VPC for ec2 instance running DB, connected via VPC Peering to another VPC with an ec2 instance running application

Hi, you could have a read to this architecture whitepaper: https://docs.aws.amazon.com/whitepapers/latest/serverless-multi-tier-architectures-api-gateway-lambda/three-tier-architecture-overview.html There are different cases depending on your scenario (https://docs.aws.amazon.com/whitepapers/latest/serverless-multi-tier-architectures-api-gateway-lambda/sample-architecture-patterns.html),but in general you could exploit reusing the same VPC and having subnets where you can deploy layers to. For instance for databases and EC2 accessing the database you may want to have in 2 separate private subnets.

Finally, searching for 3-layer architecture will usually lead you to clear aws architecture which you can assess if fit your case.

Hope it helps ;)

If you only want to separate applications and databases, you can simply divide subnets within the same VPC.
An example of dividing a VPC would be to divide it by system or by environment (production, staging, etc.). (In the first place, in this case, it is often divided by AWS account.)
It is also cumbersome to manage because it will be necessary to create flow logs for each VPC.