Document:

EX-10.9

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 Exhibit 10.9 

CERTAIN IDENTIFIED INFORMATION HAS BEEN EXCLUDED FROM THIS EXHIBIT BECAUSE IT IS BOTH (I) NOT MATERIAL AND (II) WOULD LIKELY CAUSE
COMPETITIVE HARM IF PUBLICLY DISCLOSED. [***] INDICATES THAT INFORMATION HAS BEEN REDACTED. 
 AMENDMENT NO. 1 

TO 
 RESEARCH, DEVELOPMENT
AND 
 COMMECIALIZATION AGREEMENT (the “Existing Agreement”) 

DATED MAY 24, 2004 BY AND BETWEEN VERTEX PHARMACEUTICALS 

INCORPORATED (“Vertex”) and CYSTIC FIBROSIS FOUNDATION 

THERAPEUTICS INCORPORATED (“CFFT”) 

This Amendment No. 1 (the “Amendment”) is made this 6th day of January, 2006 (the
“Effective Date”) between Vertex, a Massachusetts corporation with principal offices at 130 Waverly Street, Cambridge, MA 02139-4242 and CFFT, a Delaware corporation with principal offices at 6931 Arlington Road, Bethesda, Maryland 20814.
Vertex and CFFT are referred to hereinafter collectively as the Parties. 
 INTRODUCTION 

In 1998, CFFT made an award to Aurora Biosciences to do a feasibility study using high throughput screening for cf targets. On May 19, 2000, CFFT
selected and provided support for Aurora Biosciences to conduct high throughput screening with respect to the CFTR target identified by CFFT. Since that time, Aurora Biosciences, and then after its merger into Vertex, Vertex, have been conducting a
Research Program with CFFT’s support aimed at identification and design of Potentiator and Corrector Compounds, both of which are directed as a principal mode of therapeutic action at modulation of the biological effect of CFTR in different
ways and with different anticipated results. The Existing Agreement contemplated that during the course of the Research Program, Vertex, with CFFT’s agreement, would select either the Potentiator or the Corrector approaches as its Primary
Program, to which a majority of resources under the Research Program would be directed, and the other approach would be designated as an Alternative Program, to which the balance of resources would be directed. 

Vertex has selected the Potentiator approach as the Primary Program, with the concurrence of CFFT, and expects to designate a Potentiator Compound as a
Development Candidate on or before December 31, 2005. 
 The Parties continue to believe that it may be possible to create Corrector Compounds of
significant potential value as therapeutics in the Field. To further this effort, CFFT and Vertex agree hereinafter to provide additional funding and Vertex intends to continue its research efforts with respect to Correctors beyond the current
Research Termination Date of December 31, 2005. The purpose of this Amendment is to modify the terms of the Existing Agreement to reflect the progress made in the Research Program during its current term and to set forth the terms of the
extended Corrector Research Program. 
 Capitalized terms not otherwise defined in this Amendment shall have the meaning ascribed to them in the Existing
Agreement. If specific provisions of this Amendment are inconsistent with specific provisions of the Existing Agreement, the provisions of this Amendment shall control. 

  
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 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 In consideration of the mutual covenants set forth in this Amendment, and other good and valuable
consideration, the receipt of which is hereby acknowledged, the Parties agree as follows: 
 1. General. 

 

	1.1.	 Vertex and CFFT acknowledge that the “Primary Program” under the Existing Agreement refers to
research activities relating to Potentiator Compounds. CFFT has no further right to request under Section 2.5 of the Existing Agreement that Vertex designate Correctors as the Primary Program, or to terminate the Existing Agreement under
Section 10.5.1 thereof. 

  

	1.2.	 After December 31, 2005, the “Research Program” will refer to research undertaken under the
Existing Agreement, as amended hereby, with respect only to Corrector Compounds (except for the Potentiator research funded during 2006 as specified in the attached Research Plan). The “Research Plan” under Section 2.4 of the Existing
Agreement will mean, after December 31, 2005, the initial plan for conduct of the Research Program focused on Correctors (and to a limited extent, Potentiators, as provided in the Research Plan), subject to applicable provisions of
Section 2.4.1 of the Existing Agreement regarding modifications to that Research Plan. A copy of the initial Research Plan for continuing Corrector research (the “Initial Corrector Research Plan”) is attached to this Amendment as
Exhibit 1.2. The concepts of Primary Subplan and Alternative Subplan as referenced in Section 2.4.3 of the Existing Agreement will no longer apply to activities undertaken under the Research Program after December 31, 2005. The
terms of the Existing Agreement that provide for the allocation of resources between the Primary and the Alternative Programs will not be applicable to the Research Program after December 31, 2005. 

 

	1.3.	 The budget for the Research Program under the Existing Agreement for the one year period ending
December 31, 2005 (the “Current Budget”) is attached hereto as Exhibit 1.3, has been approved by both Parties hereto and represents an agreed allocation of funding between the Primary and the Alternative Programs for the period
ending December 31, 2005. The Parties have agreed on a separate budget (the “Initial Corrector Budget”) representing an agreed allocation of additional Corrector research funding to be provided under this Amendment, as referenced in
Section 4.1 below, for the period commencing on the Effective Date of this Amendment and ending on the Research Termination Date referenced in Section 1.4 below. 

 

	1.4.	 The Research Termination Date shall mean the end of the revised Research Program directed at the identification
and design of Corrector Drug Product Candidates (the “Corrector Research Program”) which shall be March 31, 2008, unless the Research Program under the Existing Agreement as amended hereby is otherwise extended or terminated in
accordance with its terms. 

  

	1.5.	 The term “Drug Product[s]” is amended to mean a finished dosage form that is prepared from Bulk Drug
Substance covered by Vertex CF Technology and is ready for administration to the ultimate consumer as a pharmaceutical. 

  

	1.6.	 The term “Vertex CF Technology” as defined in the Existing Agreement shall also be deemed to refer to
data, technical information, know-how, inventions (whether or not patented), trade secrets, processes and methods discovered or developed, and Controlled by Vertex or its Affiliates, in the course of the
performance of the Research Program under this Amendment, but shall not refer to Vertex’s general drug design technology whether in hardware or software form, tangible or intangible. 

  
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	1.7.	 The provisions of Section 6.3 of the Existing Agreement shall apply to this Amendment as if it were being
entered into as part of the Existing Agreement. The Parties will agree on the timing and content of a press release relating to this Amendment. 

2. Termination Provisions. 
  

	2.1.	 On the Effective Date of this Amendment, CFFT shall no longer have the right to terminate the Existing
Agreement under Section 10.5.1 (relating to a disagreement over the choice of Primary and Alternative Programs) or Section 10.6.3 (relating to termination of the Alternative Program). Therefore, those sections of the Existing Agreement are
hereby deleted. 

  

	2.2.	 Section 10.5.2 of the Existing Agreement is hereby amended to read as follows: 

“At its sole discretion, CFFT may terminate the Research Program effective June 30, 2006 or June 30, 2007, upon not less than
sixty (60) days prior written notice to Vertex (an “Early Termination Notice”).” 
  

	2.3.	 Sections 10.5.4, 10.5.6 and 10.7 of the Existing Agreement are hereby deleted. 

 

	2.4.	 Section 10.6.1 of the Existing Agreement is hereby amended by substituting the word “if” for the
word “unless” in the fourth-to-last line of that section. 

3. Other CFTR Research. 
 During the period for which
funding is provided to Vertex by CFFT under the Existing Agreement (as amended herein or subsequently from time to time), and under a separate agreement providing for continued Potentiator funding (the “Potentiator Funding Agreement”), if
such funding is provided in other than in the Existing Agreement, all of Vertex’s research efforts directed at the identification, development and commercialization of pharmaceutical products that have as their principal mode of action the
modulation of CFTR shall be conducted under the Existing Agreement (as amended herein or subsequently from time to time) and under the Potentiator Funding Agreement. During the [***] period following the later of the last date upon which CFFT
provides funding to Vertex under the Existing Agreement (as amended herein or subsequently from time to time), or the last date upon which CFFT provides continuing Potentiator funding under the Potentiator Funding Agreement, if such funding is
provided for other than in the Existing Agreement, Vertex shall not enter into any research, development or commercialization agreement (a “Third Party Agreement”) with a third party directed toward the eventual commercialization
(including the acquisition and sale of a marketed product) of a pharmaceutical product that has as its principal mode of action the modulation of CFTR and is not a Drug Product (the “New Product”), unless CFFT will receive the same royalty
rate from Vertex or the third party under the Third Party Agreement as is provided under Section 5.3.1 of the Existing Agreement (as it may be subsequently amended), on account of any Net Sales of the New Product. An agreement between Vertex
and a third party for the conduct of research activities, under which that third party does not then (or by subsequent agreement with such third party) receive any license rights to, or compensation with respect to the development or sale of, any
pharmaceutical product that has CFTR modulation as its principal mode of action, shall not be deemed a Third Party Agreement for the purposes of the foregoing restriction. The foregoing provisions of this Section 3 shall not apply to any Third
Party Agreement relating to a New Product that is a Corrector from and after the date upon which CFFT exercises its termination rights under section 10.5.2 of the Existing Agreement (as amended pursuant to this Amendment No. 1). In the event of
an Interruption under Section 10.6.2 of the Existing Agreement with respect to either Potentiator or Corrector research programs, Vertex shall not enter into any agreement with a third party for commercial purposes, for a period of [***]
after such Interruption, relating to the program to which the Interruption related. 

  
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 4. Budget and Funding. 

From and after the Effective Date of this Amendment, the following provisions shall apply to any incremental funding for Corrector research in 2005, and to the
budget and funding for all Corrector research thereafter under the Research Plan, in lieu of the provisions in Sections 4.1, 4.2 and 4.3 of the Existing Agreement. 
  

	4.1.	 The initial budget for incremental funding of the Corrector Research Program, relating to discovery,
optimization and IND-enabling activities for Corrector Compounds, is attached hereto as Exhibit 4.1 (the “Initial Corrector Budget”). The Initial Corrector Budget includes only amounts that
are incremental to the funding currently provided for Corrector research in the “Alternative Program” under the Current Budget. Any material revisions to the Initial Corrector Budget which would result in an increase in total funding for
the Corrector Research Program beyond the amount provided under this Amendment will require the prior approval of CFFT. Any other adjustments to the Initial Corrector Budget may be undertaken by Vertex with prior notice to, but without prior
approval from, CFFT. Vertex will provide CFFT with [***] reports within [***] showing expenses incurred under the Corrector Research Program during the quarter just ended against budgeted expenses for that quarter. For [***],
the report will cover the period from the Effective Date of this Amendment through the end of that quarter. 

  

	4.2.	 CFFT will fund [***] of the Initial Corrector Budget and Vertex will fund [***] of the Initial
Corrector Budget. Based on the approved Initial Corrector Budget of [***], CFFT will make the payments to Vertex specified below during the specified periods. 

 

									
	 	  	INITIAL CORRECTOR BUDGET
(millions $)	 
	 Research Period
	  	Aggregate
Budget
Amount	 	  	CFFT
Financial
Commitment	 
	 January 1, 2006—December 31, 2006
	  	 	[***	] 	  	 	[***	] 
	 January 1, 2007—March 31, 2008
	  	 	[***	] 	  	 	[***	] 

 Payments due under the Initial Corrector Budget on account of internal FTEs shall be made by CFFT [***].
Payments due under the Initial Corrector Budget on account of external costs shall be made by CFFT to Vertex [***] within [***] following [***] . All payments shall be made without deduction for withholding or similar taxes in
United States dollars to the credit of such bank account as may be designated in writing to CFFT. Any payments which fall due on a date that is a legal holiday in The Commonwealth of Massachusetts may be made on the next following day that is not a
legal holiday in The Commonwealth. On or before January 31 of 2006, 2007, 2008 and 2009, Vertex will provide CFFT with an accounting of all internal FTE costs and external Research costs (including documentary evidence of such external costs)
incurred under the Research Program during the most recently concluded calendar year. Internal FTE costs will be calculated at an annual rate of [***] per FTE. 
  

	4.3.	 If CFFT’s contribution for any reporting period is in excess of its agreed portion of the total expense
incurred by Vertex (internal and external) for the Corrector Research Program for that period, the excess amount will be carried over and applied as a credit against CFFT’s required contribution in future periods, except that any aggregate
excess contributions provided by CFFT as of the end of the Research Program Term will be refunded to CFFT within [***]thereafter. To the extent not inconsistent with the provisions of this Amendment, the provisions of Section 4.5 will
apply to the Corrector Research Program. 

  
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	4.4.	 Vertex will dedicate a minimum average of [***] FTE scientists (on an annualized basis) to the Corrector
Research Program during its term, [***]. 

 5. Royalties Outside the Field 

Section 5.3.2 of the Existing Agreement is amended as follows: 

“5.3.2 Net Sales outside the Field. Vertex shall pay CFFT a royalty of [***].” 

[Signature Page Follows] 

  
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 IN WITNESS WHEREOF, the Parties hereto have executed this Agreement the day and year first above written.

  

									
	 VERTEX PHARMACEUTICALS

INCORPORATED
	  		  	 CYSTIC FIBROSIS FOUNDATION

THERAPEUTICS, INCORPORATED

					
	By:	 	 /s/ KENNETH S. BOGER
	  	        	  	By:	 	 /s/ ROBERT J. BEALL, PH.D.

		 	 Senior Vice President
 and General
Counsel
	  		  		 	President and Chief Executive Officer

  
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 Exhibit 1.2 

Corrector Research Plan 
 [***]

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 Exhibit 1.3 

Current Budget 
 [***] 

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 Exhibit 4.1 

Initial Corrector Budget 
 [***]EX-10.10

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 Exhibit 10.10 

AMENDMENT NO. 2 to 

RESEARCH, DEVELOPMENT AND COMMERCIALIZATION AGREEMENT, 

DATED MAY 24, 2004, by and between VERTEX PHARMACEUTICALS INCORPORATED and CYSTIC FIBROSIS FOUNDATION THERAPEUTICS INCORPORATED 

This Amendment No. 2 (the “Second Amendment”) is made as of January 1, 2006 (the “Effective Date”)
by and between Vertex Pharmaceuticals Incorporated, a Massachusetts corporation with its principal offices at 130 Waverly Street, Cambridge, Massachusetts 02139-4242 (“Vertex”), and Cystic Fibrosis Foundation Therapeutics
Incorporated, a Delaware corporation with its principal offices at 6931 Arlington Road, Bethesda, Maryland 20814 (“CFFT”). 

This Second Amendment amends the Research, Development and Commercialization Agreement, dated May 24, 2004, by and between Vertex and
CFFT (the “Existing Agreement”), as amended by Amendment No. 1 to the Existing Agreement, dated January 6, 2006, by and between Vertex and CFFT (the “First Amendment”). Any reference herein to the
“Existing Agreement, as amended”, refers to the Existing Agreement and the First Amendment, unless the context otherwise requires. Vertex and CFFT are referred to herein individually as a “Party” and collectively as
the “Parties.” 
 Background 

In 1998, CFFT made an award to Aurora Biosciences Corporation (“Aurora”) to conduct a feasibility study using high throughput
screening for cystic fibrosis targets. On May 19, 2000, CFFT selected and provided support for Aurora to conduct high throughput screening with respect to the cystic fibrosis transmembrane conductance regulator (“CFTR”) target
identified by CFFT. Since that time, Aurora, and then after its merger into Vertex, Vertex, have been conducting a research program with CFFT’s support aimed at identification and design of “Potentiator” and “Corrector”
compounds, both of which are directed as a principal mode of therapeutic action at modulation of the biological effect of CFTR in different ways and with different anticipated results. 

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 On May 24, 2004, the Parties executed the Existing Agreement. The Existing Agreement
contemplated that during the course of the research program, Vertex, with CFFT’s agreement, would select either the Potentiator or the Corrector approach as its Primary Program (as defined in the Existing Agreement), to which a majority of
resources under the research program would be directed, and the other approach would be designated as an Alternative Program (as defined in the Existing Agreement), to which the balance of resources would be directed. 

In 2005, with the concurrence of CFFT, Vertex selected the Potentiator approach as the Primary Program, and designated a certain Potentiator
Compound (“VX-770”) as a Development Candidate under the terms of the Existing Agreement. 

The Parties believe that it may be possible to create Corrector Compounds of significant potential value as therapeutics. To further that
effort, on January 6, 2006, the Parties executed the First Amendment. Among other things, the First Amendment provided for continued funding for research relating to Corrector Compounds. 

In connection with the First Amendment, the Parties executed a Term Sheet (the “Term Sheet”) outlining the financial terms
upon which CFFT might consider funding for the accelerated development of Potentiator Compounds. 
 This Second Amendment is intended
to set forth the Parties’ agreement with respect to additional funding for the accelerated development of Potentiator Compounds, and to amend the Existing Agreement and the First Amendment accordingly. 

  
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 Amendment 

In consideration of the mutual covenants set forth in this Second Amendment, and other good and valuable consideration, the receipt of which
is hereby acknowledged, the Parties agree as follows: 
 Section 1. Acceleration Funding Agreement 

This Second Amendment is intended to constitute the Potentiator Funding Agreement contemplated by the First Amendment (referenced as the
“Acceleration Funding Agreement” in the Term Sheet). Capitalized terms not otherwise defined in this Second Amendment shall have the meaning ascribed to them in the Existing Agreement, as amended. If specific provisions of this
Second Amendment are inconsistent with specific provisions of the Existing Agreement, as amended, the provisions of this Second Amendment, with respect to the subject matter of this Second Amendment, shall control. Otherwise, the Existing Agreement,
as amended, shall continue to be applicable. 
 Section 2. Development and Development Funding. 

2.1. Potentiator JDC Organization and Operation. 

2.1.1 Potentiator JDC Membership. As soon as practicable after the Effective Date, Vertex will establish a Potentiator Joint Development
Committee (the “Potentiator JDC”) consisting of not fewer than 8 members, as may be determined from time to time by the Potentiator JDC. The Potentiator JDC shall continue to function until FDA approval of a Potentiator Drug
Product. During the period ending December 31, 2008, the Potentiator JDC shall include an equal number of representatives designated by each of Vertex and CFFT. Thereafter, CFFT shall be entitled to four (4) representatives on the
Potentiator JDC. In addition to members appointed by CFFT, the Potentiator JDC is expected to have members from the 

  
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 various functional groups (e.g., research, preclinical safety, clinical, regulatory, marketing) that
are or will be expected to be involved from time to time in development and launch of VX-770 or any other Potentiator Backup Compound that is substituted for VX-770
(collectively VX-770 and such Potentiator Backup Compounds are referred to hereinafter as “VX-770”). Vertex will appoint the Potentiator JDC Chair. In
addition to Potentiator JDC members, attendees of Potentiator JDC meetings may include such Vertex or CFFT representatives as may be required for presentation to or discussion with the Potentiator JDC from time to time. 

2.1.2 Potentiator JDC Operation. The Potentiator JDC will be the principal organization through which the development of VX-770 is planned and evaluated, subject to appropriate review and approval at senior management levels as required by Vertex from time to time. The Potentiator JDC will be responsible for preparation and
implementation of the development plan described in Section 2.1.3, below, with respect to VX-770. The Potentiator JDC will typically meet at least quarterly, depending on the level of current development
activity. Each of Vertex and CFFT shall have one vote on the Potentiator JDC. The objective of the Potentiator JDC shall be to reach agreement by consensus on all matters overseen by the Potentiator JDC. However, except as hereinafter provided, in
the event of a deadlock with respect to any action, the vote of the Potentiator JDC Chair rendered after reasonable and open discussion among the members of the Potentiator JDC shall be final and controlling. 

2.1.3 Development Plan. The Potentiator JDC shall review the implementation of an overall development plan for VX-770. The development plan shall describe the proposed clinical trial activities, non-clinical development activities, and supply and manufacturing activities for VX-770. The initial development plan considered by Vertex for VX-770 (the “VX-770 Benchmark Potentiator Development
Plan”) and the development plan currently being 

  
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 implemented by Vertex (the “VX-770 Accelerated Potentiator
Development Plan”), are attached hereto as Exhibits 2.1.3A and 2.1.3B, respectively. The VX-770 Accelerated Potentiator Development Plan reflects a significant acceleration into 2006 or
2007 of certain development activities previously planned for later in the development process, with the objective of significantly accelerating the time to NDA filing if VX-770 is successful. The VX-770 Accelerated Potentiator Development Plan will be reviewed and may be further refined from time to time by the Potentiator JDC, based in part on data generated in early
pre-clinical and clinical trials. However, the Parties intend that separate clinical trails will be conducted for the G5551D and dF508 CF patients, as provided in Exhibit 2.1.3B, and to that end the IND
which Vertex filed on March 14, 2006 provides for separate Phase I clinical trials targeting G5551D and dF508 CF patient groups. The actual design of those Phase I and any further clinical trails may be influenced by FDA feedback, clinical and
nonclinical trial data and other scientific and medical information. Any change in the clinical plans will be reviewed by Vertex with the Potentiator JDC with the aim of reaching consensus before being implemented. 

2.1.4 Meeting Materials. The Potentiator JDC will consider all information that is material to an assessment of the status,
direction and progress of the development program for VX-770, including clinical trial protocols, a summary of the IND package, enabling animal toxicity data reports, clinical trial protocols, clinical trials
final reports, summary data and reports. The Potentiator JDC will review progress reports prepared by Vertex, which shall be submitted to the Potentiator JDC prior to each meeting and which shall include a summary in written text of progress made
during the preceding three month period under the VX-770 Accelerated Potentiator Development Plan. The chemical structure of VX-770 will be disclosed at the written
request of CFFT to one CFFT employee reasonably acceptable to Vertex who is a 

  
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 JDC member and who executes a customary form of confidentiality agreement directly with Vertex, undertaking
to maintain the chemical structure in confidence. Vertex will also disclose the chemical structure of VX-770 to CFFT’s chemistry advisors to whom it has previously disclosed the structure, under
confidential disclosure agreements previously executed with each such advisor, provided that such agreements explicitly cover the additional disclosure or are appropriately modified to that effect. The Potentiator JDC Chair will ensure that minutes
are prepared and distributed to each member of the Potentiator JDC after each meeting. Subject to the restrictions on disclosure of chemical structures set forth above, CFFT’s representatives on the Potentiator JDC will receive all documents
and information distributed or communicated to members of the Potentiator JDC. In any event, all information presented to the JDC or otherwise disclosed to CFFT by or at the direction of Vertex shall be deemed confidential to Vertex and subject to
the confidentiality provisions of the Existing Agreement. 
 2.2 Therapeutic Development Network. CFFT will use its good faith
efforts to foster discussions between the Therapeutic Development Network (“TDN”) and Vertex so that the TDN may enter into appropriate agreements with Vertex to provide to Vertex resources and expertise of the TDN to support
development efforts for VX-770. 
 2.3 Budget and Funding. Exhibit 2.3A contains a
summary “Benchmark Potentiator Budget” that sets forth the estimated costs of the VX-770 Benchmark Potentiator Development Plan originally proposed by Vertex, and a further summary budget, the
“Accelerated Potentiator Budget,” that sets forth the estimated costs of the VX-770 Accelerated Potentiator Development Plan, in each case for the period commencing January 1, 2006 and
ending December 31, 2007 (the “CFFT Accelerated Potentiator Funding Term”). A more detailed budget for the VX-770 Accelerated Potentiator Development Plan for 2006, based on 

  
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 Vertex’s most current activity and cost assumptions, is also attached as Exhibit 2.3B. Vertex
will provide comparable budgetary information for 2007 as soon as it becomes available in late 2006. CFFT agrees to bear $13.3 million of the actual Development Costs (as defined below) for VX-770 under
the VX-770 Accelerated Potentiator Development Plan; provided that (i) CFFT’s aggregate funding obligation (the “CFFT Accelerated Potentiator Funding”) shall not exceed
50% (fifty percent) of that portion of Vertex’s Development Costs incurred during the CFFT Accelerated Potentiator Funding Term that are in excess of the aggregate Development Costs summarized in the Benchmark Potentiator Budget for the CFFT
Accelerated Potentiator Funding Term; and (ii) CFFT’s funding obligation for the year 2006 shall not exceed $7.9 million unless CFFT otherwise agrees in writing. The budget for the
VX-770 Accelerated Potentiator Development Plan may be revised by the Potentiator JDC from time to time; except that the amount of CFFT Accelerated Potentiator Funding shall not be increased without the
written consent of CFFT. For purposes of this Amendment 2, the dates specified in Section 4.3 of the Existing Agreement for Vertex to provide CFFT with an accounting of all internal FTE’s and outsource costs will be changed to no later
than January 31, 2007 and 2008, respectively; and Vertex shall exercise its good faith efforts to furnish CFFT with such accounting as early in January as is possible. Funding will be reviewed by Vertex and CFFT at the end of each calendar year
during the CFFT Accelerated Potentiator Funding Term, and any amounts paid by CFFT during the calendar year that are in excess of the CFFT Accelerated Potentiator Funding amounts required under this Second Amendment will be credited against
CFFT’s 2007 funding obligations hereunder (if paid on account of activities during 2006), or promptly refunded by Vertex (if paid on account of activities during 2007). 

  
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 For the purpose of this Second Amendment, “Development Costs” shall mean all
internal and external costs associated with the VX-770 Accelerated Potentiator Development Plan, including but not limited to all (i) costs and expenses invoiced by third parties, whether
for goods or services associated with the development plan, and (ii) FTE costs of Vertex development scientists and management personnel with respect to time properly allocated to the VX-770
Accelerated Potentiator Development Plan activities. Such internal costs may include, but not be limited to, (a) laboratory work; (b) regulatory planning, oversight and review; (c) quality
assurance activities; (d) pharmaceutical supply chain activities; (e) negotiations with clinical trial sites, institutional review boards, and suppliers; (f) development plan research;
(g) program management activities; (h) intellectual property creation and protection; (i) holding scientific discussions; (j) traveling to and attending appropriate seminars
and symposia; and (k) carrying out Potentiator JDC activities, provided, however, costs associated with (i) and (j) above shall only be allocated to the VX-770 Accelerated Potentiator
Development Plan activities if they are attributable to personnel who spent more than half of their working time on such activities. Activities included in calculating FTE’s shall not include negotiation of this Second Amendment or
modifications or extensions of this Second Amendment or the Existing Agreement, as amended, or administrative activities such as accounting, invoicing, personnel related activities or the like. FTEs allocated to activities under the VX-770 Accelerated Potentiator Development Plan shall be accounted for at the rate of $325,000 per FTE per annum. Payments for internal and external costs shall be invoiced and paid pursuant to Section 4.3 of
the Existing Agreement. 

  
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 At its sole discretion, and except as to amounts previously due to Vertex, CFFT shall have
the right to terminate the CFFT Accelerated Potentiator Funding Term and CFFT’s funding obligation hereunder effective December 31, 2006 or June 30, 2007 upon not less than sixty (60) days’ prior written notice to Vertex;
provided, however, that in the event of such a termination, the provisions of this Second Amendment will cease to apply effective as of the date of such termination (and, with respect to provisions of the Existing Agreement, as amended, which
were otherwise modified or amended by the provisions of this Second Amendment, such provisions shall be read without regard to any amendment or modification set forth in this Second Amendment). 

Section 3. Amendments to Corrector Contributions and Royalty Rates. 

3.1 Corrector Contributions. Effective as of January 6, 2006, Section 4.2 of the Existing Agreement, as amended, is further
amended as follows: the text in Section 4.2 up to and including the Initial Corrector Budget Chart is deleted, and, in its place the following is inserted: 

CFFT will fund seventy percent (70%) of the Initial Corrector Budget and Vertex will fund thirty percent (30%) of the Initial Corrector
Budget. Based on the approved Initial Corrector Budget of $27.3 million (which includes the $675,000 of Potentiator research funding referenced in the Research Plan), CFFT will make the payments to Vertex specified below during the specified
periods. 
  

									
	 	  	INITIAL CORRECTOR BUDGET
(millions $)	 
	 Research Period
	  	Aggregate
Budget
Amount	 	  	CFFT Financial
Commitment	 
	 January 1, 2006 — December 31, 2006
	  	$	12.6M	 	  	$	8.82M	 
	 January 1, 2007 — March 31, 2008
	  	$	14.7M	 	  	$	10.29M	 

 The text in the balance of Section 4.2 of the First Amendment (i.e., following the Initial Corrector Budget Chart)
remains unchanged. 
 3.2 Royalty Rates. Section 5.3.1 of the Existing Agreement is amended, as of the Effective Date, as
follows: 

  
 9 

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 (i) The number “4%” referenced in the royalty table
appearing in Section 5.3.1 of the Existing Agreement, as amended, is deleted, and in its place shall be inserted “6%”; 

(ii) The paragraph following the royalty table in Section 5.3.1 of the Existing Agreement, as amended, is deleted;
and in its place, the following is inserted: 
 Following the year in which cumulative Net Sales of all Drug Products in the Field first
exceed $1 billion, measured from the date of the First Commercial Sale of any such Drug Products, (a) the royalty rate for the first $250 million in annual Net Sales of such Drug Products in subsequent years shall be increased from
six percent (6%) to eight percent (8%); and (b) the calculation of Net Sales for any calendar year thereafter for purposes of computing the royalties referenced in Section 5.3.1, shall include all Net Sales of all Drug Products during that
year, for use in the Field, under the Existing Agreement, as amended to and including this Amendment. 
 (iii)
Section 5.3.2 of the Existing Agreement, as amended, is redesignated as Section 5.3.3, and the following new Section 5.3.2 is inserted: 

5.3.2 Additional Royalty. Vertex shall pay an additional royalty to CFFT in an amount equal to twice the amount of actual CFFT
Accelerated Potentiator Funding paid to Vertex under this Second Amendment, in two installments as set forth below. The additional royalty is assumed for illustrative purposes to be based on actual CFFT Accelerated Potentiator Funding of
$13.3 million, and based on that assumption a total of $26.6 million would be payable in the following amounts, in each case within thirty days after the first quarter in which cumulative Net Sales of Potentiator Drug Products have reached
the following levels: 
  

									
	 Cumulative Net Sales
	  	  
	 	  	Additional Royalty Amount	 
	$100 million	  				  	$	13.3 million	 
	$200 million	  				  	$	13.3 million	 
		  				  	  
	  
	 
	 Total:
	  				  	$	26.6 million	 

 For example, if the first Potentiator Drug Product is launched by Vertex on October 1, 2009, and
Cumulative Net Sales of that Drug Product reach $100 million by March 31, 2010, an Additional Royalty Amount of $13.3 million would then be payable to CFFT in addition to any other royalties due and payable under the Agreement.
Thereafter, if Cumulative Net Sales of Potentiator Drug Product reach $200 million on September 30, 2010, a further Additional Royalty Amount of $13.3 million would be payable to CFFT. 

  
 10 

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 (iv) The following new Section 5.3.4 is inserted: 

Net Sales under this Section 5.3 shall not in any event include any Net Sales of Drug Products that are the subject of the royalty
obligations set forth in the Section 5.3.3 or in Section 10.5.5. 
 Section 4. Existing Agreement Ratified. 

In all other respects, the Existing Agreement, as amended, is hereby ratified and confirmed. 

[Signature Page Follows] 

  
 11 

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 In witness whereof, the Parties hereto have executed this Agreement as of the day and year
first above written. 
  

									
	VERTEX PHARMACEUTICALS	  		 	CYSTIC FIBROSIS FOUNDATION
	INCORPORATED	  		 	THERAPEUTICS INCORPORATED
					
	By:	 	 /s/ Kenneth S. Boger
	  	        	 	By:	 	 /s/ Robert Beall

	Title: Senior VP and General Counsel	  		 	Title: President/CEO
	Date: 15 Mar 06	  		 	Date: March 16, 2006

  
 12 

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 Exhibit 2.1.3A 

[Gant chart setting forth benchmark Development Plan.] 

  
 13 

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 Exhibit 2.1.3B 

[Gant chart setting forth accelerated Development Plan.] 

  
 14 

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 Exhibit 2.3B 

Funding of VX-770 Development 

Budget Summary: The budget for the VX-770 Benchmark Potentiator Development Plan (“Benchmark Potentiator
Budget”) attached hereto as Exhibit 2.1.3A is as follows: 
  

									
	 	  	2006	 	  	2007	 
	 Benchmark Budget
	  				  			
	 Internal
	  	$	6.34 M	 	  	$	7.54 M	 
	 External
	  	 	4.64 M	 	  	 	5.19 M	 
		  	  
	  
	 	  	  
	  
	 
	 Total
	  	$	10.98M	 	  	$	12.73M	 

 The budget for the VX-770 Accelerated Potentiator Development Plan (the
“Accelerated Potentiator Budget”) attached hereto as Exhibit 2.1.3B is as follows: 
  

									
	 	  	2006	 	  	2007	 
	 Accelerated Budget
	  				  			
	 Internal
	  	$	13.18 M	 	  	$	13.82 M	 
	 External
	  	 	13.73 M	 	  	 	27.06 M	 
		  	  
	  
	 	  	  
	  
	 
	 Total
	  	$	26.91 M	 	  	$	40.88 M	 

  

 Confidential Treatment Requested by Royalty Pharma plc 

Pursuant to 17 C.F.R. Section 200.83 
  

 [Chart setting forth Detailed Accelerated Potentiator Budget.]

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