How to properly protect a laptop placed in a checked in luggage?

Considering these bags will be thrown, dropped, dropped on, exposed to unknown temperatures and possibly vulnerable to theft, there is no proper way to do it. Wrapping it with a significant amount of clothing will surely protect it from some shock damage. One of those big business laptop bags will help too if that fits in your suitcase or backpack. A hard-shell suitcase will be better than a soft-shell suitcase or even backpack, as long as the laptop cannot toss around inside. But ultimately, unless you can professionally package it for this kind of transport, it's no way to handle electronics.

The normal means of protecting stuff like this is a rigid case with foam inside with holes that match what you are trying to protect.

While I have never used their air travel versions I have used Pelican cases before for transport protection. They're heavy and pricey but the stuff inside survived being dropped more than once.