Taking a cue from prima ballerinas, you can ease painful toe rubbing on long runs by using toe spacers and toe pads designed for use in pointe shoes! Layer them on under your socks and shoes and you’re good to go! They should fit snugly, but not too tight in standard running shoes. I’m not sure how well they would fit in super lightweight/barefoot running shoes, and you’d have to forgo the pointe pads if you used any sort of “toe” shoe (although, you probably don’t have that problem with toe shoes in the first place). Pads and spacers are endlessly reusable, easy to clean, and can be purchased for relatively cheap at any dance supply store or on discount dance websites like Discount Dance, Dance Direct, & Dancewear Solutions
Optional: you can also use Toe Tape or medical adhesive tape!