Polyphenols
There are over 8,000 known naturally occurring plant phenolics, and a large proportion of these are flavonoids. Structurally, polyphenols have at least one aromatic benzene ring with several hydroxyl (–OH) groups attached. In many families, such as the flavonoids, there are two or more rings with varying degrees of hydroxylation. These hydroxyl groups are what give polyphenols many of their characteristic properties.
In herbal medicine, polyphenols are often responsible for colour (yellows, reds, blues), as well as much of the bitterness and astringency we taste in plant preparations. Their actions are frequently linked with antioxidant, anti-inflammatory, and vascular-supporting effects, and they can also show hepatoprotective activity, as seen with the flavonolignan silybin from Silybum marianum (milk thistle).
On this page, you’ll find a few key polyphenols in 3D, so you can explore their shapes while you learn what they do.
Flavonoids
Flavonoids are one of the best-known families of polyphenols, built on a three-ring backbone and often occurring in plants as glycosides, where a sugar is attached to the flavonoid core (as with rutin). They are widespread in leaves, flowers and fruits, and are among the most common plant pigments after chlorophyll and carotenoids, giving many of the yellow, orange and red colours we see in herbs and foods.
Experimental and epidemiological studies suggest that flavonoids can support the heart and circulatory system, particularly the small blood vessels and capillaries. They are sometimes described as “biological stress modifiers” because they help protect tissues against various forms of environmental and metabolic stress, and they often show synergistic effects with vitamin C. Therapeutically, flavonoids are often described as helping the body manage oxidative stress, regulate inflammatory and immune activity, maintain healthy liver function and blood pressure, and support strong, flexible capillaries and microcirculation (Middleton, 1988; Pengelly, 2004).
On this page, quercetin represents a typical flavonol, while rutin shows how attaching a sugar tail changes the size, solubility and behaviour of the molecule in the body.
Quercetin
Quercetin is a widely distributed flavonol, a member of the flavonoid family, and one of the best-studied polyphenols in herbal and nutritional medicine. It is a yellow plant pigment with a three-ring flavonoid backbone and several hydroxyl (–OH) groups, which give it strong interactions with metals and reactive oxygen species.
In plants, quercetin is less common on its own; however, it may occur free form in Asteraceae, Passifloraceae and Solanaceae plants (Hoffman, 2003). It usually appears as a glycoside, in which one or more sugar units are attached to the flavonol core. Adding sugar makes the molecule more water-soluble and easier for the plant to move, store and control. On this page, the 3D model shows the quercetin aglycone (the non-sugar part), while rutin represents a quercetin glycoside (quercetin-3-O-rutinoside), where a sugar tail has been added.
Quercetin-type flavonoids are present in many medicinal plants and everyday foods, including onion, apple, berries, nettle leaf, ginkgo, hawthorn and chamomile. In the research and herbal literature, they are often discussed in relation to how they may help the body:
buffer oxidative stress and protect tissues from free-radical damage
regulate inflammatory and immune activity
support flexible, resilient capillaries and microcirculation
modulate histamine release and allergy-type responses, particularly in flavonoid-rich herbs such as nettle leaf, chamomile, elderflower and ginkgo
contribute to overall cardiovascular and metabolic health as part of a flavonoid-rich diet and herbal regimen.
Most of this evidence comes from nutrition and pharmacology research on flavonoid-rich foods and extracts, rather than from quercetin used in isolation (Middleton, 1988; Middleton et al., 2000; Pengelly, 2021; Mills & Bone, 2013). In herbal practice, quercetin is best understood as one important constituent contributing to the actions of flavonoid-rich herbs, not as a stand-alone remedy.
Quercetin – 3D Structure
Class: Flavonol (flavonoid polyphenol)
Rotate the molecule by dragging, scroll or pinch to zoom. This viewer shows the 3D structure of Quercetin loaded from PubChem and rendered with 3Dmol.js.
Rutin
Rutin is a flavonol glycoside: essentially quercetin with a sugar tail (rutinoside) attached. It was first isolated from rue (Ruta graveolens), but is now known to be widely distributed in higher plants. Rutin shares many of the general actions discussed for quercetin and other flavonoids. In the research literature, it is often noted that:
supporting capillary tone and integrity, especially where there is a tendency to capillary fragility or varicosities
acting as a free-radical scavenger, contributing to antioxidant effects
experimental anti-inflammatory and antiviral activity in vitro
Rutin occurs in a wide range of foods and herbs. Higher levels are reported in some Allium and Brassica species (such as garlic, onions, cabbage, and kale), and in several medicinal herbs, including yarrow, buchu, calendula, elder, hawthorn, hypericum, motherwort, meadowsweet, peppermint, passionflower, sweet violet, and others.
This section is for herbal study and education only; it is not a guide to self-treatment or dosing.
Rutin (Quercetin-3-rutinoside) — 3D Structure
Class: Flavonol glycoside (polyphenolic flavonoid)
Rotate the molecule by dragging, scroll or pinch to zoom. This viewer shows the 3D structure of Rutin loaded from PubChem and rendered with 3Dmol.js.
Tannins
Tannins are a group of larger polyphenolic compounds best known for their astringent effect, that drying, puckering sensation you get from strong tea, red wine or some herbal infusions. Chemically, they bind to proteins and other macromolecules, which is central to both their therapeutic actions and their potential to irritate or overload the gut if used in excess.
For study purposes, tannins are usually divided into two main groups:
Hydrolysable tannins
Condensed tannins (proanthocyanidins)
Hydrolysable Tannins
Hydrolysable tannins are tannins built from a central core, often a sugar such as glucose, with several phenolic acids attached (commonly gallic acid or related acids). These acids are joined to the sugar by ester bonds. Under acidic conditions or in the presence of enzymes, hydrolysable tannins can be broken down (hydrolysed) into their components: the sugar core and smaller phenolic acids such as gallic acid or ellagic acid. This is where the term hydrolysable comes from.
Because of this structure, hydrolysable tannins can act both as large, locally active molecules in the gut and on tissues, and as a source of smaller phenolic acids that may be absorbed and have their own effects.
What hydrolysable tannins do
Hydrolysable tannins are best known for their:
Protein-binding and astringent actions
They bind to proteins on mucous membranes and skin, creating a tightening, drying effect and forming a light protective layer over irritated surfaces.Support for leaky or overactive tissues
By tightening and “sealing” surfaces, they can help reduce excessive secretions (for example, very loose stools or weepy mucosa) when used appropriately and short term.Antioxidant and antimicrobial contributions
The phenolic acid components (such as gallic acid) are reported to have antioxidant and antimicrobial effects in the herbal and scientific literature.
Because they bind proteins and other molecules, very high doses or long-term use of strongly tannin-rich preparations can:
Reduce absorption of some nutrients (for example, certain minerals or alkaloids/medicines)
Irritate or overly dry the gut in sensitive individuals
For this reason, herbalists often balance tannin-rich herbs with soothing demulcent plants (such as marshmallow or liquorice) and aromatic herbs, and generally avoid prolonged heavy dosing.
Herbal examples of hydrolysable tannins
Hydrolysable tannins are especially abundant in barks, galls, roots and some leaves, particularly in strongly astringent plants. Examples include:
Agrimonia eupatoria (agrimony) – leaf and flower (fol and flos)
Potentilla erecta (tormentil) – root (radix)
Quercus spp. (oak) – bark (cortex)
Hamamelis virginiana (witch hazel) – leaf and bark (fol and Cortex)
Rubus fruticosus and Rubus idaeus (blackberry and raspberry) - leaves (fol)
Geranium robertianum (herb robert) (herba)
These herbs are traditionally used in herbal medicine for short-term support of mucous membranes and skin, where astringency and tissue-tightening are desired
Gallic Acid — 3D Structure
Class: Phenolic acid (polyphenol building block)
Rotate the molecule by dragging, scroll or pinch to zoom. This viewer shows the 3D structure of Gallic acid loaded from PubChem and rendered with 3Dmol.js.
Condensed Tannins (Proanthocyanidins)
Condensed tannins, also known as proanthocyanidins, are structurally different from hydrolysable tannins. Instead of being based on a sugar core with phenolic acids, they are polymers of flavan-3-ol units, such as catechin and epicatechin.
Epicatechin is one of the basic building blocks of condensed tannins and is shown in the 3D model on this page. Under strong acid treatment, condensed tannins can yield anthocyanidins, which is where the name pro-anthocyanidins comes from.
How condensed tannins work
They share many features with hydrolysable tannins, but with some nuances:
Strong astringent effect through protein binding, especially in the gut and on mucous membranes
Significant antioxidant capacity, often highlighted in nutrition research (for example, grape seed, cocoa, berries)
Interest in their effects on vascular health, microcirculation and capillary tone
Interactions with the gut microbiota, where both the tannins and their breakdown products can influence microbial balance
At high doses or in very sensitive people, condensed tannins can also irritate the gut or affect nutrient absorption, so the same “respect the dose and duration” caution applies.
Herbs rich in condensed tannins/proanthocyanidins (examples)
Crataegus spp. (hawthorn) – leaves, flowers and berries
Vitis vinifera (grape) – seeds and skins
Vaccinium spp. (bilberry, blueberry, cranberry) – fruits
Camellia sinensis (green and black tea) – leaf
Cinnamomum spp. (cinnamon) – bark
Rubus species (raspberry/blackberry leaves and fruits)
Sambucus nigra (elderberries) – fruits
Condensed tannins (proanthocyanidins) are particularly abundant in berries, grape seeds, cocoa, tea and many astringent herbs. Plants such as hawthorn, bilberry, grape seed and raspberry leaf are well-known examples used in herbal medicine and nutrition for their astringent and antioxidant properties..
Epicatechin — 3D Structure
Class: Flavan-3-ol (condensed tannin / proanthocyanidin unit)
Rotate the molecule by dragging, scroll or pinch to zoom. This viewer shows the 3D structure of Epicatechin loaded from PubChem and rendered with 3Dmol.js.
Phenolic acids/Salicylates
Salicylic acid
Salicylic acid is a simple phenolic acid (a type of plant-derived organic acid) with one aromatic ring and two key groups attached: a hydroxyl group (–OH) and a carboxylic acid group (–COOH). Chemically, it is also known as 2-hydroxybenzoic acid.
It belongs to the wider salicylate family – compounds that have played an important role in both traditional herbal medicine and modern pharmacy. The synthetic drug acetylsalicylic acid (aspirin) was developed from salicylic acid.
Where salicylic acid comes from
In nature, salicylic acid and related salicylates are found in several plants, especially:
Willow (Salix spp.) - bark
Meadowsweet (Filipendula ulmaria) - above-ground parts
Birch (Betula spp.) - bark
Wintergreen (Gaultheria spp.) - leaves (often as methyl salicylate)
These plants have a long history of traditional use for aches, pains and feverish states, long before aspirin was developed. In modern herbal practice, they are more often used as part of a broader formula rather than at high doses on their own.
How salicylic acid behaves
Salicylic acid and its relatives are often discussed in relation to:
Modulating pain and inflammation – historically linked with the traditional use of willow and meadowsweet for rheumatic and musculoskeletal discomfort.
Fever and “heat” states – many salicylate-containing plants were used as classic “fever herbs” in European herbalism.
Skin and keratin – in conventional dermatology, salicylic acid is used topically to help soften and shed thickened skin (for example, in some preparations for acne, warts or psoriasis).
In herbal medicine, whole-plant preparations are usually preferred, as they bring a mixture of constituents (for example, tannins, flavonoids and other phenolic compounds) that can modify how salicylates are absorbed and tolerated. Meadowsweet, for instance, is often described in traditional texts as being gentler on the stomach than isolated salicylic acid.
Safety and sensitivity
Because salicylic acid is related to aspirin, some people may be sensitive to salicylates. In susceptible individuals, salicylates (from drugs or from plants) can sometimes:
Aggravate asthma or nasal polyps
Irritate the stomach or upper digestive tract
Interact with blood-thinning medication or other drugs
For that reason, salicylate-rich herbs are often avoided or used cautiously in people with known aspirin/salicylate sensitivity, significant gastric irritation, or those taking certain medicines.
Salicylic Acid — 3D Structure
Class: Phenolic acid (2-hydroxybenzoic acid)
Rotate the molecule by dragging, scroll or pinch to zoom. This viewer shows the 3D structure of Salicylic acid loaded from PubChem and rendered with 3Dmol.js.
Flavonolignan
Silybin
(Silybum marianum)
Silybin (Silibinin) — 3D Structure
Class: Flavonolignan (polyphenolic constituent of milk thistle)
Rotate the molecule by dragging, scroll or pinch to zoom. This viewer shows the 3D structure of Silybin loaded from PubChem and rendered with 3Dmol.js.
Silybin (often also called silibinin) is one of the main active constituents found in the seeds of Milk thistle (Silybum marianum). Chemically, it is a flavonolignan, a hybrid structure that combines features of a flavonoid and a lignan. It comprises a major component of silymarin, an extract from milk thistle seeds that has been widely studied in herbal and medical research (Tamayo & Diamond, 2007).
In the 3D model, you can see how complex and three-dimensional silybin is compared with simpler phenolic acids or flavonoids: multiple rings, several hydroxyl (-OH) groups and a rigid, twisted shape. These features contribute to its ability to interact with cell membranes and various enzyme systems.
Where silybin comes from
Found primarily in the seeds (fruits) of Silybum marianum
Present as part of a mixture of related flavonolignans (collectively called silymarin)
Traditional milk thistle preparations used the whole seed, whereas modern extracts often standardise to a certain percentage of silymarin/silybin
Herbalists commonly use milk thistle as a tincture, capsule or tablet, sometimes alongside other herbs in “liver support” or detox-style formulas, depending on training and tradition (Vargas-Mendoza et al., 2014).
How silybin is thought to work
Research and herbal literature discuss silybin and silymarin in relation to several key actions:
Antioxidant support
Silybin can help neutralise free radicals and may support the body’s antioxidant systems (for example, by increasing glutathione levels inside cells). This is particularly relevant in tissues exposed to metabolic or environmental “stress”, such as the liver.Membrane-stabilising and cell-protective effects
Silybin appears to interact with cell membranes, reducing the entry of certain toxins and supporting the stability and resilience of liver cells (hepatocytes) in experimental models.Support for liver regeneration
Laboratory and animal studies suggest that silybin may encourage normal liver cell repair and regeneration after injury, although how this translates to humans depends on the context and overall treatment plan.Modulating inflammation
Like many polyphenols, silybin is often described as anti-inflammatory in experimental settings, where it can influence inflammatory signalling pathways and mediators.
Because of these combined actions, silybin-rich extracts are frequently discussed in the research literature as hepatoprotective, helping protect liver cells from damage in various experimental models (Vargas-Mendoza et al., 2014).
Milk thistle in herbal practice
In Western herbal medicine, milk thistle seed is traditionally used as a liver- and digestive-support herb, often alongside dietary and lifestyle changes. Practitioners may consider it where there is a need to:
support the liver’s metabolic and detoxifying functions
promote healthy bile flow and digestion of fats
help maintain liver resilience in the face of ongoing metabolic stress (for example, modern diet, alcohol, medication load, environmental exposures).
Herbalists generally work with whole-plant preparations (tinctures, powders, extracts) rather than isolated silybin alone, as the other constituents in the seed may modify how silybin is absorbed, processed and tolerated.
References
Fisher, C. (2018). Materia Medica of Western Herbs. Aeon Books.
Hoffmann, D. (2003). Medical Herbalism: The Science and Practice of Herbal Medicine. Healing Arts Press.
Middleton, E., Jr. (1988). Plant flavonoid effects on mammalian cell systems. In L. E. Craker & J. E. Simon (Eds.), Herbs, Spices and Medicinal Plants: Recent Advances in Botany, Horticulture, and Pharmacology (Vol. 3, pp. 103–144). Oryx Press.
Middleton, E., Jr., Kandaswami, C., & Theoharides, T. C. (2000). The effects of plant flavonoids on mammalian cells: Implications for inflammation, heart disease, and cancer. Pharmacological Reviews, 52(4), 673–751.
Mills, S., & Bone, K. (2013). Principles and Practice of Phytotherapy: Modern Herbal Medicine (2nd ed.). Churchill Livingstone.
National Center for Biotechnology Information. (n.d.). PubChem [Database]. U.S. National Library of Medicine. https://pubchem.ncbi.nlm.nih.gov
National Library of Medicine. (n.d.). PubMed [Database]. U.S. National Institutes of Health. https://pubmed.ncbi.nlm.nih.gov
Pengelly, A. (2021). The Constituents of Medicinal Plants: An Introduction to the Chemistry and Therapeutics of Herbal Medicine (3rd ed.). CABI.
Rego, N., & Koes, D. (2015). 3Dmol.js: Molecular visualization with WebGL. Bioinformatics, 31(8), 1322–1324.
Tamayo, C., & Diamond, S. (2007). Review of clinical trials evaluating safety and efficacy of milk thistle (Silybum marianum [L.] Gaertn.). Integrative Cancer Therapies, 6(2), 146–157. https://doi.org/10.1177/1534735407301942
Vargas-Mendoza, N., Madrigal-Santillán, E., Morales-González, Á., Esquivel-Soto, J., Esquivel-Chirino, C., García-Luna y González-Rubio, M., Gayosso-de-Lucio, J. A., & Morales-González, J. A. (2014). Hepatoprotective effect of silymarin. World Journal of Hepatology, 6(3), 144–149. https://doi.org/10.4254/wjh.v6.i3.144