I connect to an AS400 database using DBeaver and ODBC, it lets me run CRUD operations better than the 5250 Emulator. Is there a way to run from DBeaver command lines like WRKUSRPRF or CHGUSRPRF?
You can't use commands that start with WRK without a 5250 session, some will run and produce a list of elements as a spooled file but many will just refuse to run.
You can run a command in any SQL client using QSYS2.QCMDEXC stored procedure or function
IBM i Services provide views, procedures and functions you can use to retrieve information about the system and make some changes (see CHANGE_USER_PROFILE)
If you use IBM i Access - Client Solutions maybe the "run SQL scripts" option is installed. It provides a cl:<command> syntax and can prompt statement
If what you want is more "modern" interface then you can use IBM Navigator for i depending on version and PTF installed on your server. Check http://<your server>:2001