This 3-in-1 brush from Karlskicks is great for cleaning different types of sneakers. The brush consists of three different sides. A side made especially for cleaning suede-sneakers, and another side with a nubuck block (watch this video for instructions: https://goo.gl/h2s4F4). The last side (the white/gold side) should be used to clean dirty soles and flyknit/primeknit.
The brush won’t fray the fabric or the suede on the sneaker.