Under the original terms of the CPN, Motif Bio would have had to repay around US$442,000 in interest at the end of this year in the form of shares.
Motif has now agreed to pay around US$314,000 in cash and issue 409,000 shares to Amphion in full satisfaction of interest payments through to the maturity date of 31 December 2016.
The deal will also enable Amphion to convert the principal US$3.5mln amount into Motif shares before the year is out at a conversion price of US$0.2447, well below the current share price.
In addition, Amphion has entered into an agreement with Motif Bio to provide certain corporate services such as investor relations, back office and accounting functions.
Conditional upon the latter listing on NASDAQ, Amphion would provide the services for a minimum term of 12 months for a fee of US$15,500 a month.
Shares in Amphion were up 9%, or 0.3p, to 3.55p.