Literature Search
All of the relevant data and information about the Leucas aspera was obtained from a number of sources, such as PubMed, Science Direct, Sci-hub and Google Scholar evaluation and analysis papers from published works that have been subjected to peer review. We also looked at a few materials from the so-called 'grey literature,' which included ethnobotanical books and chapters.
Softwares
PyRx is a virtual screening tool for computational drug discovery that could potentially used to test compound libraries against pharmacological targets. PyRx (PyRx - Virtual Screening Tool download | SourceForge.net) is a tool for medicinal chemists that facilitates the entire virtual screening process, from data preparation through job submission and analysis of findings, regardless of the platform being used. Although there is no magic solution in the drug discovery process, PyRx's docking wizard and user-friendly interface make it a powerful tool for CAD. In addition to its chemical spreadsheet-like features, PyRx also boasts a robust visualisation engine, both of which are crucial in the realm of Rational Drug Design.
Biovia Discovery Studio 2021
Increased specificity and safety requirements, new types of therapeutics, and intricate disease mechanisms are only some of the examples of complexity in today's biopharmaceutical sector. Understanding therapeutic behaviour more thoroughly is necessary to keep up with this complexity. Modelling and simulation techniques offer a novel approach to investigating biochemical and physical processes at the molecular level. To speed up the discovery and development process, this can help direct physical experiments. Over 30 years of scholarly work and state-of-the-art In-silico methods, including molecular mechanics, free energy calculations, biotherapeutics developability, and more, are brought together in BIOVIA Discovery Studio 2021 (Free Download: BIOVIA Discovery Studio Visualizer - Dassault Systèmes (3ds.com). From Target ID through Lead Optimisation, it equips scientists with everything they need to probe the intricacies of protein chemistry and accelerate the discovery of small and big molecule therapies.
Open Babel GUI
Open Babel GUI (https://openbabel.org) is a chemical toolbox that aims to translate between different types of chemical data. Data from molecular modelling, chemistry, solid-state materials, biochemistry, and related fields can be searched, converted, analysed, and stored in this open, collaborative effort.
ChemDraw
The powerful prediction skills in ChemDraw Ultra (https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html) make it a useful tool for creating chemical structures for use in database queries, creating figures for lab reports and scientific articles, and more.
Selection and preparation of the protein
Protein three-dimensional structures have been downloaded from the RCSB Protein Data Bank (https://www.rcsb.org/). Protein was chosen based on its ability to bind reactive compounds and the microorganisms from which it was generated. Protein 4DX5, 5V5Z, 6LW5, 1ILR, 3BJM, 6LN2 (PDB IDs) are displayed. (Figure 2)
Selection of bioactive phytoconstituent and structure
Amyl propionate, Isololiolide, Leucasperol A from Leucas aspera have been isolated and reported. [26] The phytoconstituents Amyl propionate, Isololiolide, Leucasperol A has been analysed using specific paper and PubChem (https://pubchem.ncbi.nlm.nih.gov). As the Amyl propionate, Isololiolide, Leucasperol A is not reported on PubChem, so it has been created as a MDL mol format with the help of ChemDraw Ultra and ACD/ ChemSketch and further minimization has been done. To predict ligand-protein docking, the ligands were converted to Protein Data Bank (.pdb) format using the Open Babel GUI. The molecular weight and structural formula of the phytochemicals found in Leucas aspera that passed screening for Lipinski's rule, absorption, distribution, metabolism, and toxicity (Table 4).
Table 4- Screened phytoconstituents with molecular weight and structural formula
Phyto chemicals
|
Molecular weight (gm/mol)
|
Structural Formula
|
Amyl propionate
|
144.21
|
C8H16O2
|
Isololiolide
|
196.24
|
C11H16O3
|
Leucasperol A
|
352.5
|
C20H32O5
|
The remainder of the compounds have been screened for each specific activity, and some of them have violations and errors.
Drug likeness score prediction and side effect of ligand
Following the Lipinski rule of 5, Amyl propionate, Isololiolide, and Leucasperol A to check out the drug-likeness score on the online server Molsoft L.L.C. (http://molsoft.com/mprop/). The server determines the drug-likeness score, log P value, number of hydrogen bond acceptors and donors, and molecular weight (g/mol).
Pharmacokinetics prediction (ADME) and Toxicity identification
SwissADME (http://www.swissadme.ch/) was used to make predictions about the pharmacokinetic properties of the selected phytoconstituent. To predict ADME and toxicity data, this web-based tool employs in-silico algorithms. Which has been shown with the help of the table. (Table 5)
Ligand preparation
Open Babel GUI (https://openbabel.org) was used to convert the 3D.sdf files of phytoconstituents like Amyl Propionate, Isololiolide, and Leucasperol A (Table 4) downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov).
Protein preparation
RCSB's Protein Data Bank (PDB) (https://www.rcsb.org/) was mined to locate the protein of interest (4DX5, 5V5Z, 6LW5, 1ILR, 3BJM, 6LN2). The molecules have been assembled with the ligands. To further reduce docking interference, we used the BIOVIA Discovery Studio 2021 visualising tool to remove water molecules and add polar hydrogen before saving the file in.pdb format.
Ligand protein docking
Docking the phytoconstituents with the target protein was accomplished with the help of the PyRx (PyRx - Virtual Screening Tool download | SourceForge.net). After docking, the optimal Ligand was chosen based on the binding energy (Kcal/mol) in BIOVIA Discovery Studio 2021, which further generated and visualised 2D and 3D structural representations of the binding interaction between the ligand and protein.