Exhibit 10.1

CERTAIN CONFIDENTIAL PORTIONS OF THIS EXHIBIT WERE OMITTED AND REPLACED WITH
“[***]”. A COMPLETE VERSION OF THIS EXHIBIT HAS BEEN FILED SEPARATELY WITH THE
SECRETARY OF THE SECURITIES AND EXCHANGE COMMISSION PURSUANT TO AN APPLICATION
REQUESTING CONFIDENTIAL TREATMENT UNDER RULE 24B-2 OF THE EXCHANGE ACT OF 1934

FIRST AMENDMENT TO
LOAN AND SECURITY AGREEMENT

THIS FIRST AMENDMENT to Loan and Security Agreement (this “Amendment”) is
entered into as of June 30, 2017, by and between SILICON VALLEY BANK, a
California corporation with an office located at 3003 Tasman Drive, Santa Clara,
CA 95054 (“Bank” or “SVB”), as collateral agent (in such capacity, “Collateral
Agent”), the Lenders listed on Schedule 1.1 of the Loan Agreement (as defined
below) or otherwise party thereto from time to time (each a “Lender” and
collectively, the “Lenders”) including Bank in its capacity as a Lender and
SOLAR CAPITAL LTD., a Maryland corporation with an office located at 500 Park
Avenue, 3rd Floor, New York, New York 10022 ( “Solar”) and ATYR PHARMA, INC., a
Delaware corporation with offices located at 3545 John Hopkins Court, Suite 250,
San Diego, CA 92121 (“Borrower”).

Recitals

A.Collateral Agent, Lenders and Borrower have entered into that certain Loan and
Security Agreement dated as of November 18, 2016 (as amended from time to time,
the “Loan Agreement”).

B.Lenders have extended credit to Borrower for the purposes permitted in the
Loan Agreement.  

C.Borrower has requested that Collateral Agent and Lenders (i) modify the Second
Draw Period and (ii) make certain other revisions to the Loan Agreement as more
fully set forth herein.

D.Collateral Agent and Lenders have agreed to modify such consent and to amend
certain provisions of the Loan Agreement, but only to the extent, in accordance
with the terms, subject to the conditions and in reliance upon the
representations and warranties set forth below.

Agreement

Now, Therefore, in consideration of the foregoing recitals and other good and
valuable consideration, the receipt and adequacy of which is hereby
acknowledged, and intending to be legally bound, the parties hereto agree as
follows:

1.Definitions.  Capitalized terms used but not defined in this Amendment shall
have the meanings given to them in the Loan Agreement.

2.Amendments to Loan Agreement.

2.1Section 2.2(d) (Permitted Prepayment of Term Loans).  Section 2.2(d) is
hereby amended by adding “(other than a prepayment of the Term B Loans as
permitted by Section 6.14)” after “all, but not less than all” therein.

2.2Section 6.14 ([***]).  New Section 6.14 hereby is added to the Loan Agreement
to read as follows:

“6.14

[***].Borrower shall achieve the [***] by no later than August 31, 2017.  If
Borrower fails to achieve the [***] by August 31, 2017, it shall not be an Event
of Default if Borrower immediately cash secures the principal balance of all
outstanding Term B Loans in the Pledged Account until the date on which Borrower
achieves the [***]; provided, however, that if Borrower does not achieve the
[***], Borrower may prepay on or before October 31, 2017, the Term

 

 

1

 

* Confidential information, indicated [***], has been omitted from this filing
and filed separately with the Securities and Exchange Commission.

 

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B Loans in accordance with Section 2.2(d). Borrower hereby authorizes Bank to
transfer to the Pledged Account an amount equal to the principal amount of all
outstanding Term B Loans if Borrower fails to achieve the [***] by August 31,
2017.”

 

Section 8.2 (Covenant Default).  Section 8.2(a) hereby is amended and restated
in its entirety to read as follows:

“(a)

Borrower or any of its Subsidiaries fails or neglects to perform any obligation
in Sections 6.2 (Financial Statements, Reports, Certificates), 6.4 (Taxes), 6.5
(Insurance), 6.6 (Operating Accounts), 6.7 (Protection of Intellectual Property
Rights), 6.9 (Notice of Litigation and Default), 6.10 (Phase 1 Trial
Initiation), 6.11 (Landlord Waivers; Bailee Waivers), 6.12 (Creation/Acquisition
of Subsidiaries); 6.13 (Further Assurances) or 6.14 ([***]) or Borrower violates
any covenant in Section 7; or”

 

2.3Section 13.1 (Definitions).  The following terms and their respective
definitions hereby are added or amended and restated in their entirety, as
applicable, to Section 13.1 of the Loan Agreement as follows:

“Amortization Date” is December 1, 2017; provided that, if Borrower achieves the
[***], the “Amortization Date” shall be June 1, 2018.

“[***]” is the [***] Borrower, on or after the First Amendment Effective Date
and no later than October 31, 2017, of [***].

“First Amendment Effective Date” is June 30, 2017.

“Pledged Account” means Borrower’s restricted account number ******9636 held at
Bank.

“Pledge Agreement” means that certain Bank Services Cash Pledge Agreement
executed by Borrower in favor of Bank as of the First Amendment Effective Date.

“Prepayment Fee” is, with respect to any Term Loan subject to prepayment prior
to the Maturity Date, whether by mandatory or voluntary prepayment, acceleration
or otherwise, an additional fee payable to the Lenders in amount equal to:

(i)

for a prepayment made on or after the Effective Date up to but not including the
first anniversary of the Effective Date, three percent (3.00%) of the principal
amount of the Term Loans prepaid;

 

(ii)

for a prepayment made after the date on or after the first anniversary of the
Effective Date up to but not including the second anniversary of the Effective
Date, two percent (2.00%) of the principal amount of the Term Loans prepaid;

 

(iii)

for a prepayment made on or after the date which is after the second anniversary
of the Effective Date, one percent (1.00%) of the principal amount of the Term
Loans prepaid;

 

provided that, with respect to the Term B Loans, Lenders shall waive the
Prepayment Fee if (a) Borrower does not achieve the [***] and (b) the Term B
Loans are prepaid by no later than October 31, 2017.

“Second Draw Period” is the period commencing on the First Amendment Effective
Date and ending on the earlier of (i) June 30, 2017 and (ii) the occurrence of
an Event of Default; provided, however, that the Second Draw Period shall not
commence if on the date of the occurrence of the Second Draw Period Milestones
an Event of Default has occurred and is continuing.

 

2

 

* Confidential information, indicated [***], has been omitted from this filing
and filed separately with the Securities and Exchange Commission.

 

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“Third Draw Period Milestones” is the achievement of each of the following: (i)
positive Phase 1b/2 interim data readout from Resolaris trial for either (a)
adult facioscapulohumeral muscular dystrophy, (b) early onset
facioscapulohumeral muscular dystrophy or (c) limb-girdle muscular dystrophy;
and (ii) either (x) initiation of “iMod.Fc” Phase 1 clinical trial within the
United States or the European Union or  (y) either (I) thirty days have elapsed
from the Food and Drug Administration’s receipt of an exploratory initial
investigational new drug application in connection with the  iMod.Fc clinical
trial (provided, that the achievement of the Third Draw Period Milestones shall
not occur in the event of an issuance by the Food and Drug Administration during
such thirty day period of notice that such clinical trial is subject to a
clinical hold under 21 C.F.R. § 312.42 until the earlier of (A) such time as
such clinical hold expires or is otherwise terminated or (B) the Third Draw
Period has expired), or (II) evidence of approval from the European Medicines
Agency for a clinical trial authorization in connection with the iMod.Fc
clinical trial; each in form and content reasonably acceptable to Collateral
Agent and the Lenders.

2.4Section 13.1 (Definitions).  The following term and its respective definition
set forth in Section 13.1 of the Loan Agreement hereby is deleted in its
entirety:

“Second Draw Period Milestones”

2.5Exhibit C of the Loan Agreement hereby is replaced in its entirety with
Exhibit C attached hereto.

3.Limitation of Amendment.

3.1The amendments set forth in Section 2 are effective for the purposes set
forth herein and shall be limited precisely as written and shall not be deemed
to (a) be a consent to any amendment, waiver or modification of any other term
or condition of any Loan Document, or (b) otherwise prejudice any right or
remedy which Collateral Agent or any Lender may now have or may have in the
future under or in connection with any Loan Document.

3.2This Amendment shall be construed in connection with and as part of the Loan
Documents and all terms, conditions, representations, warranties, covenants and
agreements set forth in the Loan Documents, except as herein amended, are hereby
ratified and confirmed and shall remain in full force and effect.

4.Representations and Warranties.  To induce Collateral Agent and Lenders to
enter into this Amendment, Borrower hereby represents and warrants to Collateral
Agent and Lenders as follows:

4.1Immediately after giving effect to this Amendment (a) the representations and
warranties contained in the Loan Documents are true and correct in all material
respects as of the date hereof (except to the extent such representations and
warranties relate to an earlier date, in which case they are true and correct in
all material respects as of such date), and (b) no Event of Default has occurred
and is continuing;

4.2Borrower has the power and authority to execute and deliver this Amendment
and to perform its obligations under the Loan Agreement, as amended by this
Amendment;

4.3The organizational documents of Borrower delivered to Collateral Agent and
Lenders on the Effective Date, or subsequent thereto, remain true, accurate and
complete and have not been amended, supplemented or restated and are and
continue to be in full force and effect;

4.4The execution and delivery by Borrower of this Amendment and the performance
by Borrower of its obligations under the Loan Agreement, as amended by this
Amendment, have been duly authorized;

4.5The execution and delivery by Borrower of this Amendment and the performance
by Borrower of its obligations under the Loan Agreement, as amended by this
Amendment, do not and will not contravene

 

3

 

* Confidential information, indicated [***], has been omitted from this filing
and filed separately with the Securities and Exchange Commission.

 

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(a) any material Requirement of Law, (b) any material agreement with a Person
binding on Borrower, (c) any order, judgment or decree of any court or other
governmental or public body or authority, or subdivision thereof, binding on
Borrower, except as could not reasonably be expected to have a Material Adverse
Effect or (d) the organizational documents of Borrower;

4.6The execution and delivery by Borrower of this Amendment and the performance
by Borrower of its obligations under the Loan Agreement, as amended by this
Amendment, do not require any order, consent, approval, license, authorization
or validation of, or filing, recording or registration with, or exemption by any
governmental or public body or authority, or subdivision thereof, binding on
Borrower, except as have been obtained and are in full force and effect or are
being obtained pursuant to Section 6.1(b) of the Loan Agreement or which the
failure to obtain would not reasonably be expected to result in a Material
Adverse Effect; and

4.7This Amendment has been duly executed and delivered by Borrower and is the
binding obligation of Borrower, enforceable against Borrower in accordance with
its terms, except as such enforceability may be limited by bankruptcy,
insolvency, reorganization, liquidation, moratorium or other similar laws of
general application and equitable principles relating to or affecting creditors’
rights.

5.Counterparts.  This Amendment may be executed in any number of counterparts
and all of such counterparts taken together shall be deemed to constitute one
and the same instrument.

6.Effectiveness.  This Amendment shall be deemed effective upon the due
execution and delivery to Collateral Agent and Lenders of (i) this Amendment by
each party hereto, (ii) Corporate Borrowing Certificate attached hereto, (iii)
the Pledge Agreement in favor of Bank along with Annex A thereto and (iv)
Borrower’s payment of all reasonable documented out-of-pocket Lenders’ Expenses
incurred through the date of this Amendment.

[Balance of Page Intentionally Left Blank]

 

 

 

4

 

* Confidential information, indicated [***], has been omitted from this filing
and filed separately with the Securities and Exchange Commission.

 

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In Witness Whereof, the parties hereto have caused this Amendment to be duly
executed and delivered as of the date first written above.

COLLATERAL AGENT AND LENDER:

 

SILICON VALLEY BANK

 

 

By: /s/ Anthony Flores

Name:Anthony Flores

Title:Director

 

 

 

LENDER:

 

SOLAR CAPITAL LTD.

 

By: /s/ Neil J. Bonanno

Name:Neil J. Bonanno

Title:Authorized Signatory

 

 

 

BORROWER:

 

ATYR PHARMA, INC.

 

By: /s/ Nancy D. Krueger

Name:Nancy D. Krueger

Title:VP Legal Affairs and Secretary

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

[Signature Page to First Amendment to Loan and Security Agreement]

 

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EXHIBIT C

Compliance Certificate

TO:

SILICON VALLEY BANK, as Collateral Agent and Lender
SOLAR CAPITAL LTD., as Lender

FROM:

ATYR PHARMA, INC.

The undersigned authorized officer (“Officer”) of ATYR PHARMA, INC.
(“Borrower”), hereby certifies that in accordance with the terms and conditions
of the Loan and Security Agreement by and among Borrower, Collateral Agent, and
the Lenders from time to time party thereto (the “Loan Agreement;” capitalized
terms used but not otherwise defined herein shall have the meanings given them
in the Loan Agreement),

(a)Borrower is in complete compliance for the period ending _______________ with
all required covenants except as noted below;

(b)There are no Events of Default, except as noted below;

(c)Except as noted below, all representations and warranties of Borrower stated
in the Loan Documents are true and correct in all material respects on this date
and for the period described in (a), above; provided, however, that such
materiality qualifier shall not be applicable to any representations and
warranties that already are qualified or modified by materiality in the text
thereof; and provided, further that those representations and warranties
expressly referring to a specific date shall be true and correct in all material
respects as of such date.

(d)Borrower, and each of Borrower’s Subsidiaries, has timely filed all required
tax returns and reports, Borrower, and each of Borrower’s Subsidiaries, has
timely paid all foreign, federal, state, and local taxes, assessments, deposits
and contributions owed by Borrower, or Subsidiary, except as otherwise permitted
pursuant to the terms of Section 5.8 of the Loan Agreement;

(e)No Liens have been levied or claims made against Borrower or any of its
Subsidiaries relating to unpaid employee payroll or benefits of which Borrower
has not previously provided written notification to Collateral Agent and the
Lenders.

Attached are the required documents, if any, supporting our
certification(s).  The Officer, on behalf of Borrower, further certifies that
the attached financial statements are prepared in accordance with Generally
Accepted Accounting Principles (GAAP) and are consistently applied from one
period to the next except as explained in an accompanying letter or footnotes
and except, in the case of unaudited financial statements, for the absence of
footnotes and subject to year‑end audit adjustments as to the interim financial
statements.  

Please indicate compliance status since the last Compliance Certificate by
circling Yes, No, or N/A under “Complies” column.

 

Reporting Covenant

Requirement

Actual

Complies

1)

Financial statements

Quarterly within five (5) days after filing with the SEC

 

 

Yes

No

N/A

2)

Annual (CPA Audited) statements

Earlier of (x) 180 days after FYE or (y) within five (5) days after filing with
the SEC

 

 

Yes

No

N/A

 

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3)

Annual Financial Projections/Budget (prepared on a monthly basis)

Annually, within earlier of (i) 60 days after FYE and (ii) 7 days of board
approval, and when revised

 

Yes

No

N/A

4)

A/R & A/P agings

If applicable

 

Yes

No

N/A

5)

8‑K, 10‑K and 10‑Q Filings

within 5 days of filing

 

Yes

No

N/A

6)

Compliance Certificate

Quarterly within five (5) days after filing financial statements with the SEC

 

Yes

No

N/A

7)

Total amount of Borrower’s cash and cash equivalents at the last day of the
measurement period

 

$________

 

 

 

8)

Total amount of Borrower’s Subsidiaries’ cash and cash equivalents at the last
day of the measurement period

 

$________

 

 

 

Financial Covenants

 

 

Covenant

Requirement

Actual

Compliance

1)

[***] (See Section 6.14)

[***]

$_________

Yes

No

N/A

 

Deposit and Securities Accounts

(Please list all accounts; attach separate sheet if additional space needed)

 

 

Institution Name

Account Number

New Account?

Account Control Agreement in place?

1)

 

 

Yes

No

Yes

No

2)

 

 

Yes

No

Yes

No

3)

 

 

Yes

No

Yes

No

4)

 

 

Yes

No

Yes

No

 

Other Matters

 

1)

Have there been any changes in any Responsible Officer since the last Compliance
Certificate?

Yes

No

 

 

 

 

2)

Have there been any transfers/sales/disposals/retirement of Collateral or IP
prohibited by the Loan Agreement?

Yes

No

 

 

 

 

3)

Have there been any new or pending claims or causes of action against Borrower
that involve more than Two Hundred Fifty Thousand Dollars ($250,000.00)?

Yes

No

 

 

 

 

4)

Have there been any amendments of or other changes to the capitalization table
of Borrower and to the Operating Documents of Borrower or any of its
Subsidiaries?  If yes, provide copies of any such amendments or changes with
this Compliance Certificate.

Yes

No

 

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Exceptions

 

Please explain any exceptions with respect to the certification above: (If no
exceptions exist, state “No exceptions.”  Attach separate sheet if additional
space needed.)

 

 

 

ATYR PHARMA, INC.

 

By  

Name:  

Title:  

 

Date:

 

LENDER USE ONLY

 

 

Received by:

Date:  

 

 

Verified by:  

Date:  

 

 

Compliance Status:YesNo