There is a direct couchette car from Thessaloniki to Prague, going 12.6-20.9. on Mondays, Fridays and Saturdays - departure 17:05, arrival 22:21 second day.
On the other days you have to change in Beograd. The timetable is same as above. From Thessaloniki to Beograd with Hellas Express, from Beograd to Prague with EC Avala.
Both variants are faster than the journey via Sofia.