Assuming you mean InstallShield 12, not InstallShield 2012 (yeah it's a bit of a name clash), your best bet is to create or find a prerequisite that installs .NET Framework version 4.5. Unfortunately since it's not built-in, the build won't know that it's .NET, and the warning won't necessarily go away.
(Actually the same advice goes for InstallShield 2012, but that version might include such a prerequisite already; InstallShield 12 is definitely too old for that.)