How to prevent a man-in-the-middle attack in case of a compromised server?

Question

Imagine that a server is serving public keys of the users to their partners to make encrypted communication possible. However, the server does NOT have access to the private key

Answer 1

The FAQ for PGP (Pretty Good Privacy) explains this issue.

I would also recommend reading Bruce Schneier's excellent book "Applied Cryptography" for "friendly and digestible" discussions of these topics.