In general, if the QB gets the ball out in under 2.5 seconds accurately and on time to the right guy and he catches it then nothing can stop this offense. In other words, there's no defense for the perfect pass.
A defense could, however, try to make any of those steps more difficult.
A defense can try to get pressure before 2.5 seconds (it would have to be up the middle against most play calls). (That's why moving Williams to C was such a key decision). You could see that in games where teams disrupted Brady. It was often with pressure up the middle.
They can try and confuse the QB. Teams have tried this but so far Tua has been pretty good at reading defenses and has made them pay.
They can try and flood the zones where the QB wants to go. This is the one I think is most likely. Pitt had success in the second half b/c it seemed like Minkah scared Tua off his middle of the field passes. Tua was clearly rusty that game and didn't use his outside alternatives very well. Cleveland did something similar with a ton of cover 3 and cover 6. They tried to take away the middle of the field and anything deep to force the offense to be more methodical. But Tua had better answers than against Pitt and showed much better patience.
Not only did he use more other targets, but specifically he used the backs out of the backfield a lot more. Mostert, who was never a great receiving back, caught several. And Wilson provided a huge upgrade as a receiver vs. what we got from Chase. Ingold also contributed after some drops out of the backfield early in the season. Being able to hit those backs out of the backfield is huge when you stretch the defense vertically. It's just a tough ask for LBs to get deep and take away the middle and then come back up to tackle in the short areas.
The other key is the addition of the run game. If the team can run against the better DLs, then defenses have to involve the LBs more. That, of course makes it more difficult for them to get enough depth quickly enough against really fast receivers.
So basically, a defense needs to be able to stop the run and get inside pressure with their DL, have LBs or hybrid Ss that can cover a lot of space in the middle of the field yet also get up to limit the backs out of the backfield.