13D Filing: Baker Bros. Advisors and Idera Pharmaceuticals Inc. (IDRA)

(a) and (b) Items 7 through 11 and 13 of each of the cover pages
of this Amendment No. 1 are incorporated herein by reference. Set forth below is the aggregate number of shares of Common Stock
directly held by each of the the Funds, which may be deemed to be indirectly beneficially owned by the Reporting Persons, as well
as shares of Common Stock that may be acquired upon exercise of certain warrants to purchase shares of Common Stock at an exercise
price of $0.47 per share that expire on May 7, 2018 (“2018 Warrants”), certain warrants to purchase shares of Common
Stock at an exercise price of $0.01 per share that expire on May 7, 2020 (“May 2020 Warrants”), certain warrants to
purchase shares of Common Stock at an exercise price of $0.01 per share that expire on September 25, 2020 (“September 2020
Warrants”) and certain warrants to purchase shares of Common Stock at an exercise price of $0.01 per share that expire on
February 10, 2021 (“2021 Warrants”, and together with the 2018 Warrants, May 2020 Warrants, and September 2020 Warrants,
the “Warrants”) by the Funds, subject to the limitation on exercise described below. The information set forth below
is based upon 183,013,693 shares of Common Stock that will be outstanding following the Offering including 5,000,000 shares issued
as part of the Underwriters option, as described in the Issuer’s Prospectus Supplement filed with the Securities and Exchange
Commission on October 26, 2017.

The Warrants are only exercisable to the extent that after giving
effect to such exercise the holders thereof and their affiliates would beneficially own, for purposes of Rule 13d-3 under the Securities
Exchange Act of 1934, as amended, no more than 4.999% of the outstanding shares of Common Stock of the Issuer. As a result of this
restriction, the number of shares that may be issued upon exercise of the Warrants by the above holders may change depending upon
changes in the outstanding shares of Common Stock.

Pursuant to management agreements, as amended, among the Adviser,
the Funds, and their respective general partners, the Adviser has complete and unlimited discretion and authority with respect
to the Funds’ investments and voting power over investments.

The Adviser GP, Felix J. Baker and Julian C. Baker as principals
of the Adviser GP, and the Adviser may be deemed to be beneficial owners of securities of the Issuer directly held by the Funds,
and may be deemed to have the power to vote or direct the vote of and the power to dispose or direct the disposition of such securities.

The Reporting Persons disclaim beneficial ownership of the securities
held by each of the Funds, and this Amendment No. 1 shall not be deemed an admission that the Reporting Persons are the beneficial
owners of such securities for purposes of Section 13(d) or for any other purpose.

The Adviser GP, and Felix J. Baker and Julian C. Baker as principals
of the Adviser GP, may be deemed to have the power to vote or direct the vote of and the power to dispose or direct the disposition
of the Stock Options held by Julian C. Baker and Dr. Neu.

(c) The disclosure regarding the purchase of Common Stock of
the Issuer in the Offering and the disclosure regarding the shares of Common Stock granted to Julian C. Baker and Dr. Neu on October
2, 2017, described in Item 4 are incorporated by reference herein. Except as described in this Amendment No. 1, none of the Reporting
Persons has effected any transaction in the securities of the Issuer during the past 60 days.