Document:

Exhibit 10.9

Exhibit 10.9

Indemnification Agreements

The following current directors of NuPathe Inc. are each a party to an Indemnification Agreement
with NuPathe Inc. consistent in all material respects with the Form of Indemnification Agreement
which is filed as Exhibit 10.20 to Amendment No. 2 to NuPathe Inc.’s Registration Statement on Form
S-1 filed July 9, 2010.

Michael Cola

Jeanne Cunicelli

Michael C. Diem, MD

John H. Dillon, II

Jane H. Hollingsworth

Richard S. Kollender

Gary J. Kurtzman, MD

Robert P. Roche, Jr.

Wayne P. Yetterexv4w1

Exhibit 4.1

Execution Version

AMENDMENT NO. 3

     This Amendment No. 3 dated as of November 9, 2010 (this “Agreement”) is among Stone
Energy Corporation, a Delaware corporation (“Borrower”), Stone Energy Offshore, L.L.C., a
Delaware limited liability company (“Guarantor”), the financial institutions party to the
Credit Agreement described below as Banks (“Banks”), and Bank of America, N.A., as Agent
for the Banks (“Agent”) and as Issuing Bank (“Issuing Bank”).

INTRODUCTION

     A. The Borrower, the Banks, the Issuing Bank, and the Agent have entered into the Second
Amended and Restated Credit Agreement dated as of August 28, 2008, as amended by (i) Amendment No.
1 dated as of April 29, 2009 and (ii) Amendment No. 2 dated as of January 11, 2010 (as so amended,
the “Credit Agreement”).

     B. The Guarantor entered into that certain Guaranty dated as of August 28, 2008, as amended by
Amendment No. 1 dated as of April 29, 2009 (as so amended, the “Stone Offshore Guaranty”).

     C. The Borrower plans to issue up to $150,000,000 in unsecured senior notes due 2017 pursuant
to the Indenture entered into by the Borrower, the Guarantor, and The Bank of New York Mellon Trust
Company, N.A., as Trustee dated as of January 26, 2010 (the “2010 Indenture”), in addition
to those unsecured senior notes due 2017 that are outstanding under the 2010 Indenture on the date
of this Agreement.

     D. The parties hereto desire to amend the Credit Agreement to permit the issuance of up to
$150,000,000 in unsecured senior notes pursuant to the 2010 Senior Subordinated Indenture.

     E. The Guarantor wishes to reaffirm its guarantee of the Obligations as amended by this
Agreement.

     THEREFORE, in fulfillment of the foregoing, the Borrower, the Guarantor, the Agent, the
Issuing Bank, and the Banks hereby agree as follows:

     Section 1. Definitions; References. Unless otherwise defined in this Agreement, each
term used in this Agreement which is defined in the Credit Agreement has the meaning assigned to
such term in the Credit Agreement.

     Section 2. Amendment. Upon the satisfaction of the conditions specified in
Section 6 of this Agreement, and, unless otherwise specified, effective as of the date set
forth above, the Credit Agreement is amended as follows:

          (a) The definition of “2010 Indenture” in Section 1.1 of the Credit Agreement shall be amended
to read in its entirety as follows:

 

 

     “2010 Indenture” means the Indenture, dated as of January 26, 2010,
among the Borrower, the Guarantor and The Bank of New York Mellon Trust Company,
N.A., as Trustee, as amended by the First Supplemental Indenture thereto, dated as
of January 26, 2010, and any additional supplemental indenture that is substantially
similar thereto, in each case relating to the issuance of unsecured senior notes due
2017.

          (b) Section 2.2(a) of the Credit Agreement shall be amended to read in its entirety as
follows:

          (a) The Borrowing Base has been set by the Banks and acknowledged by the
Borrower as $395,000,000 as of October 29, 2010. On the date of any issuance of
Debt after November 9, 2010 under the 2010 Indenture, the Borrowing Base shall be
reduced automatically by an amount equal to 30% of the amount of such Debt. The
automatic reduction described in this Section 2.2(a) shall not be deemed to
take the place of regularly scheduled or other redeterminations of the Borrowing
Base in accordance with this Section 2.2.

          (c) Section 6.2(b) of the Credit Agreement shall be amended to delete the words “existing on
the date hereof and” from such Section.

          (d) Schedule 6.2 of the Credit Agreement shall be replaced with Schedule 6.2 attached hereto.

     Section 3. Reaffirmation of Liens.

          (a) Each of the Borrower and the Guarantor (i) is party to certain Security Documents securing
and supporting the Borrower’s and Guarantor’s obligations under the Credit Documents, (ii)
represents and warrants that it has no defenses to the enforcement of the Security Documents and
that according to their terms the Security Documents will continue in full force and effect to
secure the Borrower’s and Guarantor’s obligations under the Credit Documents, as the same may be
amended, supplemented, or otherwise modified, and (iii) acknowledges, represents, and warrants that
the liens and security interests created by the Security Documents are valid and subsisting and
create an Acceptable Security Interest in the Collateral to secure the Borrower’s and Guarantor’s
obligations under the Credit Documents, as the same may be amended, supplemented, or otherwise
modified.

          (b) The delivery of this Agreement does not indicate or establish a requirement that any
Guaranty or Security Document requires the Borrower’s or any Guarantor’s approval of amendments to
the Credit Agreement.

     Section 4. Representations and Warranties. The Borrower represents and warrants to
the Agent and the Banks that:

          (a) the representations and warranties set forth in the Credit Agreement and in the other
Credit Documents are true and correct in all material respects as of the date of this Agreement
(except to the extent such representations and warranties relate to an earlier date, in which case
such representations and warranties shall be true and correct in all material respects

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as of such earlier date); provided that such materiality qualifier shall not apply if such
representation or warranty is already subject to a materiality qualifier in the Credit Agreement or
such other Credit Document;

          (b) (i) the execution, delivery, and performance of this Agreement are within the corporate
power and authority of the Borrower and have been duly authorized by appropriate proceedings and
(ii) this Agreement constitutes a legal, valid, and binding obligation of the Borrower, enforceable
against the Borrower in accordance with its terms, except as limited by applicable bankruptcy,
insolvency, reorganization, moratorium, or similar laws affecting the rights of creditors generally
and general principles of equity; and

          (c) as of the effectiveness of this Agreement and after giving effect thereto, no Default or
Event of Default has occurred and is continuing.

     Section 5. Reaffirmation of Guaranty. The Guarantor hereby ratifies, confirms, and
acknowledges that its obligations under the Stone Offshore Guaranty are in full force and effect
and that the Guarantor continues to unconditionally and irrevocably guarantee the full and punctual
payment, when due, whether at stated maturity or earlier by acceleration or otherwise, of all of
the Obligations (subject to the terms of the Stone Offshore Guaranty), as such Obligations may have
been amended by this Agreement. The Guarantor hereby acknowledges that its execution and delivery
of this Agreement do not indicate or establish an approval or consent requirement by the Guarantor
under the Stone Offshore Guaranty in connection with the execution and delivery of amendments,
modifications or waivers to the Credit Agreement, the Notes or any of the other Credit Documents.

     Section 6. Effectiveness. This Agreement shall become effective as of the date
hereof, and the Credit Agreement shall be amended as provided herein, upon the occurrence of all of
the following: (a) the Majority Banks’, the Borrower’s, and the Guarantor’s duly and validly
executing originals of this Agreement and delivery thereof to the Agent, (b) the representations
and warranties in this Agreement being true and correct in all material respects before and after
giving effect to this Agreement, (c) the Borrower’s having made a prepayment of Advances, and if
the Advances have been repaid in full, made deposits into the Cash Collateral Account to provide
cash collateral for the Letter of Credit Exposure, in an aggregate amount equal to the amount of
any Borrowing Base Deficiency that would exist immediately after giving effect to the reduction of
the Borrowing Base specified in Section 2(b) of this Agreement, and (d) the Borrower’s
having paid all costs, expenses, and fees which have been invoiced and are payable pursuant to
Section 9.4 of the Credit Agreement or any other written agreement.

     Section 7. Effect on Credit Documents. Except as amended herein, the Credit Agreement
and the Credit Documents remain in full force and effect as originally executed, and nothing herein
shall act as a waiver of any of the Agent’s or Banks’ rights under the Credit Documents, as
amended. This Agreement is a Credit Document for the purposes of the provisions of the other
Credit Documents. Without limiting the foregoing, any breach of representations, warranties, and
covenants under this Agreement may be a Default or Event of Default under other Credit Documents.

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     Section 8. Choice of Law. This Agreement shall be governed by and construed and
enforced in accordance with the laws of the State of Texas.

     Section 9. Counterparts. This Agreement may be signed in any number of counterparts,
each of which shall be an original.

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     THIS WRITTEN AGREEMENT AND THE CREDIT DOCUMENTS, AS DEFINED IN THE CREDIT AGREEMENT,
REPRESENT THE FINAL AGREEMENT AMONG THE PARTIES AND MAY NOT BE CONTRADICTED BY EVIDENCE OF PRIOR,
CONTEMPORANEOUS, OR SUBSEQUENT ORAL AGREEMENTS OF THE PARTIES. THERE ARE NO UNWRITTEN ORAL
AGREEMENTS BETWEEN THE PARTIES.

     EXECUTED as of the date first set forth above.

	 	 	 	 	 
	 	BORROWER:

STONE ENERGY CORPORATION

 	 
	 	By:  	/s/ David H. Welch
 	 
	 	 	Name:  	David H. Welch 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	 	 
	 	By:  	                  /s/ Kenneth H. Beer
 	 
	 	 	Name:  	Kenneth H. Beer 	 
	 	 	Title:  	Senior Vice President and

Chief Financial Officer 	 
	 
	 	GUARANTOR:

STONE ENERGY OFFSHORE, L.L.C.

 	 
	 	By:  	/s/ David H. Welch
 	 
	 	 	Name:  	David H. Welch 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	 	 
	 	By:  	                  /s/ Kenneth H. Beer
 	 
	 	 	Name:  	Kenneth H. Beer 	 
	 	 	Title:  	Senior Vice President and

Chief Financial Officer 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	

AGENT AND ISSUING BANK:

BANK OF AMERICA, N.A., as Agent and Issuing Bank

 	 
	 	By:  	/s/ Ronald E. McKaig
 	 
	 	 	Name:  	Ronald E. McKaig 	 
	 	 	Title:  	Senior Vice President 	 
	 
	 	BANKS:

BANK OF AMERICA, N.A.

 	 
	 	By:  	/s/ Ronald E. McKaig
 	 
	 	 	Name:  	Ronald E. McKaig 	 
	 	 	Title:  	Senior Vice President 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	

BNP PARIBAS

 	 
	 	By:  	/s/ Douglas R. Liftman
 	 
	 	 	Name:  	Douglas R. Liftman 	 
	 	 	Title:  	Managing Director 	 
	 
	 	 	 
	 	By:  	     /s/ Betsy Jocher
 	 
	 	 	Name:  	Betsy Jocher 	 
	 	 	Title:  	Director 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	

NATIXIS

 	 
	 	By:  	/s/ Donovan C. Broussard
 	 
	 	 	Name:  	Donovan C. Broussard 	 
	 	 	Title:  	Managing Director 	 
	 	 	 
	 	By:  	     /s/ Liana Tchernysheva
 	 
	 	 	Name:  	Liana Tchernysheva 	 
	 	 	Title:  	Director 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	

THE BANK OF NOVA SCOTIA

 	 
	 	By:  	/s/ J. Frazell
 	 
	 	 	Name:  	J. Frazell 	 
	 	 	Title:  	Director 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	

CAPITAL ONE, N.A.

 	 
	 	By:  	/s/ Paul D. Hein
 	 
	 	 	Name:  	Paul D. Hein 	 
	 	 	Title:  	Vice President 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	

TORONTO DOMINION (TEXAS) LLC

 	 
	 	By:  	/s/ Debbi Brito
 	 
	 	 	Name:  	Debbi Brito 	 
	 	 	Title:  	Authorized Signatory 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	ALLIED IRISH BANKS p.l.c.

 	 
	 	By:  	/s/ Edward M. Fenk
 	 
	 	 	Name:  	Edward M. Fenk 	 
	 	 	Title:  	Vice President 	 
	 
	 	 	 
	 	By:  	     /s/ James Giordano
 	 
	 	 	Name:  	James Giordano 	 
	 	 	Title:  	Assistant Vice President 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	BARCLAYS BANK PLC

 	 
	 	By:  	/s/ Vanessa A. Kurbatskiy
 	 
	 	 	Name:  	Vanessa A. Kurbatskiy 	 
	 	 	Title:  	Vice President 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	REGIONS BANK

 	 
	 	By:  	/s/ Tress M. Johnson
 	 
	 	 	Name:  	Tress M. Johnson 	 
	 	 	Title:  	Assistant Vice President 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	U.S. BANK NATIONAL ASSOCIATION

 	 
	 	By:  	/s/ Daria M. Mahoney
 	 
	 	 	Name:  	Daria M. Mahoney 	 
	 	 	Title:  	Vice President 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	WHITNEY NATIONAL BANK

 	 
	 	By:  	/s/ John B. Lane
 	 
	 	 	Name:  	John B. Lane 	 
	 	 	Title:  	Senior Vice President 

Whitney National Bank 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	JPMORGAN CHASE BANK, N.A.

 	 
	 	By:  	/s/ Jo Linda Papadakis
 	 
	 	 	Name:  	Jo Linda Papadakis 	 
	 	 	Title:  	Authorized Officer 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

	 	 	 	 	 
	 	SUMITOMO MITSUI BANKING CORPORATION

 	 
	 	By:  	/s/ Masakazu Hasegawa
 	 
	 	 	Name:  	Masakazu Hasegawa 	 
	 	 	Title:  	General Manager 	 

[SIGNATURE PAGE TO AMD NO. 3 TO 2nd A&R CREDIT AGREEMENT]

 

 

SCHEDULE 6.2

PERMITTED EXISTING DEBT

1. $200 million of unsecured Debt related to the 2004 issuance of 6.75% senior subordinated notes
due 2014 pursuant to the 2004 Indenture.

2. Up to $275 million of unsecured Debt related to the January 2010 issuance of 8.625% senior notes
due 2017 pursuant to the 2010 Indenture.

3. Up to $150 million of unsecured Debt related to the November 2010 issuance of senior notes due
2017 pursuant to the 2010 Indenture.

[Schedule 6.2 to Amendment No. 3 to 2nd A&R Credit Agreement]

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