This is one of the ways we get all of the secondary metabolites from plants, most of the compounds in supplements and drugs that are active in humans. They come from mutations of the existing DNA, then are able to change from there without impacting the plant's core functions due to being duplicates:

"Gene duplications drive the recruitment of genes for secondary metabolism. Gene copies are gradually modified to create genes with specificities and expression patterns adapted to the needs of the new pathway in which they are involved. Duplicated genes are often in tandem repeats, forming clusters within the plant genome. However, in some cases, clusters of nonhomologous genes have also been identified as forming a functional unit. The selective forces that have caused the establishment of new pathways are far from understood and might have changed repeatedly during evolution owing to the continuously changing environment. Recent data show that the way several classes of secondary compounds are scattered among species is attributable to independent recruitment and the inactivation of biosynthetic enzymes."

https://www.cell.com/trends/plant-science/abstract/S1360-138...

If you want to understand secondary metabolites, which is not the "how" do they work part of plant-derived molecules, but the "why" do they work?

You can follow this line of research:

"Over recent years, the consensus as to the mechanisms responsible for these effects in humans has shifted away from polyphenols having direct antioxidant effects and toward their modulation of cellular signal transduction pathways. To date, little consideration has been given to the question of why, rather than how, these plant-derived chemicals might exert these effects. Therefore, this review summarizes the evidence suggesting that polyphenols beneficially affect human brain function and describes the current mechanistic hypotheses explaining these effects. It then goes on to describe the ecologic roles and potential endogenous signaling functions that these ubiquitous phytochemicals play within their home plant and discusses whether these functions drive their beneficial effects in humans via a process of “cross-kingdom” signaling predicated on the many conserved similarities in plant, microbial, and human cellular signal transduction pathways."

https://www.sciencedirect.com/science/article/pii/S216183132...

The functional aspect of the duplicated DNA goes back to the point that humans, insects, and plants are all eukaryotes...

Scientists uncover key mechanism in evolution: Whole-genome duplication drives