At the end of a long run, the legs are inevitably tired which is to be expected. I understand the important role that the knees play in running, and they certainly carry a lot of the body’s weight and movement. Doing core exercises and strengthening and stretching the pelvis, hips, and legs will help the knees and legs remain strong during a run. Without a strong core to keep the body in a nice straight line while running, your knees will bear the brunt of any sideways movement of the body and you’ll feel the pain later.