Bangladesh J. Plant Taxon. 30(1): 53-76, 2023 (June) DOI: https://doi.org/10.3329/bjpt.v30i1.67044
© 2023 Bangladesh Association of Plant Taxonomists
QUANTITATIVE ETHNOBOTANICAL STUDY IN GAFARGAON
SUB-DISTRICT AND UNVEILING DRUG CANDIDATES THROUGH
MOLECULAR DOCKING AND DYNAMICS SIMULATION APPROACHES
SHEIKH SUNZID AHMED, M. OLIUR RAHMAN*, MOHAMMAD AJMAL ALI1
AND JOONGKU LEE2
Department of Botany, University of Dhaka, Dhaka 1000, Bangladesh
Keywords: Ethnobotany; Informant consensus factor; Fidelity; Molecular docking; Molecular
dynamics simulation; Rheumatoid arthritis; JAK1.
Abstract
An ethnobotanical investigation was carried out in Gafargaon sub-district (upazila)
under Mymensingh district, Bangladesh that unveiled a total of 79 medicinal plant
species under 74 genera and 46 families which were used to treat various ailments
through 106 formularies. In addition, molecular docking and dynamics simulation studies
were performed based on ethnobotanical outcome for the first time in Bangladesh to
unveil potential drug candidates. The study revealed that most of the species used for
primary healthcare were herbs (44.3%) followed by trees (36.7%), shrubs (10.2%) and
climbers (8.8%). Leaves were found to be the most frequently used part (34%) compared
to other plant parts. Factor of informant consensus values ranged from 0.975 to 0.984 and
the highest value was recorded for respiratory tract disorders (0.984). Maximum number
of taxa was unraveled to treat digestive and gastrointestinal disorders. Fidelity level
varied from 41.2 to 100%, where 11 species showed 100% fidelity, and the citation
frequency was found above 70% for 15 different ailments. Molecular docking study
exposed 60% Stephania japonica phytocompounds scoring higher than the control drug
Ibuprofen (-7.0 kcal/mol) targeting rheumatoid arthritis. The phytocompounds
Oxostephanine, Trilobine and Epistephanine were identified as lead drug candidates with
binding affinity of -9.7, -8.7 and -8.6 kcal/mol, respectively. Molecular interactions of
these compounds were found significant to identify potential drug surface hotspots.
Molecular dynamics simulation shed light on regional flexibility profiles and unraveled
notable structural stability of the top three phytocompounds. The present study would
offer foundational data for identifying potential bioactive compounds that could be
utilized in novel drug discovery efforts.
Introduction
Plants with medicinal uses have been a quintessential component of traditional healthcare
system since antiquity. Indigenous therapeutic uses of plants have enriched existing traditional
medicinal knowledge (TMK) which in turn, developed the pedestal of modern medicines (Pandey
and Tripathi, 2017; Mouele et al., 2022). Conservation of this traditional botanical knowledge
(TBK) through formal documentation is considered as a key factor to open new avenues for
designing and developing novel drugs (Yordi et al., 2022). According to World Health
Organization (WHO), ethnomedicine are still the primary sources of healthcare for approximately
80% of the world’s population, especially in rural areas of developing countries. Over 50% of all
*Corresponding author. Email: oliur.bot@du.ac.bd
1Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia
2Department of Environment and Forest Resources, Chungnam National University, Daehak-ro, Yuseong-gu, Daejeon,
Republic of Korea
https://doi.org/10.3329/bjpt.v30i1.67044
mailto:oliur.bot@du.ac.bd
54 AHMED et al.
pharmaceutical drugs can be traced back to their origins in ethnomedicine (Van Wyk et al., 1997;
Suchana et al., 2022). Recently, the use of ethnomedicinal plant-based formularies have gained
popularity over the use of synthetic drugs focusing issues, such as safety and efficacy which
demands a more rigorous and scientific documentation of indigenous medicinal knowledge
(Minnady et al., 2022). Lack of plant identification skill is a hindrance to this endeavor which
might results in inappropriate selection of taxa for specific ailment and at this point taxonomic
expertise is very much essential (Hadiati et al., 2022). The global market for herbal medicines has
prospered as a result of cumulative significance of ethnobotanical research. The worldwide market
was valued at approximately US$ 83 billion in 2019, and it is projected to grow significantly,
reaching an estimated worth of US$ 550 billion by 2030 (Suchana et al., 2022). This brilliant
economic outgrowth is endangered due to some factors including continuous decline in traditional
medicinal practices, reduced interests of the younger generation toward traditional treatment
systems coupled with rural depopulation, mass deforestation, and migrations of traditional
medicinal healers to other jobs (Faruque et al., 2018). All of these facts further necessitate the
need of ethnobotanical research to conserve ethnomedicinal values of plants and cultural heritage.
Molecular docking and molecular dynamics simulation (MDS) are in silico techniques which
facilitate validation of the ethnobotanical findings at the molecular level to shed light on potential
lead candidates of specific taxa to carry out drug design works. Molecular docking provides
insights into the interactions that occur at the atomic level between a small molecule (referred to as
a ligand) and a protein (referred to as a receptor). Molecular dynamics simulation is used to
inspect the temporal behavior and movement of atoms and molecules employing equations of
motion grounded in classical physics. In Structure Based Drug Design (SBDD), molecular
docking and dynamics simulation approaches help to recognize intermolecular interactions,
dynamic behavior of complexes, structural alterations, and properties exhibited by molecular
systems which drive rational designing of novel inhibitors targeting a wide range of diseases and
disorders. These comprehensive in silico strategies can save time, cost and labor on the contrary of
conventional in vitro and in vivo investigations (Azim et al., 2020; Ahmed et al., 2022). Very
recently, some ethnobotanical studies have attempted these molecular approaches to signify
ethnobotanical findings and led a possible strategy for the development of future therapeutics
targeting specific ailments based on peoples’ perception and practical perspectives (Vijayakumar
et al., 2016; Maghfiroh et al., 2021; Abdulrahman et al., 2022).
Janus Kinase 1 (JAK1) is a tyrosine kinase receptor that plays a critical role in the
pathogenesis of rheumatoid arthritis when dysregulated via production of pro-inflammatory
cytokines which mainly drive disease progression of rheumatoid arthritis (RA). Binding of
cytokines facilitates phosphorylation of JAK1 and it gets activated. This activation results in the
formation of STAT (Signal Transducers and Activators of Transcription) dimer that is translocated
to the nucleus, acts as transcription factor and initiates transcription of genes encoding pro-
inflammatory cytokines which ended up with production of malignant protein that causes
rheumatoid arthritis. Therefore, inhibition of JAK1 plays a regulatory role in the JAK-STAT
pathway to prevent the production of pro-inflammatory cytokines and consequently to stop the
disease progression of RA (Tanaka et al., 2022).
In Bangladesh, several efforts have been made to record and document the traditional
knowledge of ethnomedicinal plants, leading to a resurgence in folk medicine over the past two
decades (Hassan and Khan, 1986, 1996; Mia and Huq, 1988; Alam et al., 1996; Uddin M.Z. et al.,
2008, 2015, 2017, 2019; Uddin S.B. et al., 2011; Sajib and Uddin, 2015; Hossain and Rahman,
2018). These studies shed light on medicinal plants of particular community, specific diseases or
certain areas of Bangladesh. Nevertheless, there are still numerous areas and communities in
Bangladesh that have not been explored. Many more medicinal plants used as sources of herbal
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 55
drugs by ethnic groups, folk medicinal practitioners (FMPs), and local people are yet to be
uncovered from those unexplored areas and communities (Hossain and Rahman, 2018). In the
recent past, Rahman et al. (2019) conducted a floristic survey on the angiosperm flora of
Gafargaon sub-district, however, there has been no ethnobotanical investigation attempted
targeting this sub-district. Moreover, molecular docking and dynamics simulation analyses have
never been conducted to validate ethnobotanical outcomes in any earlier studies carried out in
Bangladesh. Therefore, the current study aimed to employ ethnobotanical protocol to unravel
peoples’ consensus regarding the ethnomedicinal uses of plants in Gafargaon sub-district via
quantitative analyses. The investigation aimed further to unleash the power of molecular docking
and dynamics simulation approaches in ethnobotany for the first time in Bangladesh to unveil
potential lead phytocompounds targeting particular ailment with specific taxon based on
informants’ consensus which would shed light on future drug design and discovery.
Materials and methods
Study area:
Gafargaon sub-district under Mymensingh district spans an area of 401.16 sq. km. and is
situated between latitudes of 24°15' and 24°33' N, and longitudes of 90°27' and 90°39' E. The sub-
district shares its borders with Trishal and Nandail sub-districts to the north, Kapasia and Sreepur
sub-districts to the south, Hossainpur and Pakundia sub-districts to the east, and Trishal, Bhaluka,
and Sreepur sub-districts to the west. Gafargaon experiences a moderate climate, similar to other
parts of the district, as it is located near to the Himalayas and falls within the tropical monsoon
zone. The temperature in the area varies from 15.1ºC to 34.4ºC, with monthly average minimum
and maximum temperatures of 22.3ºC and 31.8ºC, respectively. The average monthly rainfall is
227 mm. There are significant monthly variations in humidity levels, the maximum ranging from
81% to 97%, while the minimum varying from 47% to 79% (Rahman et al., 2019; BBS, 2022).
The sub-district boasts a variety of habitats and ecosystems, including wetlands, cultivated lands,
char (river islands), homestead areas, scrub jungles, and fallow lands. These diverse habitats
support a dense growth of angiosperms, which are crucial for the local economy, environment, and
primary healthcare system. Many individuals in the region possess traditional knowledge about
plants and their uses, which they rely on for their primary healthcare management.
Plant samples and data collection
Plant samples were collated from the study area through multiple field surveys conducted at
various seasons between May 2020 and December 2022. Collected voucher specimens were
processed using standard herbarium techniques (Hyland, 1972; Alexiades, 1996) and deposited at
the Dhaka University Salar Khan Herbarium (DUSH). All the specimens were critically studied
and identified by experts, using standard literatures and online databases (Hooker, 1872-1897;
Prain, 1903; Dassanayake and Fosberg, 1980-1991; Ahmed et al., 2008-2009; The Plant List,
2013; POWO, 2022; TROPICOS, 2022). Data on medicinal uses of these plants were collected
through semi-structured interviews, group interviews, plant interviews, discussions with key
informants, and informal conversations with folk medicinal practitioners locally referred to as
Kabiraz (Alexiades, 1996). A total of 51 informants, including 11 female and 40 male individuals,
with an average age of 55 years were interviewed.
Quantitative analyses
Factor of informant consensus (Fic):
To estimate use diversity targeting particular ailments, Fic values were determined using the
following formula (Heinrich et al., 1998):
56 AHMED et al.
Fic = ………………………… (i)
Here, Nur represents number of use reports in each category, and Ntaxa represents number of
species in each category.
Citation frequency (CF %):
CF values help to identify the most commonly used medicinal plants in the study area. CF
values were estimated employing the following formula (Friedman et al., 1986):
CF = × 100 …………………………. (ii)
Here, n refers to number of people interviewed citing species, and N represents total number
people interviewed.
Fidelity level (FL %):
FL values are useful to identify the plant species that are most preferred by informants for
treating specific ailments. FL values were calculated using the following formula (Friedman et al.,
1986):
FL = × 100 ……………………….. (iii)
Here, Ip denotes to number of informants who indicate use of a species for the same major
ailment, and Iu refers to total number of informants who mentioned the same plant for any other
use.
Active site prediction of the receptor macromolecule
CASTp 3.0 and SCFBio webservers have been utilized to predict active sites of the receptor
JAK1 (Kuman et al., 2012; Tian et al., 2018). For prediction, the PDB file was uploaded to these
servers after retrieving from the Protein Data Bank with PDB ID “4K6Z”. The CASTp 3.0 server
was utilized for single cavity-based prediction, whereas the SCFBio server was employed for
making predictions on multiple cavity basis.
Molecular docking and interaction analyses
Based on Fic (Factor informant consensus) value and novelty, Stephania japonica was
selected for molecular docking analysis targeting rheumatoid arthritis. The receptor protein, JAK1
was retrieved from the Protein Data Bank with PDB ID “4K6Z”. This transferase is frequently
targeted to search for novel inhibitors targeting rheumatoid arthritis (Singh and Singh, 2020). The
protein was prepared using AutoDock MGL tool by deleting water and heteroatoms, adding polar
hydrogens and Kollman charges and repairing missing atom residues. Subsequently, the protein
was energy minimized by SWISS-PDB viewer following Rahman and Ahmed (2022). Afterwards,
30 bioactive phytochemicals of Stephania japonica were retrieved from PubChem database
(Semwal et al., 2010). Ibuprofen, as the control drug, was retrieved from DrugBank (Grennan
et al., 1979). All the phytocompounds and control were prepared as ligands for molecular docking
by applying MMFF94 (Merck Molecular Force Field) force field based on earlier study (Ahmed
et al., 2023). Molecular docking was performed using the blind docking approach in PyRx
software version 0.8. Docked complexes were visualized using Discovery Studio visualizer for
molecular interaction analysis (Ahmed et al., 2023).
Molecular dynamics simulation
The flexibility of the ligand-protein complexes that ranked the highest was assessed using the
CABS-flex 2.0 server (http://biocomp.chem.uw.edu.pl/CABSflex2), and the results were
http://biocomp.chem.uw.edu.pl/CABSflex2),
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 57
presented using RMSF (Root Mean Square Fluctuation). CABS-flex enables rapid simulation of
protein flexibility with minimal system requirements showing a strong correlation between the
flexibility simulations obtained from this server and NMR results (Kmiecik et al., 2016; Kuriata et
al., 2018). CABS-flex provides high-resolution simulations (10 ns) of protein dynamics in
conditions close to their native state, making it a valuable tool for real-time evaluation of protein-
ligand stability. The simulation in CABS-flex was conducted using the default parameters,
consisting of 50 cycles.
Results and Discussion
Diversity of ethnomedicinal plants:
The present study unveiled traditional medicinal knowledge of 79 species belonging to 74
genera and 46 families which were used for 13 major ailments via 106 formularies. A total of 51
informants took part in the participatory rural appraisal (PRA) from diverse profession and age
groups (Table 1). The ethnomedicinally important species alongside families and vouchers, their
vernacular names, parts used, mode of administration and ailments treated for each species are
documented in Table 2. Asteraceae was found to be the most dominant plant family containing the
highest number of species (7.5%), followed by Fabaceae (6.3%), Malvaceae (5.1%) and Rutaceae
(5.1%). The most frequently used species were herbs (44.3%), followed by trees (36.7%), shrubs
(10.2%) and climbers (8.8%) (Fig. 1A). These findings have been found congruent with several
other studies where the dominant ethnomedicinal plants were herbs (Uddin et al., 2019; Suchana
et al., 2022). Traditional healers use herbs and trees as the most common sources of medicines
(Uniyal et al., 2006), which has been supported further by our study. The maximum number of
species were prepared as extract (34.9%), followed by paste (21.7%) and decoction (17.9%) prior
to administration (Fig. 1B). The percentage of plant parts administered for treating different
ailments is shown in Figure 2.
In a study conducted on the ethnomedicinal plants of Barisal district, extracts were reported as
the principal mode of administration which showed congruence with our findings (Hossain and
Rahman, 2018). However, Faruque et al. (2019) reported paste as the chief mode of preparation in
Bilaichari sub-district of Rangamati district, which was found to be inconsistent with our study.
This inconsistency might be due to the peoples’ perception driven by geographical isolation and
community composition of the two areas. About 76% of the species were recorded for internal use
and the remaining 24% showed external application. Among the parts used, leaves were found to
be the most dominant one (34%), followed by roots (14%), whole plants (13%) and fruits (12%)
(Fig. 2).
Table 1. Socio-demographic features of the informants in Gafargaon sub-district.
Variables Categories Percentage Variables Categories Percentage
Gender Male 78.4 Religion Islam 92.2
Female 21.6 Others 7.8
Age group < 30 5.8 Profession Traditional healer 25.5
31-50 19.6 Farmer 19.6
51-70 64.8 Day laborer 13.7
> 70 9.8 Small shopkeeper 13.7
Education Illiterate 33.3 Others 27.5
Primary 43.1
Secondary 17.5
University 6.1
58 AHMED et al.
A few other studies have also demonstrated that leaves are predominantly used by folk
medicinal practitioners for various therapeutic purposes (Hossain and Rahman, 2018; Uddin et al.,
2019). The inclination towards using leaves in the preparation of herbal medicines by healers
might be attributed to the year-round availability of leaves and their ease of collection, storage,
processing, and handling (Faruque et al., 2018).
Fig. 1. Comparative analysis of habits and mode of preparation of the recorded ethnomedicinally important
plants. A. Classification of species based on habits showing the percentage for treating various ailments;
B. Different modes of preparation of the recorded species.
Fig. 2. Use report of different plant parts applied to treat various ailments in Gafargaon sub-district.
A B
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 59
Table 2. Ethnobotanical uses of medicinal plants in Gafargaon sub-district with various ailments and
mode of administration.
Taxa and voucher Local name Parts
used
Ailments Mode of application
Abroma augustum (L.) L.f.
(Malvaceae); SSA-229
Ulot Kombol Stem Constipation,
menstrual
problems
Stem aqueous extract is taken after soaking it
whole night.
Root Dysentery Decoction of root is mixed with root extract of
Bombax ceiba and taken orally.
Achyranthes aspera L.
(Amaranthaceae); SSA-275
Uuhutlenga,
Apang
Whole
plant
Infertility
problem
2 ml decoction is orally taken thrice a day for
three months.
Aegle marmelos (L.) Corrêa
(Rutaceae); SSA-270
Bel Fruit Diarrhoea Infusion of fruit pulp is orally consumed.
Root Heart
palpitation
Decoction of roots is taken internally.
Allium cepa L.
(Amaryllidaceae); SSA-244
Peeaz Bulb Insect bite Extract is applied externally to treat swelling
and inflammation.
Oligomenorrhea Half teaspoon of bulb extract is taken orally
with honey early morning on an empty
stomach for two weeks.
Allium sativum L.
(Amaryllidaceae); SSA-212
Roshun Bulb Rheumatoid
arthritis
Extract is often taken orally and sometimes
boiled for external application.
Hyperlipidemia Juice is taken internally.
Amaranthus spinosus L.
(Amaranthaceae); SSA-245
Khoirakata Leaf Skin
inflammation
Paste is applied externally.
Root Skin allergy Decoction is applied externally.
Whole
plant
Jaundice Decoction is taken orally.
Amorphophallus
paeoniifolius (Dennst.)
Nicol. (Araceae); SSA-279
Oulkachu Tuber Piles Extract is consumed orally at night.
Ananas comosus (L.) Merr.
(Bromeliaceae); SSA-206
Anarosh Leaf Helminthiasis Crushed young leaves are combined with
powdered Areca catechu roots and mixed with
water for oral consumption.
Annona squamosa L.
(Annonaceae); SSA-271
Ata Fruit Cardiovascular
problem
Fruit juice is taken orally along with
Mesosphaerum suaveolens seeds.
Aphanamixis polystachya
(Wall.) R. Parker
(Meliaceae); SSA-233
Pitraj Leaf Rheumatoid
arthritis
Leaf paste is applied externally.
Averrhoa carambola L.
(Oxalidaceae); SSA-276
Kamranga Fruit Anorexia Juice is taken orally.
Azadirachta indica A. Juss.
(Meliaceae); SSA-219
Nim Leaf Allergy Leaf paste is applied externally, sometimes
consumed orally as small tablets.
Stem Toothache Young shoots are used for brushing teeth.
Bombax ceiba L.
(Malvaceae); SSA-232
Shimul Root Dhat syndrome Decoction of roots is taken internally,
sometimes after mixing with root extract of
Xanthium strumarium.
Cajanus cajan (L.) Huth
(Fabaceae); SSA-208
Aarol,
Orohor
Leaf Jaundice Juice is taken internally along with coconut
water.
Constipation Leaf paste is taken internally.
Calotropis procera (Aiton)
W.T. Aiton (Apocynaceae);
SSA-268
Aahon,
Akondo
Leaf Asthma
Body ache
Boiled leaf is inhaled, sometimes taken orally.
Leaf juice is taken internally.
60 AHMED et al.
Table 2 Contd.
Taxa and voucher Local name Parts
used
Ailments Mode of application
Carica papaya L.
(Caricaceae); SSA-266
Pabda, pepey Leaf Body ache Leaf juice is taken orally.
Jaundice Leaf paste is taken orally.
Cassia fistula L. (Fabaceae);
SSA-234
Bandor Lori Seed Jaundice Seed paste is administered internally early in
the morning for five consecutive days.
Centella asiatica (L.) Urb.
(Apiaceae); SSA-204
Dholmanik,
Thankuni
Whole
plant
Diarrhoea Decoction is taken orally.
Cold and cough Decoction is internally taken.
Chenopodium album L.
(Amaranthaceae); SSA-267
Bottoua Shak Leaf Body ache Leaf paste is orally taken.
Whole
plant
Constipation Boiled or fried as vegetables.
Chromolaena odorata (L.)
King & Rob. (Asteraceae);
SSA-277
Boro
Heyalmuti
Leaf Skin cut and
laceration
Paste of leaves is applied externally for blood
clotting and wound healing.
Cinnamomum tamala (Buch.-
Ham.) Nees & Eberm.
(Lauraceae); SSA-248
Tej Pata Leaf Cold and cough Boiled leaf extract is taken internally with tea.
Clerodendrum infortunatum
L. (Lamiaceae); SSA-253
Bhait Leaf Chronic
dysentery
Leaf juice is taken orally.
Flower Rheumatoid
arthritis
Flower paste is taken internally along with ash
of coconut shell.
Coccinia grandis (L.) Voigt
(Cucurbitaceae); SSA-203
Kauajhingi Leaf Dyspepsia and
flatulence
Boiled leaf is taken with rice.
Root Diabetes Decoction of roots is taken orally.
Cocos nucifera L.
(Arecaceae); SSA-213
Nairol Fruit Diarrhoea Coconut water is taken orally.
Colocasia esculenta (L.)
Schott (Araceae); SSA-215
Kachu Bark Skin laceration Applied externally for wound dressing.
Corchorus olitorius L.
(Malvaceae); SSA-223
Naillya Seed Pox Seed paste is applied externally along with
seed oil of Sesamum indicum.
Curcuma longa L.
(Zingiberaceae); SSA-209
Oldi, Holud Rhizome Diabetes Decoction is taken internally.
Cuscuta reflexa Roxb.
(Convolvulaceae); SSA-262
Swarnolot Whole
plant
Helminthiasis Extract is orally taken once a day for a few
days.
Cyanthillium cinereum (L.)
H. Rob. (Asteraceae) SSA-
251
Kukshima Root Dhat syndrome Extract is mixed with decoction of Xanthium
strumarium roots and consumed orally.
Cynodon dactylon (L.) Pers.
(Poaceae); SSA-264
Durba Whole
plant
Skin laceration Crushed parts are mixed with flower extracts
of Nymphaea nouchali and applied externally.
Datura metel L.
(Solanaceae); SSA-257
Dhutura Fruit Eczema and
skin rash
Raw fruit is eaten in small quantity once a
day.
Dendrocnide sinuata (Bl.)
Chew (Urticaceae); SSA-220
Chutra Leaf Skin irritation
and itching
Leaf paste is applied externally.
Dillenia indica L.
(Dilleniaceae); SSA-260
Chalta Fruit Asthenia Fruit juice is taken thrice a day.
Leaf Dysentery Extract is taken twice a day for one week.
Diospyros malabarica
(Desr.) Kostel. (Ebenaceae);
SSA-207
Gab Bark Dysentery Crushed bark is consumed orally with curd
twice a day for three days.
Eclipta prostrata (L.) L.
(Asteracae); SSA-205
Kalahuta Whole
plant
Skin laceration
and wound
healing
Applied externally to the affected area,
sometimes along with Cynodon dactylon.
Body ache Extract is taken internally twice a day.
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 61
Table 2 Contd.
Taxa and voucher Local name Parts
used
Ailments Mode of application
Ficus hispida L.f.
(Moraceae); SSA-261
Kudura Fruit Diabetes Raw fruit is eaten, sometimes fruit juice is
taken orally.
Asthenia Juice is consumed regularly.
Glycosmis pentaphylla
(Retz.) DC. (Rutaceae);
SSA-250
Motkila Stem Toothache Used to brush teeth, applied externally.
Heliotropium indicum L.
(Boraginaceae); SSA-274
Aattir Shur,
Hatishur
Leaf Eczema Leaf paste is applied externally to the affected
part of the body.
Hibiscus rosa-sinensis L.
(Malvaceae); SSA-202
Joba Leaf Flatulence Infusion of leaves is taken internally.
Flower Dyspepsia Infusion of flowers is taken internally.
Justicia adhatoda L.
(Acanthaceae); SSA-218
Adabasok Leaf Cold and cough Leaf juice is taken orally.
Kalanchoe pinnata (Lam.)
Pers. (Crassulaceae); SSA-
235
Pathor Shila Leaf Burning
sensation and
body ache
Extract is orally taken.
Lablab purpureus (L.) Sweet
(Fabaceae); SSA-255
Shim Leaf Dermatitis Leaf paste is applied externally.
Lawsonia inermis L.
(Lythraceae); SSA-239
Mendi Leaf Insect bite Leaf paste is used externally to the affected
area.
Dermatitis Leaf paste is mixed with banana and calcium
hydroxide before external application.
Leucas aspera (Willd.) Link
(Lamiaceae); SSA-216
Dol Kolosh,
Dondokolosh
Leaf Rheumatoid
arthritis
Boiled leaf is applied externally.
Litsea glutinosa (Lour.) C.B.
Rob. (Lauraceae); SSA-256
Kharajora Leaf Chronic
dysentery
Leaf juice is taken orally.
Mangifera indica L.
(Anacardiaceae); SSA-221
Aam Bark Jaundice Decoction is taken orally along with seed and
fruit extracts of Syzygium cumini and Ficus
racemosa, respectively.
Mikania cordata (Burm. f.)
B.L. Rob. (Asteraceae);
SSA-247
Asam Lata Leaf Diarrhoea Extract is taken orally twice a day for a few
days.
Mimosa pudica L.
(Mimosaceae); SSA-214
Lajonti Root Menstrual
problems
Decoction of roots is taken internally for twice
a day.
Moringa oleifera Lam.
(Moringaceae); SSA-236
Sajna Leaf Rheumatoid
arthritis
Leaf paste is taken, sometimes extract is
consumed orally.
Murraya paniculata (L.)
Jack (Rutaceae); SSA-258
Kamini Flower Body ache Infusion is taken internally.
Murraya koenigii (L.)
Spreng. (Rutaceae); SSA-
238
Karipata Root Skin
inflammation
Root paste is applied externally.
Nigella sativa L.
(Ranunculaceae); SSA-243
Kailla jira Seed Asthenia Fried seeds are eaten with rice.
Nymphaea nouchali Burm. f.
(Nymphaeaceae); SSA-263
Haluk Flower Skin cut and
laceration
Floral paste is mixed with plant extract of
Cynodon dactylon for wound healing and
blood clotting.
Ocimum sanctum L.
(Lamiaceae); SSA-201
Tulshi Leaf Acute cough Raw leaves are eaten.
Root Chronic cough,
sore throat
Decoction of roots is taken internally.
Oroxylum indicum (L.) Kurz
(Bignoniaceae); SSA-278
Kanaidingi Fruit Jaundice Infusion is taken orally.
Flower Jaundice Infusion is taken orally.
62 AHMED et al.
Table 2 Contd.
Taxa and voucher Local name Parts
used
Ailments Mode of application
Oxalis articulata Savigny
(Oxalidaceae); SSA-240
Khud Manik Whole
plant
Flatulence Extract is taken orally.
Oxalis corniculata L.
(Oxalidaceae); SSA-241
Khud Manik Whole
plant
Flatulence Extract is taken orally.
Phyllanthus acidus (L.)
Skeels (Phyllanthaceae);
SSA-225
Orboroi Leaf Pox Leaf paste is applied externally.
Phyllanthus emblica L.
(Phyllanthaceae); SSA-265
Aamloki Fruit Anorexia Raw fruits are eaten, sometimes fruit juice is
taken orally.
Phyllanthus reticulatus Poir.
(Phyllanthaceae); SSA-272
Sitkari Stem Helminthiasis Extract is used internally, sometimes mixed
with extract of Tinospora crispa.
Piper betle L. (Piperaceae);
SSA-227
Pan Leaf Constipation Juice is taken orally, especially by children.
Psidium guajava L.
(Myrtaceae); SSA-217
Hobri,
Peyara
Leaf Toothache Leaf juice is taken internally.
Ricinus communis L.
(Euphorbiaceae); SSA-228
Bhenna Bark Nausea Bark is wrapped around the neck of children.
Saccharum officinarum L.
(Poaceae); SSA-252
Aakh Stem Jaundice Juice is taken internally, sometimes
accompanied with coconut water.
Scoparia dulcis L.
(Plantaginaceae); SSA-231
Bondhone Leaf Diarrhoea Leaf juice is taken internally.
Whole
plant
Diabetes Infusion of whole plant is taken regularly to
reduce blood sugar level.
Sesamum indicum L.
(Pedaliaceae); SSA-224
Til Seed Dysentery Crushed seeds are taken internally, sometimes
seed oil is consumed.
Smilax perfoliata A. DC.
(Smilacaceae); SSA-269
Kumarilot Root Dhat syndrome Decoction of root is taken internally.
Stephania japonica (Thunb.)
Miers (Menispermaceae);
SSA-211
Mochilot Whole
plant
Rheumatoid
arthritis
Used to wrap the painful areas of the body,
applied externally.
Leaf Body ache Leaf paste is applied externally.
Diarrhoea Leaf juice is taken internally.
Streblus asper Lour.
(Moraceae); SSA-222
Sheura Root Jaundice Decoction of roots is consumed with the bark
extract of Mangifera indica.
Swietenia mahagoni (L.)
Jacq. (Meliaceae); SSA-226
Mahogoni Root Diabetes Extract is taken internally with plant extract of
Coccinia grandis.
Tagetes erecta L.
(Asteraceae); SSA-242
Genda Leaf Toothache Leaf paste is applied externally.
Tamarindus indica L.
(Fabaceae); SSA-254
Tetul Fruit Hypertention Juice is orally consumed after mixing with
Allium sativum bulb extract.
Terminalia arjuna (Roxb. ex
DC.) Wight & Arn.
(Combretaceae); SSA-230
Arjun Bark Cardiovascular
problem
Decoction of bark is orally taken with fruit
juice of Phyllanthus emblica and Terminalia
bellirica.
Tinospora crispa (L.) Hook.
f. & Thom.
(Menispermaceae); SSA-249
Padma
gurunchi
Leaf Allergy Leaf paste applied externally.
Whole
plant
Helminthiasis Infusion of whole plant is taken orally.
Vachellia nilotica (L.)
Hurter & Mabb. (Fabaceae);
SSA-273
Babla Flower Gastro-intestinal
disorder
Extract is taken orally to reduce dyspepsia and
flatulence.
Xanthium strumarium L.
(Asteraceae); SSA-259
Ghagra Root Dhat syndrome Decoction of root is often mixed with Bombax
ceiba root extract and taken orally at night.
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 63
Table 2 Contd.
Taxa and voucher Local name Parts
used
Ailments Mode of application
Xanthosoma sagittifolium
(L.) Schott (Araceae); SSA-
246
Kailla Kachu Stem Skin laceration
and wound
healing
Extract is applied externally to the affected
area.
Zingiber officinale Roscoe
(Zingiberaceae); SSA-210
Ada Rhizome
Digestive
disorder
Eaten raw, sometimes infusion is taken orally.
Cold and cough Taken orally along with honey and Nigella
sativa seeds.
Hypertention Raw rhizome is taken with tea.
Ziziphus mauritiana Lam.
(Rhamnaceae); SSA-237
Boroi Fruit Jaundice Juice is taken regularly.
Quantitative analyses:
Factor of informant consensus (Fic):
A total of 13 major ailments were evaluated using Fic values that ranged from 0.975 to 0.984
(Table 3). For different ailments the number of use reports varied from 102 to 1305, while the
number of taxa varied from 3 to 29. Among the various ailments, digestive and gastrointestinal
disorders exhibited the highest number of taxa (29), followed by skin diseases (23 taxa), and the
lowest number of taxa (3) was recorded for anorexia, colorectal problems, and asthenia (Fig. 3).
Table 3. Consensus of agreement on the uses of medicinal plants among informants.
No. Category of diseases Most cited species No. of use
reports
No. of
taxa
FIC
1 Respiratory tract disorders (acute and
chronic cough, runny nose, sore throat,
asthma, bronchitis etc.)
Justicia adhatoda 506 9 0.984
2 Cardiovascular diseases (hyperlipidemia,
hypertention, arrhythmia)
Terminalia arjuna 243 5 0.983
3 Helminthiasis Cuscuta reflexa 179 4 0.983
4 Asthenia (body weakness) Dillenia indica 121 3 0.983
5 Male sexual disorders (dhat syndrome) Bombax ceiba 171 4 0.982
6 Colorectal problems (anal fissure, piles) Xanthium strumarium 108 3 0.981
7 Anorexia (loss of appetite) Phyllanthus emblica 108 3 0.981
8 Female sexual disorders (oligomenorrhea,
labor pain, menstrual problems)
Mimosa pudica 102 3 0.98
9 Rheumatoid arthritis Stephania japonica 250 6 0.979
10 Digestive and gastrointestinal diseases
(gastritis, flatulence, diarrhoea, dysentery,
jaundice, constipation, stomach ache)
Cajanus cajan 1305 29 0.978
11 Myalgia (general body ache) and toothache Chenopodium album 328 8 0.978
12 Skin problems (inflammation, arthropod
sting, prickly heat rash, allergies, eczema,
acute and chronic dermatitis, laceration,
thermal burning)
Colocasia esculenta 979 23 0.977
13 Diabetes Curcuma longa 333 9 0.975
64 AHMED et al.
In a recent study in Sherpur sadar and Sreebardi sub-districts, Suchana et al. (2022) showed
that the highest number of taxa were used in digestive and gastrointestinal disorders which further
corroborated our findings. In the present study, the highest Fic value was recorded for respiratory
tract disorders incorporating acute and chronic cough, runny nose, sore throat, asthma and
bronchitis. Justicia adhatoda was found to be the most cited species for this disease category. The
second highest value (0.983) was observed in three different disorders, such as cardiovascular
diseases, helminthiasis and asthenia. Bombax ceiba was found as the most cited species to treat
male sexual disorders which was congruent with previous study (Hossain and Rahman, 2018). In
the case of rheumatoid arthritis, the Fic value was recorded 0.979 with Stephania japonica as the
most cited species which was found to be concordant with Mollik et al. (2010) who reported the
same use in Ashuganj sub-district of Brahmanbaria district.
Fig. 3. Number of taxa used to treat major ailments based on informant consensus factor.
Fidelity level (FL):
The present investigation revealed that the fidelity level values ranged from 41.2 to 100%
(Table 4). A total of 11 species showed fidelity levels of 100%, viz. Bombax ceiba, Centella
asiatica, Chenopodium album, Colocasia esculenta, Cuscuta reflexa, Cynodon dactylon,
Lawsonia inermis, Phyllanthus emblica, Ricinus communis, Streblus asper and Terminalia arjuna.
The ailments of these top scoring species were anorexia, body ache, cardiovascular disease,
dermatitis, dhat syndrome, gastro-intestinal disorder, helminthiasis, jaundice, nausea and skin
problems, respectively. Higher level of fidelity for multiple species was found concordant with
some recently published studies (Mitu et al., 2022; Suchana et al., 2022).
Citation frequency (CF):
The citation frequency was estimated for all 79 species and amongst them, top 15 scored
species were presented in Table 5. Citation frequency was recorded 100% for Justicia adhatoda,
Bombax ceiba, Cajanus cajan, Cuscuta reflexa and Stephania japonica. Citation frequency was
found higher than 80% for nine ailments, such as acute and chronic cough, jaundice, skin
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 65
laceration, rheumatoid arthritis, helminthiasis, diarrhoea, chronic dysentery, pox and diabetes (Fig.
4). The highest number of taxa was recorded for respiratory tract disorder, while the lowest was
found for four ailments including diarrhoea, chronic dysentery, pox and diabetes. Maximum
informants cited internal application for the most cited species which was in agreement with
previous studies (Hossain and Rahman, 2018; Mitu et al., 2022). Plants with high citation rates
could be explored further for the identification of novel phytoconstituents, which could potentially
be utilized in the development and discovery of novel therapeutics.
Table 4. Fidelity level values of frequently cited species along with major ailments.
Ailments Species No. of
informants (Ip)
Total no. of
informants (Iu)
Fidelity level
(%)
Anorexia Phyllanthus emblica 41 41 100
Body ache Chenopodium album 42 42 100
Cardiovascular disease Terminalia arjuna 48 48 100
Dermatitis Lawsonia inermis 47 47 100
Dhat syndrome Bombax ceiba 51 51 100
Gastro-intestinal disorder Centella asiatica 51 51 100
Helminthiasis Cuscuta reflexa 51 51 100
Jaundice Streblus asper 47 47 100
Nausea Ricinus communis 45 45 100
Blood clotting Colocasia esculenta 51 51 100
Skin laceration and wound healing Cynodon dactylon 51 51 100
Rheumatoid arthritis Stephania japonica 51 75 68.0
Jaundice Cajanus cajan 51 78 65.3
Toothache Glycosmis pentaphylla 36 60 60.0
Gynecological disorder Mimosa pudica 45 80 56.2
Asthenia Dillenia indica 43 81 53.0
Piles Xanthium strumarium 39 75 52.0
Diabetes Curcuma longa 49 96 51.0
Acute and chronic cough Justicia adhatoda 51 102 50.0
Allergy Tinospora crispa 42 102 41.2
Fig. 4. Number of taxa with citation frequency higher than 80% used to treat various ailments.
66 AHMED et al.
Table 5. Citation frequency (CF) of some selected medicinal plant species of the study area.
Species Ailments No. of citation Citation frequency (%)
Justicia adhatoda Acute and chronic cough 51 100
Bombax ceiba Dhat syndrome 51 100
Cajanus cajan Jaundice 51 100
Cuscuta reflexa Helminthiasis 51 100
Stephania japonica Rheumatoid arthritis 51 100
Litsea glutinosa Chronic dysentery 49 96.1
Curcuma longa Diabetes 49 96.1
Terminalia arjuna Cardiovascular disease 48 94.1
Lawsonia inermis Dermatitis 47 92.1
Mimosa pudica Gynecological disorder 45 88.2
Ricinus communis Nausea 45 88.2
Phyllanthus emblica Anorexia 41 80.4
Xanthium strumarium Piles 39 76.4
Tinospora crispa Allergy 37 72.5
Glycosmis pentaphylla Toothache 36 70.5
Active sites of the receptor macromolecule
A single pocket was detected as the active site of the JAK1 protein from the CASTp 3.0
server. The surface area of the active pocket was estimated to be 309.764 Å2 and volume to be
209.690 Å3. The active site resides were Arg27, Leu29, Gly30, Glu31, Gly32, Val37, Ala54,
Lys56, Glu73, Leu77, Val86, Met104, Glu105, Phe106, Leu107, Pro108, Ser109, Gly110, Ser111,
Glu114, Tyr115, Lys118, Arg155, Asn156, Leu158, Gly168, Asp169 and Phe170. Hence, a total
of 28 amino acid residues were predicted as active sites by the CASTp 3.0 server (Fig. 5A).
SCFBio server predicted a total of 39 cavities from where the 8th cavity was considered for
current investigation. The volume of the cavity was estimated as 854 Å3. The server did not
provide any data on the surface area of the cavity. Cavity point was provided to be -16.514, -2.456
and -5.108 for X, Y and Z axes, respectively. The active site residues were Met139, Asp140,
Tyr141, Leu142, Gly143, Ser144, Gln146, Tyr147, Val148, Arg150, Ile176, Glu177, Thr178,
Asp179, Lys180, Glu181, Tyr182, Tyr183, Pro198, Glu199, Gln203, Lys205, Phe206, Tyr207,
Ile208, Ala209, Val212, Lys278, Glu281, Phe282, Gln283, Pro284, Ser285, Asn286, Thr288,
Ser289, Phe290, Gln291, Asn292 and Glu295. Active sites were visualized using Discovery
Studio visualizer as shown in Figure 5B.
Molecular docking and interaction analyses:
Molecular docking analysis was performed for bioactive phytochemicals of Stephania
japonica targeting rheumatoid arthritis. S. japonica was selected as it showed a very high level of
citation frequency and Fic value. The docking analysis unveiled binding affinities ranging from -
5.3 to -9.7 kcal/mol. The control drug Ibuprofen scored -7.0 kcal/mol. Of the 30 phytochemicals
investigated, nearly 60% (18) compounds scored higher than the control and the remaining 40%
(12) scored lower than the control (Table 6). This indicates the potential of Stephania japonica as
a source of next generation therapeutics targeting rheumatoid arthritis. The compound
Oxostephanine with a molecular weight of 305.3 g/mol showed the highest binding affinity (-9.7
kcal/mol) followed by Trilobine (-8.7 kcal/mol) and Epistephanine (-8.6 kcal/mol). Two
dimensional chemical structures of the top three compounds along with the control Ibuprofen are
visualized in Figure 6. Among the top three potential drug candidates, molecular weight was
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 67
found to be highest for Epistephanine (606.7 g/mol) followed by Trilobine (562.7 g/mol) and
Oxostephanine (305.3 g/mol). In contrary, the lowest molecular weight was observed in Viburnitol
(164.16 g/mol) among all the phytocompounds, and this compound also exhibited the lowest
binding affinity (-5.3 kcal/mol). The docked complexes for the top three compounds along with
the control have been shown in Figure 7.
Fig. 5. Active sites of JAK1 receptor macromolecule predicted by CASTp server (A) and SCFBio server (B).
Results of molecular interactions are depicted in Table 7. Molecular interactions were
analyzed to justify drug surface hotspots and to find potential active sites in the Janus Kinase 1
receptor which are crucial for drug design and future drug development process (Ahmed et al.,
2023). All the three top scoring compounds showed hydrophobic interactions which are vital to
ensure stability when these phytocompounds will bind with receptor macromolecule (Rahman and
Ahmed, 2022). Both the Oxostephanine and Epistephanine showed conventional hydrogen
bonding with the JAK1 protein except Trilobine. Oxostephanine interacted with Leu29 only, while
Epistephanine interacted with Asn292 and Ser289 amino acid residues (Fig. 8). These hydrogen
bonds play a pivotal role in maintaining stability in ligand-receptor interactions and ensure the
specificity of ligand binding (Rahman and Ahmed, 2022).
68 AHMED et al.
Fig. 6. Two-dimensional chemical structures of three top scoring phytochemicals with the control Ibuprofen.
A. Oxostephanine; B. Trilobine; C. Epistephanine; D. Ibuprofen.
Fig. 7. Three lead phytocompounds of Stephania japonica and the control drug with rheumatoid arthritis
protein. A. Oxostephanine-complex; B. Trilobine-complex; C. Epistephanine-complex; D. Ibuprofen-
complex (control).
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 69
Hydrogen bonds donating and accepting regions were further visualized (Fig. 9). Some common
residues such as Leu29, Val37, Ala54, Met104 and Leu158 have interacted with Ibuprofen, and
two phytochemicals, viz. Oxostephanine and Epistephanine indicating that these amino acid
residues of JAK1 could be potential drug surface hotspots for future drug discoveries.
Fig. 8. Two dimensional molecular interactions of the phytochemicals of Stephania japonica along with the
control. A. Oxostephanine; B. Trilobine; C. Epistephanine; D. Ibuprofen (control).
Molecular docking in conjunction with ethnobotanical research has drawn attention to
unveil a new window for drug discovery. In the recent past, molecular docking was applied to a
few ethnobotanical studies where Abdulrahman et al. (2022) used molecular docking to validate
the ethnobotanical outcome targeting Measles in Northern Nigeria. A total of 40 phytocompounds
were docked against Measles nucleoprotein from 21 ethnomedicinal plant species and the binding
affinities ranged from -1.3 to -9.3 kcal/mol (Abdulrahman et al., 2022). In our study, both the
upper and lower thresholds of binding affinity were higher than that of Abdulrahman et al. (2022)
which justifies accuracy and potentials of Stephania japonica phytochemicals targeting
rheumatoid arthritis. Vijayakumar et al. (2016) conducted an ethnobotanical-molecular docking
70 AHMED et al.
survey of traditional Siddha medical practitioners from Thiruvarur district focusing
hepatoprotective potentials. Vijayakumar et al. (2016) docked three commercial drugs and 12
bioactive phytochemicals from different ethnomedicinal plants against hepatitis B virus receptor,
where the binding affinities varied from -5.0 to -8.08 kcal/mol, and Luteolin (-8.08 kcal/mol) was
the best scoring compound. Our investigation revealed a significantly higher binding affinity of
-9.7 kcal/mol compared to other studies providing additional support to our findings
(Abdulrahman et al., 2022; Vijayakumar et al., 2016).
Fig. 9. Three dimensional molecular interactions of the phytochemicals of Stephania japonica and the control
drug showing hydrogen bonds donating and accepting regions. A. Oxostephanine; B. Trilobine; C.
Epistephanine; D. Iburprofen (control).
Molecular dynamics simulation
Structural flexibility analysis unraveled satisfactory results for the tested protein-ligand
complexes in comparison with the control drug Ibuprofen-complex. Root Mean Square
Fluctuation (RMSF) values were found minimal for all the three lead candidates (Fig. 10). For
Oxostephanine, mean RMSF was recorded as 0.96 Å. Trilobine and Epistephanine revealed mean
RMSF values of 0.97 Å and 0.90 Å, respectively during the 10 ns simulation trajectory. Ibuprofen
showed mean RMSF of 0.82 Å which was slightly lower than the three lead candidates. This close
proximity of mean RMSF values indicated nearly same structural stability and flexibility of the
tested lead phytocompounds as compared to the control drug. The average RMSF distance in the
binding pockets was also estimated that unveiled a mean RMSF of 0.47 Å, 0.65 Å, 0.76 Å and
0.32 Å in Oxostephanine, Epistephanine, Trilobine and Ibuprofen, respectively. All the values
were found below the standard threshold of 2.5 Å which denoted very good structural stability of
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 71
Table 6. Molecular docking analysis of bioactive phytocompounds of Stephania japonica targeting rheumatoid
arthritis.
Phytocompounds PubChem
CID
Molecular
formula
Molecular weight
(g/mol)
Binding affinity
(kcal/mol)
1. Oxostephanine 343547 C18H11NO4 305.3 -9.7
2. Trilobine 169007 C35H34N2O5 562.7 -8.7
3. Epistephanine 5317122 C37H38N2O6 606.7 -8.6
4. Isotrilobine 12310578 C36H36N2O5 576.7 -8.4
5. Isochondrodendrine 197726 C36H38N2O6 594.7 -8.3
6. Stepinonine 135778935 C36H34N2O7 606.7 -8.2
7. Cyclanoline 3082134 C20H24NO4
+ 342.4 -8.2
8. Obamegine 441064 C36H38N2O6 594.7 -8.2
9. Bebeerine 12300019 C36H38N2O6 594.7 -8.1
10. Tetrandrine 73078 C38H42N2O6 622.7 -8.1
11. Fangchinoline 73481 C37H40N2O6 608.7 -8.1
12. Oxostephabenine 181354 C27H27NO8 493.5 -8.0
13. Hypoepistephanine 282017 C36H36N2O6 592.7 -8.0
14. Insularine 10348927 C38H40N2O6 620.7 -7.7
15. Stebisimine 3083913 C36H34N2O6 590.7 -7.6
16. Steponine 15432819 C20H24NO4
+ 342.4 -7.5
17. Cycleanine 121313 C38H42N2O6 622.7 -7.4
18. Lanuginosine 97622 C18H11NO4 305.3 -7.3
19. Aknadinine 159966 C20H25NO5 359.4 -6.8
20. Stepharine 98455 C18H19NO3 297.3 -6.6
21. Metaphanine 12312776 C19H23NO5 345.4 -6.5
22. Homostephanoline 627343 C20H25NO5 359.4 -6.5
23. Aknadicine 442156 C19H23NO5 345.4 -6.4
24. Oxostephasunoline 621065 C20H25NO7 391.4 -6.3
25. Stephasunoline 618654 C20H27NO6 377.4 -6.2
26. Prometaphanine 91895299 C20H25NO5 359.4 -6.2
27. Oxostephamiersine 101673501 C21H25NO7 403.4 -6.1
28. Hasubanonine 442246 C21H27NO5 373.4 -6.0
29. Epistephamiersine 91895297 C21H27NO6 389.4 -5.9
30. Viburnitol 101715 C6H12O5 164.16 -5.3
Ibuprofen (Control) 3672 C13H18O2 206.2 -7.0
Table 7. Molecular interaction analysis of the top scoring three phytocompounds of Stephania
japonica along with the control drug.
Ligands Residues in
hydrogen bonding
Residues in hydrophobic
interactions
Binding affinity
(kcal/mol)
Oxostephanine Leu29 Leu29, Val37, Ala54,
Val86, Met104, Leu158
-9.7
Trilobine No residues Leu29, Arg27, Glu114,
Arg155, Asn156, Asp169
-8.7
Epistephanine Asn292, Ser289 Asp140, Gly143, Glu181,
Ile208, Ala209, Phe290
-8.6
Ibuprofen (Control) Ser111, Leu158 Leu29, Val37, Ala54,
Met104
-7.0
72 AHMED et al.
the lead compounds in the binding cavity of the receptor macromolecule. This further justified
their potentials to be effective drug candidates against rheumatoid arthritis. Superimposed
simulation structures of each complex have been demonstrated in Figure 10.
Fig. 10. Molecular dynamics simulation showing superimposed simulated structures and regional flexibility
profiles of Stephania japonica phytochemicals – Oxostephanine (A), Trilobine (B), Epistephanine (C)
and control drug Ibuprofen (D).
This present study combines the principles of molecular docking and dynamics simulation
with ethnobotanical knowledge in Bangladesh, marking the first of its kind in this field of
research. The study uncovered some novel findings about the traditional medicinal uses of various
ETHNOBOTANICAL STUDY AND MOLECULAR DOCKING 73
plants of Gafargaon sub-district. Remarkably, Aphanamixis polystachya leaf paste was found to be
effective in treating arthritis; Calotropis procera boiled leaf inhalation was used to alleviate
asthma symptoms; Datura metel raw fruit was traditionally employed to address eczema, and
Xanthium strumarium root was used to tackle dhat syndrome. The study unveiled several threats to
medicinal plant species including habitat destruction and fragmentation, deforestation, over-
exploitation, insufficient awareness among local communities about the need for conserving
species diversity, and the planting of exotic species. Our findings further highlight the pressing
need for conservation efforts and sustainable management practices to safeguard the future of
these valuable medicinal plants. To ensure the preservation of valuable medicinal plant species in
the surveyed area, various protective measures should be implemented. These might include
establishing nurseries to propagate important and endangered medicinal plants, creating
distribution maps with precise coordinates for key species, and employing ex-situ conservation
strategies to safeguard the medicinal plants in the study area, thereby promoting their sustainable
use and development.
Species that exhibited the highest citation frequency, fidelity level and Fic value could be
subjected to in vitro studies for phytochemical screening. In addition, molecular docking and
dynamics simulation analyses might open up new avenues for the designing and discovery of
novel drugs from Stephania japonica phytocompounds to treat rheumatoid arthritis. Our findings
provide the baseline data to bridge the gap between traditional healers and scientific communities.
Based on our findings, we recommend conducting additional in vitro, in vivo, and in silico studies
on the ethnomedicinal plants identified in this venture, in order to further explore their potential
for enhancing healthcare management and drug discovery.
Acknowledgements
The authors extend their appreciation to the Researchers Supporting Project number
(RSP2023R306), King Saud University, Riyadh, Saudi Arabia. The first and second authors are
thankful to the local people and folklore practitioners of Gafargaon sub-district of Mymensingh
district for their cooperation and sharing information about the medicinal uses of plants.
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(Manuscript received on 2 January 2023; revised on 6 June 2023)