Until run profiler to know where are slow spots specifically any micro optimization is premature.
W/o other information on code structure nothing to be said;
A(B,:)=5;
is about as efficient as it gets presuming elements of B are already in A which is a class double array...the hint may be in the earlier phrase of "Each loop...". Perhaps that loop or significant portions could be vectorized or otherwise are the bottleneck but crystal ball is in shop for repair (yet again)...
