Document:

Exhibit 10.1

	
  DATED

  	
   

  	
  2007

  

 

	
  (1)

  	
   

  	
  TRIPOS DISCOVERY
  RESEARCH LIMITED

  
	
   

  	
   

  	
   

  
	
  (2)

  	
   

  	
  SOUTH WEST OF ENGLAND
  REGIONAL DEVELOPMENT AGENCY

  
	
   

  	
   

  	
   

  
	
  (3)

  	
   

  	
  TRIPOS, INC

  
	
   

  	
   

  	
   

  
	
  (4)

  	
   

  	
  COMMONWEALTH
  BIOTECHNOLOGIES, INC

  

 

Supplemental Agreement

relating to the sale of

Land and Building at

Bude Stratton
Industrial Estate

www.ashfords.co.uk

 1
 

THIS
SUPPLEMENTAL DEED is made the   day of          Two
Thousand and Seven

BETWEEN

(1)            TRIPOS DISCOVERY RESEARCH LIMITED incorporated and registered in England and Wales with company
number 02493812 whose registered office is at The Courtyard, High Street,
Ascot, Berkshire (“Tripos Discovery”)

(2)            SOUTH WEST OF ENGLAND REGIONAL DEVELOPMENT AGENCY (a body
corporate under the Regional Development Agencies Act 1998) of Sterling House,
Dix’s Field, Exeter, Devon, EX1 1QA ( “Agency”)

(3)            TRIPOS INC a company incorporated in Utah whose registered
office is situated at 1699 South Hanley Road, St. Louis, Missouri 63144, USA (“Tripos”)

(4)            COMMONWEALTH BIOTECHNOLOGIES, INC, a
company incorporated in Virginia whose registered office is situated at 601
Biotech Drive, Richmond, Virginia 23235, USA (“CBI”)

BACKGROUND

1.             The Agency and the
Tripos Discovery have Today entered into an Agreement for Sale (“the Property Sale Agreement”) in relation to
land and buildings at Bude Stratton Industrial Estate, Bude, Devon, England (“the
Property”).

2.             Tripos is the sole
shareholder in Tripos Discovery and CBI will become the sole shareholder in
Tripos Discovery under the Share Sale Agreement and Tripos and CBI have agreed
with the Agency that the proceeds of the sale of the Property will be used in
accordance with this deed.

3.             By a grant offer
letter (“the Grant Letter”) dated
23rd April 2002 the Secretary of State offered, and
Tripos Discovery accepted, a grant not exceeding £2,400,000 to carry out the
project therein described.

4.             On 24th April 2002 Tripos provided to the Secretary of
State an authorised parental undertaking and guarantee (“the Guarantee”) that if any sums became
repayable by Tripos Discovery under the terms of the Grant Letter and Tripos
Discovery did not repay on first demand, Tripos would pay the Secretary of
State the amount repayable together with interest.

5.             In April 2006 Tripos
Discovery alerted the Secretary of State to the fact that they had made staff
redundant and that their prospects of meeting the project targets were remote.

6.             The Secretary of
State is understood to be willing to release the obligations in the Grant
Letter and the Guarantee subject to receiving £591,000 and being satisfied with
the eventual plans for the continuation and development of the Tripos Discovery
business.

 2
 

IT IS
AGREED as follows:

1.             In this Agreement the
following expressions shall have the following meanings respectively:

Agency’s
Solicitors: Ashfords of Grenadier Road Exeter EX1 3LH
or such other solicitors as the Agency shall appoint for the purposes of this
deed and notify to Tripos

Condition: has the meaning given in clause 2.1

Connected
Person: has the same meaning as in section 839 of the
Income and Corporation Taxes Act 1988

Balance
Proceeds of Sale: the purchase price payable under the
Agreement for Sale less the Escrow Monies

Deed of
Release: a release of Tripos Discovery and Tripos from
the obligations under the Grant Letter (other than the obligation in Paragraph
8 of the Grant Letter in relation to enquires by the European Commission) and
the Guarantee

Escrow
Account: a client account operated by the Agency’s
Solicitors

Escrow
Monies: £520,000 from the purchase monies payable
under the Property Sale Agreement

Insolvent:  means Tripos Discovery is:

a.            Insolvent or unable to pay it’s debts within the
meaning of Section 123 Insolvency Act 1986 or has stopped paying it’s debts as
they fall due;

b.            An
order has been made, petition presented, resolution passed, meeting convened or
any steps have been taken for the winding up of Tripos Discovery;

c.            An administrator, liquidator, provisional liquidator, receiver
(including administrative receiver) has been appointed or steps have been taken
to appoint one in respect of Tripos Discovery or in respect of all or any part
of the assets of Tripos Discovery;

d.            Distress, execution or other process has been levied
or threatened in writing in respect of any asset of Tripos Discovery;

e.            A voluntary arrangement, compromise or scheme of
arrangement has been proposed, sanctioned or approved in respect of Tripos
Discovery;

f.              Tripos Discovery has been removed or there is an
application pending for the removal of Tripos Discovery from the Register of
Companies

Release Confirmations: written confirmations from:

(a) the Secretary
of State  that the Secretary of
State has agreed to grant to Tripos and Tripos Discovery a release of the
obligations under the Grant Letter and Guarantee; and

 3
 

(b) Tripos
Discovery and Tripos that the Deed of Release is in a satisfactory form.

Share Sale Agreement: an agreement dated 11 May 2007 for the acquisition by
CBI of all the share capital in Tripos Discovery

Termination Date: 24 June 2007 or such later date as all the parties
agree in writing

1.1.          In
this Deed references to;

1.1.1.       any
statute or any section thereof or legislation generally include any statutory
extension or modification, amendment or re-enactment of such statutes and
include all instruments, orders, bye-laws and regulations for the time being
made, issued or given thereunder or deriving validity therefrom, and all other
legislation of the European Community that is directly applicable to the United
Kingdom.

1.1.2.       any
clause, sub-clause, paragraph, sub-paragraph or schedule without further
designation shall be construed as a reference to the clause, sub-clause,
paragraph, sub-paragraph or schedule to this Deed so numbered;

1.1.3.       this
Deed includes any variations hereto made from time to time and any agreement
expressed to be supplemental hereto;

1.1.4.       words
importing one gender shall include both genders and the singular shall include
the plural and vice versa.

2.            Pre-Condition

2.1.          This
agreement is conditional upon; closing the Share Sale Agreement; obtaining the
Release Confirmations; and the exchange and completion of the Property Sale
Agreement, prior to the Termination Date.

2.2.          The
provisions of clauses 3, and 4 take effect from the satisfaction of the
Condition.

2.3.          If
the Condition is not satisfied by the Termination Date then this Agreement is
at an end and of no further effect.

3.            Payment to the
Secretary of State

3.1.          Tripos,
CBI and Tripos Discovery agree that the Escrow Monies shall be held in the
Escrow Account until the Agency receives the Release Confirmations.

3.2.          Upon
receipt of the last of the Release Confirmations the Agency shall procure that
the Escrow Monies are paid to the Secretary of State to be held to order
pending the completion of the Deed of Release.

3.3.          If
prior to the receipt of the of the Release Confirmations the Agency receives
notice from the Secretary of State that he has demanded payment of sums which
have become repayable by Tripos Discovery or payable by Tripos under the Grant
Letter and Guarantee respectively,  then
the Agency shall procure that the Escrow Monies are paid to the Secretary of
State towards payment of the sums demanded.

 4
 

4.            Proceeds of Sale

4.1.          Tripos,
CBI and Tripos Discovery jointly and severally undertake to the Agency that the
Balance of the Proceeds of Sale shall be retained by Tripos Discovery to be
used;

4.1.1.       as
required under the Property Sale Agreement;

4.1.2.       to
repay existing finance agreements in relation to plant and equipment at the
Property in accordance with the repayment schedule attached or such other
repayment scheme as is approved in writing by the Agency; and

4.1.3.       as
working capital for the Tripos Discovery business carried on at the Property.

4.2.          Tripos,
CBI and Tripos Discovery jointly and severally undertake to the Agency that the
Balance Proceeds of Sale will not be used to pay dividends, management charges,
or other sums now or in the future due to:

4.2.1.       Tripos
or any Connected Person to Tripos, or by other means be passed to Tripos or any
Connected Person to Tripos; or

4.2.2.       CBI
or any Connected Person to CBI, or by other means passed be to CBI or any
Connected Person to CBI.

4.3.          Tripos,
CBI and Tripos Discovery jointly and severally agree to provide the Agency with
all such information as the Agency may require in order to satisfy itself that
clauses 4.1 and 4.2 have been complied with, and shall provide access for
inspection and copying purposes only to relevant information within their
possession.

4.4.          Tripos
undertakes to the Agency to pay or repay to Tripos Discovery, or, if Tripos
Discovery becomes Insolvent or ceases to trade from the Property , as the
Agency directs, any of the Balance of the Proceeds of Sale;

4.4.1.       received
or held by Tripos, or any Connected Person to Tripos, in breach of clause 4.2;
or

4.4.2.       which
the Agency is reasonable satisfied, acting in good faith, are not used in
accordance with clause 4.1.

4.5.          CBI
undertakes to the Agency to pay or repay to Tripos Discovery, or, if Tripos
Discovery becomes Insolvent or ceases to trade from the Property, as the Agency
directs, any of the Balance of the Proceeds of Sale;

4.5.1.       received
or held by CBI, or any Connected Person to CBI, in breach of clause 4.2, or

4.5.2.       which
the Agency is reasonable satisfied, acting in good faith, are not used in
accordance with clause 4.1.

 5
 

4.6.          The
provisions of Section 4.1 and 4.4 shall be binding upon Tripos only with
regards to matters arising whilst Tripos is a shareholder of Tripos Discovery,
or whilst Tripos Discovery is acting in accordance with obligations to or the
requirements of Tripos.

4.7.          In
determining whether the Balance Proceeds of Sale have been used in accordance
with clause 4.1 and in calculating any sum to be paid or repaid under clauses
4.4 and 4.5, clause 4.1.3 shall be deemed to have been subject to the following
proviso if Tripos Discovery becomes Insolvent or ceases to trade from the
Property prior to 31 December 2008;

“PROVIDED
ALWAYS that the aggregate expenditure under this clause 4.1.3 shall not exceed
£250,000 prior to the repayment in full of all the existing finance agreements
in relation to plant and equipment at the Property”

4.8.          CBI
agrees to:

4.8.1.       comply
with such monitoring and reporting requirements relating to Tripos Discovery
and the Tripos Discovery business as the Agency may from time to time require;

4.8.2.       notify
the Agency as soon as possible of any meetings of the board of directors of
Tripos Discovery and allow a representative of the Agency to attend and
participate in such meetings.

4.9.          The
Agency confirms that in consideration of the agreements made herein, Tripos is
released from its obligations as guarantor under the Development Agreement
dated 19th June 2003.

5.            Jurisdiction

This Deed shall be governed by and construed in
accordance with the laws of England and each of the parties irrevocably submits
to the exclusive jurisdiction of the English courts and waives any objection to
proceedings in such courts on the grounds of venue or on the grounds that
proceedings have been brought in an inappropriate forum.

6.            Counterparts

This agreement may be executed in any number of
counterparts (but shall not be effective until each party has executed at least
one counterpart), each of which, when executed and delivered, shall be an
original and which together shall have the same effect as if each party had
executed and delivered the same document.

7.            Liability and
Severance

7.1.          The
Agency may take action against, or release or compromise the liability of, any
of the other parties, or grant time or other indulgence, without affecting the
liability of any other parties.

7.2.          If
any provision of this agreement (or part of any provision) is found by any
court or other authority of competent jurisdiction to be invalid, unenforceable
or illegal, the other provisions shall remain in force.

 6
 

7.3.          If
any invalid, unenforceable or illegal provision would be valid, enforceable and
legal if some part of it were deleted, the provision shall apply with whatever modification
is necessary to give effect to the commercial intention of the parties.

7.4.          The
parties agree, in the circumstances referred to in clause 7.1 and if clause 7.2
does not apply, to attempt to substitute for any invalid or unenforceable
provision a valid and enforceable provision which achieves, to the greatest
extent possible, the same effect as would have been achieved by the invalid or
unenforceable provision. The obligations of the parties under any invalid or
unenforceable provision of this agreement shall be suspended while an attempt
at such substitution is made.

This document has
been executed as a deed and is delivered and takes effect on the date stated at
the beginning of it.

	
  THE CORPORATE SEAL of

  	
  )

  
	
  the SOUTH WEST OF ENGLAND

  	
  )

  
	
  REGIONAL DEVELOPMENT

  	
  )

  
	
  AGENCY  hereto affixed is

  	
  )

  
	
  authenticated by:

  	
  )

  
	
   

  	
   

  
	
   

  	
  Authorised Signatory

  
	
   

  	
   

  
	
   

  	
  Authorised Signatory

  
	
   

  	
   

  
	
  EXECUTED as a
  deed and delivered

  	
  )

  
	
  on the date hereof by Tripos

  	
  )

  
	
  Discovery Research Limited

  	
  )

  
	
  acting by two of its directors or

  	
  )

  
	
  a director and its secretary

  	
  )

  
	
   

  	
   

  
	
   

  	
   

  
	
  /s/ John P.
  McAlister

  	
   

  	
   

  
	
  Director

  	
   

  
	
   

  	
   

  
	
   

  	
   

  
	
  /s/ Simon Cole

  	
   

  	
   

  
	
  Director/Secretary

  	
   

  

 

 7
 

 

	
  

  	
   

  
	
  EXECUTED as a deed by Tripos

  	
  )

  
	
  Inc and signed by
  John P. McAlister

  	
  )

  
	
  and Ralph Lobdell.

  	
         )

  
	
  acting, in accordance with the law

  	
  )

  
	
  of Utah under the authority of Tripos

  	
  )

  
	
  Inc pursuant to a
  resolution of the

  	
  )

  
	
  Board/shareholders dated May 30, 2007

  	
  )

  

 

 

	
  

  	
  /s/ John P.
  McAlister

  	
   

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  /s/ Ralph
  Lobdell

  	
   

  
	
   

  	
   

  
	
  EXECUTED as a
  deed by

  	
  )

  
	
  Commonwealth Biotechnologies,

  	
  )

  
	
  Inc and signed by Richard J. Freer,

  	
  )

  
	
  acting, in accordance with the law

  	
  )

  
	
  of Virginia under the authority of

  	
  )

  
	
  Commonwealth Biotechnologies,

  	
  )

  
	
  Inc pursuant to a
  resolution of the

  	
  )

  
	
  Board/shareholders dated May 1, 2007.

  	
  )

  
	
   

  	
   

  
	
   

  	
   

  
	
   

  	
  /s/ Richard J.
  Freer

  	
   

  

 

 8Exhibit 10.2

THIS DEED OF RELEASE
is made the 4th day of June Two Thousand and Seven

BETWEEN:

(1)           THE SECRETARY OF STATE FOR TRADE AND INDUSTRY whose
principal office is at 1 Victoria Street, London SW1H 0ET (“the Secretary of
State”);

(2)           TRIPOS DISCOVERY RESEARCH LIMITED (formerly Tripos Receptor
Research Limited) a company incorporated in England and Wales with company
number 02493812 whose registered office is situated at The Courtyard, High
Street, Ascot, Berkshire SL5 7HP (“Tripos Discovery”);

and

(3)           TRIPOS INC a company incorporated in Utah whose registered
office is situated at 1699 South Hanley Road, St. Louis, Missouri 63144, USA (“Tripos
Inc”)

WHEREAS:-

(A)          By grant offer letter (“the
Grant Letter”) dated 23rd April 2002 the Secretary of State offered, and
the Tripos Discovery accepted, a grant not exceeding £2,400,000 to carry out
the project therein described.

(B)           On 24th April 2002 Tripos Inc provided an authorised
parental undertaking and guarantee (“the Guarantee”) that if any sums became
repayable by Tripos Discovery under the terms of the Grant Letter and Tripos
Discovery did not repay on first demand, Tripos Inc would pay the Secretary of
State the amount repayable together with interest.

(C)           In April 2006 Tripos
Discovery alerted the Secretary of State to the fact that they had made staff
redundant and that their prospects of meeting the project targets were remote.

(D)          Pursuant to the terms of
the Grant Letter the Secretary of State is under no obligation to make further
payments to Tripos Discovery, sums have now become repayable by Tripos
Discovery, and sums have now become payable by Tripos Inc.

(E)           By an agreement dated
15th May 2007 and made between Tripos Inc and
Commonwealth Biotechnologies, Inc. (“the CBI Agreement”) Tripos Inc has agreed
to dispose of certain shares to Commonwealth Biotechnologies Inc.

(F)           Subject to the
completion of the CBI Agreement in accordance with its terms and to receiving
from Tripos Discovery and/or Tripos Inc repayments and/or payments under the
Grant Letter and the Guarantee in the aggregate sum of Five Hundred and

 1
 

Ninety One Thousand Pounds (£591,000), the Secretary of state is
willing to release Tripos Discovery and Tripos Inc from all further liability
under the terms of the Grant Letter and the Guarantee.

IT IS HEREBY AGREED:-

1.             The following
provisions of this Deed shall not come into effect unless by 15 June 2007:

a.             the CBI Agreement is
completed in accordance with its terms; and

b.             the Secretary of
State is in receipt of cleared funds in the sum of Five Hundred and Ninety One
Thousand Pounds (£591,000) from Tripos Discovery and/or Tripos Inc.

If either of the
preconditions is not met the Secretary of State shall be fully entitled, under
the terms of the Grant Letter, to require repayment of the total amount of
grant paid to Tripos Discovery under the Grant Letter.

2.             Tripos Discovery
releases and discharges the Secretary of State from all liabilities and
obligations under the Grant Letter.

3.             For the avoidance of
doubt, the Secretary of State shall be under no further obligation to provide
any further grant money.

4.             The Secretary of
State releases and discharges Tripos Discovery and Tripos Inc. and their
Successors and assigns from the performance of their duties and from all
liabilities and obligations under the Grant Letter subject to the exception in
clause 5 below.

5.             Tripos Discovery will
remain subject to the obligation in Paragraph 8 of the Grant Letter in relation
to enquires by the European Commission.

6.             This Deed of Release
shall be governed by and construed in accordance with the laws of England and
each of the parties hereby irrevocably submits to the exclusive jurisdiction of
the English courts and waives any objection to proceedings in such courts on
the grounds of venue or on the grounds that proceedings have been brought in an
inappropriate forum.

IN WITNESS WHEREOF
the Corporate Seal of the Secretary of State has been hereunto affixed and
Tripos Discovery and Tripos Inc have caused this Deed of Release  to be executed as a deed the day and year
first above written.

	
  THE CORPORATE SEAL of

  	
  )

  
	
  THE
  SECRETARY OF STATE

  	
  )

  
	
  FOR
  TRADE AND INDUSTRY

  	
  )

  
	
  here unto
  affixed is authenticated by

  	
  )

  

 

 

	
  /s/

  	
   

  
	
  an Official in
  the Department

  	
   

  
	
  of Trade and
  Industry

  	
   

  
	
   

  	
   

  

 

 2
 

 

	
  EXECUTED as a deed and delivered

  	
  )

  
	
  on the date
  hereof by Tripos

  	
  )

  
	
  Discovery
  Research Limited

  	
  )

  
	
  acting by two of
  its directors or

  	
  )

  
	
  a director and
  its secretary

  	
  )

  
	
   

  	
   

  
	
   

  	
   

  
	
  /s/ John P. McAlister

  	
   

  
	
  Director: John P.
  McAlister

  	
   

  
	
   

  	
   

  
	
   

  	
   

  
	
  /s/ Mark Allen

  	
   

  
	
  Director/Secretary:
  Mark Allen

  	
   

  
	
  Tripos Discovery
  Research Limited

  	
   

  
	
   

  	
   

  
	
   

  	
   

  
	
  EXECUTED
  as a deed by Tripos

  	
  )

  
	
  Inc and
  signed by John P. McAlister

  	
  )

  
	
  and Ralph
  Lobdell

  	
  )

  
	
  acting, in
  accordance with the law

  	
  )

  
	
  of Utah under
  the authority of Tripos

  	
  )

  
	
  Inc pursuant
  to a resolution of the

  	
  )

  
	
  Board dated 17
  May 2007

  	
   

  
	
   

  	
   

  
	
   

  	
   

  
	
  /s/ John P. McAlister

  	
   

  
	
  John P.
  McAlister

  	
   

  
	
   

  	
   

  
	
   

  	
   

  
	
  /s/ Ralph Lobdell

  	
   

  
	
  Ralph Lobdell

  	
   

  

 

 3

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