LIGAND DOCKING EXPERIMENT LAB REPORT

STUDENT NAME

INSTITUTION NAME

COURSE NAME

DUE DATE

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Table of Contents

1. INTRODUCTION..................................................................3

2. METHODOLOGY.................................................................4

3. RESULTS...............................................................................5

4. DISCUSSION.......................................................................11

5. REFERENCES.....................................................................13

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 1. INTRODUCTION

Ligand docking is a computational method extensively applied in molecular biology and drug

development. This approach entails predicting and analyzing the interactions between a small

molecule, known as the ligand, and a target receptor, typically a biomolecule like a protein. The

central goal of ligand docking is to forecast the ligand's position and binding mode with the

receptor, thereby offering insights into the nature and strength of these interactions. This method

contributes significantly to advancing our comprehension of the intricate molecular dynamics

between ligands and receptors.

This laboratory report focuses on the exploration of ligand-receptor interactions using

computational techniques, with a specific emphasis on the ligand adrenaline, which holds

considerable importance in pharmacology and physiology. The DEEPSITE online server is

utilized to forecast binding pockets on receptor surfaces. By employing adrenaline as the subject

of interest and taking into account the amino acids surrounding a suitable binding site for

pharmaceutical docking, ligand docking simulations are conducted using the Galaxy7TM. The

primary objective is to pinpoint potential binding configurations, a critical step in unraveling the

pharmacological implications of the ligand-receptor interaction.

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 2. METHODOLOGY

A pre-existing G protein-coupled receptor (GPCR) served as the foundation for generating a

three-dimensional structure of adrenaline through the molecular modeling program DEEPSITE.

The orthosteric binding pocket, identified as the largest predicted pocket, played a pivotal role in

this structural representation. The DEEPSITE online resource was then employed to identify

binding pockets on the surfaces of receptors, as well as potential locations of these pockets

within proteins. The amino acids surrounding the binding site were carefully observed and

documented.

Subsequently, a depiction of the adrenaline ligand was crafted using Molview. These identified

binding pockets were deemed suitable for ligand docking experiments, which were conducted

using the Galaxy7TM online docking server. The choice of the receptor for docking was

informed by literature data detailing the known binding target of the ligand. Molecular docking

simulations were executed to explore potential interactions and binding conformations, providing

insights into the molecular dynamics of the ligand-receptor interaction.

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 3. RESULTS

Figure 1: Adrenaline 2D ligand

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Figure 2: Adrenaline 3D Ligand

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Binding pockets (DEEPSITE)

Binding pocket 1

Figure 3: Docking Site 1

Binding pocket 2

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Figure 4: Docking site 2

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Figure 5: Ligand docking results

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 4. DISCUSSION

In the context of ligand docking studies, researchers identify and predict the binding site on the

receptor where ligands, such as drugs or signaling molecules, are likely to interact.

Computational tools and algorithms are employed to analyze the protein surface and identify

potential binding pockets.

Ligand docking simulations involve virtually placing the ligand (e.g., adrenaline) into the

predicted binding site on the 3D model of the receptor. Computational algorithms then predict

the optimal binding conformation and estimate the binding affinity, providing insights into the

potential interactions between the ligand and the receptor.

Following ligand docking, different amino acids were found to have different roles. These amino

acids were crucial in creating a precise and steady milieu in which the ligand and receptor

interacted. The results offered insightful information on the complex molecular pathways

underlying biological processes.

The contribution of lysine to ionic connections was emphasized, demonstrating its function in

augmenting the selectivity of the ligand to receptor interaction. Ionic interactions, which are

defined by charged particles, were important in giving the molecule binding process selectivity

in addition to increasing the interaction's intensity.

The results of the ligand docking research, in summary, gave rise to a thorough comprehension

of the subtle roles played by these amino acids, shedding light on the intricate process of ligand-

receptor interaction and its possible consequences for medication development.

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It was noted that tyrosine was an important role in determining how the ligand is placed inside

the binding pocket. Tyrosine had an impact on the precise configuration and orientation of

molecules, which is essential to their functional responsibilities. Leucine have been found to

have a role in the development of a hydrophobic environment that is conducive for bound

adrenaline. The stabilization of molecular structures was greatly aided by this hydrophobic

contact, especially in the watery settings seen in biological systems.

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 5. REFERENCES

Auniq, R. B. J., Chy, M. N. U., Adnan, M., Roy, A., Islam, M. A., Khan, T. N., ... & Islam, S.

(2019). Assessment of anti-nociceptive and anthelmintic activities of Vitex Peduncularis

Wall. leaves and in silico molecular docking, ADME/T, and PASS prediction studies of

its isolated compounds. J. Complement. Med. Res, 10(4), 170-185.

Hamid, N., Junaid, M., Manzoor, R., Jia, P. P., & Pei, D. S. (2020). Prioritizing phthalate esters

(PAEs) using experimental in vitro/vivo toxicity assays and computational in silico

approaches. Journal of Hazardous Materials, 398, 122851.

Lee, G. R., & Seok, C. (2016). Galaxy7TM: flexible GPCR–ligand docking by structure

refinement. Nucleic Acids Research, 44(W1), W502–W506.

Shen, C., Ding, J., Wang, Z., Cao, D., Ding, X., & Hou, T. (2020). From machine learning to

deep learning: Advances in scoring functions for protein–ligand docking. Wiley

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