Yes, alcohol breaks down peptidoglycan. It does this through the process of denaturation.

Alcohol molecules are amphiphile chemical compounds. This means that they have both water and fat-loving properties. When a bacterial cell is exposed to alcohol, the amphiphile alcohol molecules bond with and break down the peptidoglycan molecules that form the outermost part of the bacterial cell wall. With the breaking down of the peptidoglycan molecules leaves the bacteria wall-less and exposes its core components to the outside environment. This results in the bacteria ceasing to function and it dies soon after.