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Contents
1
Introduction: Biologically Active Compounds .....................................
Part I
2
3
4
1
Biologically Active Substances in Cropping Systems
Free, Bounded, and Included in Humic Acids Amino Acids:
Thermal Properties of Humic Acids from Cropping Systems ............
25
Conversions and Pathways of Organic Carbon and Organic
Nitrogen in Soils ......................................................................................
53
Free Sulfuric Amino Acids and Rhodanese in Soils Under
Rye Cropping and Crop Rotation .........................................................
91
5
Amino Acids, Indole-3-Acetic Acid, Stable and Transient
Radicals, and Properties of Humic and Fulvic Acids as
Affected by Tillage System ..................................................................... 113
6
Rate of Leaching of Organic and Inorganic Compounds
in Tilled and Orchard Soils .................................................................... 131
7
Impact of Long-Term Agricultural Management and Native
Forest Ecosystem on the Chemical and Biochemical Properties
of Retisols’ Organic Matter .................................................................... 149
v
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vi
Contents
Part II The Physiological Importance of Biologically
Active Substances
8
Auxin, One Major Plant Hormone, in Soil ........................................... 175
Junichi Ueda, Marian Saniewski, and Kensuke Miyamoto
9
Transformations of Organic Matter in Soils Under Shelterbelts
of Different Ages in Agricultural Landscape ........................................ 211
Lech Wojciech Szajdak, Victoria Maryganova,
Eugene Skakovskii, and Ludmila Tychinskaya
10 Phytohormone in Peats, Sapropels, and Peat Substrates .................... 247
Lech Wojciech Szajdak
11 Cranberry: A Plant Growing on Organic Soils with
a Broad Spectrum of Pharmaceutical and Medical Use...................... 273
Lech Wojciech Szajdak and Lydia I. Inisheva
12 The Importance of Horticultural Growing Media
and Biochemical Processes ..................................................................... 287
Lech Wojciech Szajdak, Katarzyna Styła, Wioletta Gaca,
Teresa Meysner, Marek Szczepański, and Jacek Stanisław Nowak
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Chapter 1
Introduction: Biologically Active Compounds
Abstract Each chemical compound possesses numerous biological activities.
Biological activity spectrum of a compound should be predicted on the basis of the
structure-activity-relationships. The biological activity spectrum of a compound
shows its all actions and its participation in the biological, physiological and metabolically pathways despite the difference in the experimental conditions. The biological activity spectrum of a compound shows compound’s all actions and the
participation in the biological, physiological and metabolically pathways despite the
difference in the experimental conditions. If the differences in species, sex, age,
dose, and the participation in the metabolic processes and pathways etc. are neglected,
the biological activity may be identified only qualitatively. Thus the biological activity spectrum is defined as the “intrinsic” property of a substance depending only on
its structure and physicochemical characteristics. Structure-activity-relationship
(SAR) is an approach to finding the relationships between the chemical structure (or
structural-related properties) and the biological activity of studied compounds. It
links the chemical structure to a chemical property (e.g., water solubility) or the
biological activity including toxicity.
Keywords Chemical compounds • Biological potential • Biological activity spectrum • Structure-activity-relationship
Each chemical compound possesses numerous biological activities. However, its
activity always depends on the object, dose, and participation in the chemical conversions or biochemical pathways. On the other hand, the biological potential of the
substance may be discovered under the specific experimental conditions.
As per the Oxford Dictionary, “Biochemistry refers the biological activity of a
substance demonstrated in living organisms.” The biologically active substances are
often from biological origin. Biological activity characterizes the biological effectiveness of a substance and describes the changes caused by biological material like
enzymes, hormones, vitamins, etc., in a tissue or in an organ under constant condi-
1
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L.W. Szajdak
tions as compared with certain international standard. Certain biological activity is
measurable in quantity, and the international unit (IU) corresponds to a certain
amount of a biologically active substance which produces a certain biological
response. However, another measure is the IC50—value corresponding to that
amount of an effective substance, which inhibits the biochemical reaction in target
organism by 50 % effectiveness. Concentration in this context means the concentration of a given substance in the target tissue—often in mg/kg or g/kg (Uosukainen
and Pihlaja 2006).
Some scientists call the biological potential the biological activity spectrum.
Biological activity spectrum of the compound should be predicted based on the
structure–activity relationships. The biological activity spectrum of a compound
shows compound’s all actions and the participation in the biological, physiological,
and metabolic pathways despite the difference in the experimental conditions. If the
differences in species, sex, age, dose, participation in the metabolic processes and
pathways, etc., are neglected, the biological activity may be identified only qualitatively. Thus, “the biological activity spectrum” is defined as the “intrinsic” property
of a substance depending only on its structure and physicochemical characteristics
(Filimonov and Poroikov 1996; Filimonov et al. 1999).
The molecular structure of an organic compound determines its properties (Jurs
et al. 1988).
Molecular
Structures
Properties
Structural
Description
The term active substance has been used in this chapter to refer to raw material
(organic matter, mineral and organic soil, peat, moorsh, sapropel) substrates and
growing media for agriculture and horticulture. Relationship between the molecular
structure and biological activity or molecular structure and physical properties can
be investigated for most organic compounds using different analytical methods.
High-performance liquid chromatography (HPLC), gas chromatography, infrared
analysis, UV-VIS spectrophotometry, spectrofluorimetry, colorimetric test, thermal
analysis, electron paramagnetic resonance, enzyme activity, etc., are recommended
for the quantitative and qualitative determination of chemical and biochemical compounds, their metabolites, and degradation products.
Specification for the active substances should include the tests for (i) appearance,
(ii) identification, (iii) content/assay, (iv) impurities (residual solvents, ash, heavy
metals, and related substances, metabolites, and the products of the degradation),
and (v) other parameters relevant to the individual substances (water content, loss
on drying, the presence or ratio of isomers, optical rotation, melting point and the
clarity, color and pH of solutions).
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1
Introduction: Biologically Active Compounds
3
Structure–activity relationship (SAR) is an approach to find the relationships
between chemical structure (or structural-related properties) and its biological
activity of studied compounds. It links the chemical structure to a chemical property
(e.g., water solubility) or biological activity including toxicity. Qualitative SARs
and quantitative SARs are collectively named (Q)SARs. Qualitative relationships
are derived from non–continuous data (e.g., yes or no data), while quantitative relationships are derived from continuous data (e.g., toxic potency data). The approach
is not new [AFA Cros in 1863 noted in “Action de l’alcool amylique sur l’organisme,”
the relationship between the toxicity of primary aliphatic alcohols and their water
solubility (Chirico and Gramatica 2012)]. The concept of structure biodegradability
relationships (SBR) explains the variability in persistence of organic chemicals in
the environment.
The main concept of SAR is that the structure of compound is responsible for the
activity. Therefore, similar molecules should reveal similar biological activities.
Thus, the SAR approach assumes that the structure of a molecule (e.g., its geometric, electronic properties) contains the features responsible for its physical, chemical, and biological properties (Nantasenamat et al. 2009, 2010; Thompson et al.
2006).
Biological activity (e.g., mutagenicity, cancerogenicity, teratogenicity, inhibition
of enzyme activity, toxicity) of substances is governed by their properties, which in
turn are determined by their chemical structure. The objectives of SAR are
twofolds:
(i) To accurately determine the limits of variation in the structure of a chemical
that are consistent with the production of a specific effect (e.g., can a chemical
elicit a specific toxic endpoint)
(ii) To define the ways, which alters the structure and thereby the overall properties
of a compound to influence the endpoint potency (Patani and LaVoie 1996;
Brown 2012)
The action of biologically active substances in soil depends upon the environmental conditions (such as temperature, light, water, oxygen tension, and availability of nutrients). Biologically active substances exert their greatest effects on
increasing the plant yield, when conditions are suboptimal for plant growth.
Chemical compounds may be classified according to several criteria. One common method is based on the specific elements present (oxides, hydrides, halides,
halogens). Organic compounds are those compounds with a backbone of carbon
atoms, and all the remaining compounds are classified as inorganic. As the name
suggests, organometallic compounds are organic compounds bonded to metal
atoms. Another classification scheme for chemical compounds is based on the types
of bonds that the compound contains. Ionic compounds contain ions and are held
together by the attractive forces among the oppositely charged ions. Common salt
(sodium chloride) is one of the best-known ionic compounds.
However, molecular compounds contain discrete molecules, which are held
together by sharing electrons (covalent bonding), e.g., water (contains H2O molecules), methane (contains CH4 molecules), and hydrogen fluoride (contains HF
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4
L.W. Szajdak
molecules). Furthermore, another classification system is based on reactivity—specifically, the types of chemical and biochemical reactions, conversions, and pathways that the compounds are likely to undergo.
Some biologically active substances act at low concentrations. Phytohormones
can be also considered in the same category as antagonisms as they affect the plant
growth. Vitamins from B group are normal constituents of fertile soils. Their presence is due to release from organic residues, liberation from plant roots, and synthesis by soil microorganisms. Phenolic acids derived from the lignin decay by
microorganisms influence the activity of peroxidase in soils (Stevenson 1982).
The following organic compounds occur in soil under continuous cropping, and
intensive rotations are ecotoxic and allelopathic (Smyk 1992; Szajdak and
Życzyńska-Bałoniak 1994):
1. Aliphatic and aromatic amines (primary, secondary, tertiary) as the precursors
of nitrozoamines
2. Amides, imides, esters, derivatives of carboxylic and hydroxycarboxylic acids,
peptides (Fig. 1.1)
3. Phenols: hydroxyphenolic acids (p-hydroxybenzoic, p-coumaric, ferulic, salicylic, syringic, vanillic, protocatechuic), catechol, quinone, hydroquinone, resorcine, derivatives of o,m,p, p-aminophenols and nitrophenols (Table 1.1)
4. Coumarins and their derivatives (Table 1.2) (Fig. 1.2 and 1.3)
5. Terpenoids (saponins, diterpenoids)
6. Flavonoids as per IUPAC nomenclature (Table 1.3):
NH2 (γ)
NH2 (γ)
L
H2N
DAB
L
Leu
L DAB
D
Fen
L Tre
L
L
D
DAB
Leu
L DAB
D
Fen
L DAB
NH2(γ)
L DAB
L Tre
OH
NH2(γ)
OH
(γ)H2N
L DAB
L
NH2
L DAB (à)
DAB
DAB
L DAB
NH2 (γ)
L Tre
OH
NH2(γ)
IPEL
D
DAB
NH2 (γ)
IPEL
(I)
(II)
Fig. 1.1 Polymyxin B—the product of Bacillus polymyxa strains. Structure of polymyxin B from
eight (I) or seven (II) of amino acids (Szajdak 2011)
Bond CO–NH, Tre threonine, DAB L-α,γ-diaminobutyric acid, Fen phenylalanine, Leu leucine,
IPEL isopelargonic acid
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1
5
Introduction: Biologically Active Compounds
Table 1.1 Phenolic acids in soils
Chemical compound
Benzoic acid
Structure
COOH
O
Cinnamic acid
OH
O
o-Hydroxycinnamic acid
OH
OH
Vanillic acid
COOH
O
CH3
OH
O
p-Coumaric acid
OH
HO
Ferulic acid
H3CO
Caffeic acid
HO
COOH
HO
COOH
HO
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L.W. Szajdak
O
O
O
Warfarin
O
Angelicin
Psoralen
O
HO
7-Hydroxycoumarin
Compounds
Dicumarol
Table 1.2 Derivatives of coumarin in soils
Structure
O
OH
O
O
O
O
O
O
O
O
O
6
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Introduction: Biologically Active Compounds
7
NH
NH
Me
O
OH
O
Me
O
Me
OH
O
O
Me
Me
NH
NH
Me
Me
MeO
O
O
Me
MeO
O
H2N
Me
MeO
Me
Coumermycin
Compounds
Novobiocin
Structure
OH
Me
O
OH
Me
O
O
O
OH
O
NH
OH
O
NH
O
OH
(continued)
1
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L.W. Szajdak
Me
NH
O
Me
Compounds
Clorobiocin
Table 1.2 (continued)
Structure
MeO
Me
OH
O
Cl
O
OH
O
NH
O
OH
8
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1
Introduction: Biologically Active Compounds
O
9
HO
O O
7-hydroxycoumarin
O
HO
O O
6-hydroxycoumarin
OH
8-hydroxycoumarin
OH
CH2CH2COOH
o-hydroxyphenylpropionic acid
OH
HO
O O
Coumarin
O O
5-hydroxycoumarin
CH CHCOOH
o-coumaric acid
HO
HO
OH
OH
O O
Esculetin
O O
3-hydroxycoumarin
O O
4-hydroxycoumarin
O H
H
O O
3,4-epoxide
OH
CH2CHOHCOOH
o-hydroxyphenyllactic acid
OH
CH2CHO
o-hydroxyphenylacetaldehyde
OH
CHCOOH
o-hydroxyphenylacetic acid
Fig. 1.2 Conversion of coumarin. All biotransformations are possible (Lacy and O’Kennedy
2004)
(i) Flavones, derivatives of 2-phenylchromen-4-one (2-phenyl-1,4benzopyrone) (examples: quercetin, rutin)
(ii) Isoflavonoids,
derivatives
of
3-phenylchromen-4-one
(3-phenyl-1,4-benzopyrone)
(iii) Neoflavonoids,
derivatives
of
4-phenylcoumarin
(4-phenyl-1,2-benzopyrone)
7. Nitrozoamines and nitrozoamides
8. Mycotoxins
9. Polycyclic aromatic hydrocarbons: anthracene, chrysene, corannulene, naphthalene, phenanthrene, triphenylene, benzo[α]pyrene, coronene, tetracene, pentacene, pyrene, ovalene (Table 1.4)
10. Heterocyclic compounds (Table 1.5)
11. Glycosides (Table 1.6)
12. Alkaloids—ergot alkaloids and others (Table 1.7)
13. Phytoalexins (gossypol, capsidiol, camalexin, pisatin, etc.) (Table 1.8)
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L.W. Szajdak
CHO
COOH
COOH
CHO
CH
CH
CH
CH
CH
CH
CH
CH
OH
3
OH
CH3
OCH3
OH
1
OH
2
4
COOH
CH
COOH
COOH
CH
OCH3
OH
OH
OH
5
OH
6
COOH
COOH
7
COOH
OH
HO
OH
OH
OH
OH
8
OH
OH
9
10
OH
HO
OH
11
Fig. 1.3 The mechanism of the conversion of methoxyphenyl acids in fungi Epicoccus nigrum
(Haider and Martin 1967), (1) coniferyl aldehyde, (2) ferulic acid, (3) p-hydroxycinnamic acid, (4)
p-hydroxycinnamic aldehyde, (5) vanillic acid, (6) caffeic acid, (7) p-hydroxybenzoic acid, (8)
gallic acid, (9) protocatechuic acid, (10) 2,3,4-trihydroxybenzoic acid, (11) pyrogallol
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11
Introduction: Biologically Active Compounds
Table 1.3 Flavonoids in soils
Compound
Flavone
Structure
O
O
Isoflavone
O
Neoflavonoids
O
O
OH
Quercetin
OH
HO
OH
OH
O
OH
Epicatechin
HO
O
OH
OH
OH
OH
Rutin
O
HO
OH
HO
O
OH
OH
OH
O
O
O
H 3C
HO
O
HO
OH
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12
Table 1.4 Polycyclic aromatic hydrocarbons in soils
Compound
Anthracene
Structure
Chrysene
Naphthalene
Phenanthrene
Triphenylene
Benzo[α]pyrene
Coronene
Tetracene
Pentacene
Pyrene
(continued)
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13
Introduction: Biologically Active Compounds
Table 1.4 (continued)
Compound
Ovalene
Table 1.5 Heterocyclic
compounds in soils
Structure
Compound
Indole
Structure
NH
Anthraquinone
CO
CO
Fluorene
CO
Quinoline
NH
Carbazole
N
H
Furan
O
Thiophene
S
Pirolle
N
Benzofuran
O
Benzothiophene
S
(continued)
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14
Table 1.5 (continued)
Compound
Benzopirol
Structure
NH
CO
Xanthol
O
Purine
N
H
N
Pyrimidine
NH
N
N
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Introduction: Biologically Active Compounds
15
HO
O
O
HO
HO
HO
Compound
Solanine
Table 1.6 Glycosides in soils
Structure
OH
O
OH
OH
O
O
O
OH
OH
H
H
H
H
H
N
H
(continued)
1
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H
OH
HO
O
O
HO
OH
O
O
HO
Structure
Compound
Tomatine
Table 1.6 (continued)
OH
O
O
HO
OH
OH
OH
O
OH
O
OH
H
H
H
H
H
O
L.W. Szajdak
HN
16
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Introduction: Biologically Active Compounds
17
O
C
O
HO
HO
HO
HO
OH
OH
CH2OH
O
HO
Amygdalin
Compound
Quercetin glycoside
Structure
OH
O
O
OH
O
O
N
O
OH
OH
(continued)
1
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HO
HO
CH3
C
N
CH3
Linamarin
H
HO
OH
OH
OH
OH
O
O
N
C
Structure
Compound
Lotaustralin
Table 1.6 (continued)
O
L.W. Szajdak
O
18
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19
Introduction: Biologically Active Compounds
Table 1.7 Alkaloids in soils
Compounds
Mitomycin
Structure
O
N
NH
O
H2N
O
O
O
H 2N
Ergotamine
O
O
NH
OH
N
H
O
H
N
O
N
HN
Ergocristine
H
HO
O
HN
O
N
O
N
O
N
H
NH
Ergometrine
OH
NH
H
N
HN
(continued)
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L.W. Szajdak
20
Table 1.7 (continued)
Compounds
Ergocryptine
Structure
H
O
O
NH
N
H
H
N
O
O
N
CH3
H
HN
H
Solanidine
H
N
H
H
H
H
HO
Sparteine
H
N
N
H
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21
Introduction: Biologically Active Compounds
Table 1.8 Phytoalexins in
soils
Compound
Pisatin
Structure
O
Me
OH
O
O
O
Camalexin
N
S
NH
Gossypol
O
OH
OH
HO
OH
OH
HO
O
OH
Capsidiol
CH2
HO
CH3
CH3
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L.W. Szajdak
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