Hmm I think it must be The Island of Dr. Brain or The Castle of Dr. Brain. I remember that I have played one of these games at a friend, back in the good old days. I remember a book as well.
http://www.abandonia.com/game.php?genre=puzzle&ID=224 Island
http://www.abandonia.com/game.php?genre=puzzle&ID=49 Castle
cu, Spaceball