I am SO sorry this is happening to you and your ds. Is he in 2nd grade? I have a 2nd grader who has loved school -- and this year he is being targeted by a girl in his class. It breaks my heart and makes me think some very uncharitable things.
Someone suggested skipping a grade, which might help, but there is another side to it; I know that my brother and I were both recommended to skip a grade (me, fourth grade, and my brother, sixth grade) and our parents chose not to. I am really glad they didn't, because I made some of my best and lifelong friends in fourth grade. My brother is also glad he wasn't advanced a grade, because he was socially awkward at that age and felt a grade skip would have made things even worse.
Some of the things we are doing is working VERY CLOSELY with the school. I am not assuming that they are going to handle things. He is one of 150 second graders and it is simply impossible to monitor the children all the time. I had a conference with the classroom teacher, the auxiliary teachers, and the school counselor, and gave them some information on teaching positive peer interaction. Basically, it tries to build empathy among peers by showing that we are all alike, and we are all different. "Who likes to ride bikes? Everyone? Wow! We all like to ride bikes in our class. Who likes to eat ice cream? Lots of ice-cream eaters, too. Ok, who likes to play chess? Ahh. Just a few chess players. Isn't it interesting, how we are all alike in some ways, but we are all different too?" Blah blah -- you probably get the picture, but it's a good program (I think) for that age group. I want to empower my son to be able to handle negative interactions AND I want other children to know a better way of talking to their peers. I know it helps my son tremendously to focus on how everyone is alike, rather than on how he is different, and it changes their perspective too.
Do you know any parents of children in his class? The first year my son was in a traditional school, I made friends with several parents, and their children were his playmates. Some of the friendships stuck, some didn't, but it helped him to have people at school who were inclusive and friendly. School days are too long to feel isolated.
I also volunteer in his classroom -- it gives me a better feel for what happens in the day. I can tell from his face if it's been a good day or a hard one.
Another thing we do in our family is really downplay the "smart" thing. Yes, since preK he's been labeled "the smart kid" but that isn't who he is, and his self-worth shouldn't be caught up in that title. He loves to play basketball, likes sports, geography, telling jokes, lots of things. Those are the skills and areas of interest we are trying to build on, for now. The academics come effortlessly to him, so the challenge is the social stuff; and when we focus less on the differences, and more on the samenesses, he feels better about himself. We are all alike; we are all different
Good luck to you -- I know how hard it is, and your heart must ache for your ds. I would just advise being very proactive and keeping on top of the situation.