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20
Molecular Pharmacognosy
Piyushkumar Sadhu, Mamta Kumari, Ghanshyam Parmar, Chitrali Talele
Department of Pharmacy, Sumandeep Vidyapeeth Deemed to be University, Vadodara, India
20.1 Introduction
The structure of DNA, discovered by Watson and Crick in
1953, marked a pivotal moment in life sciences, profoundly
influencing medicine and reshaping intellectual perspectives. This prompted a renewed exploration of life’s fundamental nature at the biological macromolecular level.
Though not directly impacting pharmacognosy, the discovery had an immeasurable influence on the broader life sciences landscape. This transformative period saw rapid
advancements in molecular biology, seamlessly integrating
with applied biomedicine. Notably, polymerase chain reaction (PCR)-based molecular marker technology flourished,
significantly contributing to the growth.
Molecular pharmacognosy is a branch of pharmacognosy that applies molecular biology techniques to study the
classification, identification, cultivation, conservation, and
production of crude drugs and their active components.
Crude drugs are natural substances derived from plants,
animals, or minerals that are used for medicinal purposes
or as raw materials for pharmaceuticals [1, 2]. Molecular
pharmacognosy aims to provide a scientific basis for the
quality, standardization, and authentication of traditional
medicines, especially traditional Chinese medicine (TCM),
which has a long history and rich diversity of medicinal
materials. It has emerged as a new interdisciplinary field
that integrates the knowledge and methods of pharmacognosy, molecular biology, genomics, proteomics, metabolomics, and biotechnology. Notably, advancements in
molecular biology techniques, such as next-generation
sequencing and metabolomics, have revolutionized the
investigation of plant-derived drugs at a molecular level,
providing insights into their composition and pharmacological activities [3, 4].
20.1.1 History and Evolution of Pharmacognosy
Pharmacognosy has its roots in the medical uses of plants
in many different cultures, and it emerged from their healing traditions in older times. Herbal medicines can be
found in ancient Chinese books like the Shen Nong Ben
Cao Jing, which demonstrates a precocious knowledge of
plants’ healing abilities. Ancient Indian Ayurvedic texts,
such as the Charaka Samhita, detailed the use of herbal
medicines [5, 6]. Concurrently, in the Mediterranean area,
individuals such as Dioscorides amassed vast herbal collections, augmenting the understanding of therapeutic
flora [7]. Arabic manuscripts were used during the Middle
Ages to preserve and disseminate pharmacognostic information. The monumental work as Avicenna’s The Canon
of Medicine brought together the knowledge of therapeutic herbs. An increase of interest in natural history and
therapeutic plants occurred in Europe during the
Renaissance, as seen by the work of individuals, such as
Nicholas Culpeper and Leonhart Fuchs [8, 9]. Pharmacognosy evolved into a distinct discipline during the
eighteenth and nineteenth centuries. The establishment
of pharmacopeias, such as the London Pharmacopeia in
1618, standardized the identification and preparation of
medicinal substances [10]. A significant advance in the
extraction of active ingredients from plants was made in
the nineteenth century when Friedrich Serturner isolated
morphine from opium [11]. The twentieth century saw
396 20 Molecular Pharmacognosy
significant developments in chemistry and technology
that revolutionized pharmacognosy. The transition toward
isolating active ingredients was characterized by the separation of quinine from cinchona bark, and the identification of salicin as the precursor to aspirin exemplified the
shift toward isolating active constituents [12, 13]. Compound identification was transformed by technological
advancements, such as spectroscopy and chromatography.
Pharmacognosy has adopted cutting-edge technologies in
the twenty-first century. Through the integration of genomics, metabolomics, and molecular biology approaches,
the sub-discipline of molecular pharmacognosy investigates the molecular foundation of medicinal plants [14].
Drug discovery from natural sources has been expedited
by bioinformatics and high-throughput screening techniques. In the contemporary period, pharmacognosy
remains a crucial resource for drug discovery.
20.1.2 Current Trends in Pharmacognosy
In the dynamic field of pharmacognosy, current trends
reflect a paradigm shift toward advanced methodologies and
interdisciplinary collaboration. Molecular pharmacognosy
stands at the forefront, utilizing techniques such as DNA
barcoding and next-generation sequencing (NGS) to precisely identify and authenticate medicinal plants, ensuring
the quality and consistency of herbal products [15, 16].
Metabolomics and metabolic profiling contribute to the
exploration of plant metabolites, offering insights into
biosynthetic pathways and chemical variations influenced
by geographical factors and cultivation methods [17].
Biotechnological approaches, including plant tissue culture
(PTC) and genetic engineering, play a pivotal role in sustainable production, optimizing bioactive compound yields in
engineered plants [18]. The integration of ethnopharmacology and traditional knowledge validates the historical uses
of medicinal plants, guiding modern drug discovery efforts.
Pharmacovigilance and quality control measures, crucial in
the globalization of herbal products, ensure the safety and
efficacy of traditional medicines, emphasizing regulatory
compliance [5, 14]. Furthermore, the field thrives on interdisciplinary collaborations, where partnerships with molecular biologists, chemists, and pharmacologists contribute to
a deeper understanding of the intricate interactions between
plant compounds and biological targets.
20.1.3 Scope and Objectives
Molecular pharmacognosy is a science that deals with the
study of medicinal plants and animals at the molecular
level. It has several research topics and applications, such
as using DNA markers to verify the identity and quality of
traditional medicinal materials [1–3]; finding new sources
of bioactive compounds or functional genes by studying
the genetic diversity and evolution of medicinal plants
and animals [2, 4]; preserving and reproducing the germplasm of rare and endangered medicinal species by using
molecular techniques, such as in vitro propagation, cryopreservation, genetic engineering, and synthetic biology
[4]; modifying or introducing genes that affect the production and transport of active ingredients in medicinal plants
by using genetic engineering and gene editing tools, such
as CRISPR-Cas9 [19]; analyzing the genome, transcriptome, proteome, and metabolome of medicinal plants by
using high-throughput sequencing and bioinformatics,
and revealing the molecular mechanisms and gene networks that control their growth, development, and secondary metabolism [20]; producing natural or novel
bioactive compounds in heterologous hosts, such as bacteria, yeast, or plant cells, by using synthetic biology
approaches, such as metabolic engineering, enzyme engineering, and artificial gene circuits [21]; and investigating
the genetic and environmental factors that influence the
quality and efficacy of Daodi herbs, which are medicinal
materials that are grown in specific regions with optimal
ecological conditions and cultivation practices, by using
molecular markers and omics technologies [22, 23]. It is a
promising and prospective field that can contribute to the
development and innovation of natural medicine and
pharmacology. It can also provide new insights and solutions for the challenges and opportunities faced by the
global health and wellness industry.
20.2 Molecular Biology Techniques in Pharmacognosy
Molecular pharmacognosy is a rapidly growing field that
combines pharmacognosy and molecular biology, focusing
on the genetic classification of medicinal plants, particularly Chinese herbs. It involves taxonomy, phylogenetic
evolution, identifying raw materials, metabolic pathways,
and regulating secondary metabolites [3]. Advances in biotechnology, systems biology, genomics, proteomics, and
metabolomics have made molecular biology techniques
more reliable for identifying bioactive components in
medicinal plants [24, 25]. These techniques also aid in
pharmacogenetic authentication, ensuring the accuracy
and authenticity of herbal compounds. Molecular biology
techniques ensure the efficacy and safety of natural products, speed up drug development, and improve research
accuracy [26, 27].
39720.2 Molecular Biology Techniques in Pharmacognosy
20.2.1 DNA Extraction, Polymerase Chain Reaction, Sequencing, and Cloning
Recent developments in molecular biology have brought
about some change in pharmacognosy, the study of naturally occurring substances having potential medical uses.
Researchers have become increasingly reliant on DNA
extraction, PCR, sequencing, and cloning as techniques to
reveal a deeper understanding of medicinal plants and
their bioactive components [28]. Cloning, PCR, DNA
extraction, and sequencing have all changed the face of
pharmacognosy [29]. With the use of these cutting-edge
molecular biology approaches, scientists may explore
medicinal plants in greater depth, discovering new and
effective natural medicines that have latent promise. The
future of pharmacognosy holds great promise for innovative healthcare discoveries as these approaches progress
and become more accessible. Now, we will examine each
method in detail and see how it contributes to pharmacognosy [30]. DNA extraction: All subsequent uses are based
on the isolation of high-quality DNA from plant material.
To extract the appropriate DNA types from plants, pharmacognosy makes use of a wide variety of extraction techniques. Liquefaction and grinding: the first step in
extracting valuable plant compounds is homogenizing the
material in order to release the contents of the cells by
breaking down their walls. Additional dissolving of cell
membranes and other components is accomplished using
lysis buffers. In the purification process, proteins, polysaccharides, and RNA are removed using techniques such as
phenol-chloroform extraction, column chromatography,
and magnetic bead separation. As a quality control measure, we check the extracted DNA for concentration, purity,
and integrity to make sure it is good to go ahead [31]. PCR:
Researchers can use this amplification technique to dramatically boost the concentration of a specific DNA fragment in a sample. Important genes found in medicinal
plants often have low numbers; therefore, this is essential
for their analysis. The design of primers involves selecting
specific oligonucleotide sequences to round the desired
area of DNA. Denaturation, annealing, and extension are
the three steps that DNA goes through in amplification
cycles [32]. New copies of the target DNA are generated
in each cycle by DNA polymerase by extending primers
that have hybridized to their complementary sequences.
Pharmacognosy uses PCR for a number of things, such as
amplifying and sequencing particular genes involved in the
production of medicinally relevant chemicals, which are
key steps in gene identification and characterization. By
comparing DNA sequences, molecular authentication may
tell closely related plant species apart despite their shared
morphologies. Detection of adulterants: Finding synthetic
compounds diluted with real plant extracts. Sequencing:
DNA molecules’ nucleotide orders (A, C, G, and T) can be
deciphered using sequencing technology. Here, we may
find important details on the gene’s sequence, any mutations, and the proteins that are encoded. For tiny DNA fragments, the tried-and-true Sanger sequencing approach
yields accurate and trustworthy results. For the purpose of
evaluating whole genomes or transcriptomes, NGS is a
great option because it is a high-throughput technology
that generates enormous volumes of sequencing data.
Sequencing has several uses in pharmacognosy, including
gene discovery, which is the process of finding new genes
that may be involved in making bioactive substances. To
better understand plant metabolism and compound manufacturing, functional genomics seeks to understand gene
regulation and expression [33]; pharmacogenomics seeks
to understand how individual genetic differences impact
drug response and to tailor medicine based on medicines
obtained from plants. Cloning: This method enables scientists to replicate a little piece of DNA, which opens up new
possibilities for studying its structure and function. The
first step in cloning DNA is selecting a suitable vector,
which can be a plasmid or a bacterial artificial chromosome (BAC). DNA insertion: Ligases and restriction
enzymes are used to introduce the target DNA into the vector. The process of transformation and selection involves
inserting DNA into a host organism (such as bacteria) and
then having the recombinant vector proliferate alongside
the DNA [34]. Using these selective methods, we can be
sure that only cells with the specific DNA fragment we
need will be propagated. Pharmacognosy applications:
With cloning, it is possible to produce an excessive amount
of protein encoded by a gene of interest in order to study its
biochemical and pharmacological properties, which is
known as overexpression of the gene [35]. Introducing specific mutations into genes to learn how they work and how
they affect chemical synthesis is known as mutagenesis.
Finding and studying the genes that code for certain biochemical pathways that produce useful pharmaceutical
molecules is the goal of functional gene cloning [36].
20.2.2 Significance of Different Molecular Biology Techniques
Pharmacognosy is the study of therapeutic compounds
found in plants and microbes through the application of
molecular biology. Molecular techniques like PCR, DNA
extraction, and sequencing are useful tools for establishing
genetic databases for medicinal organisms, evaluating
genetic diversity, and identifying species. In addition to regulating or improving medicinal chemical biosynthesis, these
398 20 Molecular Pharmacognosy
strategies aid researchers in identifying metabolic pathways,
such as genes involved in medical drug manufacture. To
ensure the best possible harvest of medicinal plants, molecular methods, such as quantitative polymerase chain reaction (QPCR) and reverse transcription-polymerase chain
reaction (RT-PCR) can be used to explore the effects of environmental variables, stages of development, and elicitors on
pharmacognostic studies, genetic and molecular markers
are used to select plants with desirable features. These methods enhance the dependability of herbal remedies, maintain
the use of medicinal plants, and quicken the process of discovering and developing natural therapeutic substances
[39]. Some of the techniques of molecular biology are repre-
sented in Table 20.1 [40].
the gene expression of drugs [37]. To guarantee the genuineness of medicinal plant material, DNA barcoding stops
herbal product adulteration, mislabeling, and substitution.
Biotechnological medication production is made possible
through cloning and recombinant DNA, which allows for
larger-scale synthesis with better yields and purity
compared to natural extraction [38]. Finding naturally
occurring therapeutic options and developing pharmacologically active medications for a variety of illnesses are two
more areas where molecular techniques contribute to
pharmaceutical development. To promote sustainable agriculture and guarantee high-quality plant material for
Table 20.1 Techniques used to identify, authenticate, and characterize medicinal plants and their active compounds with the help
of molecular biology.
Technique
Significance in
pharmacognosy
Identification Authentication Characterization
20.2.3 Different Examples of Molecular
Markers, Barcodes, and Databases for
Molecular Identification and Authentication
of Medicinal Plants
Researchers have embraced a world of advanced molecu-
lar technologies to guarantee the purity and authenticity
of therapeutic plants. DNA barcoding, which is similar to
a plant’s distinctive genetic fingerprint, uses certain areas
of DNA to accurately identify species [41]. Single nucleo-
tide polymorphisms (SNPs) identify small differences for
DNA barcoding and
sequencing
Random amplified
polymorphic DNA
(RAPD)
Inter-simple sequence
repeat (ISSR)
Polymerase chain
reaction (PCR)
Gel electrophoresis Separates DNA fragments
DNA microarrays and
RNA-sequencing
Protein profiling and
analysis
Analyzes unique DNA
regions for accurate species
identification, even for
morphologically similar
plants.
Generates DNA fingerprints
for differentiating
populations and detecting
adulteration.
Another fingerprinting
technique for genetic
diversity analysis and
authentication.
Amplifies specific DNA
sequences for targeted
identification and detection
of marker genes.
based on size for
visualization and analysis.
Analyze gene expression
patterns to understand
biosynthetic pathways and
identify novel bioactive
compounds.
Characterizes proteins
involved in plant metabolism
and identifies specific
biomarkers for quality
control.
✓ ✓ ✓
✓ ✓ Limited
✓ ✓ Limited
✓ ✓ ✓
✓ (indirectly) ✓ ✓ (indirectly)
× ✓ ✓
× ✓ ✓
20.3 Molecular Genetics and Genomics of Medicinal Plants
399
Technique
High-performance
liquid chromatography
(HPLC)
Mass spectrometry (MS) Identifies and characterizes
Nuclear magnetic
resonance (NMR)
Significance in
pharmacognosy
Separates and quantifies
bioactive compounds for
standardization and quality
control.
unknown compounds based
on their mass and
fragmentation patterns.
Elucidates the structure and
composition of complex
molecules for deeper
characterization.
Sample
Preparation
Barcode
Identification
Identification Authentication Characterization
× × ✓
× × ✓
× × ✓
DNA Extraction
Molecular Identification
and Authentication of
Medicinal Plants
PCR
Amplification
AAT GC
Figure 20.1 Molecular markers, barcodes, and databases for molecular identification and authentication of medicinal plants.
Source: Ghanshyam Parmar.
even tighter separation, other markers, such as random
amplified polymorphic DNA (RAPD) and inter-simple
sequence repeat (ISSR) provide quick screening [42].
continually appearing, melding the course of medicinal
plant authentication [9], and some of the databases are
represented in Figure 20.1.
Gel
Electrophoresis
These identifiers are linked to large databases that store
reference sequences for species confirmation and comparison, such as GenBank, BoLC, and PDBC [43]. In addition, DNA microarrays help with focused breeding and
20.3 Molecular Genetics and
Genomics of Medicinal Plants
compound discovery by revealing genes implicated in
therapeutic qualities [44]. Additional information on
applications, chemistry, and traditional knowledge can be
found in resources, such as GloPIS, TCM Database [45],
and HerbalGram. Standardized, high-quality medicinal
plant products are now within reach, thanks to this
molecular arsenal that enables correct identification and
combats adulteration [46]. Keep in mind that the most
effective strategy frequently makes use of a combination
of approaches and that fascinating new methods are
The analysis of the molecular genome and genetics of
medicinal plants represents a fascinating intersection of
botanical science, genetics, and pharmacology. It emerges
from a collective recognition of the immense therapeutic
potential bear within the genetic makeup of plant species
traditionally valued for their healing properties. The background of this topic probes into the evolution of scientific
inquiry that seeks to interpret the intricate genetic codes
underlying the combination of bioactive compounds in
400 20 Molecular Pharmacognosy
medicinal herbs. Historically, the usage of medicinal
plants predates the advent of modern science, with ancient
civilizations relying on empirical knowledge passed down
through generations. Traditional healers intuitively
selected plants based on their observable effects, unaware
of the molecular intricacies governing these therapeutic
properties [47]. As technology advanced, the twentieth
century witnessed a paradigm shift in our understanding
of plant biology, catalyzed by breakthroughs such as DNA
structure discovery.
The presentation of the double helix structure of DNA by
James Watson and Francis Crick in 1953 laid the foundation
for molecular biology, providing scientists with a tool to
explore the genetic blueprints of all living organisms,
including medicinal plants. This revelation marked the
commencement of a new era in botanical research, wherein
the focus shifted from mere observation of plant characteristics to a detailed examination of the molecular mechanisms orchestrating their growth, development, and
production of bioactive compounds. Advancements in
molecular genetics techniques, such as DNA sequencing
and genome mapping, empowered scientists to unravel the
inherited codes of various plant species, revealing the
molecular basis of their medicinal properties. The genomic
era allowed researchers to categorize key genes indulged in
the biosynthesis of therapeutic compounds, shedding light
on the intricate pathways responsible for the synthesis of
alkaloids, flavonoids, terpenoids, and other bioactive molecules. Moreover, the advent of functional genomics and
genetic engineering provided tools to manipulate and
enhance the production of beneficial compounds in medicinal plants [48]. Scientists began to explore the potential of
altering gene expression to amplify the yield of specific
metabolites or even introduce novel pathways for synthesizing desired compounds. These technological strides opened
roads for the sustainable production of medicinal compounds, reducing dependency on wild plant populations.
Medicinal plants have been an integral component of traditional medicine systems across diverse cultures for centuries, serving as the foundation of healing practices that have
withstood the test of time. The intrinsic connection between
humans and the botanical realm has been forged through
an intricate tapestry of empirical knowledge, passed down
through generations, and cultivated through keen observation of nature’s remedies. The significance of medicinal
plants in traditional medicine transcends mere herbalism; it
embodies a profound understanding of the symbiotic relationship between humanity and the plant kingdom. The
roots of traditional medicine run deep, grounded in the wisdom of indigenous communities and ancient civilizations.
Across continents and cultures, traditional healers have
harnessed the therapeutic potential of botanical treasures,
unlocking the secrets embedded in the leaves, roots, and
seeds of various plant species. These age-old remedies,
often shrouded in traditional stories and cultural practices,
provide not only relief from ailments but also offer a complete approach to well-being, addressing the intricate balance between the physical, mental, and spiritual dimensions
of health. In the face of modern advancements in pharmaceuticals, the relevance of medicinal plants in traditional
medicine endures. The compounds found in these plants,
often the result of intricate biochemical pathways developed over millennia, continue to inspire scientific inquiry
and serve as the foundation for the development of contemporary medicines. Furthermore, the holistic approach of
traditional medicine, which considers not only the symptoms but also the overall well-being of individuals, resonates with a growing awareness of the importance of
integrative healthcare in today’s world. This exploration
into the significance of medicinal plants in traditional medicine aims to unravel the deep-rooted connections between
humanity and the botanical world [49].
20.3.1 Genomics of Medicinal Plants
The finding of the double helical structure of DNA guided
a new phase of life science investigation. The primary origins of a species are determined by DNA sequences, which
are life’s most elementary genetic data. A new age in the
study and use of species is heralded by the decoding of
genome sequences, which contain all of a species’ genetic
information. Decoding the genome arrangement of a
medicinal plant with significant therapeutic and commercial potential will advance scientific study, molecular
breeding, and genetic modification of the plant. The first
era of sequencing technology was formed in 1977 when
Frederick Sanger devised the chain-terminating sequencing technique [50, 51]. Furthermore, the discipline has
entered the post-genome era with the advent of the third
era of single-molecule sequencing technology and the second era of high-throughput sequencing technologies.
Whole genome sequencing is not now the exclusive domain
of model creatures because of the advancements in
sequencing technology and falling sequencing costs. More
and more significant commercial crops and medicinal
herbs are the subject of genome sequencing studies, which
offer a wealth of data resources for functional genomic
studies on medicinal plants.
At this point, genomes have been sequenced for over 360
species. In contrast to the widespread release of genetic data,
the biological function of a very small percentage of genes
remains unknown. The goal of the post-genome period is to
analyze how huge genomic data functions in biology.
Genome sequences give insight on physiological and genetic