Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia (original) (raw)
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Pharmacognosy Journal, 2019
Objective: Development of novel drugs is an important challenge in the pharmaceutical world and industry. In-silico methods are often considered in refinement / correction processes of drug design because they may lower the costs. The in-silico drug discovery process requires a three-Dimensional Structure (3DS) of the chemical compounds as input. Computational 3DSs often exhibit structural mismatches thus affecting the validity of the in-silico drug design process. In a previous study, a 3DS database with 1405 of Indonesian herbal compounds was developed, named HerbalDB. In this database, various structural mismatches were identified in some of the 3DSs. Our study aimed to identify and correct the structural mismatches in the herbalDB and to determine the best method in creating correct 3DS of chemical compounds. Methods: Structural mismatches in the herbal database were identified by molecular visualization. Results: The identification process yielded 170 compounds with structural mismatches that were corrected with 10 different parameters using the MarvinSketch and VegaZZ software, evaluated by molecular visualization. Conclusions: based on 3DS of chemical compound visualization, *.mol and *.sdf file format created using Dreiding force fields of MarvinSketch are the best method to construct the proper structure of Indonesian medicinal plant's chemical compound database compared with MMFF94, AMBER and CHARMM forcefields.
Evidence Based Validation of Traditional Medicines, 2021
In the current scenario of medicine, products from natural source have been significantly contributing towards the therapeutic approach in the treatment of disease ailments ranging from simple to complicated ones. The World Health Organization has stated that approximately 80% of the global population rely on herbal medicines/products for their healthcare benefits. But in many cases, the utilization of herbal products as medicine has slowed down due to their lack of standardization involving botanical, chemical and biological (activity/toxicity) aspects. Standardization of medicinal plants and its active constituents has been the major event in the field of plant science involving ethnopharmacology, phytomedicine and pharmacognosy. The conventional or traditional standardization method of medicinal plant research is a cumbersome process, expensive, time-consuming and to a less extent outdated. Hence, a computational technique incorporating in silico molecular docking simulation study has become an essential tool for drug discovery, standardization and screening of phytochemicals. In this chapter, a comprehensive information have been discussed on the approach, significance and application of molecular docking study towards the ligand-protein interaction taking examples of pure active
MAPS Database: Medicinal plant Activities, Phytochemical and Structural Database
Drug development from natural sources is an important and fast developing area. Natural sources (plants) have been used to cure a range of diseases for Thousands of years. Different online medicinal plant databases provide information about classifications, activities, phytochemicals and structure of phytochemicals in different formats. These databases do not cover all aspects of medicinal plants. MAPS (Medicinal plant Activities, Phytochemicals & structural database) has been constructed with uniqueness that it combines all information in one web resource and additionally provides test targets on which particular plant found to be effective with reference to the original paper as well. MAPS database is user friendly information resource, including the data of > 500 medicinal plants. This database includes phytochemical constituents, their structure in mol format, different activities possessed by the medicinal plant with the targets reported in literature.
An Update on Docking Analysis of Some Pharmacological Activity in Japanese Knotweed Leaf Compounds
Turkish computational and theoretical chemistry, 2023
The proof of concept presents the results of molecular docking analysis of Japanese knotweed leaf compounds interacting with the four different proteases 4GQQ, 2B17, 2FW3 and 1ZB6 from the Protein Data Bank. Several of these compounds exhibit binding energies for the various proteases and according to our data, compare favorably to known antibacterial, anti-inflammatory, antidiabetic and antioxidant drugs. The advancement of improved docking techniques has also made it possible to more accurately predict the biological activity of substances. This paper provides compounds of Japanese knotweed leaf to determine the result of gas chromatography-mass spectrometry for calculation of binding energy in comparison to standard drugs. The lowest value of binding energy for good biological activity. The compound Undecane had a higher negative binding energy than cyclohexanecarboxylic acid 2-hydroxyethyl ester. As we can see from the docking results, by comparing the values of the binding energies of the four proteins from the Protein Data Bank (4GQQ, 2B17, 2FW3 and 1ZB6), we propose that the Undecane compound is better antibacterial, anti-inflammatory, antidiabetic and antioxidant nature then cyclohexanecarboxylic acid 2hydroxyethyl ester compound. The density function theory (DFT) results of the energy difference between the highest molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) (ΔE =-0.44 eV) showed that the compounds were more reactively.
Molecular Docking Studies on Plant Derived Bioactive Compounds
Research journal of Agricultural Sciences, 2023
In the current scenario medicinal products from natural source have been significantly contributing towards the therapeutic approach in the treatment of diseases ranging from simple to complicate. The utilization of herbal products has slowed down due to lack of standardization involving botanical, chemical and biological (activity /toxicity) aspects. Hence a computational technique incorporating in silico molecular docking simulation study has become an essential tool for drug discovery, standardization and screening of phytochemicals. In this molecular docking study, the ligand-protein interaction of pure active phytol against the targeted fusarium protein is done.
2021
Due to advancement in the bioinformatics, there is a rapid increase in the computational method to predict the interaction between the interface of two biological origin molecules. Bioinformatics reduces the tedious task to perform the repeated analysing of various molecules interaction and gives the best interface interaction as an output. Prediction and experiment are the ways that undergo simultaneously and provides best route. It gives the promising result with a good precision value. The virtual screening method has been broadly acceptable as it omits the undesirable molecules from the compound repositories and gives a platform with a low cost and timeconsuming process. In our present study we have carry out the computational approach to predict and find out the anticancerous protein from curry leaves. We have selected the target from PDB and the ligand from the PubChem data base. For the preparation of target, we have removed the water molecules and added the polar hydrogen group. And for the preparation of ligand, we have detected the torsion root where docking can be processed. All the files of target and ligand were saved in pdbqt format. We have taken three breast cancerous protein into consideration for the molecular docking against the three anticancerous drugs obtained from PubMed are Oestradiol (PDB ID-3HB5), HER2 (PDB ID-1N8Z) and NUDT-5(PDB ID-5NQR). Oestradiol is a well characterized sex hormone that stimulates breast cancer in female. HER2 protein, when inappropriately activated leads to proliferation and differentiation of breast cancer cells. NUDT 5 has the importance in the gene regulation and the proliferation of breast cancer cells. After the molecular docking via Auto dock Vina Mahanine and Pyrayafoline D showed least interaction energy with the breast cancerous protein. The cancerous protein taken into consideration is also responsible for the other types of cancer but we are mainly focused on the breast cancer. Our present study concludes that the Murraya koenigii may serve as a potential source of bioactive compounds in the prevention of cancer. The potential for developing an anticancerous drugs from higher eukaryotic plants appears rewarding for the mankind as it leads to the development of new drugs that will be helpful for the cancer patient in present date.
Screening and Docking Studies of 266 Compounds
2010
Various proteins play important roles in hypertension and a number of plants have been tested for their efficacy in modulating hypertension. Angiotensin 1-converting enzyme, renin and extracellular regulated kinase 2(ERK2) proteins, respectively, has major role in hypertension and therefore protein ligand interaction studies were performed on 266 compounds from different parts of 7 plants (Allium sativum, Coriandrum sativum, Dacus carota, Murrayya koneigii, Eucalyptus globus, Calendula officinalis and Lycopersicon esculentum). Analysis was conducted using GOLD (Genetic Optimisation for Ligand Docking) software as docking program and the molecules drawn in ISIS Draw software are energy minimized using cosmic optimize 3D module of Tsar (Tools for structure activity relationships) software. Before docking plant compounds, software validation was performed and found that all co-crystallized ligands are within 2.0 A°. Further, docking and re-scoring of 266 compounds with GOLD, Molegro an...
Screening and Docking Studies of 266 Compounds from 7 Plant Sources as Antihypertensive Agents
Journal of Computer Science & Systems Biology, 2010
Various proteins play important roles in hypertension and a number of plants have been tested for their efficacy in modulating hypertension. Angiotensin 1-converting enzyme, renin and extracellular regulated kinase 2(ERK2) proteins, respectively, has major role in hypertension and therefore protein-ligand interaction studies were performed on 266 compounds from different parts of 7 plants (Allium sativum, Coriandrum sativum, Dacus carota, Murrayya koneigii, Eucalyptus globus, Calendula officinalis and Lycopersicon esculentum). Analysis was conducted using GOLD (Genetic Optimisation for Ligand Docking) software as docking program and the molecules drawn in ISIS Draw software are energy minimized using cosmic-optimize 3D module of Tsar (Tools for structure activity relationships) software. Before docking plant compounds, software validation was performed and found that all co-crystallized ligands are within 2.0 A°. Further, docking and re-scoring of 266 compounds with GOLD, Molegro and eHiTS followed by rank-sum technique revealed high binding affinity of compound 27, from Allium sativum, with Angiotensin converting enzyme, 1UZE and Renin, 2IKO. The docked pose of compound 27 (Phytic acid) exactly fits into the active site region and the ligand formed more number of H-bond interactions than the co-crystallized ligand. The best compound that exhibited high binding affinity with 3ERK was molecule 23 (Stigmasterol) from Lycopersicon esculentum.
Journal of Health and Allied Sciences NU
The success or failure of a potential drug depends on its absorption, distribution, metabolism, excretion and toxicity (ADMET) characteristics, and these features are usually rate-limiting in the drug development process. Hence, it is essential to know about the predicted ADMET properties of the most promising leads to avoid the risk of late-stage attrition. This project focuses on in silico screening of ADMET properties of phytochemicals found in Dakshina Kannada's medicinal plants, which include Tinospora cordifolia, Azadirachta indica, Ocimum sanctum, and Plectranthus amboinicus, mainly known for their antimicrobial properties.The physicochemical properties, bioactivity scores, ADMET, and molecular interactions of the selected phytoconstituents were determined by QikProp, Molinspiration, ADMETlab 2.0, ProTox-II, and GLIDE. In addition, molecular docking checked for their binding interactions with target proteins 1JIJ and 4 HOE of Staphylococcus aureus and Candida albicans, re...
Background: Cancer is one of the leading causes of death worldwide, and the pain associated with it is very intense. Plants are a significant source of medications, particularly anticancer and analgesic medicines. One significant plant, Strobilanthes Kunthiana, is well-known for its assortment of medical applications. As a result, additional studies were carried out using these two Phytocosntituents, lupeol and betulin, to examine their analgesic and anticancer characteristics using PDB IDs 2MUB and 4XI3. The examination on the basis of molecular docking and ADME profiles served as the foundation for this study. Objective: Based on molecular docking investigations, to suggest a mechanism of Strobilanthes Kunthiana Phytocosntituents for anticancer and analgesic activity. Method: Molecular docking studies of Phytoconstituents of Strobilanthes Kunthiana were performed using the PyRx Virtual Screening software. Results:According to the results of molecular docking, numerous ingredients,...