Intercept Ctrl + S keyboard shortcut in editor for custom editor

You can not intercept built in Unity keyboard shortcuts.

You can however define your own to do what you want. In the sample editor script below I show you how to do the same thing with two different keyboard shortcuts.

 using UnityEngine;
 using UnityEditor;
 using System.Collections;
 using UnityEditor.SceneManagement;
 using UnityEngine.SceneManagement;
 
 public class UnityExtededShortKeys : ScriptableObject
 {
     [MenuItem("HotKey/Run _F5")]
     [MenuItem("HotKey/Run2 _%H")]
     static void PlayGame()
     {
         EditorSceneManager.SaveScene(SceneManager.GetActiveScene(), "", false);
         EditorApplication.ExecuteMenuItem("Edit/Play");
     }
 }

Here is a link to how to use Unity Editor Extensions.