Plants are the main storage house of most food products, medicines, and nutritional supplements that exist. There are basically two kinds of phytochemicals in plants: these include primary and secondary metabolites. Primary metabolites play a crucial role in the biological functioning of plants because they play a major role in the processes of mitosis, respiration, metabolism, growth, and reproduction. Secondary metabolites are not just mere by-products of primary metabolism in plants; their effects stretch much further into plant defense mechanisms, ecology, and evolution. The substances formed by living things do not support their growth and development, yet they have numerous other roles to play such as that of a cofactor. It is common to find compounds derived from glycolysis, TCA cycle, and shikimic acid pathway being utilized as the starting materials to produce secondary metabolites estimated to be tens of thousands. In comparison to variations within primary metabolic pathways, whose mechanisms remain highly conserved across species, there exist much more variations within secondary metabolic pathways at various biological organization levels. In addition, the high degree of catalytic promiscuity displayed by secondary metabolism, which may be explained due to the fact that secondary metabolism is relatively new to deviating from primary metabolism and faces less selective pressure on its enzymes than those of primary metabolism, is another factor that is considered important in the tremendous diversity of secondary metabolism. Secondary metabolites can be produced through different metabolic pathways, which include the MEP pathway for phenols and the shikimic acid pathway for aromatics and alkaloids. However, one of the main pathways besides these two is the malonyl pathway that links glycolysis to the precursor acetyl CoA.

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1. Corradini E, Foglia P, Giansanti P, Gubbiotti R, Samperi R, Laganà A. Flavonoids: Chemical properties and analytical methodologies of identification and quantitation in foods and plants. Nat Prod Res. 2011;25(5):469–95.
2. Winkel-Shirley B. Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol. 2001;126(2):485–93.
3. Shah AA, Pandey N, Rai N, Bachheti RK, Gupta A. Exploring the anti-inflammatory and anti-arthritic potential of Malus peel phenolics: A comprehensive comparative analysis of “Royal Delicious,” “Delicious,” “Golden Delicious,” and “Maharaji” cultivars from Kashmir, India. Appl Fruit Sci. 2025;67(1).
4. Panche AN, Diwan AD, Chandra SR. Flavonoids: An overview. J Nutr Sci. 2016;5.
5. Palazon J, Alcalde MA. Secondary metabolites in plants. Plants. 2025;14(14):2146.
6. Guo C, Wang X, Wang Q, Zhao Z, Xie B, Xu L, et al. Plant defense mechanisms against ozone stress: Insights from secondary metabolism. Environ Exp Bot. 2023;217:105553.
7. Gong G, Qin Y, Huang W, Zhou S, Yang X, Li D. Rutin inhibits hydrogen peroxide-induced apoptosis through regulating reactive oxygen species-mediated mitochondrial dysfunction pathway in human umbilical vein endothelial cells. Eur J Pharmacol. 2010;28(1–3):27–35.
8. Guevara-García A, San Román C, Arroyo A, Cortés ME, Gutiérrez-Nava ML, León P. Characterization of the Arabidopsis clb6 mutant illustrates the importance of posttranscriptional regulation of the methyl-D-erythritol 4-phosphate pathway. Plant Cell. 2005;17(2):628–43.
9. Liu B, Jian Z, Li Q, Li K, Wang Z, Liu L, et al. Baicalein protects human melanocytes from H2O2-induced apoptosis via inhibiting mitochondria-dependent caspase activation and the p38 MAPK pathway. Free Radic Biol Med. 2012;53(2):183–93.
10. De Pascual-Teresa S, Moreno DA, García-Viguera C. Flavanols and anthocyanins in cardiovascular health: A review of current evidence. Int J Mol Sci. 2010;11(4):1679–703.
11. Duchnowicz P, Broncel M, Podsędek A, Koter-Michalak M. Hypolipidemic and antioxidant effects of hydroxycinnamic acids, quercetin, and cyanidin 3-glucoside in hypercholesterolemic erythrocytes (in vitro study). Eur J Nutr. 2012;51(4):435–43.
12. Waisundara VY, Siu SY, Hsu A, Huang D, Tan G. Baicalin upregulates the genetic expression of antioxidant enzymes in type-2 diabetic Goto-Kakizaki rats. J Funct Foods. 2011;3? [Bibliographic details require verification].
13. Wang ZH, Kang KA, Zhang R, Piao MJ, Jo SH, Kim JS, et al. Myricetin suppresses oxidative stress-induced cell damage via both direct and indirect antioxidant action. Environ Toxicol Pharmacol. 2010;29(1):12–18.
14. Annadurai T, Muralidharan AR, Joseph T, Hsu MJ, Thomas PA, Geraldine P. Antihyperglycemic and antioxidant effects of a flavanone, naringenin, in streptozotocin-nicotinamide-induced experimental diabetic rats. J Physiol Biochem. 2012;68(3):307–18.
15. Thines E, Aguirre J, Foster AJ, Deising HB. Genetics of phytopathology: Secondary metabolites as virulence determinants of fungal plant pathogens. In: Esser K, Lüttge U, Beyschlag W, Murata J, editors. Progress in botany. Vol. 67. Berlin: Springer; 2006.
16. Shah AA, Gupta A. Secondary metabolite basis of elicitor- and effector-triggered immunity in pathogen elicitation amid infections. In: Interdisciplinary biotechnological advances. 2023. p. 225–51.
17. Twaij BM, Hasan MN. Bioactive secondary metabolites from plant sources: Types, synthesis, and their therapeutic uses. Int J Plant Biol. 2022;13(1):4–14.
18. Havsteen BH. The biochemistry and medical significance of the flavonoids. Pharmacol Ther. 2002;96(2–3):67–202.
19. Kay CD, Hooper L, Kroon PA, Rimm EB, Cassidy A. Relative impact of flavonoid composition, dose and structure on vascular function: A systematic review of randomised controlled trials of flavonoid-rich food products. Mol Nutr Food Res. 2012;56(11):1605–16.
20. Marzocchella L, Fantini M, Benvenuto M, Masuelli L, Tresoldi I, Modesti A, et al. Dietary flavonoids: Molecular mechanisms of action as anti-inflammatory agents. Recent Pat Inflamm Allergy Drug Discov. 2011;5(3):200–20.
21. Shah AA, Singh S, Saini S, Pundir A, Saxena K, Gupta A. A perusal of phenolics within polar peel fractions of Malus domestica var Maharaji via hyphenated techniques cum anti-microbial with REMA and tyrosinase inhibitory potential thereof. J Pure Appl Microbiol. 2023;17(4):2215–31.
22. González-Paramás AM, Santos-Buelga C, Dueñas M, González-Manzano S. Analysis of flavonoids in foods and biological samples. Mini Rev Med Chem. 2011;11(14):1239–55.
23. Chae SC, Lee JH, Park SU. Phenolic compounds in bitter melons collected from different regions of Korea. Asian J Chem. 2014;26(16):5313–14.
24. Morales J, Günther G, Zanocco AL, Lemp E. Singlet oxygen reactions with flavonoids: A theoretical-experimental study. PLoS One. 2012;7(7).
25. Iwashina T. Flavonoid properties in plant families synthesizing betalain pigments (review). Nat Prod Commun. 2015;10(6):1041–46.
26. Manach C, Scalbert A, Morand C, Rémésy C, Jiménez L. Polyphenols: Food sources and bioavailability. Am J Clin Nutr. 2004;79(5):727–47.
27. Szkudelska K, Nogowski L. Genistein—A dietary compound inducing hormonal and metabolic changes. J Steroid Biochem Mol Biol. 2007;105(1–5):37–45.
28. Ram RS, Rupa B, Noopur S. An in-silico perspective towards target ability of available drugs in infectious disease treatment: A possible strategy. J Bioinform Genomics. 2017;2(4).
29. Dixon RA, Pasinetti GM. Flavonoids and isoflavonoids: From plant biology to agriculture and neuroscience. Plant Physiol. 2010;154(2):453–57.
30. Hertog MGL, Hollman PCH, van de Putte B. Content of potentially anticarcinogenic flavonoids of tea infusions, wines, and fruit juices. J Agric Food Chem. 1993;41(8):1242–46.
31. Li R, Yuan C, Dong C, Shuang S, Choi MMF. In vivo antioxidative effect of isoquercitrin on cadmium-induced oxidative damage to mouse liver and kidney. Naunyn Schmiedebergs Arch Pharmacol. 2011;383(5):437–45.
32. Park CE, Yun H, Lee EB, Min BI, Bae H, Choe W, et al. The antioxidant effects of genistein are associated with AMP-activated protein kinase activation and PTEN induction in prostate cancer cells. J Med Food. 2010;13(4):815–20.
33. Mira L, Fernandez MT, Santos M, Rocha R, Florêncio MH, Jennings KR. Interactions of flavonoids with iron and copper ions: A mechanism for their antioxidant activity. Free Radic Res. 2002;36(11):1199–208.
34. Garazd MM, Garazd YaL, Khilya VP. Neoflavones. Part 2. Methods for synthesizing and modifying 4-arylcoumarins. ChemInform. 2006;37(7).
35. Shah AA, Gupta A. Venturia inaequalis post-infection enhancement of secondary metabolites in the peels of Delicious apple variety. Mater Today Proc. 2023;73:151–62.
36. Sutariya S, Shah AA, Bajpai A, Sharma RJ, Pandhurnekar CP, Gupta A. Fourier transform infrared spectroscopy (FTIR) analysis, antioxidant and anti-inflammatory activities of leaf and fruit extracts of Gymnosporia montana. Mater Today Proc. 2023;73:134–41.
37. Grassi D, Desideri G, Ferri C. Flavonoids: Antioxidants against atherosclerosis. Nutrients. 2010;2(8):889–902.
38. Hou X, Rivers J, León P, McQuinn RP, Pogson BJ. Synthesis and function of apocarotenoid signals in plants. Trends Plant Sci. 2016;21(9):792–803.
39. Buer CS, Imin N, Djordjevic MA. Flavonoids: New roles for old molecules. J Integr Plant Biol. 2010;52(1):98–111.
40. Benavente-García O, Castillo J. Update on uses and properties of citrus flavonoids: New findings in anticancer, cardiovascular, and anti-inflammatory activity. J Agric Food Chem. 2008;56(15):6185–205.
41. Alvarez Y, Chen K, Reynolds AL, Waghorne N, O’Connor JJ, Kennedy BN. Predominant cone photoreceptor dysfunction in a hyperglycaemic model of non-proliferative diabetic retinopathy. Dis Model Mech. 2010;3(3–4):236–45.
42. Hodgson JM, Prince RL, Woodman RJ, Bondonno CP, Ivey KL, Bondonno N, et al. Apple intake is inversely associated with all-cause and disease-specific mortality in elderly women. Br J Nutr. 2016;115(5):860–67.
43. Knekt P, Kumpulainen J, Järvinen R, Rissanen H, Heliövaara M, Reunanen A, et al. Flavonoid intake and risk of chronic diseases. Am J Clin Nutr. 2002;76(3):560–68.
44. Aharoni A, Galili G. Metabolic engineering of the plant primary-secondary metabolism interface. Curr Opin Biotechnol. 2011;22(2):239–44.

Plants are the main storage house of most food products, medicines, and nutritional supplements that exist. There are basically two kinds of phytochemicals in plants: these include primary and secondary metabolites. Primary metabolites play a crucial role in the biological functioning of plants because they play a major role in the processes of mitosis, respiration, metabolism, growth, and reproduction. Secondary metabolites are not just mere by-products of primary metabolism in plants; their effects stretch much further into plant defense mechanisms, ecology, and evolution. The substances formed by living things do not support their growth and development, yet they have numerous other roles to play such as that of a cofactor. It is common to find compounds derived from glycolysis, TCA cycle, and shikimic acid pathway being utilized as the starting materials to produce secondary metabolites estimated to be tens of thousands. In comparison to variations within primary metabolic pathways, whose mechanisms remain highly conserved across species, there exist much more variations within secondary metabolic pathways at various biological organization levels. In addition, the high degree of catalytic promiscuity displayed by secondary metabolism, which may be explained due to the fact that secondary metabolism is relatively new to deviating from primary metabolism and faces less selective pressure on its enzymes than those of primary metabolism, is another factor that is considered important in the tremendous diversity of secondary metabolism. Secondary metabolites can be produced through different metabolic pathways, which include the MEP pathway for phenols and the shikimic acid pathway for aromatics and alkaloids. However, one of the main pathways besides these two is the malonyl pathway that links glycolysis to the precursor acetyl CoA.

🔒 This is a subscription article

Full text is available to subscribers and institutional members. Please choose an option below to access it.

1. Corradini E, Foglia P, Giansanti P, Gubbiotti R, Samperi R, Laganà A. Flavonoids: Chemical properties and analytical methodologies of identification and quantitation in foods and plants. Nat Prod Res. 2011;25(5):469–95.
2. Winkel-Shirley B. Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol. 2001;126(2):485–93.
3. Shah AA, Pandey N, Rai N, Bachheti RK, Gupta A. Exploring the anti-inflammatory and anti-arthritic potential of Malus peel phenolics: A comprehensive comparative analysis of “Royal Delicious,” “Delicious,” “Golden Delicious,” and “Maharaji” cultivars from Kashmir, India. Appl Fruit Sci. 2025;67(1).
4. Panche AN, Diwan AD, Chandra SR. Flavonoids: An overview. J Nutr Sci. 2016;5.
5. Palazon J, Alcalde MA. Secondary metabolites in plants. Plants. 2025;14(14):2146.
6. Guo C, Wang X, Wang Q, Zhao Z, Xie B, Xu L, et al. Plant defense mechanisms against ozone stress: Insights from secondary metabolism. Environ Exp Bot. 2023;217:105553.
7. Gong G, Qin Y, Huang W, Zhou S, Yang X, Li D. Rutin inhibits hydrogen peroxide-induced apoptosis through regulating reactive oxygen species-mediated mitochondrial dysfunction pathway in human umbilical vein endothelial cells. Eur J Pharmacol. 2010;28(1–3):27–35.
8. Guevara-García A, San Román C, Arroyo A, Cortés ME, Gutiérrez-Nava ML, León P. Characterization of the Arabidopsis clb6 mutant illustrates the importance of posttranscriptional regulation of the methyl-D-erythritol 4-phosphate pathway. Plant Cell. 2005;17(2):628–43.
9. Liu B, Jian Z, Li Q, Li K, Wang Z, Liu L, et al. Baicalein protects human melanocytes from H2O2-induced apoptosis via inhibiting mitochondria-dependent caspase activation and the p38 MAPK pathway. Free Radic Biol Med. 2012;53(2):183–93.
10. De Pascual-Teresa S, Moreno DA, García-Viguera C. Flavanols and anthocyanins in cardiovascular health: A review of current evidence. Int J Mol Sci. 2010;11(4):1679–703.
11. Duchnowicz P, Broncel M, Podsędek A, Koter-Michalak M. Hypolipidemic and antioxidant effects of hydroxycinnamic acids, quercetin, and cyanidin 3-glucoside in hypercholesterolemic erythrocytes (in vitro study). Eur J Nutr. 2012;51(4):435–43.
12. Waisundara VY, Siu SY, Hsu A, Huang D, Tan G. Baicalin upregulates the genetic expression of antioxidant enzymes in type-2 diabetic Goto-Kakizaki rats. J Funct Foods. 2011;3? [Bibliographic details require verification].
13. Wang ZH, Kang KA, Zhang R, Piao MJ, Jo SH, Kim JS, et al. Myricetin suppresses oxidative stress-induced cell damage via both direct and indirect antioxidant action. Environ Toxicol Pharmacol. 2010;29(1):12–18.
14. Annadurai T, Muralidharan AR, Joseph T, Hsu MJ, Thomas PA, Geraldine P. Antihyperglycemic and antioxidant effects of a flavanone, naringenin, in streptozotocin-nicotinamide-induced experimental diabetic rats. J Physiol Biochem. 2012;68(3):307–18.
15. Thines E, Aguirre J, Foster AJ, Deising HB. Genetics of phytopathology: Secondary metabolites as virulence determinants of fungal plant pathogens. In: Esser K, Lüttge U, Beyschlag W, Murata J, editors. Progress in botany. Vol. 67. Berlin: Springer; 2006.
16. Shah AA, Gupta A. Secondary metabolite basis of elicitor- and effector-triggered immunity in pathogen elicitation amid infections. In: Interdisciplinary biotechnological advances. 2023. p. 225–51.
17. Twaij BM, Hasan MN. Bioactive secondary metabolites from plant sources: Types, synthesis, and their therapeutic uses. Int J Plant Biol. 2022;13(1):4–14.
18. Havsteen BH. The biochemistry and medical significance of the flavonoids. Pharmacol Ther. 2002;96(2–3):67–202.
19. Kay CD, Hooper L, Kroon PA, Rimm EB, Cassidy A. Relative impact of flavonoid composition, dose and structure on vascular function: A systematic review of randomised controlled trials of flavonoid-rich food products. Mol Nutr Food Res. 2012;56(11):1605–16.
20. Marzocchella L, Fantini M, Benvenuto M, Masuelli L, Tresoldi I, Modesti A, et al. Dietary flavonoids: Molecular mechanisms of action as anti-inflammatory agents. Recent Pat Inflamm Allergy Drug Discov. 2011;5(3):200–20.
21. Shah AA, Singh S, Saini S, Pundir A, Saxena K, Gupta A. A perusal of phenolics within polar peel fractions of Malus domestica var Maharaji via hyphenated techniques cum anti-microbial with REMA and tyrosinase inhibitory potential thereof. J Pure Appl Microbiol. 2023;17(4):2215–31.
22. González-Paramás AM, Santos-Buelga C, Dueñas M, González-Manzano S. Analysis of flavonoids in foods and biological samples. Mini Rev Med Chem. 2011;11(14):1239–55.
23. Chae SC, Lee JH, Park SU. Phenolic compounds in bitter melons collected from different regions of Korea. Asian J Chem. 2014;26(16):5313–14.
24. Morales J, Günther G, Zanocco AL, Lemp E. Singlet oxygen reactions with flavonoids: A theoretical-experimental study. PLoS One. 2012;7(7).
25. Iwashina T. Flavonoid properties in plant families synthesizing betalain pigments (review). Nat Prod Commun. 2015;10(6):1041–46.
26. Manach C, Scalbert A, Morand C, Rémésy C, Jiménez L. Polyphenols: Food sources and bioavailability. Am J Clin Nutr. 2004;79(5):727–47.
27. Szkudelska K, Nogowski L. Genistein—A dietary compound inducing hormonal and metabolic changes. J Steroid Biochem Mol Biol. 2007;105(1–5):37–45.
28. Ram RS, Rupa B, Noopur S. An in-silico perspective towards target ability of available drugs in infectious disease treatment: A possible strategy. J Bioinform Genomics. 2017;2(4).
29. Dixon RA, Pasinetti GM. Flavonoids and isoflavonoids: From plant biology to agriculture and neuroscience. Plant Physiol. 2010;154(2):453–57.
30. Hertog MGL, Hollman PCH, van de Putte B. Content of potentially anticarcinogenic flavonoids of tea infusions, wines, and fruit juices. J Agric Food Chem. 1993;41(8):1242–46.
31. Li R, Yuan C, Dong C, Shuang S, Choi MMF. In vivo antioxidative effect of isoquercitrin on cadmium-induced oxidative damage to mouse liver and kidney. Naunyn Schmiedebergs Arch Pharmacol. 2011;383(5):437–45.
32. Park CE, Yun H, Lee EB, Min BI, Bae H, Choe W, et al. The antioxidant effects of genistein are associated with AMP-activated protein kinase activation and PTEN induction in prostate cancer cells. J Med Food. 2010;13(4):815–20.
33. Mira L, Fernandez MT, Santos M, Rocha R, Florêncio MH, Jennings KR. Interactions of flavonoids with iron and copper ions: A mechanism for their antioxidant activity. Free Radic Res. 2002;36(11):1199–208.
34. Garazd MM, Garazd YaL, Khilya VP. Neoflavones. Part 2. Methods for synthesizing and modifying 4-arylcoumarins. ChemInform. 2006;37(7).
35. Shah AA, Gupta A. Venturia inaequalis post-infection enhancement of secondary metabolites in the peels of Delicious apple variety. Mater Today Proc. 2023;73:151–62.
36. Sutariya S, Shah AA, Bajpai A, Sharma RJ, Pandhurnekar CP, Gupta A. Fourier transform infrared spectroscopy (FTIR) analysis, antioxidant and anti-inflammatory activities of leaf and fruit extracts of Gymnosporia montana. Mater Today Proc. 2023;73:134–41.
37. Grassi D, Desideri G, Ferri C. Flavonoids: Antioxidants against atherosclerosis. Nutrients. 2010;2(8):889–902.
38. Hou X, Rivers J, León P, McQuinn RP, Pogson BJ. Synthesis and function of apocarotenoid signals in plants. Trends Plant Sci. 2016;21(9):792–803.
39. Buer CS, Imin N, Djordjevic MA. Flavonoids: New roles for old molecules. J Integr Plant Biol. 2010;52(1):98–111.
40. Benavente-García O, Castillo J. Update on uses and properties of citrus flavonoids: New findings in anticancer, cardiovascular, and anti-inflammatory activity. J Agric Food Chem. 2008;56(15):6185–205.
41. Alvarez Y, Chen K, Reynolds AL, Waghorne N, O’Connor JJ, Kennedy BN. Predominant cone photoreceptor dysfunction in a hyperglycaemic model of non-proliferative diabetic retinopathy. Dis Model Mech. 2010;3(3–4):236–45.
42. Hodgson JM, Prince RL, Woodman RJ, Bondonno CP, Ivey KL, Bondonno N, et al. Apple intake is inversely associated with all-cause and disease-specific mortality in elderly women. Br J Nutr. 2016;115(5):860–67.
43. Knekt P, Kumpulainen J, Järvinen R, Rissanen H, Heliövaara M, Reunanen A, et al. Flavonoid intake and risk of chronic diseases. Am J Clin Nutr. 2002;76(3):560–68.
44. Aharoni A, Galili G. Metabolic engineering of the plant primary-secondary metabolism interface. Curr Opin Biotechnol. 2011;22(2):239–44.