Basically, someone who introduced as a protagonist become a villain while the villain become protagonist halfway through, similar to Samurai Deeper Kyo and Sengoku Youko. Any other manga which do this in similar way?
What I'm looking for is the case for main protagonist. So something like Naruto where Sasuke become villain while Gaara become one of the good guy doesn't count because the main MC is still Naruto.

What about the protagonist becoming the villain (but a different antagonist at first)?

Immortal Regis and its sequel

I can't think of many where both switch places like that. But I know of some with either one or the other.

These are some where a protagonist is presented as an antagonist at first:
Kokumin Quiz
Vampire Juujikai

The protagonist becomes villainous:
Murasakiiro no Qualia
(I suppose Death Note technically fits this but I'm sure you already know about that one)

And I'm still not sure about this one:
Babel no Toshokan