I cannot address the motives a pharmaceutical company would or would not pursue research/production into compounds which may or may not have potential to be patented, but can point to the process on the NIH side of things. NCI, as I have pointed out has a Natural Products Group who is responsible for screening naturally occurring products for anti-tumor and anti-viral properties. Another group will take promising compounds; analyze them and determine their chemical structure. Another group will try to synthesis the compounds and determine if they are still biologically active. If so, a biopharmaceutical pilot plant will develop and streamline production of the compound for both animal and phase 1 human clinical trials. Compounds that successful go through the phase 1 trails are then expanded to other Cancer Clinical Centers. Many successful treatments have been developed by this process and are now used worldwide. All done in the open, with no nefarious motives, peer reviewed scientific and medical publications ensure access to the information.

Yes, patents are pursued, which are generally used to prevent the compounds from being patented by commercial pharmaceutical companies. The government maintains the rights to the patent and companies can obtain the right to produce the material though licensing agreements, which attempts to recoup the costs for developing the compounds. There is a big emphasis on lab to bedside research, making the patient the focus of research.

Pete