Prefix Dr. or Mr./Ms. if I have an MD but not a Ph.D. in medicine?
First, note that the title that you give to a ScholarOne manuscript handling system probably doesn't matter at all --- more than anything else, that is in there to avoid offending you if you are particular about being given your title.  The actual publication of the paper will typically omit titles, so putting in the title just regulates what the system will call you in email.

That said, Dr. is a correct title to use as an M.D.  In fact, many people will argue that opposite, that it is Ph.D.-holders whose use of the title is dubious!