Your question has a broad sense. You does not focus metabolism of any class. However I want to focus Phenolic acids.

Plant secondary metabolites and gut health: the case for phenolic acids. 

Russell W Duthie G.

Proceedings of the Nutrition Society 2011 Aug;70(3):389-96.

Plant-based diets contain a plethora of secondary metabolites that may impact on health and disease prevention. Much attention has been focused on the potential bioactivity and nutritional relevance of several classes of phytochemicals such as flavonoids, carotenoids, phyto-oestrogens and glucosinolates. Less attention has been paid to simple phenolic acids that are widely found in fruit, vegetables, herbs, spices and beverages. Daily intakes may exceed 100 mg. In addition, bacteria in the gut can perform reactions that transform more complex plant phenolics such as anthocyanins, procyanidins, flavanones, flavonols, tannins and isoflavones into simple phenolic metabolites. The colon is thus a rich source of potentially active phenolic acids that may impact both locally and systemically on gut health. Both the small and large intestine (colon) contain absorption sites for phenolic acids but low post-prandial concentrations in plasma indicate minimal absorption early in the gastrointestinal tract and/or rapid hepatic metabolism and excretion. Therefore, any bioactivity that contributes to gut health may predominantly occur in the colon. Several phenolic acids affect the expression and activity of enzymes involved in the production of inflammatory mediators of pathways thought to be important in the development of gut disorders including colon cancer. However, at present, we remain largely ignorant as to which of these compounds are beneficial to gut health. Until we can elucidate which pro-inflammatory and potentially carcinogenetic changes in gene expression can be moderated by simple phenolic acids, it is not possible to recommend specific plant-based foods rich in particular phenolics to optimise gut health.

I hope I try my best to give you essence of Phenolic acids metabolism in gut.

Regards

SALMAN AHMED

Ph.D Fellow

Please read the real story. I think by reading this story you will get the actual answer of your question.

• After absorption and intestinal metabolism, the major products in the hepatic portal vein are most certainly glucuronides and perhaps methylated glucuronides.
• These polar conjugates gain access to hepatocytes and are further modified. Quercetin glucuronides can be taken up by Hepatic G2 cells. Where these glucuronides become sulphated and methylated.
• Certain glucuronides can be hydrolysed and re-glucouronidated at a different position and conjugated with sulphate.
• I am also sending you the picture of Flavonoid, absorption, metabolism and elimination for your better understanding.

If I really satisfy you and succeed to give you right answer. Up vote my both answers to encourage me.

Regards

SALMAN AHMED

Ph.D Fellow

Now the story of alkaloids

The metabolism of corynantheidine and 9-methoxycorynantheidine-type alkaloids by liver microsomes

A.H. Beckett, D.M. Morton

Biochemical Pharmacology, Volume 16, Issue 8, August 1967, Pages 1609–1615

The qualitative and quantitative metabolism by liver microsome preparations of corynantheidine-type alkaloids, with and without aromatic ring substitution, is influenced significantly by the stereochemistry of the alkaloids. Normal, allo and epiallo isomers are metabolized principally by O-demethylation, whereas the alkaloids possessing the pseudo configuration are metabolised by a different process to yield unidentified products. O-Dealkylation of the enol ether group occurs more readily in planar than in non-planar isomers, and increased metabolism is observed with alkaloids possessing aromatic methoxy substitution.

I appreciate and welcome the suggestions given by Salman. The metabolic processes do affect the efficacy of pharmacological agents. We have worked with Karanjin, a furanoflavonol, a type of flavonoid of Pongamia pinnata (Karanja) and have experienced the significant variation in the efficacy during oral route of administration and dermal.

A simple answer cannot be given for such a broad question "How are plant secondary metabolites metabolized inside the body?" Its a vast field. "Pharmacokinetic profiling of phytochemicals". Each and every class of them undergo their own metabolic processes based on their structures and functional groups and that definitely will and should affect the efficacy of its pharmacological actions. 

Salman had given some interesting examples with flavonoids and alkaloids.

My focus is on hydrolysable tannins as they are complex structured high molecular weight polyphenols which are preferred by intraperitoneal route and not by oral in rats. 

Hydrolyzed tannins are gallic acid polymers as opposed to proanthocyanins, which were earlier known as tannins, and which mainly contain catechin and epicatechin units. They are polymeric compounds. Grape seed, skin and chocolate contain substantive quantities of proanthocyanins. Molecular size determines absorption and plasma bioavailibility. Phenolic polymers ranging in molecular size of about 600 -900 seem to be absorbed and bioavailable (example, chocolate phenolics) in humans when ingested.

You have all made useful contributions. Metabolic processes can influence the pharmacological properties of secondary metabolites. The effect and extent vary  with individuals and prevailing metabolic conditions. Although, some effects may  be general observations. The presence of other pharmacogical agent at the point of administration might also be a factor.

I have very interesting publication regarding pharmacokinetic studies of  antioxidant phytochemicals (polyphenols).

• Absorption and Bioavailability of Antioxidant Phytochemicals and Increase of Serum Oxidation Resistance in Healthy Subjects Following Supplementation with Raisins.

Read the attached article carefully.

Hopefully it will share different pharmacokinetic aspects of antioxidants.

http://download.springer.com/static/pdf/876/art%253A10.1007%252Fs11130-013-0389-2.pdf?auth66=1418490792_ebc465eb41f42872edd0682fb2fdc386&ext=.pdf