Document:

Exhibit 10.1
    

    
      OMNIBUS AMENDMENT TO ALL OUTSTANDING 12% CONVERTIBLE SECURED
PROMISSORY
      NOTES OF OPEXA THERAPEUTICS, INC. AND
ASSOCIATED REGISTRATION
      RIGHTS AGREEMENT
    

    
      This Omnibus Amendment to All Outstanding 12% Convertible Secured
      Promissory Notes of Opexa Therapeutics, Inc. and Associated Registration
      Rights Agreement (this “Amendment”) is made effective as of
      September 20, 2013 (or such later date as described in Section 5
      below), by and among Opexa Therapeutics, Inc., a Texas corporation (the “Company”),
      and certain holders of the Company’s outstanding 12% convertible secured
      promissory notes (the “Notes”), but shall apply to all of
      the outstanding Notes (and, with respect to the Notes, to bind all
      holders thereof) as well as the Registration Rights Agreement (defined
      below) for all intents and purposes, as described below.
    

    
      WHEREAS, the Notes were issued by the Company in a private placement on
      July 25, 2012, and are evidenced by individual Notes issued to holders
      (each an “Investor”) in the amount of such Investor’s
      individual investment.  The Notes are currently convertible into shares
      of the Company’s Series A convertible preferred stock, no par value (the
      “Series A”), at a conversion price of $100, and the Series
      A is convertible into shares of the Company’s Common Stock, $0.01 par
      value (“Common Stock”), at a conversion price of
      $3.1225.  In connection with issuance of the Notes, the Company and each
      Investor also entered into a Registration Rights Agreement of even date
      (the “Registration Rights Agreement”).  An aggregate of
      $3,185,000 in principal amount of the Notes is currently outstanding.
    

    
      WHEREAS, as a result of the Company’s August 2013 underwritten public
      offering of Common Stock, the Company met the conditions precedent
      stated in the Notes in order to convert the Notes, at the Company’s
      election, into shares of Series A.
    

    
      WHEREAS, pursuant to Section 10 of the Notes, any term or provision of
      the Notes may be waived or amended in any respect with the written
      consent of the Company and holders of at least 66-2/3% in principal
      amount of the then outstanding Notes; provided, that any
      such amendment or waiver must apply to all Notes, and provided
      further, that terms and provisions of the Notes regarding
      payment or conversion require the written consent of holders of at least
      75% in principal amount of the then outstanding Notes (the “Requisite
      Holders”).  Pursuant to Section 7(a) of the Registration Rights
      Agreement, the Registration Rights Agreement may be amended or waived
      only by a writing signed by (i) the Company and (ii) the Investors
      holding 66-2/3% of the Issuable Shares (as defined in the Registration
      Rights Agreement).  Inasmuch as no transfers of the Notes have taken
      place since their original issuance, execution of this Amendment by the
      Requisite Holders will satisfy the requirement of Section 7(a) of the
      Registration Rights Agreement (in addition to execution by the Company)
      in order to amend the Registration Rights Agreement as provided herein.
    

    
      WHEREAS, the Company and the Requisite Holders desire to amend certain
      terms of the Notes relating to conversion features such that, in
      addition to the existing conversion arrangements, the Notes are
      convertible based upon a conversion price stated herein directly into
      shares of Common Stock (rather than any intermediate conversion to
      Series A).  Upon execution of this Amendment by the Company and the
      Requisite Holders, this Amendment shall apply to all outstanding Notes
      (and, with respect to the Notes, to bind all holders thereof) as well as
      the Registration Rights Agreement.
    

    
      
        

        

      

      
        

        

        
          

        

      

      
        

        

      

    

    

    

    
      NOW, THEREFORE, in consideration of the foregoing recitals and for other
      good and valuable consideration, the receipt and sufficiency of which
      are hereby acknowledged, the Company and the Requisite Holders agree as
      follows:
    

    
      1.  Conversion into Common Stock.  At the sole election
      of the Company, the outstanding principal balance of each and every
      outstanding Note plus any accrued but unpaid interest through the
      conversion date (the “Outstanding Balance”), shall be
      convertible directly into shares of Common Stock.  The number of shares
      of Common Stock into which the Outstanding Balance is convertible (the “Conversion
      Shares”) shall be determined by dividing (i) the
      Outstanding  Balance by (ii) the “Conversion Price.”
      The Conversion Price shall be the most recent closing market price of
      the Company’s Common Stock on the NASDAQ Stock Market at the time of the
      Company’s election to convert the Outstanding Balance into shares of
      Common Stock as provided herein (the “Conversion Time”).  For
      the avoidance of doubt, any election by the Company pursuant to this
      Section 1 shall apply uniformly to all Notes outstanding at the time of
      such election.  Notwithstanding any provision herein to the contrary,
      however, the Company may not elect to convert the Outstanding Balance
      into shares of Common Stock if the Conversion Price would, for purposes
      of such conversion, be less than $1.50 per share of Common Stock or more
      than $2.25 per share of Common Stock.  Promptly following its election,
      the Company will send written notice to each holder of a Note (each a “Noteholder”)
      of the Company’s election to convert the Outstanding Balance into shares
      of Common Stock, with such notice to be transmitted to each Noteholder
      via email at the email address appearing below the Noteholder’s
      signature hereto or in the Company’s records.
    

    
      2.  Registration of Common Stock.  The Company has
      previously filed a Registration Statement on Form S-3 (the “First
      S-3”) with respect to certain shares of Common Stock issuable with
      respect to the Notes and the Warrants (as defined in the Registration
      Rights Agreement); however, the First S-3 does not cover the
      Conversion Shares as contemplated by this Amendment.  Promptly following
      the Conversion Time, the Company shall prepare and file another
      Registration Statement on Form S-3 (the “Second S-3”),
      including the prospectus to be used in connection therewith, covering
      the resale by the Noteholders of their respective Conversion
      Shares.  Subject to any comments of the U.S. Securities and Exchange
      Commission, the Second S-3 shall include the plan of distribution
      attached to the Registration Rights Agreement as Exhibit A.  The Company
      shall use its commercially reasonable efforts to cause the Second S-3 to
      be declared effective under the Securities Act of 1933, as amended, as
      promptly as reasonably practicable after the filing thereof.  Each
      Noteholder shall use its commercially reasonable efforts to furnish to
      the Company such information regarding itself, the Conversion Shares and
      any other securities of the Company held by it, as shall be reasonably
      required of a selling shareholder in order to effect registration of the
      Conversion Shares pursuant to the Second S-3.  Except for the provisions
      of Section 2(a) of the Registration Rights Agreement (inasmuch as such
      provisions relate to the First S-3, which the parties hereto acknowledge
      have been fully satisfied), the parties hereto agree that the provisions
      of the Registration Rights Agreement shall apply to the Second S-3, such
      that the Registration Rights Agreement is modified and amended hereby as
      appropriate to apply to the Second S-3 as though it were the
      “Registration Statement” referenced therein (but with such Registration
      Statement applicable solely to the Conversion Shares as contemplated
      hereby – i.e., as though the Conversion Shares are, for
      purposes of the Second S-3, the only “Registrable Securities” as
      referenced in the Registration Agreement).
    

    
      
        

        

      

      
        
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      3.  No Further Amendment.  Except as otherwise
      expressly provided herein, the Notes and the Registration Rights
      Agreement are unaffected hereby and remain in full force and effect in
      accordance with their respective terms.  Without limiting the foregoing,
      the preexisting conversion features of the Notes continue to remain in
      full force and effect (including, without limitation, the Company’s
      right to effect a conversion into shares of Series A as provided in the
      Notes), and the provisions of this Amendment shall not be deemed to
      limit such features or otherwise be in derogation of the Company’s
      rights with respect thereto.
    

    
      4.  Counterparts.  This Amendment may be executed in
      one or more counterparts, each of which shall be deemed an original, but
      all of which together shall constitute one and the same instrument.  A
      signature to this Amendment transmitted electronically shall have the
      same authority, effect and enforceability as an original signature.
    

    
      5.  Binding Effect.  Upon execution of this Amendment
      by the Company and the Requisite Holders, this Amendment shall (i) amend
      and be deemed to amend all outstanding Notes, irrespective of whether or
      not the individual Noteholder has executed this Amendment, and (ii)
      amend the Registration Rights Agreement.  The Amendment shall be
      effective as of September 20, 2013 or, if necessary, such later date
      when the Company and sufficient Requisite Holders constituting 75% of
      the outstanding Notes have executed this Amendment.
    

    
      [Signature Pages Follow]
    

    
      
        

        

      

      
        
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                IN
      WITNESS WHEREOF, the parties have executed this Amendment or caused
      their duly authorized officer to execute this Amendment as of the date
      first above written.
    

    	
           
        	
          
            THE COMPANY:
          

        
	

        	

        	
           
        
	

        	
          
            OPEXA THERAPEUTICS, INC.
          

        
	

        	

        	
           
        
	

        	

        	
           
        
	

        	
          
            By:
          

        	
          
            /s/ Neil K. Warma                             
          

        
	

        	
          
            Name:
          

        	
          
            Neil K. Warma
          

        
	

        	
          
            Title:
          

        	
          
            President and Chief Executive Officer
          

        

    

    

    

    
      [signature page to Omnibus Amendment]
    

    
      
        

        

      

      
        

        

        
          

        

      

      
        

        

      

    

    

    

    
                IN WITNESS WHEREOF, the parties have executed this Amendment
      or caused their duly authorized officer to execute this Amendment as of
      the date first above written.
    

    	
           
        	
          
            THE NOTEHOLDER:
          

        	

        
	

        	

        	

        	
           
        
	

        	

        	

        	
           
        
	

        	
          
            By:
          

        	
           
        	
           
        
	

        	
          
            Printed Name:
          

        	
           
        	
           
        
	

        	
          
            Title (if applicable):
          

        	
           
        	
           
        
	

        	
          
            Entity Name (if applicable):
          

        	
           
        	
           
        
	

        	
          
            Email:
          

        	
           
        	
           
        

    

    	
           
        	
          
            Delivery instructions for Conversion Shares:
          

        
	

        	
           
        
	

        	
          
            1. _____ Physical certificate
          

        
	

        	
           
        
	

        	
          
            Address:
          

        
	

        	
           
        
	

        	
           
        
	

        	
           
        
	

        	
           
        
	

        	
          
            or (check only one)
          

        
	

        	
           
        
	

        	
          
            2. ____ DWAC
          

        

    

    	
           
        	
          
            Account name:
          

        	
           
        
	

        	
          
            Broker name:
          

        	
          
             
          

        
	

        	
          
            DTC#:
          

        	
           
        
	

        	
          
            Account No.:
          

        	
          
             
          

        

    

    

    

    
      [signature page to Omnibus Amendment]Ex-4.6 Form of Service Agreement for Specified Executive

 Exhibit 4.6 

Form of Service Agreement for Specified Executive (Mr Andrew Mackenzie) 

Chief Executive Officer – BHP Billiton 

1.    Term 
 Mr Mackenzie is employed
under a single contract of service with the BHP Billiton Group with no fixed term. The contract is effective from 10 May 2013; the date of Mr Mackenzie’s appointment as Chief Executive Officer. The contract can be terminated by the Group
on 12 months notice and by Mr Mackenzie on 6 months notice. Payment can be made in lieu of notice, the details of which are set out in section 6 below. Mr Mackenzie’s performance and remuneration will be reviewed at the end of each financial
year. 
 2.    Fixed Salary and retirement benefits 

Mr Mackenzie is paid a base salary of US$1,700,000 per annum. 

He is entitled to an additional sum equal to 25 per cent of base salary (which at the commencement of the contract was US$425,000 per annum) which he may
pay into a superannuation or pension scheme, take as cash in lieu of retirement benefits or take in cash on retirement. 

3.    Benefits 
 Mr Mackenzie was
required to relocate from London, UK to the Company’s head office in Melbourne, Australia. He has received benefits to cover the cost of his relocation from the UK to Australia in accordance with BHP Billiton’s normal policy in respect of
such transfers, including relocation allowance, costs of international transfer, health insurance, life and disability insurance and the preparation of multi-jurisdictional taxation returns. 

4.    Incentive arrangements 
 For the
remainder of FY2013, Mr Mackenzie continued to participate in the Group Incentive Scheme (GIS) in regard to short-term incentives, and in the Long Term Incentive Plan (LTIP) in regard to long-term incentives. The GIS and the LTIP were initially
approved by shareholders in 2004 and amendments have been approved at subsequent Annual General Meetings. From FY2014, the GIS will be replaced by a new Short Term Incentive Plan (STIP) and it is proposed that the LTIP will be replaced by a new Long
Term Incentive Plan (new LTIP), and Mr Mackenzie will participate in these new plans. The new LTIP is subject to shareholder approval at BHP Billiton’s Annual General Meetings in October and November 2013. Copies of the current rules of the
LTIP and the rules of the proposed new LTIP are available on the BHP Billiton website at www.bhpbilliton.com. 
 Short Term Incentives 

Under the rules of the GIS and the STIP, Mr Mackenzie is entitled to incentive awards calculated by reference to his base salary. For performance at the target
level, which requires Mr Mackenzie to meet the rigorous performance hurdles set by the Board, including delivery against designated health and safety measures and the budget, Mr Mackenzie would receive a bonus of 160 per cent of his base
salary. Half is paid in cash and half in deferred equity. The deferred equity must be held for two years. 
 For performance at the maximum level Mr
Mackenzie would receive a bonus of 240 per cent of his base salary. 
 The grant of deferred equity will be subject to the approval of shareholders
where required by applicable listing rules, and will be valued and reported each year in the Remuneration Report which forms part of the Annual Report. The valuation will be subject to audit by the Group’s auditors. 

The GIS rules provided for a maximum bonus of two times the target level (i.e. 320 per cent of base salary); however, the Board and Remuneration
Committee have decided to reduce the maximum bonus to 1.5 times the target level (i.e. 240 per cent of base salary). This reduced maximum will apply to awards provided under the STIP to Mr Mackenzie and all of his direct reports from the 2014
financial year. 

 Long Term Incentives 

Long term incentives will be issued under the terms of the new LTIP if approved by shareholders at the 2013 Annual General Meetings, or otherwise will be
provided under the terms of the current LTIP. 
 The number of LTIP awards allocated under either plan will be determined by the Board on the recommendation
of the Remuneration Committee and must be approved by shareholders each year. LTIP awards are subject to performance hurdles which are set out in the rules of the LTIPs and measured five years after the effective date of the grant. Performance
hurdles are not subject to re-testing. 
 Under either LTIP, the performance hurdle requires BHP Billiton’s total shareholder return (TSR) over a five
year performance period to be measured against the TSR of an index of comparator companies. If BHP Billiton’s TSR is below the index TSR no LTIP awards vest and the awards are forfeited. Twenty five per cent of the LTIP awards vest if BHP
Billiton’s TSR is equal to the index TSR. 
 For all the LTIP awards to vest, BHP Billiton’s TSR must exceed the index TSR by a specified
percentage. The Remuneration Committee determines the percentage each year. For the 2012 financial year the percentage was set at 5.5 per cent per annum over the five year performance period. 

For performance between the index TSR and the percentage determined by the Remuneration Committee, vesting occurs on a sliding scale. 

For the 2013 calendar year, Mr Mackenzie will receive an LTIP award with a face value equal to 400 per cent of base salary (subject to shareholder
approval at the 2013 Annual General Meetings). The fair value of the LTIP award (as calculated by the Remuneration Committee’s independent advisor Kepler Associates) is 41 per cent of the face value, thus the LTIP award has a fair value
equal to 164 per cent of base salary. The value and number of shares awarded to Mr Mackenzie will be reported in the subsequent Remuneration Report that forms part of the Annual Report. The Remuneration Report will be subject to audit by the
Group’s auditors. 
 Grants are subject to an overriding discretion held by the Remuneration Committee to reduce the number of awards that will vest in
circumstances where the performance hurdle has been met or partially met. The Committee does not have power to approve the vesting of awards where the performance hurdle has not been met. In exercising that discretion the Committee will decide if
the value at the time of vesting is proportionate to the overall performance of the Company, the CEO’s individual performance and the prevailing remuneration levels in the relevant market. 

Dividends 
 A dividend equivalent payment is
provided on GIS, STIP and LTIP awards when the vesting period is over and the GIS or STIP deferred equity and the LTIP awards vest or are exercised. No payment is made in respect of unvested or lapsed GIS, STIP and LTIP awards. 

The Board and Remuneration Committee has determined that dividend equivalent payments in respect of future GIS and STIP deferred equity and LTIP awards will
be made in the form of shares, instead of cash as has been prior practice. 
 5.    Minimum shareholding requirement 

The Board and Remuneration Committee has determined that Mr Mackenzie as CEO is required to hold BHP Billiton securities with a value at least equal to five
times his pre-tax (gross) annual base salary. This is an increase from the previous level for the CEO which was three times pre-tax annual base salary. The value of the securities for the purposes of this requirement is the market value of the
underlying shares. Unvested awards do not qualify. 

 The equivalent requirement for Mr Mackenzie’s direct reports is three times (previously two times) pre-tax
(gross) annual base salary. 
 Where sufficient securities are not held to meet the relevant requirement, it is expected that participants will grow their
holdings to the required level over an acceptable timeframe in accordance with the scheduled vesting of equity awards. 

6.    Termination of contract 
 The
Group retains the right to terminate the contract by giving 12 months’ notice or by making payment in lieu of notice to 12 months base salary plus the amount paid in lieu of a contribution to a superannuation or retirement scheme (i.e. a total
of US$2,125,000). Mr Mackenzie would also be entitled to any accrued entitlements such as earned but untaken leave. 

7.    Entitlements under the GIS, STIP and LTIPs on termination 

The rules of the GIS, STIP and LTIPs set out the entitlement of participants on termination of employment. These are described in the Remuneration Report which
forms part of the Annual Report. 
 Resignation or termination for cause 

Where employment is terminated by the resignation of the executive, or by the Group for cause, a participant is not entitled to any cash incentive for the year
in question. All GIS, STIP and LTIP awards that have been allocated but which are not yet exercisable lapse. 
 Retirement or termination by mutual
agreement 
 If Mr Mackenzie retires or his employment terminates by mutual agreement: 

 

	•	 	Any GIS awards that had been granted, but which were not exercisable at the date of departure, would vest in full; 

  

	•	 	Any STIP awards that had been granted, but which were not exercisable at the date of departure, would be retained by Mr Mackenzie but would not vest until the scheduled vesting date (after departure); 

 

	•	 	He may at the Remuneration Committee’s discretion be considered for a pro rata short term cash incentive for his period of service during that year based on performance; and 

 

	•	 	Mr Mackenzie would have a right to retain entitlements to LTIP awards that have been granted but that are not exercisable, pending satisfaction of future performance hurdles. The number of entitlements Mr Mackenzie
would be permitted to retain would be reduced pro rata to reflect his period of service. These entitlements would become exercisable only if the performance hurdles are ultimately met and the Remuneration Committee approves vesting.

 Other circumstances 
 Special
provisions relate to events described as “uncontrollable” such as death, serious injury. In those circumstances, all of the GIS and STIP deferred equity and LTIP awards that have been awarded but which are not exercisable become
immediately exercisable by Mr Mackenzie or his estate.

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