Is the remaining amount from selling a medicine at a price higher than the company's price permissible, and is that considered usury and trade?

Since you are working as an agent for the company, you only have the authority to act within the scope authorized by the company, and it is not permissible for you to take any commission for yourself without its knowledge. The amount exceeding the set selling price belongs to the company, and it is not permissible for you to take it except with its permission and knowledge.