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Phytochemical 6-Gingerol -A promising Drug of choice for COVID-19

May 2020
International Journal of Advanced Science and Engineering 06(04)

DOI:10.29294/IJASE.6.4.2020.1482-1489

Authors:

Thirumalaisamy Rathinavel

Sona College of Arts and Science

Palanisamy Srinivasan

Mahendra Arts & Science College

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COVID-19 Proteins Targets and its 3D Docking Pose with 6-gingerol

…

Molecular interaction of 6-gingerol with different COVID-19 Protein targets

…

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Int. J. Adv. Sci. Eng. Vol.6 No.4 1482-1489 (2020) 1482 E-ISSN: 2349 5359; P-ISSN: 2454-9967

Thirumalaisamy Rathinavel et al.,

International Journal of Advanced Science and Engineering www.mahendrapublications.com

Phytochemical 6-Gingerol – A promising Drug of choice

for COVID-19

Thirumalaisamy Rathinavel1, Murugan Palanisamy2,

Srinivasan Palanisamy1, Arjunan Subramanian*1, Selvankumar Thangaswamy*1

1Department of Biotechnology, Mahendra Arts & Science College (Autonomous),

Namakkal (Dt) -637 501, Tamil Nadu, India

2Nichi Asia Life Sciences Sdn Bhd, Kota Damansara, Malaysia

1. INTRODUCTION

Corona virus is the group of viruses that have a

crown-like appearance when viewed under the

electronic microscope. Corona viruses cause

respiratory tract infections in humans, which can

cause a wide range of illnesses from the mild

common cold to lethal SARS and MERS. There are no

vaccines and anti-viral drugs are available yet to

treat corona viral infections. Corona virus possesses

positive sense single-stranded enveloped RNA as

their genetic material. The genome of corona virus is

the largest group among the viruses is host specific

which is based on the receptor specificity of their S-

Protein. It is an enveloped virus that is made up of

glycoprotein.

In December 2019, the novel corona virus

(2019-nCoV or SARS CoV-2), cause corona virus

disease 2019 (COVID-19) in humans, was an

outbreak in Wuhan, China. The epidemic disease of

SARS CoV-2 in Wuhan has occurred human to human

transmission among close contacts, which becomes

emerged as a pandemic disease from January 2020

spread through international travelers across the

different countries and enters almost all the

countries except few of them. As of 10th April 2020,

there have been over 1.6 million cases with over 0.1

million deaths for the COVID-19 outbreak worldwide

[1] However, there are currently no effective

medications against SARS CoV-2. Several national

and international research groups are working on

the development of vaccines to prevent and treat the

SARS CoV-2, but effective vaccines are not available

yet. There is an urgent need for the development of

effective prevention and treatment strategies for

SARS CoV-2 outbreak. Indian people are consuming

Indian traditional medicinal herb extract and Indian

spices to boost the immune system to fight COVID -

19.

Ginger (Zingiber officinale) is the herbaceous

plant native to South Asia belonging to the family of

Zingiberaceae. The characteristic pungent flavor of

the ginger rhizome is used extensively in foods and

beverages [2]. Ginger is a common Indian spice and

traditional medicinal plants have important

pharmacologic activities such as antibacterial,

antiviral, anti-hypertensive, antioxidant, analgesic

and antipyretic properties [3]. Ginger has been

proved to be effective on various viruses [4-8].

Ginger rhizome possesses several outstanding

bioactive non-volatile phenolic compounds such as

gingerols, paradols, shogaols, and zingerones [9].

Ginger is one of the best choices of bioactive Phyto-

compound in traditional medicine in Ayurvedic,

Chinese and Unani systems to treat different diseases

in ancient times.

6-gingerol is a bioactive phenolic

phytocompound found in the fresh ginger rhizome.

6-gingerol is a promising drug candidate to treat

various diseases associated with inflammation,

ABSTRACT: Recently, a novel corona virus (COVID-19), identified as one of the acute respiratory syndrome

corona virus (SARS CoV-2) and emerged as a pandemic disease in Asia and European countries in 2020. The

World Health Organization (WHO) has declared the current outbreak as a global public he alth crisis. Due to the

variability in the amino acid and amino acid sequences, it does not develop suitable vaccines against the viral

proteins. Hence, the inhibitor to be developed against the viral proteins of the corona virus is a promising idea to

develop structure-based drugs from the photochemical compounds. Here, the novel drug was identified and well

studied against the viral receptors by using the molecular docking technique. Phytocompound 6-gingerol

possesses excellent drug likeliness with zero violations and very good pharmacokinetic properties with the

highest binding affinity ranging from -2.8764 KJ/mol to -15.7591 KJ/mol with various COVID-19 viral protein

targets. Our study reveals that 6-gingerol from ginger could act as a promising drug of choice to treat COVID-19.

KEYWORDS: SARS-CoV-2; COVID-19; 6-Gingerol, corona virus; respiratory infection.

*Corresponding Authors: pavima08@gmail.com & selvankumar75@gmail.com

Received: 18.01.2020 Accepted: 21.03.2020 Published on: 18.04.2020

Int. J. Adv. Sci. Eng. Vol.6 No.4 1482-1489 (2020) 1483 E-ISSN: 2349 5359; P-ISSN: 2454-9967

Thirumalaisamy Rathinavel et al.,

International Journal of Advanced Science and Engineering www.mahendrapublications.com

cancer, and viral disease. Fresh ginger possesses

anti-viral activity against human respiratory

syncytial virus due to the presence of bioactive

phenolic phytocompound 6-gingerol [10]. Hence, the

present study aims to examine phytocompound 6-

gingerol from the ginger plant (Zingiber officinale)

that could act as a promising drug against COVID-19

proteins and screened through in silico approach.

MATERIALS AND METHOD

1.1. Ligand generation

The 2D structure of Zingiber officinale

phytocompound 6-gingerol (CID 442793) was

retrieved from Pubchem, a database of chemical

molecules [11]. The retrieved 2D SDF file format of

6-gingerol was submitted to “Online SMILES

convertor and Structure file generator‟ [12] and

converted into 3D SDF format.

1.2. Drug Likeliness and Absorption,

Distribution, Metabolism, Extraction and

Toxicity [ADME] Calculations

Swiss ADME online server was used to calculate

Drug Likeliness parameters. Drug likeliness of the

phytocompounds gingerol was examined based on

Violations of the following rules such as Lipinski,

Ghose, Veber, Egan, and Muegge. Pharmacokinetic

properties of phytocompounds gingerol were

screened by preADMET is a web-based application to

determine the pharmacological efficiency of

phytocompounds. PreADMET predicts the various

parameters associated with ADME and toxicity

behavior of phytocompounds.

1.3. Preparation of Receptor and its Binding Site

Novel corona viral (SARS-CoV-2 or COVID-19)

Proteases, Spike protein, RNA binding protein, N-

terminal RNA binding domain are the key viral

molecules involved in attachment and replication

and reproduction of viral particle in the human host

cells. These Protein target molecules served as a

novel target to inhibit the viral lifecycle in human

host cells. Three-dimensional structures of SARS

CoV-2 nine molecules of main proteases (5R7Y,

5R80, 5R81, 5R83, 5R84, 6LU7, 6LVN, 6M03, 6Y84),

one spike protein (6VSB), one RNA binding protein

(6W4B) and one N-terminal binding domain (6M3M)

was retrieved from RCSB PDB database

(https://www.rcsb.org/) [13].To determine the

binding affinities between the ligand and receptor,

the amino acids with the binding pockets were

predicted at the Q-site finder server [14].

1.4. Flexible docking

The generated gingerol SDF structures were

docked with the predicted binding site of all selected

protein target binding site by using teaching version

of FlexX [15] with following parameters i) default

general docking information ii) base placement using

triangle matching, iii) scoring of full score

contribution and threshold of 0.70 iv) Chemical

parameters of clash handling values for protein-

ligand clashes with maximum allowed overlap

volume of 2.9 A03 and intra-ligand clashes with clash

factor of 0.6 and considering the hydrogen in

internal clash tests. v) Default docking details values

of 200 for both the maximum number of solutions

per iteration and a maximum number of solutions

per fragmentation.

1.5. Prediction of ligand-receptor interactions

The interactions of phytocompound gingerol

with twelve SARS CoV-2 proteins targets in the

docked complex were analyzed by the pose-view of

LeadIT [16]. 2D and 3D pose view of SARS COV-2

protein target-phytocompound gingerol was

generated and analyzed using LeadIT.

1.6. Density Functional Theory DFT Analysis

DFT calculation for phytocompound gingerol

was performed using Gaussian 09 software. DFT

used to calculate HOMO–LUMO orbital providing

energy gap between highest occupied molecular

orbital (HOMO) and lowest unoccupied molecular

orbital (LUMO) providing high and low electron

density regions on the compounds.

2. RESULT AND DISCUSSION

2.1. Drug Likeliness and ADME Calculation

Drug likeliness calculation for phytocompound

gingerol was made in Swiss ADME server and

revealed that 6-gingerol possess a molecular weight

of 294.39 g/mol, the number of hydrogen bond

acceptor and donor are 4 & 6 respectively. Gingerol

also possess excellent TPSA(topological polar surface

area), lipophilicities (iLog P) and water solubility

(Log S ESOL) values of 66.76, 3.48 & -2.96

respectively which proved there are nil (zero)

violations for drug likeliness rules such as Lipinski,

Ghose, Veber, Egan, and Muegge essential for better

drug likeliness properties

ADME property of gingerol calculated by

preADMET web-based application revealed that very

good pharmacokinetic properties such as absorption,

bioavailability and distribution parameters of 6-

gingerol such as HIA 86.75%, the pure water

solubility of 0.3460 mg/ml, 100% plasma protein

binding, which are tabulated and presented in Table

Figure 1- 2D & 3D structures of 6-Gingerol

Int. J. Adv. Sci. Eng. Vol.6 No.4 1482-1489 (2020) 1484 E-ISSN: 2349 5359; P-ISSN: 2454-9967

Thirumalaisamy Rathinavel et al.,

International Journal of Advanced Science and Engineering www.mahendrapublications.com

Table 1 - ADME properties of 6-gingerol from

ginger plant

ABSORPTION

Human intestinal absorption (HIA, %)

86.75456

Caco-2 cell permeability (nm/sec)

13.5496

MDCK cell permeability (nm/sec)

0.627041

skin permeability (logKp, cm/hour)

-2.36594

BIOAVAILABILITY

Buffer solubility (mg/ml)

0.7135

Pure water solubility (mg/ml)

0.3460

DISTRIBUTION

Plasma protein binding (%)

100

Blood-brain barrier penetration

0.69481

2.2. Docking Study

Different COVID-19 target proteins (proteases,

spike protein, RNA binding protein) and their

docking score and 3D pose with 6-gingerol are

presented in Table 2 and their detailed molecular

interaction between them is tabulated and presented

in Table 3 & Figure 2.

The results of a flexible docking study by flexX

software between COVID-19 viral targets and

gingerol was exhibit the binding affinity and docking

score ranging from -2.8764 KJ/mol to -15.7591

KJ/mol. Gingerol exhibit the highest binding affinity

(-15.7591 KJ/mol) with 5R7Y COVID-19 main

protease essential for replication and reproduction

of SARS Cov-2. Corona Viral protease 5R7Y residues

such as His 164, Glu166, Thr190, Gln192 from

hydrogen-bonded interaction with phytocompound

gingerol, it also forms form non bonded interaction

with the residues of His164, Met 165, Glu166,

Leu167, Pro168, Arg188, Gln189, Thr190.

Gingerol exhibits binding affinity of -11.4082

KJ/mol, -12.9523 KJ/mol and -12.8835 KJ/mol with

COVID-19 viral RNA binding protein (6W4B), N-

Terminal RNA Binding Protein (6VSB), Spike

glycoprotein (6M3M) respectively. Molecular

interaction between COVID-19 viral spike

glycoprotein with Gingerol forms hydrogen-bonded

interaction with Glu63, Arg89, Thr92, Asp129

residues and form non bonded interaction with

Glu63, Lys66, Arg89, Thr92, Leu168, Pro169

residues of COVID-19 spike glycol protein.

Molecular interaction between COVID-19 viral

RNA binding protein with Gingerol makes hydrogen

bonded interaction with Val42, Pro58, Ser60, Thr68

residues and form non bonded interaction with

Arg40, Phe41, Val42, Phe57, Pro58, Lys59, Ser60,

Ile66, Thr68, Ile92 residues of COVID-19 spike glycol

protein.

The previous study reported that several

phytocompounds of flavonoids and phenolic

substances possess antiviral activities [17-19]

especially 6-gingerol possess antiviral activities. Siti

Khaerunnisa et al. [20] reported that 6-gingerol

binds with the COVID-19 main protease active sites

with the binding affinity of -5.40 K.Cal/mol.

Table 2 . COVID-19 Proteins Targets and its 3D Docking Pose with 6-gingerol

S.No

COVID-19

Protein

Targets

Details

Protein 3D Structure

Docking

Score

(KJ/mol)

Docking

5R7Y

Crystal Structure of

COVID-19 main

protease in

complex with

Z45617795

-15.7591

5R80

Crystal Structure of

COVID-19 main

protease in

complex with

Z18197050

-7.0885

Int. J. Adv. Sci. Eng. Vol.6 No.4 1482-1489 (2020) 1485 E-ISSN: 2349 5359; P-ISSN: 2454-9967

Thirumalaisamy Rathinavel et al.,

International Journal of Advanced Science and Engineering www.mahendrapublications.com

5R81

Crystal Structure of

COVID-19 main

protease in

complex with

Z1367324110

-8.2021

5R83

Crystal Structure of

COVID-19 main

protease in

complex with

Z44592329

-7.4778

5R84

Crystal Structure of

COVID-19 main

protease in

complex with

Z31792168

-9.5168

6LU7

COVID-19 main

protease in

complex with an

inhibitor N3

-2.8764

6LVN

Structure of the

2019-nCoV HR2

Domain

-4.5961

6M03

The crystal

structure of

COVID-19 main

protease in apo

form

-8.6837

Int. J. Adv. Sci. Eng. Vol.6 No.4 1482-1489 (2020) 1486 E-ISSN: 2349 5359; P-ISSN: 2454-9967

Thirumalaisamy Rathinavel et al.,

International Journal of Advanced Science and Engineering www.mahendrapublications.com

6M3M

SARS-CoV-2

nucleocapsid

protein N-terminal

RNA binding

domain

-12.9523

6VSB

Prefusion 2019-

nCoV spike

glycoprotein with a

single receptor-

binding domain up

-12.8835

6W4B

Nsp9 RNA binding

protein of SARS

CoV-2

-11.4082

6Y84

SARS-CoV-2 main

protease with

unliganded active

site (2019-nCoV,

coronavirus

disease 2019,

COVID-19)

-9.7625

2.3. DFT Study

DFT study is used to explain the accurate

structural and electronic properties of

phytocompounds. The electronic distribution

phytocompound 6-gingerol could provide a clear

picture of SARS CoV-2 protein-gingerol interactions,

which will be useful to explore the inhibition

potentials of the phytocompound 6-gingerol. HOMO

and LUMO orbital energies of 6-gingerol are shown

in Figures 3 & 4. The calculated various HOMO-

LUMO orbital energies are presented in Table 4.

The localization of HOMO and LUMO orbitals in

the compound is very important in intermolecular

interactions with SARS CoV-2 protein targets. 6-

gingerol (-0.20606eV, 0.10303eV, and 9.3187eV)

showed more stability and biological activity as it

shows less energy gap, low hardness, and more

softness. Thus the DFT calculations performed here

better evidence highest binding affinity of 6-gingerol

with SARS CoV-2 protein targets in molecular

docking.

Similar comparative DFT study of phytochemical

constituents of present in the bark extract of Ficus

racemosa β-Amyrin (-0.06277eV, 0.031385eV and

31.86235eV) showed more stability and biological

activity as it shows less energy gap, low hardness,

and more softness followed by Betulinic acid (-

0.23987eV, 0.119935eV and 8.33784eV) and

Stigmasterol (-0.26925 eV, 0.134625 eV and 7.42804

eV) [21]. It was possible to characterize the

compounds as well as their characteristics of

electron donor/electron acceptor compared with

other biological properties of the phytocompound by

DFT analysis.

Int. J. Adv. Sci. Eng. Vol.6 No.4 1482-1489 (2020) 1487 E-ISSN: 2349 5359; P-ISSN: 2454-9967

Thirumalaisamy Rathinavel et al.,

International Journal of Advanced Science and Engineering www.mahendrapublications.com

Table 3 .Molecular interaction of 6-gingerol with different COVID-19 Protein targets

S.No.

COVID-19

Proteins

Target PDB

CODE

Gingerol and COVID-19 Target Protein Interactions

Hydrogen-Bonded Interactions

Non-Bonded Interactions

5R7Y

His 164, Glu166, Thr190, Gln192

His 164, Met 165, Glu166, Leu167, Pro168, Arg188,

Gln 189, Thr190

5R80

Phe 219, Asn 221, Asn 277, Arg 279

Trp218,Trp219, Asn221, Glu270, Leu271, Asn274,

Asn277, Arg279

5R81

Asp295,Arg298,Gln299,Thr304

Met6, Phe8,Pro9, Ile152, Tyr154, Arg298, Val 303,

Thr304

5R83

Thr25, His41, Ser46, Gly143

5R84

Pro108,Gln110,His246

Pro108,Gly109,Gln110,Pro132,

Ile200,Val202,Glu240,Ile249, Phe294

6LU7

Glu270,Gly275,Arg279

Phe223,Glu270,Leu271,Asn274

6LVN

Gln13,Asn20,Lys24

Gln13,Ile16,Asn20,Ala23,Lys24,Asn27

6M03

Gln110,Thr111,Phe294

Phe8,Gln110,Asn151,Phe294,Arg298,Val303

6M3M

Glu63, Arg89, Thr92, Asp129

Glu63, Lys66, Arg89, Thr92, Leu168, Pro169

6VSB

Gln773, Gln954, Ile1013, Arg1019

Glu773, Gln954, Ile1013, Arg1014, Glu1017,

Arg1019

6W4B

Val42, Pro58, Ser60, Thr68

Arg40, Phe41, Val42, Phe57, Pro58, Lys59, Ser60,

Ile66, Thr68, Ile92

6Y84

Met6, Ile152, Tyr154

Met6, Phe8, Pro9, Ile152, Tyr154, Arg298, Gln298,

Val303, Thr304

(a) (b)

Figure 2 – Interaction plot for 6-Gingerol with

COVID-19 Protein Targets (a-l)

a).Interaction of Gingerol with 5R7Y (-15.7591

KJ/mol) b).Interaction of Gingerol with 5R80

(-7.0885 KJ/mol)

C).Interaction of Gingerol with with 5R81

(-8.2021KJ/mol)

d).Interaction of Gingerol with with 5R83

(-7.4778KJ/mol)

(e) (f)

e).Interaction of Gingerol with 5R84

(9.5168KJ/mol)

f).Interaction of Gingerol with 6LU7

(-2.8764KJ/mol)

(g) (h)

g).Interaction of Gingerol with 6LVN

(-4.5961KJ/mol)

h).Interaction of Gingerol with 6M03

(-8.6837 KJ/mol)

Int. J. Adv. Sci. Eng. Vol.6 No.4 1482-1489 (2020) 1488 E-ISSN: 2349 5359; P-ISSN: 2454-9967

Thirumalaisamy Rathinavel et al.,

International Journal of Advanced Science and Engineering www.mahendrapublications.com

(i) (j)

(i)Interaction of Gingerol with 6M3M

(-12.9523 KJ/mol)

(j)Interaction of Gingerol with 6VSB

(-12.8835KJ/mol)

(k) (l)

(k)Interaction of Gingerol with 6W4B

(-11.4082 KJ/mol)

(l)Interaction of Gingerol with 6Y84

(-9.7625 KJ/mol

Figure 3 . HOMO orbital energy for 6-Gingerol

Figure 4.LUMO orbital energy for 6-Gingerol

3. CONCLUSION

The present study was attempted to prove that

phytocompound 6-gingerol from Zingiber officinale

acts as a promising drug to treat COVID-19. 6-

Gingerol possesses excellent drug likeliness

parameters with zero violations of different rules

and very good ADME pharmacokinetic properties.

Finally, 6-gingerol proves anti-viral efficiency against

SARS CoV-2 by showing the highest binding affinity

and interaction with multiple targets of COVID-19

including Viral proteases, RNA binding protein, Spike

protein. DFT study finally evidences the reason

behind the highest binding affinity between 6-

gingerol and COVID-19 protein targets. The present

study proves that 6-gingerol from the ginger plant

could be served as a promising drug to treat the

novel COVID-19.

Acknowledgments

This work is partially supported by the PG &

Research Department of Biotechnology, Mahendra

Arts and Science College (Autonomous), and the

Department of Science and Technology, Government

of India (DST-FIST sponsored - Ref. No.

SR/FST/College-232/2014).

Table.4. HOMO LUMO Orbital Energies for 6-

Gingerol through DFT calculations

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Network pharmacology, molecular docking, and dynamics analyses to predict the antiviral activity of ginger constituents against coronavirus infection

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May 2024

COVID-19 is a global pandemic that caused a dramatic loss of human life worldwide, leading to accelerated research for antiviral drug discovery. Herbal medicine is one of the most commonly used alternative medicine for the prevention and treatment of many conditions including respiratory system diseases. In this study, a computational pipeline was employed, including network pharmacology, molecular docking simulations, and molecular dynamics simulations, to analyze the common phytochemicals of ginger rhizomes and identify candidate constituents as viral inhibitors. Furthermore, experimental assays were performed to analyze the volatile and non-volatile compounds of ginger and to assess the antiviral activity of ginger oil and hydroalcoholic extract. Network pharmacology analysis showed that ginger compounds target human genes that are involved in related cellular processes to the viral infection. Docking analysis highlighted five pungent compounds and zingiberenol as potential inhibitors for the main protease (M pro ), spike receptor-binding domain (RBD), and human angiotensin-converting enzyme 2 (ACE2). Then, (6)-gingerdiacetate was selected for molecular dynamics (MD) simulations as it exhibited the best binding interactions and free energies over the three target proteins. Trajectories analysis of the three complexes showed that RBD and ACE2 complexes with the ligand preserved similar patterns of root mean square deviation (RMSD) and radius of gyration (Rg) values to their respective native structures. Finally, experimental validation of the ginger hydroalcoholic extract confirmed the existence of (6)-gingerdiacetate and revealed the strong antiviral activity of the hydroalcoholic extract with IC

_{50}

50 of 2.727 \upmu \hbox {g}/\hbox {ml} μ g / ml . Our study provides insights into the potential antiviral activity of (6)-gingerdiacetate that may enhance the host immune response and block RBD binding to ACE2, thereby, inhibiting SARS-CoV-2 infection.

Efficacy and safety of Link Natural Sudarshana, an Ayurvedic herbal preparation in COVID-19 patients: A phase II multicenter double-blind randomized placebo-controlled trial

Article

Full-text available

Jan 2024
J ETHNOPHARMACOL

Role of different Medicinal Plants in the prevention and management of Covid-19 : A Comprehensive Review

Article

Full-text available

Aug 2024
J Cardiovasc Dis Res

The global pandemic of SARS-CoV-2, or severe acute respiratory syndrome coronavirus, in 2020 claimed millions of lives globally. The clinical manifestation of this virus is called COVID-19, and it can cause everything from flu-like symptoms to severe clinical consequences and even death. The global health organization (WHO) created awareness campaigns to reduce infection rates and slow the virus's rapid spread because there was no proven medication that could treat this infection or lessen its problems with little to no negative effects on the health of the patients. Despite the fact that vaccinations have been created as preventative measures, people still prefer to use conventional herbal drugs because it offers exceptional health benefits and, with comparatively minor side effects, can either prevent a viral infection or restrict the development of serious symptoms through various mechanistic pathways. This thorough analysis offers empirical data clarifying the protective effect of various plants against SARS-CoV-2, opening the door for additional research to reevaluate plant-based extracts—rich in bioactive compounds—in more sophisticated clinical evaluations to determine their effect on COVID-19 patients.

Assessing the Role of Medicinal Plants in Combating Respiratory Diseases: A Questionnaire Based Survey in Kohat, Pakistan

Article

Full-text available

Jul 2024

Background: The impact of respiratory disorders on healthcare systems is still a major problem for global health. Despite the fact that modern medicine has made great strides in treating these ailments, complementary and alternative ways of managing respiratory health are gaining popularity. Objective: The main objective of this study was to assess the efficiency of medicinal plants in combating respiratory diseases in Kohat, Pakistan. Methodology: A questionnaire-based survey was conducted at DHQ Teaching Hospital Kohat from April 2022 to March 2023. The study included 82 patients diagnosed with respiratory disorders, who provided informed consent to participate. Descriptive statistics, such as frequencies and percentages, were utilized to characterize the participant's demographic characteristics and consumption habits for medicinal plants. Results: Among the 82 patients, a greater number of participants (n=57; 69.51%) reported utilizing medicinal herbs to treat respiratory conditions. Liquorice (n=13; 23%) was the most often utilized medicinal plant, followed by Puthkanda (n=11; 19%) and Ginger (n=9 ;16%). The leaves (n=19; 34%), fruits (n=15; 26%), and stem (n=12; 21%) were the most often used plant components, while decoction (n=14; 25%) and extract (n=13; 23%) were the favored preparation techniques. More than one-third of patients (n=46; 80.70%) suggested using medicinal plants to treat respiratory conditions. Conclusion: The survey reveals significant utilization of medicinal plants for managing respiratory diseases in Kohat, Pakistan, emphasizing their potential as complementary approaches to conventional treatments. Integrating traditional knowledge into modern healthcare practices could lead to improved respiratory health outcomes and overall well-being.

BioScientific Review (BSR) Title: Protective Effect of Commonly Used Foods and Natural Products against COVID-19 Affiliation (s): History: Citation

Article

Full-text available

May 2024

COVID-19 caused by the SARS-COV-2 virus has swiftly turned into a pandemic, leading to an ongoing health crisis worldwide. This disease has a zoonotic origin, and its symptoms range from asymptomatic, mild to severe, potentially leading to death. Given its pandemic nature, researchers around the world have expedited efforts to find the treatment. While synthetic drugs have been developed for treatment, their efficacy is still under evaluation, and their side effect is the primary concern. This situation necessitates the need to explore treatment options that are not only effective but also safe. Natural products could help COVID-19 prevention and treatment given their historical role in the treatment of other viruses such as HIV, MERS-CoV, and influenza. This study aims to evaluate the potential role of natural products against COVID-19, their mechanisms of action, and previous use against other viruses. This study aims to evaluate the potential role of natural products against COVID-19, their mechanisms of action, and previous use against other viruses. The comprehensive review focuses on natural products such as ginger, garlic, clove, black pepper, red pepper, black seeds, honey, turmeric, onion, ginseng, and thyme. The findings aim to contribute valuable insights to the development of anti-COVID-19 natural products.

A critical review on phytochemicals as antiviral medications for SARS-CoV-2 virus infection

Article

Full-text available

Oct 2024
N Schmied Arch Pharmacol

A pandemic of acute respiratory infection, which was specified as coronavirus disease 2019, was instigated by a different strain of the virulent coronavirus SARS-CoV-2 that first appeared in late 2019. Since viral infections spread fast and there is presently no effective treatment, the use of plants with a long history of use in treating these infections has been explored regularly. The pandemic of coronavirus disease 2019 (COVID-19) has brought to light the dearth of medications with approval to treat acute viral illnesses. Because of this, the illness had a high fatality rate. The mortality rate was initially quite high and varied according to the patient’s geographic location. For instance, among Chinese patients, the rate was 3·6%, whereas 1·5% of COVID-19-related deaths were documented outside of China. As of 2020, India has a 1.4% case fatality rate (CFR) of COVID-19 mortality, compared to 2.8% in Brazil and 1.8% in the USA. Many studies are being conducted to create pharmaceutical compounds specifically targeting important SARS-CoV-2 proteins. Several drug discovery initiatives are being undertaken to find powerful inhibitors by combining biochemical assay and computer-aided drug design techniques. Although plant-derived compounds have not had much success in the dominion of antivirals, plants are, however, believed to be a limitless supply of medications for a variety of diseases and clinical conditions. The scientific foundation required for developing novel natural source medications is provided by the chemical characterization and analysis of plant components. Most viral infections treated by ethnobotanical applications and historical literature on ayurveda, and traditional medicine are generally attributed to phytochemicals, which are compounds derived from medicinal plants. In this review, we have described the application of vascular plant-derived chemicals, such as tannins, polyphenols, alkaloids, and flavonoids, as antivirals, especially for managing COVID-19. This article discusses novel bioactive compounds and their molecular structures that target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as prospective candidates for anti-coronavirus disease drugs. Moreover, to confirm the effectiveness of the phytochemicals that have demonstrated antiviral activity, clinical trials would need to be conducted in addition to the preclinical research that has already been done. To ensure spectacular findings, more applications of the compound would need to be studied to fully understand the effects of those phytochemicals whose clinical usefulness has already been established.

Antiviral activity of natural compounds extracted from Mediterranean medicinal plants against SARS-CoV-2

Article

Aug 2024

In vitro cancer cell line luminescence-based validation of anticancer phytocompounds obtained from Leucas biflora against HELA cervical and A549 lung cancer cells

Article

Full-text available

Aug 2024
LUMINESCENCE

Current research aims to screen the anticancer prospective of Leucas biflora phytocompounds against apoptotic regulator target protein essential for cancer progression. In gas chromatography–mass spectrometry analysis major phytocompounds such as tetracosahexaene, squalene, phytol, 22‐stigmasten‐3‐one, stigmasterol, fluorene, and 1,4‐dihydro were identified in ethanolic leaf extract of Leucas biflora . In vitro, the free radical scavenging potential of ethanolic leaf extract of Leucas biflora was examined through its DPPH and ABTS radical scavenging potential IC 50 value 15.35 and 13.20 μg/ml, respectively. Dose‐dependent cytotoxicity was monitored against both A549 lung cancer and HELA cervical cancer cells. Leucas biflora ethanolic leaf extract highly reduces the cell viability of both HELA and A549 cells in in vitro cytotoxicity assays. Leucas biflora ethanolic extract produces 23.76% and 29.76% viability rates against A549 lung and HELA cervical cancer cell lines, and their IC 50 values differ slightly at 95.80 and 90.40 μg/ml, respectively. In molecular docking analysis lung cancer target protein–ligand complex 5Y9T‐16132746 showed a maximum score of −14 kcal/mol by exhibiting stable binding affinity and interactions among all screened complexes. Based on docking score nine phytocompounds from Leucas biflora and two reference standard drugs were chosen for further analysis. Further validation reveals that the fluorene, 1,4‐dihydro possess good ADMET, Bioactivity and density functional theory indices.

Anti-obesity Impact of Natural Products Modulated by Peroxisome Proliferator-Activated Receptor Gamma and CCAAT/Enhancer-Binding Protein-Alpha via Wnt/β-Catenin Signaling Pathway

Article

Jul 2024

In an effort to investigate the critical relationship between natural products and obesity management, this narrative review was conducted to provide a comprehensive, scientific evidence-based assessment of the impact and interplay between them through the modulation of the Wnt/β-catenin signaling pathway. Obesity is universally acknowledged to be a significant danger to human wellness and frequently coincides with several comorbidities, such as diabetes mellitus type II, dyslipidemia, and cardiovascular diseases. Adipogenesis is a mechanism by which adipocyte precursor cells expand and differentiate into mature adipocytes. The molecular mechanisms and related factors involved in adipogenesis should be identified to serve as suitable therapeutic targets against obesity. This narrative review aims at demonstrating a scientific evidence-based source to evaluate the impact of natural products in the modulation process of adipogenic transcription elements such as peroxisome proliferator-activated receptor gamma (PPAR-γ) and CCAAT/enhancer-binding protein-alpha (C/EBP-α). They are contributive in various signaling pathways, with a significant influence in Wnt/β-catenin signaling pathway, which diminishes adipogenesis and consequently controls obesity. This pathway’s activation stabilizes and accumulates a protein inside the nucleus called β-catenin, leading to suppression of transcription elements involved in adipogenesis especially C/EBP-α and PPAR-γ, preventing adipocyte differentiation and thus obesity. The information presented in this review would educate plant researchers on the significance of natural products of plant origin in activating Wnt/β-catenin pathway, which is a key development essential for managing obesity.

The efficacy and safety of ginger (Zingiber officinale) rhizome extract in outpatients with COVID-19: A randomized double-blind placebo-control clinical trial

Article

May 2024

Background Ginger, a potent antiviral, anti-inflammatory, and antioxidant remedy, is a potential therapeutic option for COVID-19. However, there was not enough clinical evidence about ginger and COVID-19. We evaluated the efficacy and safety of ginger on clinical and paraclinical features in outpatients with COVID-19. Methods In this randomized controlled trial, the outpatients with confirmed COVID-19 were randomly assigned in a 1:1 ratio to receive ginger (1000 mg 3 times a day for 7 days) or placebo. The primary outcome was viral clearance after the end of the intervention. Oxygen saturation (S P O 2 ), body temperature, respiratory rate (RR), hospital admission, and the incidence of adverse events were also assessed. Results A total of 84 patients (42 in the ginger and 42 in the control groups) were randomized. The viral clearance was not statistically improved in the ginger group (41.6%) compared to the placebo group (42.8%). The findings indicated that S P O 2 , body temperature, and RR had no significant difference between the groups at the end of the intervention. The imaging finding indicated pulmonary infiltrate significantly reduced on the 7 th day of the intervention in the ginger group. The percentage of patients with S P O 2 <96% in the ginger group decreased over the study compared to the placebo group. Moreover, the need for hospital admission and the incidence of adverse drug events were not different between the groups over the follow-up period. Conclusions Ginger had no significant impact on the clinical and paraclinical parameters of patients. However, this intervention demonstrated a safe profile of adverse events and reduced pulmonary infiltrate. Trial registration The trial was registered as IRCT20200506047323N1.

Potential Inhibitor of COVID-19 Main Protease (Mpro) From Several Medicinal Plant Compounds by Molecular Docking Study

Preprint

Full-text available

Mar 2020

COVID-19, a new strain of coronavirus (CoV), was identified in Wuhan, China, in 2019. No specific therapies are available and investigations regarding COVID-19 treatment are lacking. Liu et al. (2020) successfully crystallised the COVID-19 main protease (Mpro), which is a potential drug target. The present study aimed to assess bioactive compounds found in medicinal plants as potential COVID-19 Mpro inhibitors, using a molecular docking study. Molecular docking was performed using Autodock 4.2, with the Lamarckian Genetic Algorithm, to analyse the probability of docking. COVID-19 Mpro was docked with several compounds, and docking was analysed by Autodock 4.2, Pymol version 1.7.4.5 Edu, and Biovia Discovery Studio 4.5. Nelfinavir and lopinavir were used as standards for comparison. The binding energies obtained from the docking of 6LU7 with native ligand, nelfinavir, lopinavir, kaempferol, quercetin, luteolin-7-glucoside, demethoxycurcumin, naringenin, apigenin-7-glucoside, oleuropein, curcumin, catechin, epicatechin-gallate, zingerol, gingerol, and allicin were -8.37, -10.72, -9.41, -8.58, -8.47, -8.17, -7.99, -7.89, -7.83, -7.31, -7.05, -7.24, -6.67, -5.40, -5.38, and -4.03 kcal/mol, respectively. Therefore, nelfinavir and lopinavir may represent potential treatment options, and kaempferol, quercetin, luteolin-7-glucoside, demethoxycurcumin, naringenin, apigenin-7-glucoside, oleuropein, curcumin, catechin, and epicatechin-gallate appeared to have the best potential to act as COVID-19 Mpro inhibitors. However, further research is necessary to investigate their potential medicinal use.

Inhibition of SARS-CoV 3CL protease by flavonoids

Article

Full-text available

Nov 2019

There were severe panics caused by Severe Acute Respiratory Syndrome (SARS) and Middle-East Respiratory Syndrome-Coronavirus. Therefore, researches targeting these viruses have been required. Coronaviruses (CoVs) have been rising targets of some flavonoids. The antiviral activity of some flavonoids against CoVs is presumed directly caused by inhibiting 3C-like protease (3CLpro). Here, we applied a flavonoid library to systematically probe inhibitory compounds against SARS-CoV 3CLpro. Herbacetin, rhoifolin and pectolinarin were found to efficiently block the enzymatic activity of SARS-CoV 3CLpro. The interaction of the three flavonoids was confirmed using a tryptophan-based fluorescence method, too. An induced-fit docking analysis indicated that S1, S2 and S3′ sites are involved in binding with flavonoids. The comparison with previous studies showed that Triton X-100 played a critical role in objecting false positive or overestimated inhibitory activity of flavonoids. With the systematic analysis, the three flavonoids are suggested to be templates to design functionally improved inhibitors.

Identification of Anti-Diabetic Phytocompounds from Ficus racemosa and its Validation through In Silico Molecular Modeling

Article

Full-text available

Jun 2019

In the present study, anti-diabetic phyto compounds of Ficus racemosa bark methanolic extract was screened through GCMS and evaluated its anti-diabetic potential in vitro and in silico (molecular docking and DFT analysis) approaches. The anti-diabetic phyto compounds β-Sitosterol, β-amyrin, betulinic acid and stigmasterol were explored through GCMS analysis. In vitro anti-diabetic α-amylase inhibitory effect of the plant (IC50 19.50 µg) was found equipotent when compared with standard acarbose drug (IC50 11.25 µg). In silico molecular docking study of Ficus racemosa phytocompounds and reference standard drug acarbose with four crucial targets of diabetes (GLP-1, GSK, GK & IRTK) revealed that phytocompound β-amyrin shows highest binding affinity with all four screened targets -6.9,-9.1,-8.9,-10.7 kcal/mol than standard drug acarbose -4.7, -8.1, -7.7 & -8.8 kcal/mol respectively. Further DFT analysis of top 3 ant-diabetic phytocompounds (β-amyrin, betulinic acid and stigmasterol) of F.raemosa and standard acarbose was done. It was found that β-amyrin possess more stability and biological activity as it shows less energy gap, low hardness, and more softness -0.06277eV, 0.031385eV and 31.86235eV than reference standard acarbose possess more energy gap, more hardness, and low softness -0.24436 eV, 0.12218 eV and 8.18464 eV respectively.

Flavonoids: promising natural compounds against viral infections

Article

Full-text available

Sep 2017
ARCH VIROL

Flavonoids are widely distributed as secondary metabolites produced by plants and play important roles in plant physiology, having a variety of potential biological benefits such as antioxidant, anti-inflammatory, anticancer, antibacterial, antifungal and antiviral activity. Different flavonoids have been investigated for their potential antiviral activities and several of them exhibited significant antiviral properties in in vitro and even in vivo studies. This review summarizes the evidence for antiviral activity of different flavonoids, highlighting, where investigated, the cellular and molecular mechanisms of action on viruses. We also present future perspectives on therapeutic applications of flavonoids against viral infections.

PubChem 2019 update: improved access to chemical data

Article

Oct 2018
NUCLEIC ACIDS RES

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a key chemical information resource for the biomedical research community. Substantial improvements were made in the past few years. New data content was added, including spectral information, scientific articles mentioning chemicals, and information for food and agricultural chemicals. PubChem released new web interfaces, such as PubChem Target View page, Sources page, Bioactivity dyad pages and Patent View page. PubChem also released a major update to PubChem Widgets and introduced a new programmatic access interface, called PUG-View. This paper describes these new developments in PubChem.

Pa-9: A flavonoid extracted from plectranthus amboinicus inhibits HIV-1 protease

Article

Jun 2016

221 extracts from various parts of 33 Indian medicinal plants were tested to identify their protease inhibitor potential. The aqueous extract of Aporosa lindleyana, methanol and aqueous extracts of Baliospermum montanum, chloroform extract of Gymnema sylvestre, aqueous extract of Hedyotis corymbosa and aqueous extract of Plectranthus amboinicus showed significant inhibition of α-Chymotrypsin, Leucine Amino peptidase and Papain.The aqueous extracts of Plectranthus amboinicus exhibited significant inhibition of HIV -1 specific Protease. A biology guided fractionation methodology devised in this study pinpointed the flavonoid bioactive fraction PA-9 to exhibit inhibition of HIV-1 protease at 100μg/ml. © 2016, International Journal of Pharmacognosy and Phytochemical Research. All rights reserved.

Fresh ginger (Zingiber officinale) has anti-viral activity against human respiratory syncytial virus in human respiratory tract cell lines

Article

Oct 2012

Ethnopharmacological relevance: Ginger, Zingiber officinale Roscoe, is a common spice and also a widely used medicinal plant in ancient China. Ginger is an ingredient of Ge-Gen-Tang (Kakkon-to; GGT). GGT has been proved to have antiviral activity against human respiratory syncytial virus (HRSV). However, it is unknown whether ginger is effective against HRSV. Aim of the study: To find a readily available agent to manage HRSV infection, the authors tested the hypothesis that ginger can effectively decrease HRSV-induced plaque formation in respiratory mucosal cell lines. Materials and methods: Effect of hot water extracts of fresh and dried gingers on HRSV was tested by plaque reduction assay in both human upper (HEp-2) and low (A549) respiratory tract cell lines. Ability of ginger to stimulate anti-viral cytokines was evaluated by enzyme-linked immunosorbent assay (ELISA). Results: Fresh ginger dose-dependently inhibited HRSV-induced plaque formation in both HEp-2 and A549 cell lines (p<0.0001). In contrast, dried ginger didn't show any dose-dependent inhibition. 300 μg/ml fresh ginger could decrease the plaque counts to 19.7% (A549) and 27.0% (HEp-2) of that of the control group. Fresh ginger was more effective when given before viral inoculation (p<0.0001), particularly on A549 cells. 300 μg/ml fresh ginger could decrease the plaque formation to 12.9% when given before viral inoculation. Fresh ginger dose-dependently inhibited viral attachment (p<0.0001) and internalization (p<0.0001). Fresh ginger of high concentration could stimulate mucosal cells to secrete IFN-β that possibly contributed to counteracting viral infection. Conclusions: Fresh, but not dried, ginger is effective against HRSV-induced plaque formation on airway epithelium by blocking viral attachment and internalization.

SMILES, A Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules

Article

Feb 1988

David Weininger

SMILES (Simplified Molecular Input Line Entry System) is a chemical notation system designed for modern chemical information processing. Based on principles of molecular graph theory, SMILES allows rigorous structure specification by use of a very small and natural grammar. The SMILES notation system is also well suited for high-speed machine processing. The resulting ease of usage by the chemist and machine compatability allow many highly efficient chemical computer applications to be designed including generation of a unique notation, constant-speed (zeroeth order) database retrieval, flexible substructure searching, and property prediction models.

Ginger — chemistry, technology, and quality evaluation: Part 1

Article

Feb 1982

V S Govindarajan

Ginger is used in more ways than any other spice. This monograph, published in two parts, comprehensively reviews production, trade, processing, chemistry, and evaluation of quality. Botany, world varieties, agronomy, crop improvement and potential are reviewed briefly with emphasis on the yield of functional components. Processing for the market, international trade patterns, and factors influencing them are discussed. Derived products such as ginger powder, syruped ginger, volatile oil, and oleoresin are discussed in greater detail. The increasing world demand for quality products of added value such as the oleoresin and volatile oil show prospects for their production in the growing countries. The chemistry of the components which contribute aroma and pungency that characterize ginger is critically reviewed. The second part deals with evaluation of quality. The physico-chemical parameters prescribed as a measure of quality for ginger and its products in the existing standards can assure only hygienic quality and purity, and possibly the source, when new parameters such as GC-fingerprints are included. The importance of sensorily evaluating flavor quality is emphasized to understand the variation in flavor quality required by the industrial and retail markets. Related areas, such as problems in sensory evaluation of intense flavored substances, objective flavor profile analysis, and correlation of instrumental and sensory data, are discussed and our recent work in this area is summarized. Areas where more research are needed are indicated. Other areas briefly discussed are functional, physiological, and toxicological properties in use of ginger; biosynthetic aspects of the components stimulating flavor; and structure and pungency and chemistry of spices from allied species and genera. A comprehensive bibliography is provided to aid in further study and research.

Isolation of Antirhinoviral Sesquiterpenes from Ginger (Zingiber officinale)

Article

Jun 1994

The dried rhizomes of Indonesian ginger, Zingiber officinale, were investigated for antirhinoviral activity in the plaque reduction test. Fractionation by solvent extraction, solvent partition, and repeated chromatography guided by bioassay, allowed the isolation of several sesquiterpenes with antirhinoviral activity. The most active of these was beta-sesquiphellandrene [2] with an IC50 of 0.44 microM vs. rhinovirus IB in vitro.