CHAPTER-I Introduction to natural products and bioactive compounds A review
CHAPTER-I Introduction to natural products and bioactive compounds: A review
1.1.Introduction to natural products and bioactive compounds Organic chemistry is an art executed science.The art of synthesis and isolation of natural products and bioactive compounds makes it one of the most interesting and finest areas of modern chemistry. As an eminent scientist says,If we wish to catch with nature,we shall need to use the same methods as she does,and I can foresee a time in which physiological chemistry will not only make greater use of natural enzymes but will actually resort to creating synthetic ones- Emily Fischer,1902.These words reflected an extensive chemical synthesis and isolation of natural products and bioactive compounds for the welfare of human kind in the future thereafter The key role played by plant-based systems in the healthcare of different cultures has been extensively documented,and the World Health Organization(WHO)has estimated that approximately 65-80% of the world's population rely mainly on plant-derived traditional medicines for their primary health care.1 Most of these natural products are secondary plant metabolites.Keeping this in view,we felt an urge to synthesize some natural products and test their bioactivity and also planned for the isolation of some bioactive natural compounds. Natural products have played a key role in health care and prevention of diseases for the past thousands of years.Several ancient civilizations,such as Indians,Chinese,and North Africans have provided written evidence for the use of natural sources for curing
1.1. Introduction to natural products and bioactive compounds Organic chemistry is an art executed science. The art of synthesis and isolation of natural products and bioactive compounds makes it one of the most interesting and finest areas of modern chemistry. As an eminent scientist says, If we wish to catch with nature, we shall need to use the same methods as she does, and I can foresee a time in which physiological chemistry will not only make greater use of natural enzymes but will actually resort to creating synthetic ones– Emily Fischer, 1902. These words reflected an extensive chemical synthesis and isolation of natural products and bioactive compounds for the welfare of human kind in the future thereafter. The key role played by plant-based systems in the healthcare of different cultures has been extensively documented, and the World Health Organization (WHO) has estimated that approximately 65-80% of the world’s population rely mainly on plant-derived traditional medicines for their primary health care.1 Most of these natural products are secondary plant metabolites. Keeping this in view, we felt an urge to synthesize some natural products and test their bioactivity and also planned for the isolation of some bioactive natural compounds. Natural products have played a key role in health care and prevention of diseases for the past thousands of years. Several ancient civilizations, such as Indians, Chinese, and North Africans have provided written evidence for the use of natural sources for curing
various ailments.2 Sumerian clay tablet is known to be the earliest known written document that was used as a remedy for various illnesses.3 The importance of natural products as anticancer agents can be seen between the years 1981-2006,where about a hundred anticancer agents have been developed,of which,nine were pure natural products,eleven were derived from a natural product pharmacophore,eighteen were natural product mimics,and twenty five were natural product derivatives,4 thus making the natural sources as significant contributors to the health care system A few words below convey a subtle idea about the importance of natural products as medicines over the last 4000 years 2000 BC:Here,eat this root. 1000 AD:That root is heathen!Here,say this prayer. 1850 AD:That prayer is superstition!Here,drink this potion. 1935 AD:That potion is snake oil!Here,swallow this pill. 1975 AD:That pill is ineffective!Here,take this antibiotic. 2000 AD:That antibiotic is poison!Here,eat this root. -Anonymous 1.2.Characterization of natural products and bioactive compounds The characterization of natural products and bioactive compounds in the past decades has utilized spectroscopic techniques as well as chemical methods to determine the structures.The use of ultraviolet- visible and infrared spectrophotometry,nuclear magnetic resonance
various ailments.2 Sumerian clay tablet is known to be the earliest known written document that was used as a remedy for various illnesses.3 The importance of natural products as anticancer agents can be seen between the years 1981-2006, where about a hundred anticancer agents have been developed, of which, nine were pure natural products, eleven were derived from a natural product pharmacophore, eighteen were natural product mimics, and twenty five were natural product derivatives,4 thus making the natural sources as significant contributors to the health care system. A few words below convey a subtle idea about the importance of natural products as medicines over the last 4000 years. 2000 BC: Here, eat this root. 1000 AD: That root is heathen! Here, say this prayer. 1850 AD: That prayer is superstition! Here, drink this potion. 1935 AD: That potion is snake oil! Here, swallow this pill. 1975 AD: That pill is ineffective! Here, take this antibiotic. 2000 AD: That antibiotic is poison! Here, eat this root. -Anonymous 1.2. Characterization of natural products and bioactive compounds The characterization of natural products and bioactive compounds in the past decades has utilized spectroscopic techniques as well as chemical methods to determine the structures. The use of ultravioletvisible and infrared spectrophotometry, nuclear magnetic resonance
spectroscopy(NMR),mass spectrometry(MS),high performance liquid chromatography(HPLC),polarimetry,and circular dichroism can yield complementary information that is used to determine the structures of the compounds.When NMR data and degradative studies are inconclusive,a total synthesis and spectroscopic comparison between the synthetic and natural product is the easiest way for stereochemical determination and confirmation.s 1.3.Dereplication Dereplication is the rapid identification of known compounds within a sample.These known compounds interfere with in vitro assays,leading to false-positive results in bioassays.In order to avoid known or interfering compounds,various dereplication methods are applied to the bioactive samples.The currently used popular dereplication methods include mass spectrometry (MS)-based methods,NMR-based methods,chromatographic methods,and activity profiling. 1.3.1.MS-based methods. It includes liquid chromatography-MS (LC-MS),LC-UV-MS,and LC-MS-NMR methods.These methods allow for an easy determination of the molecular weights of compounds in either a purified or crude sample.6 In some methods,the LC-MS,UV,and bioactivity profiles of a particular crude extract can be compared with a library of characterized compounds,and a particular known active compound can be rapidly identified.7.8
spectroscopy (NMR), mass spectrometry (MS), high performance liquid chromatography (HPLC), polarimetry, and circular dichroism can yield complementary information that is used to determine the structures of the compounds. When NMR data and degradative studies are inconclusive, a total synthesis and spectroscopic comparison between the synthetic and natural product is the easiest way for stereochemical determination and confirmation.5 1.3. Dereplication Dereplication is the rapid identification of known compounds within a sample. These known compounds interfere with in vitro assays, leading to false-positive results in bioassays. In order to avoid known or interfering compounds, various dereplication methods are applied to the bioactive samples. The currently used popular dereplication methods include mass spectrometry (MS)-based methods, NMR-based methods, chromatographic methods, and activity profiling. 1.3.1. MS-based methods: It includes liquid chromatography-MS (LC-MS), LC-UV-MS, and LC-MS-NMR methods. These methods allow for an easy determination of the molecular weights of compounds in either a purified or crude sample.6 In some methods, the LC-MS, UV, and bioactivity profiles of a particular crude extract can be compared with a library of characterized compounds, and a particular known active compound can be rapidly identified.7,8
1.3.2.NMR based methods: These rely on the ability of NMR-based techniques to resolve signals given by different functional groups within a molecule,or different molecules in a mixture,and help in the rapid identification of functional groups and structural motifs.DEPT,COSY or HSQC spectra are some of them.9.10 1.3.3.Chromatographic methods. Prefractionation methods depend on the ability to selectively remove a few undesirable classes of compounds.Selective removal of tannins by use of polyamide chromatography is one of the most widely used prefractionation-dereplication methods.Sephadex LH-20 and HP20 MCI gelll were been reported to selectively remove tannins from plant extracts.The remaining extract can then be evaluated for bioactivity. 1.3.4.Activity profiling: It is a dereplication method where the bioactivity of an extract is profiled in several different assays.The COMPARE algorithm used with the NCI's sixty-cell line panel is one of the most well-known methods.COMPARE method considers ICso values,which represent the concentration of a compound inhibiting the cell growth by 50%.12 1.4.Biogenesis and classification of natural products: The classification of natural products can be made on the basis of biogenesis where the process of photosynthesis plays a lead role Carbohydrates,the initial products of photosynthesis undergo alterations and leads to the formation of low molecular weight pool of
1.3.2. NMR based methods: These rely on the ability of NMR-based techniques to resolve signals given by different functional groups within a molecule, or different molecules in a mixture, and help in the rapid identification of functional groups and structural motifs. DEPT, COSY or HSQC spectra are some of them.9,10 1.3.3. Chromatographic methods: Prefractionation methods depend on the ability to selectively remove a few undesirable classes of compounds. Selective removal of tannins by use of polyamide chromatography is one of the most widely used prefractionation-dereplication methods. Sephadex LH-20 and HP20 MCI gel11 were been reported to selectively remove tannins from plant extracts. The remaining extract can then be evaluated for bioactivity. 1.3.4. Activity profiling: It is a dereplication method where the bioactivity of an extract is profiled in several different assays. The COMPARE algorithm used with the NCI's sixty-cell line panel is one of the most well-known methods. COMPARE method considers IC50 values, which represent the concentration of a compound inhibiting the cell growth by 50%.12 1.4. Biogenesis and classification of natural products: The classification of natural products can be made on the basis of biogenesis where the process of photosynthesis plays a lead role. Carbohydrates, the initial products of photosynthesis undergo alterations and leads to the formation of low molecular weight pool of
organic compounds.The final natural product is formed from a sequence of biosynthetic reactions and the process is termed as biogenesis(Fig.1.1).13 H.O glucose shikimate nins, pyruvate polyacetates shikimates acetyl-CoA mevalonate reb terp8Rol。nd coumarins amino acids proteins alkaloids Fg.1.1 1.5.Sources: Natural products generally have a prebiotic origin or they originate from plants,microbes,or animal sources (Fig.1.2).14.5 Plants and microorganisms such as fungi,bacteria have proven to be an excellent source of novel natural products including peptide antibiotics
organic compounds. The final natural product is formed from a sequence of biosynthetic reactions and the process is termed as biogenesis (Fig. 1.1).13 CO2 hν photosynthesis H2O erythrose-4 phosphate glucose mono-, oligo-, polyosides glycosides phenols, quinones, polyacetylenes, macrolides, fatty acids, lipids... phospho-enol pyruvate shikimate flavonoids, anthocyanins, tannins shikimates cinnamates, lignans, coumarins, quinones... pyruvate acetyl-CoA Krebs cycle amino acids mevalonate terpenoids and steroids alkaloids essential oils, sesqui- and diterpenes, saponins... proteins polyacetates Fig. 1.1 1.5. Sources: Natural products generally have a prebiotic origin or they originate from plants, microbes, or animal sources (Fig. 1.2).14,15 Plants and microorganisms such as fungi, bacteria have proven to be an excellent source of novel natural products including peptide antibiotics
polyketides and classes of other bioactive compounds.16 Some of the microbial metabolites are used as antineoplastic agents,antimicrobial agents and bioinsecticides.17 (Animal sources Microbial sources Natural Product Sources Plant sources (Marine sources Fg.1.2 The marine environment is a rich source of natural bioactive compounds as more than 70%of earth's surface is covered by oceans.18-20 Thus we broadly have four categories of natural product sources. 1.5.1.Natural products from plant sources. Since ages,plants have been an excellent source for the bioactive natural products.Several plant extracts were used as medicines in the treatment of various diseases.Higher plants are extremely popular for the production of variety of biologically active compounds that include,paclitaxel 1,morphine 2 and others.21.22 9 OH HO Paclitaxel(1) morphine (2) Source:Taxus brevifolia Source:Papaver somniferum
polyketides and classes of other bioactive compounds.16 Some of the microbial metabolites are used as antineoplastic agents, antimicrobial agents and bioinsecticides.17 Microbial sources Natural Product Sources Marine sources Plant sources Animal sources Fig. 1.2 The marine environment is a rich source of natural bioactive compounds as more than 70% of earth’s surface is covered by oceans.18-20 Thus we broadly have four categories of natural product sources. 1.5.1. Natural products from plant sources: Since ages, plants have been an excellent source for the bioactive natural products. Several plant extracts were used as medicines in the treatment of various diseases. Higher plants are extremely popular for the production of variety of biologically active compounds that include, paclitaxel 1, morphine 2 and others.21,22 O NH OH O O O O O H O O HO O HO OH H Paclitaxel (1) Source: T axus brevif olia HO O H HO H N morphine (2) Source: Papaver somnif erum
1.5.2.Natural products from marine organisms Spongouridine(3)and spongothymidine(4)23 were known to be the first bioactive nucleotide compounds to be isolated from the Carribean sponge Cryptotheca crypta in 1950's.These compounds were potent anticancer and antiviral agents.Some of the marine organisms lead a sedentary lifestyle,and thereby synthesize several complex and extremely potent chemicals for their defense from predators.20 The potential of these chemicals can be utilized to treat various ailments, especially cancer.Discodermolide(5),isolated from the marine sponge Discodermia dissoluta,is one such example which has a similar mode of action when compared to that of paclitaxel and possesses a strong anticancer activity.Infact,a combination therapy of the above two drugs has led to reduced tumor growth in certain cancers.24 H HN o- -0 HO HN 0 OH OH Spongouridine(3) Spongothymidine(4倒 Discodermolide (5) 1.5.3.Natural products from microorganisms. The discovery of penicillin in 1929 opened the gates for microorganisms as a source of potential drug candidates.Since then, a large number of microorganisms were screened for drug discovery which led to the discovery of antibacterial agents like cephalosporins-
1.5.2. Natural products from marine organisms: Spongouridine (3) and spongothymidine (4) 23 were known to be the first bioactive nucleotide compounds to be isolated from the Carribean sponge Cryptotheca crypta in 1950’s. These compounds were potent anticancer and antiviral agents. Some of the marine organisms lead a sedentary lifestyle, and thereby synthesize several complex and extremely potent chemicals for their defense from predators.20 The potential of these chemicals can be utilized to treat various ailments, especially cancer. Discodermolide (5), isolated from the marine sponge Discodermia dissoluta, is one such example which has a similar mode of action when compared to that of paclitaxel and possesses a strong anticancer activity. Infact, a combination therapy of the above two drugs has led to reduced tumor growth in certain cancers.24 O OH HO N HN O O Spongouridine (3) HO O OH HO N HN O O Spongothymidine (4) HO O O H2N OH OH OH O HO O Discodermolide (5) 1.5.3. Natural products from microorganisms: The discovery of penicillin in 1929 opened the gates for microorganisms as a source of potential drug candidates. Since then, a large number of microorganisms were screened for drug discovery which led to the discovery of antibacterial agents like cephalosporins-
cefprozil (6),antidiabetic agents like acarbose (7),and anticancer agents like epirubicin(8).25 OH HO HO. Cefprozil(6) HO OH OH OH Acarbose(☑ OMe O OH O Ho 7o Epirubicin(8) 1.5.4.Natural products from animal sources Animals also form a source of some interesting bioactive compounds.Epibatidine (9),a nitrogen containing heterocyclic compound isolated from the skin of an Ecuadorian poison frog,was found to be ten times more potent than morphine.26 Venoms and toxins from animals have played a significant role in designing a multitude of cures for several diseases.Teprotide,a toxic venom, extracted from a Brazilian viper,has led to the development of cilazapril (10)and captopril(11),which were found to be effective against hypertension.27
cefprozil (6), antidiabetic agents like acarbose (7), and anticancer agents like epirubicin (8).25 NH2 HO N H O N O S O OH H Cefprozil (6) HN HO OH OH OH O O OH HO HO HO OH OH OH OH Acarbose (7) O O OH OMe OH O OH O O HO H2N Epirubicin (8) HO 1.5.4. Natural products from animal sources: Animals also form a source of some interesting bioactive compounds. Epibatidine (9), a nitrogen containing heterocyclic compound isolated from the skin of an Ecuadorian poison frog, was found to be ten times more potent than morphine.26 Venoms and toxins from animals have played a significant role in designing a multitude of cures for several diseases. Teprotide, a toxic venom, extracted from a Brazilian viper, has led to the development of cilazapril (10) and captopril (11), which were found to be effective against hypertension.27
Epibatidine( Cilazapril (10) Captopril(11) 1.6.Bioassay: Once a compound is synthesized or isolated,it needs to be screened for its biological activity.Screening is an attractive and key area towards the drug discovery programmes.28 It is crucial for successful isolation of bioactive compounds.Generally,bioassays are broadly classified into two types.They are mechanism based assays and cell based assays.29 1.6.1.Mechanism based assays: It involves the testing of a specific drug against a specific enzyme, DNA,receptor etc.As these assays are conducted in artificial environment which is different from physiological environment,it must be properly configured for accuracy.A properly handled assay can determine the activity of a compound even at lower concentrations.30 Though these assays are useful in determining the biological activity of the compounds,the disadvantage is that they approximate the in vivo environment due to incomplete system generated from the absence of certain pathways 1.6.2.Cell based assays It involves a drug-cell interaction with the complete intact cell rather than just isolated system and is by far more superior to the mechanism based assay.This method has the advantage of screening
Cl N H N Epibatidine (9) N N HO NH O O O O Cilazapril (10) HS N O Captopr il (11) HOOC 1.6. Bioassay: Once a compound is synthesized or isolated, it needs to be screened for its biological activity. Screening is an attractive and key area towards the drug discovery programmes.28 It is crucial for successful isolation of bioactive compounds. Generally, bioassays are broadly classified into two types. They are mechanism based assays and cell based assays.29 1.6.1. Mechanism based assays: It involves the testing of a specific drug against a specific enzyme, DNA, receptor etc. As these assays are conducted in artificial environment which is different from physiological environment, it must be properly configured for accuracy. A properly handled assay can determine the activity of a compound even at lower concentrations.30 Though these assays are useful in determining the biological activity of the compounds, the disadvantage is that they approximate the in vivo environment due to incomplete system generated from the absence of certain pathways. 1.6.2. Cell based assays: It involves a drug-cell interaction with the complete intact cell rather than just isolated system and is by far more superior to the mechanism based assay. This method has the advantage of screening
