Other way around - the machines were using human brains as a substrate for computing.

If they can get Doom to run on a pregnancy test surely they could get it running on human brain cells?

Speaking of earlier concepts of The Matrix, there's an old 1973 German movie/mini series World on a Wire that's really good.

Wasn't the matrix using humans as some sort of power source/batteries? I may be misremembering though, as that seems pretty silly in retrospect ..