There are places on the web that offer conversion from .pub to other formats, such as .doc, .html, .rtf, and others. You can then convert any of those to an ebook format. I don't know of, nor could I find, any programs that convert directly from .pub to .epub or .mobi, but you may have more success than I if you look around.
Zamzar is one site I found that offers conversion from .pub to other formats.
The mention of this site isn't meant to be construed as a recommendation, as all I know about it is I found it a few minutes ago via a search engine, but you may want to check it out.
I've never worked with MS Publisher. Does it offer the option to "save as" anything other than .pub? If it's able to save documents as .html or .rtf, for example, you could convert it to ebook form with Calibre. (And Calibre I
do recommend!)