Document:

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                                                                     Exhibit 4.5

                         PARTNERSHIP EXCHANGE AGREEMENT

          THIS PARTNERSHIP EXCHANGE AGREEMENT (this "Agreement") is made as of
December 13, 2004, by and between Advanced Life Sciences Holdings, Inc., a
Delaware corporation ("Holdings"), and Flavin Ventures, LLC, a Delaware limited
liability company ("Ventures").

                                   WITNESSETH:

          WHEREAS, Advanced Life Sciences, Inc., an Illinois corporation
("ALS"), and Michael T. Flavin ("Flavin") entered into that certain Amended and
Restated Partnership Agreement, dated as of December 22, 2001 (the "Partnership
Agreement"), relating to Advanced Life Sciences General Partnership (the
"Partnership"); and

          WHEREAS, under the terms of the Partnership Agreement, Flavin made
capital contributions to the Partnership in the amount of $7,793,968 (the
"Flavin Contribution Amount") from December 1999 through September 2002; and

          WHEREAS, Flavin contributed and assigned his entire interest in the
Partnership to Ventures pursuant to that certain Contribution, Assignment and
Assumption Agreement dated as of September 30, 2002; and

          WHEREAS, from October 2002 through and including the date hereof,
Ventures has made capital contributions to the Partnership in the amount of
$3,717,509 (the "Ventures Contribution Amount" and, together with the Flavin
Contribution Amount, the "Total Partnership Contribution Amount"); and

          WHEREAS, ALS is undergoing a recapitalization and reorganization (the
"Recapitalization") as of the date hereof pursuant to which, among other things,
ALS has become a wholly-owned subsidiary of Holdings pursuant to that certain
ALS Exchange Agreement dated as of the date hereof between Holdings, the Michael
T. Flavin Revocable Trust and Karen Stec; and

          WHEREAS, pursuant to the Recapitalization, Ventures desires to
exchange with Holdings its Interest (as defined in the Partnership Agreement) in
the Partnership for shares of common stock, $.01 per share, of Holdings
("Holdings Stock").

          NOW, THEREFORE, in consideration of the covenants, agreements,
representations and warranties contained in this Agreement, the parties hereto
agree as follows:

          SECTION 1. EXCHANGE

          1.01   PARTNERSHIP INTEREST. At the Closing (as hereinafter defined),
on the terms and subject to the conditions set forth herein, Ventures agrees to
sell, transfer, assign and deliver to Holdings, free and clear of all liens,
pledges, encumbrances, claims and equities of every kind, its Interest in the
Partnership.

          1.02   HOLDINGS STOCK. In exchange and as consideration for the
transfer of Ventures' Interest to Holdings, at the Closing, on the terms and
subject to the conditions set forth herein, Holdings agrees to sell, transfer,
assign and deliver to Ventures, free and clear of all liens, pledges,
encumbrances, claims and equities of every kind, a number of shares of Holdings
Stock determined by dividing (a) the Total Partnership Contribution Amount by
(b) $5.82 (the "Exchange").

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          1.03   THE CLOSING. The closing of the Exchange (the "Closing") will
take place at the offices of Winston & Strawn LLP, 35 West Wacker Drive,
Chicago, Illinois 60601, at such date and time and as may be agreeable to the
parties.

          SECTION 2. CONDITIONS PRECEDENT TO THE EXCHANGE

          2.01   CONDITIONS TO THE OBLIGATION OF VENTURES. The obligation of
Ventures to transfer the Interest as provided in Section 1.01 hereof on the
Closing Date is subject to the satisfaction as of the date of the Closing of the
following conditions:

          (a)    REPRESENTATIONS AND WARRANTIES. The representations and
     warranties of Holdings contained in Section 3 hereof shall be true and
     correct at and as of the Closing.

          (b)    CLOSING DOCUMENTS. At the Closing, Holdings will have delivered
     to Ventures:

                 (i)    certificates representing 1,977,917 shares of Holdings
          Stock issued pursuant to Section 1.02; and

                 (ii)   such other documents relating to the transactions
          contemplated by this Agreement as Ventures may reasonably request.

          (c)    SIMULTANEOUS CLOSINGS. The Closing shall take place
     substantially simultaneously with the closings of the other agreement and
     other transactions contemplated by the Recapitalization (the
     "Recapitalization Transactions").

          (d)    PROCEEDINGS. All corporate, legal and other proceedings taken
     or required to be taken in connection with the transactions contemplated
     hereby to be consummated at or prior to the Closing and all documents
     incident thereto shall be satisfactory in form and substance to Ventures.

          (e)    WAIVER. Any condition specified in Section 2.01 may be waived
     if consented to by Ventures.

          2.02   CONDITION TO HOLDINGS' OBLIGATION AT THE CLOSING. The
obligation of Holdings to deliver the Holdings Stock on the Closing Date
pursuant to Section 1.02 is subject to the satisfaction as of the date of the
Closing of the following conditions:

          (a)    REPRESENTATIONS AND WARRANTIES. The representations and
     warranties of Ventures contained in Section 3 hereof shall be true and
     correct at and as of the Closing.

          (b)    RECEIPT OF PARTNERSHIP INTERESTS. At the closing, Holdings
     shall have received Ventures' Interest in the Partnership.

          (c)    CLOSING DOCUMENTS. On or prior to the Closing, Ventures will
     have delivered to Holdings such other documents relating to the
     transactions contemplated by this Agreement as Holdings may reasonably
     request.

          (d)    SIMULTANEOUS CLOSINGS. The Closing shall take place
     substantially simultaneously with the closings of the other
     Recapitalization Transactions.

                                       -2-
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          (e)    PROCEEDINGS. All corporate, legal and other proceedings taken
     or required to be taken in connection with the transactions contemplated
     hereby to be consummated at or prior to the Closing and all documents
     incident thereto shall be satisfactory in form and substance to Holdings.

          (f)    WAIVER. Any condition specified in Section 2.02 may be waived
     if consented to by Holdings.

          SECTION 3. REPRESENTATIONS AND WARRANTIES

          (a)    Holdings and Ventures expressly disclaim any and all
     representations and warranties, express or implied, except that:

                 (i)    Holdings warrants to Ventures that (A) it is duly
          organized and validly existing under the laws of the State of
          Delaware, (B) it has the requisite corporate power and authority to
          make, deliver and perform this Agreement, (C) it has taken all
          necessary action to authorize the execution, delivery and performance
          of this Agreement and the transactions contemplated thereby, (D) this
          Agreement has been duly executed and delivered on behalf of Holdings
          and (E) this Agreement constitutes a legal, valid and binding
          obligation of Holdings, enforceable against Holdings in accordance
          with its terms; and

                 (ii)   Ventures warrants to Holdings that (A) it is duly
          organized and validly existing under the laws of the State of
          Delaware, (B) it has the requisite limited liability company power and
          authority to make, deliver and perform this Agreement, (C) it has
          taken all necessary action to authorize the execution, delivery and
          performance of this Agreement and the transactions contemplated
          thereby, (D) this Agreement has been duly executed and delivered on
          behalf of Ventures and (E) this Agreement constitutes a legal, valid
          and binding obligation of Ventures, enforceable against Ventures in
          accordance with its terms.

          (b)    Holdings and Ventures acknowledge that they have had complete
     access to all information relating to the other parties necessary to make
     an informed decision regarding the Exchange, and have had the opportunity
     to negotiate the terms and conditions of the Exchange.

          SECTION 4. MISCELLANEOUS

          4.01   EXPENSES. Holdings shall pay all of the expenses incurred by
all parties to this Agreement in connection with this Agreement, including
without limitation, all legal fees.

          4.02   SURVIVAL OF REPRESENTATIONS AND WARRANTIES. All representations
and warranties contained herein will survive the execution and delivery of this
Agreement.

          4.03   SUCCESSORS AND ASSIGNS. All terms and conditions contained in
this Agreement shall bind and inure to the benefit of the respective successors
and assigns of the parties hereto.

          4.04   SEVERABILITY. Whenever possible, each provision of this
Agreement will be interpreted in such manner as to be effective and valid under
applicable law, but if any provision of this Agreement is held to be prohibited
by or invalid under applicable law, such provision will be ineffective only to
the extent of such prohibition or invalidity, without invalidating the remainder
of this Agreement.

                                       -3-
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          4.05   COUNTERPARTS. This Agreement may be executed simultaneously in
counterparts, any one of which need not contain the signatures of more than one
party, but all such counterparts taken together will constitute one and the same
agreement.

          4.06   DESCRIPTIVE HEADINGS. The descriptive headings of this
Agreement are inserted for convenience only and do not constitute a part of this
Agreement.

          4.07   GOVERNING LAW. This Agreement shall be governed by and
construed and enforced in accordance with, the laws of the State of Illinois,
without regard to conflicts of laws principles.

          4.08   ENTIRE AGREEMENT. This Agreement constitutes the entire
agreement of the parties in respect of the subject matter hereof and supersedes
any and all prior understandings (whether written or oral) in respect of such
subject matter.

                            [signature page follows]

                                       -4-
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          IN WITNESS WHEREOF, the parties hereto have caused this Agreement to
be duly executed and delivered as of the day and year first above written.

                                        ADVANCED LIFE SCIENCES HOLDINGS, INC.

                                        /s/ John L. Flavin
                                        ---------------------------------------
                                        By:    John L. Flavin
                                        Title: President

                                        FLAVIN VENTURES, LLC

                                        /s/  Michael T. Flavin
                                        ---------------------------------------
                                        By:    Michael T. Flavin
                                               Member

Consent to the transfer of
Interest pursuant to Section 7.1
of the Partnership Agreement:

ADVANCED LIFE SCIENCES, INC.

/s/ John L. Flavin
---------------------------------------
By:     John L. Flavin
Title:  President

                         PARTNERSHIP EXCHANGE AGREEMENT<Page>

                                                                     Exhibit 4.6

                             ALS EXCHANGE AGREEMENT

          THIS ALS EXCHANGE AGREEMENT (this "Agreement") is made as of December
13, 2004, by and between Advanced Life Sciences Holdings, Inc., a Delaware
corporation ("Holdings"), the Michael T. Flavin Revocable Trust, an Illinois
trust (the "Trust"), and Karen Stec, and individual residing in the State of
Illinois ("Stec" and, together with the Trust, the "Shareholders").

                                   WITNESSETH:

          WHEREAS, the Trust owns 400,000 shares and Stec owns 10,500 shares of
common stock, no par value, of Advanced Life Sciences, Inc., an Illinois
corporation ("ALS"), representing all issued and outstanding shares of common
stock of ALS (the "ALS Shares"); and

          WHEREAS, ALS is undergoing a recapitalization and reorganization as of
the date hereof (the "Recapitalization"); and

          WHEREAS, in connection with the Recapitalization, the Shareholders
desire to transfer to Holdings the ALS Shares and, in return, Holdings desires
to deliver to the Shareholders an equivalent number of shares of Holdings'
common stock, $.01 par value per share ("Holdings Common Stock").

          NOW, THEREFORE, in consideration of the covenants, agreements,
representations and warranties contained in this Agreement, the parties hereto
agree as follows:

          SECTION 1.  EXCHANGE

          1.01  THE EXCHANGE. At the Closing (as hereinafter defined), on the
terms and subject to the conditions set forth herein, the Shareholders agree to
sell, transfer, assign and deliver to Holdings, free and clear of all liens,
pledges, encumbrances, claims and equities of every kind, the ALS Shares, and
Holdings agrees to sell, transfer, assign and deliver to the Shareholders, free
and clear of all liens, pledges, encumbrances, claims and equities of every
kind, 410,500 shares of Holdings Common Stock (the "Holdings Shares") (the
exchange of the ALS Shares and the Holdings Shares is hereafter referred to as
the "Exchange").

          1.02  ALLOCATION BETWEEN SHAREHOLDERS. In the Exchange, the Trust
shall receive 400,000 Holdings Shares and Stec shall receive 10,500 Holdings
Shares.

          1.03  THE CLOSING. The closing of the Exchange (the "Closing") will
take place at the offices of Winston & Strawn LLP, 35 West Wacker Drive,
Chicago, Illinois 60601, at such date and time and as may be mutually agreeable
to Holdings and the Shareholders.

          SECTION 2.  CONDITIONS PRECEDENT

          2.01  CONDITIONS TO THE SHAREHOLDERS' OBLIGATION AT THE CLOSING. The
obligation of the Shareholders to deliver the ALS Shares as provided in Section
1 hereof on the Closing Date is subject to the satisfaction as of the date of
the Closing of the following conditions:

          (a)   REPRESENTATIONS AND WARRANTIES. The representations and
     warranties of Holdings contained in Section 3 hereof shall be true and
     correct at and as of the Closing.

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          (b)   CLOSING DOCUMENTS. At the Closing, Holdings will have delivered
     to the Shareholders:

                (i)   certificates representing the newly issued Holdings
          Shares; and

                (ii)  such other documents relating to the transactions
          contemplated by this Agreement as the Shareholders may reasonably
          request.

          (c)   SIMULTANEOUS CLOSINGS. The Closing shall take place
     substantially simultaneously with the closings of the other agreement and
     other transactions contemplated by the Recapitalization (the
     "Recapitalization Transactions").

          (d)   PROCEEDINGS. All corporate, legal and other proceedings taken or
     required to be taken in connection with the transactions contemplated
     hereby to be consummated at or prior to the Closing and all documents
     incident thereto shall be satisfactory in form and substance to the
     Shareholders.

          (e)   WAIVER. Any condition specified in Section 2.01 may be waived if
     consented to by each Shareholder.

          2.02  CONDITION TO HOLDINGS' OBLIGATION AT THE CLOSING. The obligation
of Holdings to deliver the Holdings Shares to the Shareholders on the Closing
Date is subject to the satisfaction as of the date of the Closing of the
following conditions:

          (a)   REPRESENTATIONS AND WARRANTIES. The representations and
     warranties of the Shareholders contained in Section 3 hereof shall be true
     and correct at and as of the Closing.

          (b)   CLOSING DOCUMENTS. At the Closing, the Shareholders will have
     delivered to Holdings:

                (i)   certificates representing the ALS Shares, each of which
          certificates shall be duly endorsed or accompanied by a duly executed
          stock power; and

                (ii)  such other documents relating to the transactions
          contemplated by this Agreement as Holdings may reasonably request.

          (c)   SIMULTANEOUS CLOSINGS. The Closing shall take place
     substantially simultaneously with the closings of the other
     Recapitalization Transactions.

          (d)   PROCEEDINGS. All corporate, legal and other proceedings taken or
     required to be taken in connection with the transactions contemplated
     hereby to be consummated at or prior to the Closing and all documents
     incident thereto shall be satisfactory in form and substance to Holdings.

          (e)   WAIVER. Any condition specified in Section 2.02 may be waived if
     consented to by Holdings.

          SECTION 3. REPRESENTATIONS AND WARRANTIES

          (a)   Holdings and the Shareholders expressly disclaim any and all
     representations and warranties, express or implied, except that:

                                       -2-
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                (i)   Holdings warrants to the Shareholders that (A) it is duly
          organized and validly existing under the laws of the State of
          Delaware, (B) it has the requisite corporate power and authority to
          make, deliver and perform this Agreement, (C) it has taken all
          necessary action to authorize the execution, delivery and performance
          of this Agreement and the transactions contemplated thereby, (D) this
          Agreement has been duly executed and delivered on behalf of Holdings
          and (E) this Agreement constitutes a legal, valid and binding
          obligation of Holdings, enforceable against Holdings in accordance
          with its terms; and

                (ii)  Each Shareholder warrants to Holdings that (A) it has the
          requisite power and authority to make, deliver and perform this
          Agreement, (B) this Agreement has been duly executed and delivered on
          behalf of such Shareholder and (C) this Agreement constitutes a legal,
          valid and binding obligation of such Shareholder enforceable against
          such Shareholder in accordance with its terms.

          (b)   Holdings and the Shareholders each acknowledge that they have
     had complete access to all information relating to the other necessary to
     make an informed decision regarding the Exchange, and have had the
     opportunity to negotiate the terms and conditions of the Exchange.

          SECTION 4. MISCELLANEOUS

          4.01  EXPENSES. Holdings shall pay all of the expenses incurred by all
parties to this Agreement in connection with this Agreement, including without
limitation, all legal fees.

          4.02  SURVIVAL OF REPRESENTATIONS AND WARRANTIES. All representations
and warranties contained herein will survive the execution and delivery of this
Agreement, regardless of any investigation made by the Shareholders or Holdings
or on behalf of the Shareholders or Holdings.

          4.03  SUCCESSORS AND ASSIGNS. All terms and conditions contained in
this Agreement shall bind and inure to the benefit of the respective successors
and assigns of the parties hereto.

          4.04  SEVERABILITY. Whenever possible, each provision of this
Agreement will be interpreted in such manner as to be effective and valid under
applicable law, but if any provision of this Agreement is held to be prohibited
by or invalid under applicable law, such provision will be ineffective only to
the extent of such prohibition or invalidity, without invalidating the remainder
of this Agreement.

          4.05  COUNTERPARTS. This Agreement may be executed simultaneously in
counterparts, any one of which need not contain the signatures of more than one
party, but all such counterparts taken together will constitute one and the same
agreement.

          4.06  DESCRIPTIVE HEADINGS. The descriptive headings of this Agreement
are inserted for convenience only and do not constitute a part of this
Agreement.

          4.07  GOVERNING LAW. This Agreement shall be governed by and construed
and enforced in accordance with, the laws of the State of Illinois, without
regard to conflicts of laws principles.

          4.08  ENTIRE AGREEMENT. This Agreement constitutes the entire
agreement of the parties in respect of the subject matter hereof and supersedes
any and all prior understandings (whether written or oral) in respect of such
subject matter.

                                       -3-
<Page>

          IN WITNESS WHEREOF, the parties hereto have caused this Agreement to
be duly executed and delivered as of the day and year first above written.

                                        THE MICHAEL T. FLAVIN REVOCABLE
                                        TRUST

                                        /s/ Michael T. Flavin
                                        ----------------------------------
                                        By:    Michael T. Flavin
                                               Trustee

                                        /s/ Karen Stec
                                        ----------------------------------
                                        Karen Stec, in her individual capacity

                                        ADVANCED LIFE SCIENCES HOLDINGS, INC.

                                        /s/ John L. Flavin
                                        ----------------------------------
                                        By:    John L. Flavin
                                        Title: President

                             ALS EXCHANGE AGREEMENT

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