'deprotect' is formed in modern English by prefixing the Latin-derived prefix 'de-' (meaning 'remove' or 'from') to 'protect', which itself ultimately comes from Latin.

'protect' entered English via Old French 'proteger' from Latin 'protegere' (from pro- 'in front' + tegere 'to cover'). The verb 'deprotect' is a later technical formation (notably in chemistry) made by adding 'de-' to 'protect'.

Initially the elements meant 'remove' + 'cover/protect', and the combined modern technical sense is 'to remove protection (e.g., a protecting group)'; the core idea of removing protection remains.