http://winscp.net/eng/docs/faq_su

If you are connecting to a Unix/Linux server, you can specify following command as custom shell on the SCP/Shell tab of Login dialog:

sudo su -

You can do this only if you are allowed to do sudo su without being prompted with password. See sudo documentation to learn how to do that. For example you can add following line to sudoers file (/etc/sudoers):

yourusername ALL=(ALL) NOPASSWD: ALL

Note that as WinSCP does not allocate TTY, you need to have sudoers option requiretty turned off (what is default).