Villamayor dragged fellow GM Mikhail Ulibin into a four-hour battle of wits in their French defense game but eventually succumbed to the Russian ace and resigned after 49 moves.
Mariano lost in the intricacies of a King’s Indian and bowed to 11th seed GM Pavel Eljanov of Ukraine, who made a temporary Queen sacrifice in the middle game to win the exchange of rook-for-bishop in 50 moves and then eventually promoted his pawn en route to the victory.
Nadera, on the other hand, fell to GM Artashes Minasian of Armenia in 46 moves of a Benoni defense after the latter broke through the queenside and was on the verge of winning a knight when the Filipino resigned.
The setbacks dropped the three Filipinos to joint 15th place with 3.5 points apiece.
Among the leaders, second seed GM Krishnan Sasikiran of India held top seed GM Liviu-Dieter Nisipeanu to a draw.
Nisipeanu shares the lead with Eljanov, Minasian and GM Shakriya Mamedyarov of Azerbaijan at 4.5 points each.
Eleven players follow the lead pack with four points apiece.
The nine-round Swiss system event, which drew 45 grandmasters in a field of 134 players from 39 countries, offers a total pot of $40,000.
With four more rounds to go, Mariano and Nadera still have chances of earning GM norms.
In round 6, Mariano plays white against GM Alexey Kuzmin of Russia, Nadera is black against fourth seed GM Viorel Iordachescu of Moldova while Villamayor plays IM Abdul Hameed El Arousy of Egypt.