Natural Products Chemistry PDF

Natural Products Chemistry Introduction Metabolism Sum of all the chemical reactions that take place in a living organism. Includes primary and secondary metabolism Metabolite Intermediates of metabolic processes Include primary and secondary metabolites Primary Metabolites Directly in...

Natural Products Chemistry Introduction Metabolism Sum of all the chemical reactions that take place in a living organism. Includes primary and secondary metabolism Metabolite Intermediates of metabolic processes Include primary and secondary metabolites Primary Metabolites Directly involved in the normal growth, development, reproduction etc. of a living organism Fermentation products – acetic acid, ethanol, lactic acid, citric acid Cell constituents – lipids, vitamins, polysaccharides Secondary Metabolites Not directly involved in those processes (i.e. normal growth, development, reproduction etc.) and usually has a function but is not that important for the organism No nutritional or structural function. What is the Function of a Secondary Metabolite? Color (identification) - Scent (attraction or repulsion) Sexual attraction Social communication Defense (e.g., plant toxins and antibiotics) Many still have unknown function in the organism in which they are found. What is a Natural Product? A chemical substance produced by a living organism A term used commonly in reference to chemical substances found in nature that have distinctive pharmacological effects. What is a Natural Product? Generally taken to mean a secondary metabolite Small compounds that are generally characteristic of a particular species or family, i.e., closely related  arctiin Source: Int. J. Mol. Sci. 2021, 22(6), 3009 What is Natural Products Chemistry? Branch of chemistry that focuses on the study of naturally occurring compounds derived from plants, animals, and microorganisms, which have the potential to be used in drug discovery programs. Natural Products Chemistry Ethnobotany and the Traditional Sources of Natural Products Traditional Chinese Medicine PEOPLE ANTHROPOLOGY ETHNOBOTANY PLANTS BOTANY Ganoderma lucidum Common name: Reishi, Ling Zhi Effect: Increases qi Natural Products Chemistry Ethnobotany and the Traditional Sources of Natural Products Ayurvedic Medicine (India) PEOPLE ANTHROPOLOGY ETHNOBOTANY PLANTS BOTANY Elettaria cardamomum Common name: Cardamom Effect: Antiinflammatory Natural Products Chemistry Ethnobotany and the Traditional Sources of Natural Products Kampo Medicine (Japan) PEOPLE ANTHROPOLOGY ETHNOBOTANY PLANTS BOTANY Agaricus blazei Common name: Himematsutake, Almond mushroom Natural Products Chemistry Ethnobotany and the Traditional Sources of Natural Products African Medicine PEOPLE ANTHROPOLOGY ETHNOBOTANY PLANTS BOTANY Prunus africana Common name: pygeum Effect: Antiinflammatory Natural Products Chemistry Ethnobotany and the Traditional Sources of Natural Products Native American Medicine PEOPLE ANTHROPOLOGY ETHNOBOTANY PLANTS BOTANY Salvia sp. Common name: Sage Effect: Helps with problems in digestive system Natural Products Chemistry Ethnobotany and the Traditional Sources of Natural Products Philippine Folkloric Medicine PEOPLE ANTHROPOLOGY ETHNOBOTANY PLANTS BOTANY Psidium guajava Common name: Guava Effect:, anti-inflammatory, References https://www.stuartxchange.org/ Natural Products Chemistry Non-Plant Sources of Secondary Metabolites Conidae Cone snails Source of conotoxin, analgesic peptide Osteocephalus verruciger Ecuadorian frog Source of epibatidine, an analgesic Natural Products Chemistry Non-Plant Sources of Secondary Metabolites Opiophagus hannah Cobra Source of bungarotoxin, a peptide poison Tetraodontidae Pufferfish Source of tetrodotoxin, a non- peptide poison Natural Products Chemistry Non-Plant Sources of Secondary Metabolites Penicillium notatum Fungi Source of penicillin, an antimicrobial agent Actinopyga lecanora Seacucumber Source of antimicrobial peptides Drug Discovery and Natural Products Natural Products Chemistry Sourcing of Natural Products Identificatio GPS Tagging Selection of n of Plant Plant Part Material Geographical Different Folkloric use location plant parts of plant affects the will have A member of metabolite different a family of profile or the metabolites plant with ratio of present known metabolites Fresh vs activity present dried Employs samples knowledge in traditional medicine and botany Natural Products Chemistry Isolation of Natural Products Done using organic solvents (e.g., E methanol, ethanol) X T Separation of soluble compounds from the R marc A C Product: Crude extract T Done by liquid-liquid partitioning (i.e., water- SE organic phase separation) PA Product: Crude extract separated into aqueous RA TE and organic extracts Done by chromatography (e.g., column ISOLAT chromatography) E Product: Pure compound Natural Products Chemistry Extraction Methods: Steam Distillation Natural Products Chemistry Extraction Methods: Solvent Extraction Natural Products Chemistry Extraction Methods: Solvent Extraction Figure 1. Fresh Syzygium samarangense leaves prepared for air drying (left) and dried, macerated S. samarangense leaves soaked in methanol (right). Natural Products Chemistry Extraction Methods: Solvent Extraction Figure 2. Filtration of “soaking” to remove marc (left) and pre-concentration to obtain crude extract. Natural Products Chemistry Extraction Methods: Supercritical Fluid Extraction supercritical CO2 flows through pressure is reduced so that the solute is the raw material and not soluble and dissolves the precipitates extractable components Source: https://www.ucm.es/leffs/supercritical-fluid-extraction Natural Products Chemistry Separation by Liquid Partitioning Figure 3. Crude extract dissolved in water and partitioned with hexane.  Natural Products Chemistry Separation and Isolation by Chromatography Figure 4. S. samarangense extract subjected to vacuum liquid chromatography to separate components. Natural Products Chemistry Separation and Isolation by Chromatography Figure 5. S. samarangense fractions obtained after column chromatography. Natural Products Chemistry Separation and Isolation by Chromatography Figure 6. Isolated compound from S. samarangense leaves. The compound is suspected to be dimethylcardamonin.  Natural Products Chemistry Other Separation Techniques: Separation of Nonpolar Compounds THIN LAYER CHROMATOGRAPHY Stationary phase is silica adsorbed over an inert plate Mobile phase can be pure or a mixture of nonpolar and relatively low polarity solvents (e.g., hexane, ethyl acetate, DCM) Figure 7. Thin layer chromatogram of S. For small amount of samarangense fractions after vacuum filtration chromatography. material  Natural Products Chemistry Other Separation Techniques: Separation of Nonpolar Compounds COLUMN CHROMATOGRAPHY Stationary phase is packed resin in a column (e.g., silica, alumina, cellulose) Mobile phase is similar to those used in TLC For relatively larger Figure 8. Flash chromatography using TLC-grade silica as stationary phase and amount of material a binary mobile phase (hexane-ethyl  Natural Products Chemistry Other Separation Techniques: Separation of Nonpolar Compounds GAS CHROMATOGRAPHY Useful for volatile analyte (e.g., fatty acids and methyl ester derivatives, terpenes) ION EXCHANGE CHROMATOGRAPHY Useful for separation of charged species (recall: AnEx, CatEx)  Natural Products Chemistry Other Separation Techniques: Separation of Polar Compounds CHARCOAL CHROMATOGRAPHY Works via adsorption of molecules ADVANTAGES: Abundant, cheap, and can be used with both organic and polar solvents (e.g., aqueous methanol) HIGH PERFORMANCE LIQUID CHROMATOGRAPHY A column chromatography Most usual mode is the reverse phase mode which uses C-18 columns  Natural Products Chemistry Other Separation Techniques: Separation of Polar Compounds CAPILLARY ELECTROPHORESIS Useful for separation of charged species based on rate of migration of charged species under the influence of an electric field Figure 9. Setup for capillary zone electrophoresis.  Natural Products Chemistry Other Separation Techniques: Separation of Polar Compounds POLYAMIDE GEL CHROMATOGRAPHY Typical column chromatography which uses a resin capable of forming hydrogen bonds with target Useful in separation of polyphenolic compounds, flavanols and flavonoids. SIZE EXCLUSION CHROMATOGRAPHY Typical column/resin used is Sephadex LH20 Separates molecules based on molecular weight When the solvent used is organic, it is called gel permeation chromatography Can be used to “clean” extracts by removal of Natural Products Chemistry Structure Elucidation Requires piecing together a combination of chemical and spectroscopic information Nuclear Magnetic Resonance (NMR) UV and IR Spectroscopy Mass Spectroscopy Circular Dichroism (CD) X-ray Crystallography  Natural Products Chemistry Structure Elucidation by Spectroscopy IR SPECTROSCOPY Used to determine the functional group(s) present in a molecule  Natural Products Chemistry Structure Elucidation by Spectroscopy UV-VIS SPECTROSCOPY Used to determine λmax of compound Can be used to check whether a suggested structure is plausible by comparing the theoretical with the experimental λmax  Natural Products Chemistry Structure Elucidation by Spectroscopy MASS SPECTROSCOPY Used to determine the molecular weight In tandem with IR spectroscopy, can be used to suggest plausible molecular formula  Natural Products Chemistry Structure Elucidation by Spectroscopy MASS SPECTROSCOPY Mass spectrum records the quantity of ions of particular mass-to- charge ratios. Peak heights recorded on a mass spectrum are proportional to the number of ions of  Natural Products Chemistry Structure Elucidation by Spectroscopy UCLEAR MAGNETIC RESONANCE SPECTROSCOPY Most powerful technique in structure elucidation Uses powerful magnets to determine spin systems in molecules Includes 1H-NMR and 13 C-NMR Many nuclei have spin and all nuclei are electrically charged. If an external magnetic field is applied, an energy transfer is possible between the base energy to a higher energy level. The energy transfer takes place at a wavelength that corresponds to radio frequencies and when the spin returns Natural Products Chemistry Structure Elucidation by Spectroscopy  Natural Products Chemistry Structure Elucidation by Spectroscopy Circular Dichroism (CD) An absorption spectroscopy based on the differential absorption of left and right circularly polarized light. Optically active chiral molecules will preferentially absorb one direction of the circularly polarized light. The difference in absorption of the left and right circularly polarized light can be measured and quantified. Used to investigate structural aspects of optically active chiral media.  Natural Products Chemistry Structure Eludcidation by X-ray Crystallography X-ray Crystallography Used to determine the arrangement of atoms of a crystalline solid in three dimensional space. Provides full structural information on the position and identity of each atom in the crystal of a compound. The underlying principle is that the crystalline atoms cause a beam of X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a 3D picture of the density of electrons within the crystal.  Natural Products Chemistry Structure Eludcidation by X-ray Crystallography Figure 2.10. Principle of X- Figure 2.11. Viral capsid structure ray crystallography. obtained by X-ray crystallography. Source: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/x-ray- crystallography Putting everything together  MS determine the molecular weight identify the presence of isotopes patterns for Cl or Br UV is the system conjugated ? Having completed an analysis of IR the available spectra, list the identify the functional groups that are present pieces that have been identified check the pieces the MW and / 13C-NMR or molecular formula and refine how many types of carbon ? the pieces to fit. Assemble the what types of carbon ? pieces paying particular H-NMR attention to H-NMR chemical shifts and coupling patterns how many types of hydrogen ? how many of each type ? Once you think you have the answer, check it with the what types of hydrogen ? H-NMR very carefully... it is probably the most critical how are they connected ? test to pass. Terpenes Class of >20,000 compounds containing carbon atoms in multiples of five Non-saponifiable lipids Include some fat-soluble vitamins, carotenoids, and certain co-enzymes Terpenes Synthesized from a 5-carbon building block called an isoprene unit Head Basic molecular formulae: (C H ) where n is 5 8 n the number of linked isoprene units. (isoprene rule or the C5 rule) Terpenes Isoprene units linked in a “head-to-tail” fashion Monoterpene  Terpenes Diterpenes are composed of four isoprene units and have the molecular formula C20H32 Examples taxadiene retinol taxol Terpenes Triterpenes consist of six isoprene units and have the molecular formula C30H48. Terpenes Tetraterpenes contain eight isoprene units and have the molecular formula C40H64. Biologically important tetraterpenes include the acyclic lycopene, the monocyclic gamma- carotene, and the bicyclic alpha- and beta- carotenes. Terpenes Sesterterpenes, terpenes having 25 carbons and five isoprene units, are rare relative to the other sizes. geranylfarnesol Terpenes Polyterpenes consist of long chains of many isoprene units. Natural rubber consists of polyisoprene in which the double bonds are cis. How to Identify a Terpene Look for the 2-methylbuta-1,3-diene structure, although because of addition reactions, the double bond positions will have changed or been removed. How to Identify a Terpene Look for a chain of 4 carbons, where there is a methyl group branched from carbon number 2 in the chain. 2 4 1 3 How to Identify a Terpene 2 1 3 Isoprene’s molecular formula is C5H8. 4 The number of 4 3 carbons in a terpene will be a multiple of 5. 2 The number of 1 hydrogens do not always follow the same pattern, because of further reactions that can How many isoprene units are found in a farnesol molecule? 2 4 1 3 3 4 4 2 3 1 2 1 Which of the following is a terpene? A B C D Natural Product Examples The Terpene Camphor Ninkuu, Vincent & Zhang, Lin & Yan, Jianpei & Yang, Tengfeng & Zeng, Hongmei. (2021). Biochemistry of Terpenes and Recent Advances in Plant Protection. International Journal of Molecular Sciences. 22. 5710. 10.3390/ijms22115710. Tetali, Sarada. (2019). Terpenes and isoprenoids: a wealth of compounds for global use. Planta. 249. 10.1007/s00425- 018-3056-x. Phenolic Compounds A group of small molecules characterized by their structures having at least one phenol unit. Involved in plant adaptation to environmental stress conditions Exhibit antioxidant, antimicrobial, and anti- inflammatory properties Closely associated with the flavor, color, foam, colloidal, and sensory properties of beer. Basic backbone  B A C Basic backbone Natural Product Examples Phenolic Compounds from the Willow Bark Alkaloids (N-containing Compounds) A class of naturally occurring organic nitrogen-containing bases. Generally contain at least one nitrogen atom in an amine-type structure React with acids to form salts Most have one or more of their nitrogen atoms as part of a ring of atoms Names generally end in the suffix -ine Alkaloids (N-containing Compounds) The function of alkaloids in plants is not yet understood. Waste product of plants’ metabolic processes May play a role in formation of seeds. May also protect some plants from destruction by certain insect species. Natural Product Examples Alkaloids and the Presence of Nitrogen: Nicotine Sulfur-Containing Compounds Some plants like the Brassicaceae plants (cabbage family) have evolved the ability to synthesize a wide range of sulfur-containing secondary metabolites Glucosinolates Thiosulfinates (allicin, derived from cysteine sulfoxides) Reactive sulfur species (H S and sodium 2 sulfate) Natural Product Examples Sulfur in Nature: Garlic The End