The Magpies failed with a loan bid for the Atletico Paranaense star in January, but then looked to rekindle talks with a view to signing the Brazilian World Cup winner in the summer.
However, Atletico's representatives reportedly failed to show up for a meeting with Shepherd and operating officer Russell Cushing.
The no-show of the Brazilian club and their representatives means that Newcastle are highly unlikely to come back again for the South American.
Newcastle have also poured cold water on suggestions of a renewed bid for West Ham United's Lee Bowyer.
The Toon were just one of a number of clubs to look at Bowyer when his availability at Leeds became known, but he opted to return to his London-roots.
The England international, however, only signed with West Ham until June and is available on a free transfer.
Newcastle were reportedly looking to link Bowyer up with his former Elland Road team-mate Jonathan Woodgate on Tyneside.
Shepherd, though, doubts the player will leave the capital.
"Sir Bobby Robson didn't get to first base when he was interested in Bowyer at the end of last year and the lad went to West Ham," he said.
"Bowyer wanted to go back to London and I think you will find that is where he will stay."
