Computational Docking study of phytochemicals isolated from Barleria albostellata C.B Clarke.

Molecular docking is a crucial aspect of computer-aided drug design (CADD) technique to study how a small molecule (ligand/drug) interacts with a macromolecule (protein/enzyme, DNA, etc.). Molecular docking basically addresses three key goals - virtual screening, pose prediction, and binding affinity estimation.¹ Docking is performed using free or licensed molecular docking software such as Autodockvina, PyRx, CCDC GOLD, Schrodinger, MOE, GLIDE, among others provide varied approaches to simulate these interactions.By retrieving protein structures from the PDB, researchers can analyze how different compounds interact with specific enzymes, aiming to find the most energetically favorable configuration for a ligand-enzyme complex.² This process helps in understanding potential interactions between molecules, aiding drug design and discovery.Docking serves as a crucial tool in rational drug design by predicting how small molecule candidates bind to protein targets. A statistical scoring function translates interacting energy into numerical docking scores, offering insights into the strength of molecular interactions. This process aids in assessing the affinity and activity of potential drugs within the body.

Docking is most used in the field of drug design and docking is applied to:

• Hit identification: Docking with a scoring function efficiently screens drug databases in silicoto identify molecules likely to bind to a specific protein target.
• Lead optimization: Docking predicts the ligand's binding orientation to a protein, aiding in the design of more potent and selective analogs based on this information.
• Bioremediation: Protein-ligand docking predicts enzyme interactions degrading pollutants, aiding in identifying potential biodegradation pathways for environmental cleanup efforts.³

The primary aim of this study was to determine the optimal positions and orientations for ligands within the enzyme or receptor's binding center. It also aimed to assess the impact of isolated phytoconstituents from Barleria albostellata on their antialzhemier properties.Material and Methods

1. Docking software

Among the different types of software’s available for docking, it used the Autodock4.2 software for the molecular docking investigation of proteins involved in anti-alzheimer Activity.^4-9

2. Phytoconstituents / Ligands

The Ligands were collected from an article published by Manohar Reddy and his co- workers (2022). Phytoconstituents or ligands like Carbamic Acid, Pentadecanoic Acid, Eicosanoic Acid, 9 Oxononanoic Acid, Heptafluorobutyric Acid and Sulphurous Acid were used for molecular docking studies.¹⁰

3. Potential targets and binding sites

The 3D structures of antialzhemier drug targets such as acetylcholinesterase are obtained from protein database bank. Based on these ligands in crystallized structures the active sites in receptors were determined.^4-9

4. Docking

Docking was executed to acquire probable conformations and positions for the ligand-receptor complexes at the binding site. Binding site was determined using the previous knowledge of the original ligand’s interaction site. For the stimulation runs, each ligand was kept flexible, but the amino acid residues of active site were kept rigid and default parameters values were taken. Alzheimer targets for various proteins were selected based on the literature survey. The structures of all the receptors were obtained from PDB format. Docking studies were performed against acetylcholinesterase using Autodock 4.2 software with isolated phytoconstituents and standard Rivastigmine as ligands. The results obtained in the form of binding energy and amino acids interactions by hydrogen bonding.^10-11

RESULTS AND DISCUSSION

In silico methods are computer-based methods widely used in the pharmacological field of science to help discover inhibitors with high binding capabilities with a protein target. In silico methods have been used to create various inhibitors for a spectrum of diseases. Molecular Docking is an important method in molecular biology and computeraided drug design. Ligand- protein docking helps predict the binding mode of a Ligand and Protein of known 3-dimensional structures. Evaluation of molecular docking analysis of isolated phytoconstituents from methanolic extracts of Barleria albostellata whole plant phytoconstituents such as Carbamic Acid, Eicosanoic Acid, 9 Oxononanoic Acid,Heptafluorobutyric Acid, Pentadecanoic Acid, Sulphurous Acid were docked with antialzhemier drug target proteins such acetyl choline esterase using Autodock 4.2 software. The binding energy of phytoconstituents from methanolic extracts of Barleria albostellata whole plant such as Carbamic Acid, Pentadecanoic Acid, Eicosanoic Acid, 9 Oxononanoic Acid, Heptafluorobutyric Acid and Sulphurous Acid with acetyl choline esterase was found to be -4.65, -4.89, -4.92, -4.21,6.58 and -5.48 Kcal/mol. Heptafluorobutyric acid was interaction with 10 amino acids. Heptafluorobutyric acid (-6.58 Kcal/mol) has significant bind energy with acetylcholine esterase when compared with standard Rivastigmine (-10.56Kcal/mol) (Table.1&2 and Figure.1&2). Methanolic extracts of Barleria albostellata whole plant phytoconstituent such Heptafluorobutyric acid has highly bind with acetyl choline esterase and inhibited it to possess the antialzheimer activity.

Table.1: Phytoconstituents of Barleria albostellata docking with acetyl cholinesterase

1. 1. Sulphurous acid

                                                  3D Structure                                       2D Structure

Docking binding Energy (Kcal/mol)

2. Carbamic acid

                                                            3D Structure                    2D Structure

Docking binding Energy (Kcal/mol)

3. Pentadecanoic acid

3D Structure                          2D Structure

Docking binding Energy (Kcal/mol)

4. Eicosanoic acid

                                                   3DStructure                                2D Structure

Docking binding Energy (Kcal/mol)

5. Heptafluorobutyric acid

3D Structure    2D Structure

Docking binding Energy (Kcal/mol)

6. 9 Oxononanoic acid

                                                         3D Structure                2D Structure

Docking binding Energy (Kcal/mol)

Table.2: Standard drug Rivastigmine docking with acetyl cholinesterase

Fig.2 3D,2D structure and binding energy of Rivastigmine docking with acetyl cholinesterase

3D Structure    2D Structure

Docking binding Energy (Kcal/mol)