• Journal of the Korean Magnetic Resonance Society
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• v.15 no.1
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• pp.80-89
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• 2011

3D structures of STAM1 UIM-ubiquitin complex were presented to predict and analyze the interaction between UIM and ubiquitin. To generate the protein-peptide complex structure, the RosettaDock method was used with and without NMR restraints. High resolution complex structure was acquired successfully and evaluated electrostatic interaction in the protein-peptide binding with several charged residues at the binding site. From docking results, the Rosettadock method could be useful to acquire essential information of protein-protein or protein-peptide interaction with minimal biological evidences.

• Journal of Integrative Natural Science
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• v.11 no.1
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• pp.9-13
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• 2018

KiSS1-derived peptide receptor, a GPCR protein, binds with the hormone Kisspeptin plays a major role in the neuroendocrine regulation of reproduction. It is important in the onset of puberty and triggers the release of gonadotrophin-releasing hormone. It is a potential drug target for the disorders related to GnRH, hence, analysing the structural features of the receptor becomes important. The three dimensional of the receptor modelled in a previous study was utilised. In this study, we have analysed the protein - protein interaction of the receptor with Kisspeptin 10 and 15. The study revealed the important residues which are involved in the interaction. The result of this study could be helpful in understanding the mechanism of Kiss1 receptor activation and the pathophysiology of the disorders related to the receptor.

• Natural Product Sciences
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• v.27 no.2
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• pp.99-114
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• 2021

Type 2 diabetes mellitus (T2DM) and its complications are important noncommunicable diseases with high mortality rates. Protein tyrosine phosphatase 1B (PTP1B) and aldose reductase inhibitors are recently approached and advanced for T2DM and its complications therapy. Matricaria chamomilla L. is acknowledged as a worldwide medicinal herb that has many beneficial health effects as well as antidiabetic effects. Our research was designed to determine the most potential antidiabetic phytochemicals from M. chamomilla employing in silico study. 142 phytochemicals were obtained from the databases. The first screening employed iGEMdock and Swiss ADME, involving 93 phytochemicals. Finally, 30 best phytochemicals were docked. Molecular docking and visualization analysis were performed using Avogadro, AutoDock 4.2., and Biovia Discovery Studio 2016. Molecular docking results demonstrate that ligand-protein interaction's binding affinities were -5.16 to -7.54 kcal/mol and -5.30 to -12.10 kcal/mol for PTP1B and aldose reductase protein targets respectively. In silico results demonstrate that M. chamomilla has potential antidiabetic phytochemical compounds for T2DM and its complications. We recommended anthecotulide, quercetin, chlorogenic acid, luteolin, and catechin as antidiabetic agents due to their binding affinities against both PTP1B and aldose reductase protein. Those phytochemicals' significant efficacy and potential as antidiabetic must be investigated in further advanced research.

• Journal of Integrative Natural Science
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• v.10 no.1
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• pp.1-6
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• 2017

Demand for a new anti-malarial drug has been dramatically increasing in the recent years. Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR) plays a vital role in fatty acid elongation process, which now emerged as a new important target for the development of anti-microbial and anti-parasitic molecules. In the present study, 19 compounds namely alginic acid, atropine, chlorogenic acid, chrotacumine A & B, coenzyme $Q_1$, 4-coumaric acid, curcumin, ellagic acid, embelin, 5-O-methyl embelin, eugenyl glucoside, glabridin, hyoscyamine, nordihydroguaiaretic acid, rohitukine, scopolamine, tlatlancuayin and ursolic acid were evaluated on their docking behaviour on P. falciparum enoyl-acyl carrier protein reductase (PfENR) using Auto dock 4.2. The docking studies and binding free energy calculations exhibited that glabridin gave the highest binding energy (-8.07 kcal/mol) and 4-coumaric acid in contrast showed the least binding energy (-4.83 kcal/mol). All ligands except alginic acid, ellagic acid, hyoscyamine and glabridin interacted with Gln409 amino acid residue. Interestingly four ligands namely coenzyme $Q_1$, 4-coumaric acid, embelin and 5-O-methyl embelin interacted with Gln409 amino acid residue present in both chains (A & B) of PfENR protein. Thus, the results of this present study exhibited the potential of these 19 ligands as P. falciparum enoyl-acyl carrier protein reductase (PfENR) inhibitory agents and also as anti-malarial agents.

• Journal of Integrative Natural Science
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• v.7 no.3
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• pp.159-165
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• 2014

Pyrazole, hydroxyimino, aldehyde and isoxazole derivatives exhibit a broad spectrum of biological activities such as antimicrobial, anti-inflammatory and antitumor activities. With growing application on their synthesis and bioactivity, chemists and biologists in recent years have considerable attention on the research of these derivatives. In the view of potential importance of these derivatives, we have crystallized few of the derivatives and its report has been published. The present study focuses on docking studies of these derivatives against Phospholipases $A_2$ enzyme. This enzymes has implicated as potential targets for anti-inflammatory drug design. co-crystal structure (PDB ID: 1POE) of $PLA_2$ deposited in Protein Data Bank has been retrieved for docking analysis. Docking studies using Schrodinger's GLIDE reveals that these derivatives shows better binding energy and score in the defined active site. These results may provide a guiding role to design a lead molecule which may reduce inflamation.

• CELLMED
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• v.3 no.2
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• pp.12.1-12.4
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• 2013

Identification of target protein is an important procedure in the course of drug discovery. Because of complexity, action mechanisms of herbal medicine are rather obscure, unlike small-molecular drugs. Inverse docking simulation is a reverse use of molecular docking involving multiple target searches for known chemical structure. This methodology can be applied in the field of target fishing and toxicity prediction for herbal compounds as well as known drug molecules. The aim of this review is to introduce a series of in silico works for predicting potential drug targets and side-effects based on inverse docking simulations.

• Journal of Integrative Natural Science
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• v.10 no.3
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• pp.137-140
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• 2017

Diabetes mellitus has become a major growing public health problem worldwide. More than 90% of all diabetes cases are classified as type 2 diabetes (T2D), which is also known as non-insulin dependent diabetes. Protein tyrosine phosphatase 1B (PTP1B) plays an important role in the negative regulation of insulin signal transduction pathway and has emerged as novel therapeutic strategy for the treatment of type 2 diabetes. PTP1B inhibitors enhance the sensibility of insulin receptor (IR) and have favorable curing effect for insulin resistance-related diseases. Recently twelve anti-diabetic xanthones were isolated from the bark of Garcinia xanthochymus. Hence, in the present study, molecular docking was carried out for these twelve xanthones. The objective of this work is to study the interaction of the newly isolated xanthones with PTP1B. The docking results showed that xanthones have good interactions and has better docking score with PTP1B and suggest LYS120 and ASP181 are the important residues involved in interaction between PTP1B enzyme and the xanthones.

• Journal of Integrative Natural Science
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• v.5 no.1
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• pp.18-21
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• 2012

The resistance of tumour cells against cytotoxic drug is significant limitation in successful chemotherapeutic treatment of cancer. To date, no crystal structure is available for human P-gp. We developed homology model for human P-gp NBD2 by using coordinates of transporter associated protein (TAP1). Docking study was performed for 8-geranyl-chrysin (Flavonoids) inhibitor in the NBD2 model. Ligand-protein interactions were determined which indicates that the 8-geranyl chrysin shares two overlapping sites in the cytosolic domains of P-gp, the ATP site and a hydrophobic steroid-binding site.

• Journal of Integrative Natural Science
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• v.6 no.4
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• pp.205-210
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• 2013

Human P-gp is a protein responsible for the multidrug resistance (MDR) and causes failure of cancer chemotherapy. Till date no X-ray crystal structure is reported for this membrane protein, which hampers active research in the field. We performed homology modeling to develop three dimensional (3D) model of P-gp, and docking studies of the verapamil and curcumin have been performed to gain insight into the interaction mechanism between inhibitors and P-gp. It was identified that the inhibitors docked into the upper part of P-gp and interacted through the hydrophobic interactions.

• Journal of Integrative Natural Science
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• v.15 no.4
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• pp.153-161
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• 2022

c-Jun N-terminal kinases (JNKs) are members of MAPK family. Many genes can relay signals that promote inflammation, cell proliferation, or cell death which causes several diseases have been associated to mutations in the JNK gene family. The JNK2 gene is significantly more important in cancer development than the JNK1 and JNK3 genes. There are several different ways in which JNK2 contributes to breast cancer, and one of these is through its role in cell migration. As a result, this study's primary objective was to employ computational strategies to identify promising leads that potentially target the JNK2 protein in a strategy to alleviate breast cancer. We have derived these anticancer compounds from marine brown seaweed called Turbinaria conoides. We have identified compounds Ethane, 1, 1-diethoxy- and Butane, 2-ethoxy as promising anti-cancer drugs by molecular docking, DFT, and ADME study.