$ cat ips
111.222.333.444
55.66.77.88

$ cat text
Line 1 nothing to comment
Line 2 111.222.333.444 should be commented
Line 3 11.22.33.44 do not comment
Line 4 55.66.77.88 should be commented

$ perl -pe '@l = `cat ips`;chomp @l; %h = map {$_=>1} @l; s/(\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3})/$h{$1}?"#$1":$1/e;' <text