If you are working with serial communication (sending data from PC to Arduino simulation), use the tool in Proteus.
: Supports system-level simulation of microcontrollers, including direct support for over 50 Arduino shields and breakout boards. Visual Designer
Once your simulated Arduino code works perfectly with the circuit, use Proteus ARES to design a custom shield or a standalone board (using an ATmega328P instead of the entire Uno module). Export Gerber files directly.