares then held by Pillaras compared to (B)the total number of shares then outstanding, which pro rata amount shall not exceed 19.99% of such additional financing or

(b)enter into a loan financing for the purpose of raising capital and not for the purpose of purchasing equipment, or privately sell and issue convertible debt securities or preferred stock of the Issuer that ranks senior to the Preferred Stock, Pillarshall have the option to participate in such loan financing or other senior financings, on the same terms and conditions offered by the Issuer to the other participants or purchasers of securities in such senior financings, up to that percentage ofthe amount of the loan financing or of the securities sold in such senior financing equal to the product of:

(I) A fraction, the numerator of which equalsthe number of shares then held by Pillar and the denominator of which equals the total number of shares issued to Pillar; and

(II) If the closing date ofthe senior financing is on or prior to (i)November4, 2012, 50%, (ii)November4, 2013, 40%, or (iii)November4, 2014, 30%.

Registration Rights Agreement

In connection with theSeries D Purchase Agreement, Pillar entered into a Registration Rights Agreement, dated November4, 2011 (the “Series D Registration Rights Agreement”), with the Issuer.The Series D Registration Rights Agreement providesthat the Company will file a resale registration statement (the “Series D Resale Registration Statement”) covering the shares of Common Stock issuable upon conversion of the Series D Preferred Stock and exercise of the Series DWarrants. The Issuer agreed to use its reasonable best efforts to cause to become effective the Series D Resale Registration Statement on or prior to February2, 2012.

If (i)the Series D Resale Registration Statement is not declared effective on or before March4, 2012 or (ii)after the Series D ResaleRegistration Statement has been declared effective, sales of any of the Registrable Securities (as defined in the Series D Registration Rights Agreement) cannot be made pursuant to such Series D Resale Registration Statement because such Series DResale Registration Statement has been suspended (except as a result of a permitted suspension as provided in the Series D Registration Rights Agreement), then the Issuer shall pay to Pillar an amount equal to the product of (A)the aggregatepurchase price of the Series D Preferred Stock then held by Pillar, multiplied by (B)one hundredths (.01), for each thirty (30)day period thereafter. Notwithstanding the foregoing, in no event shall the Issuer be obligated to makepayments to Pillar in an aggregate amount that exceeds 10% of the aggregate purchase price paid by Pillar for the Series D Preferred Stock.

The Issuerwill pay all registration expenses, other than underwriting discounts and commissions, related to the Issuer’s performance of the Series D Registration Rights Agreement. The Series D Registration Rights Agreement contains customarycross-indemnification provisions.

The foregoing descriptions of the Series D Purchase Agreement and the Series D Registration Rights Agreement and of theterms the Certificate of Designations, Preferences and Rights of the Series D Preferred Stock and the Form of Series D Warrant issued to Pillar (collectively, the “Series D Transaction Documents”), do not purport to be complete andare qualified in their entirety by the terms of each such document, which are attached hereto as Exhibit 2, Exhibit 3, Exhibit 4 and Exhibit 5, respectively, and are incorporated herein by reference.

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Series E Financing

Convertible Preferred Stock and Warrant Purchase Agreement

On November9, 2012, Pillar II, Participations Besancon and the Issuer entered into a Convertible Preferred Stock and Warrant Purchase Agreement (the“Series E Purchase Agreement”) pursuant to which (i)Pillar II acquired from the Issuer (a)313,341 shares of Series E Preferred Stock (convertible into 6,266,820 shares of Common Stock) and (b)Series E Warrants topurchase 6,266,820 shares of Common Stock, and (ii)Participations Besancon acquired from the Issuer (a)110,901 shares of Series E Preferred Stock (convertible into 2,218,020 shares of Common Stock) and (b)Series E Warrants topurchase 2,218,020 shares of Common Stock for an aggregate purchase price of $6,999,993. The transaction closed on November9, 2012 (the “November Closing Date”). In connection with the closing of the transaction, Abdul-WahabUmari, a managing partner of Pillar GP, was elected to the Board upon the recommendation of its Nominating and Corporate Governance Committee effective immediately following the closing of the transactions contemplated by the Series E PurchaseAgreement. The source of funds for the purchase by Pillar II was the working capital of Pillar II and the source of funds for the purchase by Besancon was the working capital of Besancon. As of the date of this filing, the Series E Preferred Stockhas been converted to Common Stock of the Issuer.

Limitations on Transfer

The Series E Purchase Agreement provides restrictions on the transfer of any securities issued to Pillar II and Besancon (including securities convertible intoor exercisable for Common Stock) pursuant to the Series E Purchase Agreement, including to not sell or transfer any such securities in one or a series of transactions if such transfer would, in the aggregate, result in the transfer more than 5% ofthe then outstanding combined voting power of the outstanding securities of the Company (excluding from this restriction certain transfers to permitted transferees or in connection with an underwritten public offering by the Company that has beenapproved by the Board).

Limitations on Conversion and Exercise

The terms of the Series E Preferred Stock and the Series E Warrants provide that the Issuer shall not effect (i)any conversion of Series E PreferredStock or (ii)any exercise of Series E Warrants, for a number of shares of Common Stock in excess of that number of shares of Common Stock which, upon giving effect to such conversion or exercise, as the case may be, would cause (A)theaggregate number of shares of Common Stock beneficially owned by Pillar II, Besancon and/or its affiliates to exceed 19.99% (subject to an increase to 35% upon the approval by the stockholders of the Company of the issuance and sale by the Companyto Pillar II and Besancon (together with all prior issuances and sales to Pillar) of a number of Shares of Common Stock (including securities convertible into or exercisable for Common Stock) that is greater than 19.99% of the outstanding CommonStock or outstanding voting power of the Company after such issuance and sale in accordance with Nasdaq Listing Rule 5636(b) (the “Nasdaq Proposal”)) of the total number of issued and outstanding shares of Common Stock of the Issuer as ofthe November Closing Date, or (B)the combined voting power of the securities of the Issuer beneficially owned by Pillar II, Besancon and/or its affiliates to exceed 19.99% (subject to an increase to 35% upon stockholder approval of the NasdaqProposal) of the combined voting power of all of the securities of the Issuer outstanding as of the November Closing Date.

Standstill

The Series E Purchase Agreement provides that, for so long as the total number of shares of Common Stock beneficially owned by Pillar II, Besancon and/or itsaffiliates exceeds 15% of the then outstanding shares of Common Stock, neither Pillar II, Besancon nor their respective affiliates will, directly or indirectly (unless specifically invited in writing by the Issuer to do so):

(a) effect or seek, initiate, offer or propose (whether publicly or otherwise) or participate in, any acquisition of any securities (or beneficial ownershipthereof) or assets of the Issuer; any tender or exchange offer, merger, consolidation or other business combination involving the Issuer; any recapitalization, restructuring, liquidation, dissolution or other extraordinary transaction with respectto the Issuer; or any “solicitation” of “proxies” or consents to vote any voting securities of the Issuer; provided, that this clause (a)shall not restrict the ability of any director of the Issuer that is affiliated withPillar II or Besancon to (i)acquire, exercise or dispose of any stock options or other equity securities of the Issuer received as compensation for serving as a director or (ii)perform his or her duties as a director of the Issuer;

(b) form, join or in any way participate in a “group” with respect to any securities of the Issuer;

(c) otherwise act, alone or in concert with others, to seek to control or influence the management, Board or policies of the Issuer;

(d) nominate or otherwise support the election of any person as a director of the Company except as approved by the Board, subject to certain exceptions;

(e) take any action which could reasonably be expected to force the Issuer to make a public announcement regarding any of the types of matters set forth inclause (a), (b), (c)or (d)above; or

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(f) enter into any agreements, discussions or arrangements with any third party with respect to any of theforegoing.

This standstill provision shall not restrict Pillar II’s or Besancon’s ability to exercise its preemptive rights as more fullydescribed below under the heading “Preemptive Rights”.

Voting; Protective Provisions

For so long as at least 84,849 shares of Series E Preferred Stock (subject to adjustment) remain outstanding, the Company has agreed that it will not, directlyor indirectly, (a)amend the Certificate of Incorporation or bylaws of the Company in a manner that adversely and uniquely affects the Series E Preferred Stock, (b)except as expressly permitted by the Certificate of Designations for theSeries E Preferred Stock, purchase or redeem or pay or declare any dividend or make any distribution on, any shares of capital stock of the Company, or (c)recapitalize or reclassify any of the Common Stock, without in each case the writtenconsent or affirmative vote of the holders of at least 51% of the then outstanding shares of Series E Preferred Stock (in addition to any other vote required by law or the Certificate of Incorporation).

Unless and until the stockholders of the Company approve the Nasdaq Proposal, the Series E Preferred Stock will have no voting rights. Subject to andeffective upon the date that the stockholders of the Company approve the Nasdaq Proposal, each holder of outstanding shares of Series E Preferred Stock will be entitled to cast a number of votes equal to the lesser of (a)the number of wholeshares of Common Stock into which the shares of Series E Preferred Stock held by such holder are convertible and (b)the product of the Voting Adjustment Percentage (as defined in the Certificate of Designations for the Series E PreferredStock) multiplied by the number of whole shares of Common Stock into which the shares of Series E Preferred Stock held by such holder are convertible. The intent of the Voting Adjustment Percentage is to provide that the maximum aggregate votingpower that the holders of Series E Preferred Stock and their affiliates may hold does not exceed 35% of the total outstanding voting power of the Company at any time. The Voting Adjustment Percentage does not modify the provisions set forth in theSeries E Purchase Agreement that require the Pillar II, Besancon and their affiliates to vote any shares held by them in excess of the number of shares equal to 19.99% or 25%, as applicable, of the outstanding Common Stock (including shares ofCommon Stock issuable upon conversion or exercise of securities that are convertible into or exercisable for shares of Common Stock held by them and their affiliates) in the same manner and percentage as the holders of the Common Stock (other thanPillar II, Besancon and their affiliates) vote on such matter as more fully described below.

The Series E Purchase Agreement provides that, for so longas the total number of shares of Common Stock beneficially owned by Pillar II, Besancon and/or its affiliates exceeds 19.99% (subject to an increase to 25% upon stockholder approval of Nasdaq Proposal) of the then outstanding shares of Common Stock,in any election of directors and in any other vote to be taken by the stockholders of the Issuer (whether taken at an annual or special meeting of stockholders or by written action), Pillar II, Besancon and/or its affiliates will vote such number ofshares of Common Stock beneficially owned by Pillar II, Besancon and/or its affiliates in excess of 19.99% (subject to an increase to 25% upon stockholder approval of Nasdaq Proposal) in the same manner as, and in the same proportion to, the votescast by the other holders of the Company’s Common Stock or other voting securities.

Each of Pillar II and Besancon agreed to refrain from exercisingany dissenters’ rights or rights of appraisal under applicable law at any time with respect to any sale of the Company to the extent such sale has been approved by the Board.

Preemptive Rights

The Series E Purchase Agreementprovides that, in the event the Issuer on or prior to the earlier of (i)November9, 2015 and (ii)the day that Pillar II or Besancon, respectively, holds a number of shares of Series E Preferred Stock (including shares of CommonStock issued upon conversion of the Series E Preferred Stock) which is less than 50% of the number of shares of Series E Preferred Stock purchased by Pillar II or Besancon, respectively, proposes to:

(a) privately sell and issue securities of the Issuer, Pillar II and Besancon, respectively, shall have the option to purchase, on the same terms andconditions offered by the Issuer to the other purchasers of such securities in such additional financing, up to that percentage of the securities sold in such additional financing equal to (A)the number of shares then held by each of Pillar IIand Besancon, respectively, as compared to (B)the total number of shares then outstanding, which pro rata amount shall not exceed 19.99% (subject to an increase to 35% upon stockholder approval of Nasdaq Proposal) of such additional financingor

(b) enter into a loan financing for the purpose of raising capital and not for the purpose of purchasing equipment, or privately sell and issueconvertible debt securities or preferred stock of the Issuer that ranks senior to the Series E Preferred Stock, each of Pillar II and Besancon, respectively, shall have the option to participate in such loan financing or other senior financings, onthe same terms and conditions offered by the Issuer to the other participants or purchasers of securities in such senior financings, up to that percentage of the amount of the loan financing or of the securities sold in such senior financing equalto the product of:

(I) A fraction, the numerator of which equals the number of shares then held by each of Pillar II and Besancon, respectively, and thedenominator of which equals the total number of shares issued to each of Pillar II and Besancon, respectively; and

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(II) If the closing date of the senior financing is on or prior to (i)November9, 2013, 50%,(ii)November9, 2014, 40%, or (iii)November9, 2015, 30%.

Automatic Adjustments to Series D Preferred Stock and Series DWarrants

As a result of the transactions contemplated by the Series E Purchase Agreement, the conversion price of the Series D Preferred Stockautomatically adjusted downward to $1.46 and the exercise price of the Series D Warrants automatically adjusted downward to $1.46.

Registration RightsAgreement

In connection with the Series E Purchase Agreement, Pillar II and Besancon entered into a Registration Rights Agreement, datedNovember9, 2012 (the “Series E Registration Rights Agreement”), with the Issuer. The Series E Registration Rights Agreement provides that the Company will file a resale registration statement (the “Series E ResaleRegistration Statement”) covering the shares of Common Stock issuable upon conversion of the Series E Preferred Stock and exercise of the Series E Warrants. The Issuer agreed to use its reasonable best efforts to cause to become effectivethe Series E Resale Registration Statement on or prior to February7, 2013.

If (i)the Series E Resale Registration Statement is not declaredeffective on or before March30, 2013 or (ii)after the Series E Resale Registration Statement has been declared effective, sales of any of the Registrable Securities (as defined in the Series E Registration Rights Agreement) cannot bemade pursuant to such Series E Resale Registration Statement because such Series E Resale Registration Statement has been suspended (except as a result of a permitted suspension as provided in the Series E Registration Rights Agreement), then theIssuer shall pay to Pillar II and Besancon an amount equal to the product of (A)the aggregate purchase price of the Series E Preferred Stock then held by Pillar II and Besancon, multiplied by (B)one hundredths (.01), for each thirty(30)day period thereafter. Notwithstanding the foregoing, in no event shall the Issuer be obligated to make payments to Pillar II and Besancon in an aggregate amount that exceeds 10% of the aggregate purchase price paid by Pillar II andBesancon for the Series E Preferred Stock.

The Issuer will pay all registration expenses, other than underwriting discounts and commissions, related tothe Issuer’s performance of the Series E Registration Rights Agreement. The Series E Registration Rights Agreement contains customary cross-indemnification provisions.

Amendment No.1 to Series D Convertible Preferred Stock and Warrant Purchase Agreement

In connection with the Series E Purchase Agreement, Pillar entered into Amendment No.1 to Convertible Preferred Stock and Warrant Purchase Agreement,dated November9, 2012 (the “Purchase Agreement Amendment”), with the Issuer. The Purchase Agreement Amendment provides that, for so long as the total number of shares of Common Stock beneficially owned by Pillar or itsaffiliates exceeds 19.99% (subject to an increase to 25% upon stockholder approval of the Nasdaq Proposal) of the then outstanding shares of Common Stock, in any election of directors and in any other vote to be taken by the stockholders of theIssuer (whether taken at an annual or special meeting of stockholders or by written action), Pillar or its affiliates will vote such number of shares of Common Stock beneficially owned by Pillar or its affiliates in excess of 19.99% (subject to anincrease to 25% upon stockholder approval of the Nasdaq Proposal) in the same manner as, and in the same proportion to, the votes cast by the other holders of the Company’s Common Stock or other voting securities. Pillar agreed to refrain fromexercising any dissenters’ rights or rights of appraisal under applicable law at any time with respect to any sale of the Company to the extent such sale has been approved by the Board.

The Purchase Agreement Amendment also provides for certain restrictions on the transfer of any securities issued to Pillar (including securities convertibleinto or exercisable for Common Stock) pursuant to the Series D Purchase Agreement, including to not sell or transfer any such securities in one or a series of transactions if such transfer would, in the aggregate, result in the transfer more than 5%of the then outstanding combined voting power of the outstanding securities of the Company (excluding from this restriction certain transfers to permitted transferees or in connection with an underwritten public offering by the Company that has beenapproved by the Board).

Amendment No.1 to Common Stock Purchase Warrant

In connection with the Series E Purchase Agreement, Pillar entered into Amendment No.1 to Common Stock Purchase Warrant, dated November9, 2012 (the“Warrant Amendment”), with the Issuer. The Warrant Amendment provides that the exercise limitation set forth therein shall be amended to increase the 19.99% limitation on exercise to 35% upon the Company’s receipt ofstockholder approval of the Nasdaq Proposal.

The foregoing descriptions of the Series E Purchase Agreement and the Series E Registration Rights Agreementand of the terms the Certificate of Designations, Preferences and Rights of the Series E Preferred Stock and the Form of Series E Warrant issued to Pillar and Besancon, the Purchase Agreement Amendment and the Warrant Amendment (collectively, the“Series E Transaction Documents”), do not purport to be complete and are qualified in their entirety by the terms of each such document, which are attached hereto as Exhibit 6, Exhibit 7, Exhibit 8, Exhibit 9, Exhibit 10 and Exhibit11, respectively, and are incorporated herein by reference.

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Amendments to Series D and Series E

April22 Amendment Agreement

On April22, 2013,Pillar I and Pillar II entered into an agreement with the Issuer pursuant to which, in connection with a public offering of the Issuer on May7, 2013 (the “Offering”), Pillar I irrevocably agreed to waive and not exercise therights, powers, preferences and other terms of the Series D Preferred Stock under Section6 of the Certificate of Designations, Preferences and Rights of Series D Preferred Stock (the “Series D Certificate of Designations”), includingwithout limitation the right to require the Issuer to purchase all or any portion of the shares of the Issuer’s Series D Preferred Stock at a price equal to the original Series D Preferred Stock purchase price per share plus all accrued ordeclared but unpaid dividends thereon upon the occurrence of specified fundamental changes such as mergers, consolidations, business combinations, stock purchases or similar transactions resulting in a person or group unaffiliated with any holder ofthe Series D Preferred Stock owning 66.67% or more of the outstanding voting securities of the Issuer or successor entity.

Under the agreement, theIssuer and Pillar I and Pillar II agreed, among other things:

to an amendment to the Series D Certificate of Designations for the Series D Preferred Stock that would cause:

the dividend provisions of the Series D Certificate of Designations to change the date after which the Issuer may elect to pay dividends in shares of its common stock from December31, 2014 to October1, 2013,and to allow for the payment of such dividends in shares of a to-be-created new series of non-voting preferred stock in the event that payment of such dividends may not be made in shares of its common stock; and

in connection with the waiver of the right to require the Issuer to purchase the Series D Preferred Stock upon the occurrence of specified fundamental changes, to modify the Series D Certificate of Designations toprovide, in the event of a sale of the Issuer, for the distribution of any assets that remain available for distribution to the Issuer’s stockholders, after payment to the holders of the Issuer’s Series A Convertible Preferred Stock andany other class of the Issuer’s capital stock that ranks senior to the Series D Preferred Stock, to the holders of the Series D Preferred Stock on a pro rata basis with the holders of the Issuer’s common stock, Series E Preferred Stock andsuch new series of non-voting preferred stock; and

to an amendment to the Certificate of Designations, Preferences and Rights of Series E Preferred Stock (the “Series E Certificate of Designations”), that:

modified the dividend provisions of the Series E Certificate of Designations to allow for the payment of dividends in shares of the Issuer’s common stock commencing October1, 2013; and

allowed for the payment of dividends in shares of a to-be-created new series of non-voting preferred stock in the event that payment of such dividends may not be made in shares of the Issuer’s common stock as aresult of the application of the beneficial ownership and voting power limitations set forth in the Series E Certificate of Designations.

In addition, the Issuer agreed to seek approval from its stockholders at the 2013 annual meeting of stockholders of amendments to the Series D Certificate ofDesignations and Series E Certificate of Designations to effect these changes to the dividend provisions of the Series D Preferred Stock and Series E Preferred Stock, the redemption rights of the holders of the Series D Preferred Stock and therights of the holders of the Series D Preferred Stock to distributions in the event of a sale of the Issuer. Each of Pillar I and Pillar II agreed:

to vote, and to cause its affiliates to vote, all shares of the Issuer’s voting stock held by Pillar I, Pillar II and their affiliates, and over which they have the power to vote, in favor of such amendments; and

not to, and to cause their affiliates not to, sell or transfer any shares of common stock, Series D Preferred Stock or Series E Preferred Stock held by them to any person, entity or group unless such proposed transfereeagrees in a written instrument executed by such transferee, the applicable entity and the Issuer to take and hold such securities subject to, among other things, the agreement and to be bound by the terms of the agreement, including the waiver ofrights, voting agreements and restrictions on transfer set forth therein.

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The agreement became effective upon the consummation of the May7 Offering on May7, 2013.

April22 Amendment Warrants

Under the April22agreement, in consideration of the agreements of Pillar I and Pillar II under the agreement and the delivery of the waiver by Pillar I, and for no additional cash consideration, the Issuer agreed to issue to Series D Pillar Warrants to purchase upto 1,000,000 shares of the Issuer’s common stock. These Series D Pillar Warrants have an exercise price per share equal to $0.61. The Pillar I Warrants are exercisable immediately, and will expire if not exercised on or prior to the fifthanniversary from the date of issuance. The Series D Pillar Warrants provide that, after the second anniversary of the date of issuance, the Issuer may redeem the Series D Pillar Warrants for $0.01 per share of common stock issuable on exercise ofthe Series D Pillar Warrants following notice to the holder thereof if the closing price of the Issuer’s common stock for 20 or more trading days in a period of 30 consecutive trading days is greater than or equal to $2.80 per share.

April30 Amendment Agreement

On April30,2013, Pillar I, Pillar II and Besancon entered into an agreement with the Issuer pursuant to which Pillar I, in its capacity as holder of 100% of the Series D Preferred Stock, irrevocably agreed to waive the right of the holders of the Series DPreferred Stock under Section2.1 of the Series D Certificate of Designations to receive, in the event of a voluntary or involuntary liquidation, dissolution or winding up of the Issuer (a “Liquidation”) an amount per share of SeriesD Preferred Stock equal to the original issue price of such share of Series D Preferred Stock plus any dividends accrued or declared but unpaid thereon to the extent such amount is greater than the amount that would have been payable with respect tosuch share had all shares of Series D Preferred Stock been converted into shares of the Issuer’s Common Stock immediately prior to such Liquidation, and that upon a Liquidation the holders of the Series D Preferred Stock will receive an amountper share of Series D Preferred Stock equal to the amount that would be payable with respect to such share had all shares of Series D Preferred Stock been converted into shares of the Issuer’s Common Stock immediately prior to such Liquidation.

In addition, under the agreement, Pillar II and Besancon, together the holders of 100% of the Issuer’s Series E Preferred Stock, irrevocably agreedto waive the right of the holders of the Series E Preferred Stock under Section2.1.1 of the Series E Certificate of Designations to receive, in the event of a Liquidation, an amount per share of Series E Preferred Stock equal to the originalissue price of such share of Series E Preferred Stock plus any dividends accrued or declared but unpaid thereon to the extent such amount is greater than the amount that would have been payable with respect to such share had all shares of Series EPreferred Stock been converted into shares of the Issuer’s Common Stock immediately prior to such Liquidation, and that upon a Liquidation the holders of the Series E Preferred Stock will receive under Section2.1 of the Series ECertificate of Designations an amount per share of Series E Preferred Stock equal to the amount that would be payable with respect to such share had all shares of Series E Preferred Stock been converted into shares of the Issuer’s Common Stockimmediately prior to such Liquidation.

Under the agreement, the Issuer agreed to seek approval from its stockholders at its 2013 annual meeting ofstockholders of amendments to the Series D Certificate of Designations and Series E Certificate of Designations to effect these changes to the liquidation provisions of the Series D Preferred Stock and Series E Preferred Stock, and each of Pillar I,Pillar II and Besancon agreed:

to vote, and to cause its affiliates to vote, all shares of the Issuer’s voting stock held by them or their affiliates, and over which they have the power to vote, in favor of such amendments; and

not to, and to cause their affiliates not to, sell or transfer any shares of Common Stock, Series D Preferred Stock or Series E Preferred Stock held by them to any person, entity or group unless such proposed transfereeagrees in a written instrument executed by such transferee, the applicable entity and the Issuer to take and hold such securities subject to, among other things, the agreement and to be bound by the terms of the agreement, including the waiver ofrights, voting agreements and restrictions on transfer set forth therein.

The agreement became effective upon the consummation of theMay7 Offering on May7, 2013.

April30 Amendment Warrants

In consideration of the agreements of Pillar I, Pillar II and Besancon under the April30 agreement and the delivery of the waivers by Pillar I, Pillar IIand Besancon, and for no additional cash consideration, the Issuer agreed to issue to Pillar I, Pillar II and Besancon warrants (the “Pillar/Besancon Warrants” and together with the Series D Pillar Warrants, the “AmendmentWarrants”) to purchase up to an aggregate of 1,000,000 shares of the Issuer’s Common Stock (with each of Pillar I, Pillar II and Besancon receiving its pro rata portion thereof). The Pillar/Besancon Warrants have an exercise price pershare equal to $0.79.

CUSIPNo. 45168K30613D Page 17 of 22 pages

Registration Rights Agreement

In addition, Pillar I, Pillar II and Besancon entered into a Registration Rights Agreement with the Issuer pursuant to which the Issuer agreed to file aregistration statement with the Securities and Exchange Commission regarding the resale of the shares of common stock issuable upon exercise of the Amendment Warrants. The Issuer will be subject to specified cash penalties if it fails to file andmaintain an effective registration statement. Such penalties are limited to a cumulative maximum penalty equal to 10% of the aggregate exercise price of the Amendment Warrants then held by Pillar I, Pillar II and Besancon which are not able to besold pursuant to a registration statement. The Issuer will be required to use its reasonable best efforts to maintain the registration statement’s effectiveness until no shares of common stock issued or issuable upon exercise of the AmendmentWarrants remain outstanding or issuable, as applicable.

The foregoing descriptions of the Amendment Warrants, the April22 Amendment Agreement, theApril30 Amendment Agreement, and the Registration Rights Agreement and of the terms the amended Series D and Series E preferred stock and Amendment Warrants , do not purport to be complete and are qualified in their entirety by the terms ofeach such document, which are attached hereto as Exhibit 12, Exhibit 13, Exhibit 14, Exhibit 15, and Exhibit 3, respectively, and are incorporated herein by reference.

May 2013 Underwritten Public Offering

OnMay1, 2013, the Issuer priced an underwritten public offering of its Common Stock and Warrants to Purchase Common Stock. In that offering, (i)Pillar Pharmaceuticals III, L.P. purchased 2,600,000 shares of Common Stock and Warrants toPurchase 2,600,000 shares of Common Stock from the underwriter for gross proceeds of $1,300,000 and (ii)Besancon purchased 2,400,000 shares of Common Stock and Warrants to Purchase 2,400,000 shares of Common Stock from the underwriter forgross proceeds of $1,200,000. The public offering closed on May7, 2013.

September 2013 Underwritten Public Offering

On September26, 2013, the Issuer priced an underwritten public offering of its Common Stock and Warrants to Purchase Common Stock. In that offering,(i)Pillar Pharmaceuticals IV, L.P. purchased 845,161 shares of Common Stock from the underwriter for gross proceeds of $1,310,000 and (ii)Besancon purchased 929,032 shares of Common Stock from the underwriter for gross proceeds of$1,440,000. The public offering closed on September30, 2013.

October 2016 Underwritten Public Offering

On October7, 2016, the Issuer priced an underwritten public offering of its Common Stock. In that offering, (i)Pillar Pharmaceuticals V, L.P.purchased 875,000 shares of Common Stock from the underwriter for gross proceeds of $1,750,000 and (ii)Besancon purchased 1,000,000 shares of Common Stock from the underwriter for gross proceeds of $2,000,000. The public offering closed onOctober13, 2016.

Additional Disclosure

TheSeries D Preferred Stock, Series E Preferred Stock, Series D Warrants, Series E Warrants, Amendment Warrants, Common Stock and Warrants to Purchase Common Stock reported herein were acquired solely for investment purposes. The Reporting Persons donot have any present plans or proposals that relate to or would result in any change in the business, policies, management, structure or capitalization of the Issuer.

The Reporting Persons will continue to evaluate the business and prospects of the Issuer, and its present and future interest in, and intentions with respectto, the Issuer, and in connection therewith expects from time to time to consult with management and other stockholders of the Issuer. The Reporting Persons reserve the right to formulate plans and/or make proposals, and take such actions withrespect to their investment in the Issuer, including subject to applicable law, (i)to hold its shares as a passive investor or as an active investor (whether or not as a member of a “group” with other beneficial owners of Shares orotherwise), (ii)to acquire beneficial ownership of additional shares in the open market, in privately negotiated transactions or otherwise, (iii)to dispose of all or part of its holdings of the shares, (iv)to take other actionswhich could involve one or more of the types of transactions or have one or more of the results described in Item4 of this Amendment No.1 to Schedule 13D, or (v)to change its intention with respect to any or all of the mattersreferred to in this Item4.

CUSIPNo. 45168K30613D Page 18 of 22 pages

Other than as described above and as set forth in the Series D Transaction Documents and the Series ETransaction Documents and the related amendment agreements executed in connection with certain amendments to the Series D and Series E preferred stock, the Reporting Persons do not have any plans or proposals which would result in any of thefollowing:

(a) The acquisition by any person of additional securities of the Issuer, or the disposition of securities of the Issuer;

(b) An extraordinary corporate transaction, such as a merger, reorganization or liquidation, involving the Issuer or any of its subsidiaries;

(c) A sale or transfer of a material amount of assets of the Issuer or any of its subsidiaries;

(d) Any change in the present Board or management of the Issuer, including any plans or proposals to change the number or term of directors or to fill anyexisting vacancies on the Board;

(e) Any material change in the present capitalization or dividend policy of the Issuer;

(f) Any other material change in the Issuer’s business or corporate structure;

(g) Changes in the Issuer’s charter, bylaws or instruments corresponding thereto or other actions that may impede the acquisition of control of the Issuerby any person;

(h) Causing a class of securities of the Issuer to be delisted from a national securities exchange or to cease to be authorized to bequoted in an inter-dealer quotation system of a registered national securities association;

(i) A class of equity securities of the Issuer becomingeligible for termination of registration pursuant to Section12(g)(4) of the Securities Exchange Act of 1934, as amended; or

(j) Any action similarto any of those enumerated above.

Idera Pharmaceuticals, Inc Institutional Sentiment

Latest Security and Exchange filings show 82 investors own Idera Pharmaceuticals, Inc. The institutional ownership in Q3 2015 is high, at 35.89% of the outstanding shares. This is decreased by 7474957 the total institutional shares. 52520603 were the shares owned by these institutional investors. In total 9 funds opened new Idera Pharmaceuticals, Inc stakes, 24 increased stakes. There were 12 that closed positions and 30 reduced them.

Natixis is an institutional investor bullish on Idera Pharmaceuticals, Inc, owning 3148916 shares as of Q3 2015 for 0.22% of its portfolio. Julian Baker And Felix Baker Baker Bros Advisors Lp owns 6976162 shares or 0.22% of its portfolio. NY Broadfin Capital Llc have 0.97% of their stock portfolio for 5213979 shares. Further, Palo Alto Investors Llc reported stake worth 0.20% of its US stock portfolio. The CA Hollencrest Securities Llc owns 177570 shares. Idera Pharmaceuticals, Inc is 0.10% of the manager’s US portfolio.

Business Profile

Idera Pharmaceuticals, Inc. is a clinical-stage biopharmaceutical company focused on the discovery, development and commercialization of therapeutics for oncology and rare diseases. The Company utilizes two drug discovery technology platforms to design and develop drug candidates, which include Toll-like receptor (TLR) targeting technology and third-generation antisense (3GA) technology. Using TLR technology, the Company designs synthetic oligonucleotide-based drug candidates to act by modulating the activity of specific TLRs. Using its 3GA technology, the Company is developing drug candidates to turn off the messenger ribo nucleic acid (mRNA) associated with disease causing genes. The Company’s drug candidates include IMO-8400; IMO-2125/IMO-2055, and IMO-9200. The Company’s TLR antagonist lead drug candidates are IMO-8400 and IMO-9200, which are both antagonists of TLR7, TLR8 and TLR9. Its TLR agonist lead drug candidates are IMO-2055 and IMO-2125, which are both agonists of TLR9.

SEC Form 13D is filed within 10 days, by anyone who acquires beneficial ownership of 5%+ of any public firm. Activist investors and practices such as: company breakups, hostile takeovers, and change of control events, are permitted for this form filers. A filer must promptly update its 13D filing in case of acquisition or disposition of 1% or more of the securities that are the subject of the filing.

Insitutional Activity: The institutional sentiment increased to 1.25 in Q2 2016. Its up 0.22, from 1.03 in 2016Q1. The ratio increased, as 9 funds sold all Idera Pharmaceuticals Inc shares owned while 15 reduced positions. 3 funds bought stakes while 27 increased positions. They now own 34.46 million shares or 16.20% less from 41.12 million shares in 2016Q1.

Moreover, Cambridge Invest Rech has 0% invested in Idera Pharmaceuticals Inc (NASDAQ:IDRA) for 18,000 shares. Barclays Public Lc accumulated 4 shares or 0% of the stock. Voya Investment Management Llc has invested 0% of its portfolio in Idera Pharmaceuticals Inc (NASDAQ:IDRA). Pnc Services Grp Inc Inc last reported 227 shares in the company. Oxford Asset Mgmt last reported 0.01% of its portfolio in the stock. The Illinois-based Guggenheim Capital Ltd has invested 0% in Idera Pharmaceuticals Inc (NASDAQ:IDRA). Carl Domino last reported 0.04% of its portfolio in the stock. Art Advisors Llc last reported 0% of its portfolio in the stock. Citigroup last reported 17,066 shares in the company. D E Shaw And Communication Inc last reported 94,970 shares in the company. Blackrock Limited Liability Corporation owns 40,602 shares or 0% of their US portfolio. Blackrock Incorporated has invested 0% of its portfolio in Idera Pharmaceuticals Inc (NASDAQ:IDRA). Wall Street Associates has invested 0.24% of its portfolio in Idera Pharmaceuticals Inc (NASDAQ:IDRA). Private Advisor Grp Ltd Liability Co accumulated 27,200 shares or 0% of the stock. Nationwide Fund last reported 58,157 shares in the company.

Insider Transactions: Since May 12, 2016, the stock had 4 insider purchases, and 0 insider sales for $6.57 million net activity. 3.25 million shares were bought by BAKER JULIAN, worth $6.50M. The insider Casey Mark J bought 34,450 shares worth $49,608. 10,000 shares with value of $13,400 were bought by GERAGHTY JAMES A on Friday, May 13. $10,824 worth of Idera Pharmaceuticals Inc (NASDAQ:IDRA) was bought by ZEIN YOUSSEF EL.

Analysts await Idera Pharmaceuticals Inc (NASDAQ:IDRA) to report earnings on November, 4. They expect $-0.12 EPS, down 20.00% or $0.02 from last year’s $-0.1 per share. After $-0.11 actual EPS reported by Idera Pharmaceuticals Inc for the previous quarter, Wall Street now forecasts 9.09% negative EPS growth.

About 151,578 shares traded hands. Idera Pharmaceuticals Inc (NASDAQ:IDRA) has declined 11.88% since March 14, 2016 and is downtrending. It has underperformed by 17.49% the S&P500.

Idera Pharmaceuticals, Inc. is a clinical-stage biopharmaceutical firm focused on the discovery, development and commercialization of therapeutics for oncology and rare diseases. The company has a market cap of $248.99 million. The Firm utilizes two drug discovery technology platforms to design and develop drug candidates, which include Toll-like receptor targeting technology and third-generation antisense (3GA) technology. It currently has negative earnings. Using TLR technology, the Company creates synthetic oligonucleotide drug candidates to act by modulating the activity of specific TLRs.

More recent Idera Pharmaceuticals Inc (NASDAQ:IDRA) news were published by: Fool.com which released: “Why Idera Pharmaceuticals Inc Stock Is Falling Again” on October 07, 2016. Also Fool.com published the news titled: “Why Idera Pharmaceuticals Inc. Is Down Big Today” on October 06, 2016. Fool.com‘s news article titled: “How Much Potential Does Idera Pharmaceuticals’ Pipeline Really Have?” with publication date: October 09, 2016 was also an interesting one.

According to Zacks Investment Research, “Idera Pharmaceuticals, Inc. is a drug discovery and development company that is developing drug candidates to treat cancer and infectious, respiratory, and autoimmune diseases, and for use in combination with therapeutic and prophylactic vaccines. Idera’s proprietary drug candidates are designed to modulate Toll-like Receptors, the body’s first line of immune defense. Idera’s pioneering DNA chemistry expertise enables it to identify drug candidates for internal development and creates opportunities for multiple collaborative alliances.”

IDRA Company Profile

Idera Pharmaceuticals, Inc., incorporated on August 24, 2005, is a clinical-stage biopharmaceutical firm focused on the discovery, development and commercialization of therapeutics for oncology and rare diseases. The Firm utilizes two drug discovery technology platforms to design and develop drug candidates, which include Toll-like receptor (TLR) targeting technology and third-generation antisense (3GA) technology. Using TLR technology, the Company creates synthetic oligonucleotide drug candidates to act by modulating the activity of specific TLRs. Using its 3GA technology, the Company is developing drug candidates to turn off the messenger ribo nucleic acid (mRNA) associated with disease causing genes. The Company’s drug candidates include IMO-8400; IMO-2125/IMO-2055, and IMO-9200.

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