If the molecule itself is new, useful and nonobvious, it may be patented and claimed as a compound, otherwise aka composition of matter. That entitles the patent owner, ordinarily, to enforce its patent against those who make, use, offers to sell or imports that claimed subject matter, and seek to enjoin those parties as infringers of that patent grant. 35 USC 151-154 and particularly 35 USC 271(a).
Dew is thinking of a patent that claims a method of use, or process. A different method or process of use sometimes gets a little trickier but, in general, see also 35 USC 100(b): "the term 'process' means process, art or method, and includes a new use of a known process, machine, manufacture, composition of matter, or material.
There likely are cases going in all directions if the patentee has limited its claims to a particular process or method of use, particularly if the prior art forced such a limited patent grant.