Stewart, Souter and McGowan are alleged to have killed Mr Munro at the flat in Morgan Street on 10 January.
They are also accused of a separate charge of abducting Mr Munro between 9 and 10 January last year.
El-Nakla is not accused of being involved in the alleged killing.
He is separately accused of being concerned in the supply of cocaine in Dundee.
Along with Stewart and McGowan, he faces a similar charge in relation to heroin.
Lawyers for Stewart, Souter and McGowan also pleaded not guilty on their behalf.
Stewart and Souter have each lodged a special defence of incrimination.
The trial is scheduled to take place in December in Edinburgh.
BBC News
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