Insilico molecular docking, Studies of drug Betulin , Sterole against SARS COV-2,

NSP-12 ( Receptor)

THESIS
SUBMITTED TO
MAHARSHI MARKANDESHWER (DEEMED TO BE UNIVERSITY) MULLANA –
AMBALA
FOR THE AWARD OF B.Tech. DEGREE

IN
BIOTECHNOLOGY
SUBMITTED BY
SUMAN KUAMR
(Roll No. 11204518)

SUPERVISOR
Dr. Hardeep Singh Tuli
(Assistant Professor)

DEPARTMENT OF BIOSCIENCES &TECHNOLOGY MAHARSHI

MARKANDESHWER (DEEMED TO BE UNIVERSITY) MULLANA – AMBALA
(HARYANA)
2020-2024
 DEPARTMENT OF BIO-SCIENCES AND TECHNOLOGY

MAHARISHI MARKANDESHWAR (DEEMED TO BE UNIVERSITY)

MULLANA-AMBALA

CERTIFICATE

This is to certify that the review work included in the dissertation report entitled “Insilico
molecular docking, Studies of drug Betulin , Sterole against SARS COV-2, NSP-12
( Receptor) ” submitted in partial fulfillment of requirement for the award of degree of
B.Tech Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-
Ambala is a bonafide work done by Suman Kumar under my guidance.

Dr. Hardeep Singh Tuli Dr. Adesh K. Saini

Assistant Professor (Professor and Head)
 DECLARATION

I, Suman Kumar hereby declare that the review work entitled “Insilico molecular docking,
Studies of drug Betulin , Sterole against SARS COV-2, NSP-12 ( Receptor) ” done by
me under the guidance of Dr. Hardeep Singh Tuli , Assistant Professor, Maharishi
Markandeshwar (Deemed to be University), Mullana-Ambala is submitted in partial
fulfillment for the award of degree of B. Tech Biotechnology.

I declare that this review work is purely original and is not submitted for the award of any
other degree or diploma to any other institute or university in India or abroad.

Date:

Place: Mullana Signature of the Candidate

In Silico Molecular Docking Analysis of Dibutyl phthalate

In the quest to discover new medicines, scientists embark on a journey from lab bench to

patient bedside—a journey often marked by long and challenging paths. But imagine a

shortcut, a virtual leap forward made possible by the magic of computers. That's where

insilico molecular docking steps in, revolutionizing the way we discover drugs and speeding

up the pace of innovation in pharmaceuticals.

Think of insilico molecular docking as a digital matchmaker, predicting how small drug-like

molecules will interact with their target proteins. It's like watching a molecular dance unfold,

where tiny molecules (the ligands) and proteins (the receptors) twirl and twist, finding just

the right fit for each other.

So how does it work? Well, first, scientists figure out the 3D shapes of these molecules and

proteins, using fancy techniques like X-ray crystallography or virtual modeling. Then, using

powerful algorithms, they simulate thousands or even millions of possible interactions

between them, predicting which combinations are most likely to hit it off.

One of the best things about insilico molecular docking? It's like having a super-speedy

assistant who can sift through massive libraries of chemicals in no time. Instead of tediously

testing one compound after another in the lab, researchers can quickly pinpoint the most

promising candidates for further investigation.

But the magic doesn't stop there. With insilico docking, scientists can explore a vast universe

of chemical possibilities that go beyond what's possible in a physical lab. By tweaking the

properties of molecules in virtual simulations, they can design custom-made compounds

tailored to specific needs, like minimizing side effects or boosting effectiveness.

Of course, there are challenges too. Like any matchmaker, insilico docking isn't perfect.

Predictions need to be double-checked in real-life experiments to make sure they're accurate.

And the quality of those predictions depends a lot on the initial data and settings used in the

simulations, which means constant fine-tuning and validation are essential.

In the end, though, insilico molecular docking represents a game-changer in drug discovery.

It's like having a high-tech compass guiding scientists through the complex world of

molecular interactions, helping them find their way with speed and precision. And as

technology continues to evolve, the possibilities for insilico docking are endless, promising a

future filled with exciting breakthroughs in medicine.[1][2]

Betulin

Betulin (BE) and betulinic acid (BA) are natural compounds found in birch tree bark, known

for their diverse medicinal properties including anticancer, antiviral, antibacterial, antifungal,

and anti-inflammatory effects. However, their therapeutic potential is limited due to low

bioavailability and poor solubility in water.

Inflammation, while crucial for combating pathogens and neoplasms, can also contribute to

pathological responses. Conditions like psoriasis and chronic dermatitis can benefit from

reducing inflammation in skin tissue. In tumors, decreased inflammation reduces the

accessibility of tumor-propagation factors and prevents tumor growth and infiltration into

neighboring tissues.

Macrophages, key players in inflammation, release inflammatory factors and depend on

them, making them significant in tumor microenvironment formation. Attenuating

inflammation may hinder tumor progression and the stimulation of cancer cell replication.

Although high-dose dexamethasone is effective, it leads to various side effects, necessitating

safer alternatives.
Derivatives of BE and BA with higher bioavailability and targeted activity are in demand.

Amino acid esters of BE synthesized in recent years exhibit increased water solubility and

anticancer properties. Current research focuses on their anti-inflammatory activity compared

to BE, BA, and dexamethasone. In vitro studies assess immunomodulatory properties,

cytokine secretion, intracellular protein content, COX-2 activity, and cytotoxicity on P388D1

cells. Computational analysis aids in identifying new biologically active compounds.[3][4]

Sterole Against SARS COV-2

In the relentless battle against the COVID-19 pandemic, researchers are exploring every

possible avenue to find effective treatments and preventive measures. One intriguing area of

study focuses on natural compounds called sterols, which are found in a variety of plants,

fungi, and animals. While still in the early stages of investigation, preliminary findings

suggest that certain sterols may offer promising benefits in combating the SARS-CoV-2

virus, which causes COVID-19. Let's take a closer look at the potential of sterols and their

role in our fight against this global health crisis.

So, what exactly are sterols? They're a diverse group of organic molecules with vital roles in

biological processes, including maintaining cell membranes and supporting immune function.

Examples of sterols include cholesterol, which many are familiar with, as well as plant-based

phytosterols and ergosterol found in fungi.

Recent studies have hinted at the antiviral properties of certain sterols, sparking interest in

their potential application against SARS-CoV-2. These compounds might interfere with the

virus's ability to replicate and spread within the body, offering hope for mitigating COVID-

19 symptoms and reducing transmission rates.

One intriguing aspect of sterols is their potential to regulate the immune response to SARS-

CoV-2 infection. Research suggests that sterols might help balance the body's inflammatory

response, preventing it from going into overdrive—a common issue in severe COVID-19

cases. By keeping inflammation in check, sterols could potentially lessen the severity of

symptoms and improve patient outcomes.

Moreover, sterols may disrupt the lipid layer that surrounds viral particles, including those of

coronaviruses like SARS-CoV-2. By destabilizing this viral membrane, sterols could impede

the virus's ability to infect host cells, potentially slowing down its spread and reducing the

risk of transmission.

While these findings are promising, it's essential to approach them with caution. Further

research, including clinical trials, is necessary to fully understand the effectiveness and safety

of sterols in treating COVID-19. Nevertheless, ongoing investigations offer hope for new and

innovative approaches to combatting the pandemic.

In summary, sterols represent a fascinating area of research in our fight against COVID-19.

Their natural origins and multifaceted properties make them attractive candidates for the

development of treatments and preventive strategies. As scientists continue to explore the

potential of sterols, we may be one step closer to finding effective solutions to this global

health crisis.[5][6]

NSP-12 ( Receptor)

A cluster of pneumonia episodes in patients connected to a seafood market in Wuhan, China,

in late 2019 led to the discovery of a novel coronavirus (SARS-CoV-2) (Saurabh Kumar et
al., 2021). Humans were infected by SARS-CoV-2, which led to the development of COVID-

19 (Gautam et al., 2020). Over 542.18 million individuals had been infected as of June 29th,

2022, and 6.32 million had died as a result of the infection (World Health Organization,

2021). Notably, the biggest number of COVID-19 cases has been officially reported from the

United States of America (USA), Russia, Brazil, France, Germany, and India (Grey, I., Arora,

T., Thomas, J., Saneh, A., Tohme, P., & Abi-habib et al., 2020). SARS-CoV-2 has a

substantially lower projected death ratio (2.96%) than the previously reported SARS (Severe

Acute Respiratory Syndrome), which was first identified in 2003 (WHO, 2020). In the case

of SARS-CoV-2, the number of cases is substantial and growing quickly. As the virus

continues to infect people, the fact that the majority of infection cases are asymptomatic

raises substantial health concerns (Sumit Kumar et al., 2020). Researchers in the academic

and industrial sectors are currently in urgent need of COVID-19 remedies, including vaccines

to stop the virus's spread (Centers for Disease Control and Prevention [CDC], 2014). A key

strategy for finding anti-COVID drugs is to target several enzymes with treatments (Khatri &

Mago, 2020; Ojha et al., 2021). As a result, using in-silico approaches to search for promising

compounds against a variety of protein targets can be done quickly and easily (Chandel et al.,

2020; Sumit Kumar et al., 2021; Raghavendra et al., 2018; Vincetti et al., 2015). The FDA-

approved Prestwick Chemical Library's 1520 compounds (Prestwick Chemical Library®:

1520 Drugs Mainly FDA-Approved - Prestwick Chemical Libraries, n.d.) were used to test

the antiviral activity of MERS-CoV and SARS-CoV, two previously reported coronaviruses

(PCL) (Dyall et al., 2014). Tuli et al in 2022 used molecular docking (MD) studies to target

spike protein of SARS-CoV-2 with three phytochemicals Quercetin, Kaempferol, and

Apigenin and showed that Quercetin can be used as potential inhibitor against SARS-CoV-2.

Recent studies suggest that the development of effective SARS-CoV treatments may benefit

with using natural plant-based substances such phytochemicals, including flavonoids,

alkaloids, and others (Silveira et al., 2020; Tuli, Sak, et al., 2021; Tuli, Sood, et al., 2021;

Vardhan & Sahoo, 2020). Vardhan and Sahoo's (2020) in silico computational investigation

of phytochemicals, such as limonin, glycyrrhizic acid, 7-deacetyl-7-benzoylgedunin,

corosolic acid, maslinic acid, ursolic acid, and obacunone revealed that these compounds

could be useful as potential therapeutics to target SARS-CoV-2 proteins. Similar to this, Hall

and Ji (2020) investigated the in-silico potential of the proteinase inhibitors Zanamivir,

Indinavir, Saquinavir, and Remdesivir against SARS-CoV-2 spike glycoprotein and 3CL

protease (Hall & Ji, 2020). Non-structural proteins (NSP) present in SARS-CoV-2, are

responsible for the virus's capacity to endure and be safeguarded in the host environment. In a

recent study, authors synthesized two new active compounds (ZG-5 and ZG-7) and found that

these compounds had inhibitory action against NSP-12 (GERÇEK et al., 2021). In 2020,

Lucas-G'omez conducted a study by using Betalains and Alfa-Bisabolol, natural compounds

aginst NSP-12 and demonstrated their role as potential inhibitors against NSP-12 (Lucas-

gómez et al., 2020). Kumar et al in 2021 used Diosmin, a flavanoid against NSP-3, NSP-9,

NSP-12, NSP-15 and revealed its multi-target role against SARS-COV-2 (Sumit Kumar et

al., 2021). Therefore, we decided to use MD techniques to target SARS-CoV-2 non-structural

protein (NSP-12, PDB ID: 6NUR) using phytochemicals compounds.

By eliminating molecules with zero affinities and focusing on those molecules to synthesise

and test experimentally, docking studies are a non-prevalent approach to identify

physiologically active chemicals towards a certain protein. When it comes to natural

compounds, new molecules are continually being described in the scientific literature, and

their biological effectiveness must be evaluated in comparison to proteins that stand in for

issues that have an influence on society. In this instance, the study shows that it is feasible to

use the docking study to find potential inhibitors of the SARS-CoV protein (important for the

virus' replication machinery that produces Covid-19). The most effective ligand can be
chosen as a potential therapeutic candidate for further investigation. Using software for

molecular interaction, the natural substance stigmasterol has been examined In silico for

possible interactions with the SARS-CoV-2 non-structural protein NSP-12. Stigmasterol

should be considered a strong contender for the development of a treatment for SARS-CoV-2

NSP-12 since studies have showed that it was an effective inhibitor of the virus [7][8][9].

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