I think the important thing to remind him is that he has a lot of years in front of him, and once he gets to college it all changes again. Most high school friends drift away from each other during/after college, so it is a great time to make new friends who have broader, shared interests.
In the meantime, can he join any extracurricular activities at school? My son's high school has art club, language clubs, math clubs, chess clubs, and on and on. Your son may be able to meet people with shared interests that way. While I get the not liking the Beiber Boy - encourage your son to begin learning about pop-culture. My parents helped us balance Mozart and Zeppelin when I was coming up and I am doing the same with my son. Increasing his knowledge about pop-culture will give him more things to talk to about other teens with. Also, talk to the guidance counselor at his school...he/she may have some other ideas about on campus activities that may work for him.
Other ideas - Youth groups at church, Boys & Girls Clubs, YMCA, Big Brother/Big Sister, Police Youth Explorers, MENSA, youth leadership programs.
Have you tried volunteering? It is a great way to get out and meet people, experience new things, and help others. He could tutor younger students, visit the elderly, walk dogs at the local animal shelter.
Most importantly you must teach him that although he is smarter than his peers, he is not better than his peers. I have found that very smart teens tend to be more awkward than their peers simply because they do understand more and see the world differently. His peers may be uncomfortable with him because he is uber-intelligent and may feel intimidated by him...which makes it their problem, not his.
You need to bolster his self esteem. Being smart doesn't mean being confident.
If you think his depression is getting out of hand then please talk to his physician and consider medication. My son has taken Zoloft to counter depression problems caused by self esteem issues directly related to his father being an absent parent....it wasn't fun to admit that my boy needed more help than I could give him - but he sure is happier and once the depression lifted was able to see his emotional reactions more clearly.
Oh, and remind him to look up the "popular" kids in 20 years...many peak in high school and don't get farther than that. What is popular in high school is not popular in college, were intellect is more valued. And what is popular in college is not popular in your 40s.
Help him learn to be more adaptive, find interests outside of school, and know that this too shall pass.
Good Luck and God Bless