scholarly journals Virtual Screening: Prediksi potensi 8-shogaol terhadap c-Jun N-Terminal Kinase (JNK)

2020 ◽  
Vol 4 (1) ◽  
pp. 1 ◽  
Author(s):  
Yohanes Bare ◽  
Mansur S ◽  
Sri Sulystyaningsih Natalia Daeng Tiring ◽  
Dewi Ratih Tirto Sari ◽  
Andri Maulidi
Keyword(s):  
Hydrogen Bond ◽  
Amino Acid ◽  
Virtual Screening ◽  
Protein Data Bank ◽  
Van Der Waals ◽  
Data Bank ◽  
Software Visualization ◽  
Amino Acid Residues ◽  
Discovery Studio ◽  
Protein Model

JNK adalah gen yang berperan dalam metabolisme DMT2. Dalam pengobatan T2DM digunakan JNK sebagai potensi terapi dengan menggunakan bahan alam. 8-shogaol adalah komponen kimia yang terkandung dalam jahe yang memiliki aktivitas antioksidan. Tujuan dari penelitina ini adalah menginversitagasi dan menganalisis peran 8-shogaol terhadap JNK. Protein JNK (ID: 464Y) diperoleh dari Protein Data Bank dan ligan 8-shogaol (CID:6442560 ) didapat dari pubchem. Ligan dan protein didocking menggunakan Hex 8.0.0. File dalam bentuk pdb divisualtisasi dan analisis menggunakan Discovery Studio Client 4.1 software. Interaksi ligan-protein menunjukan ikatan hidrogen pada residu asam amino LYS93 dan van der Waals pada 18 residu asam amino dengan energi ikatan-289.68cal/mol. Interkasi ini berpotensi sebagai penghambat kerja JNK dan dapat digunakan dalam terapi DMT2.Virtual screening: potential prediction of 8-shogaol againts c-Jun N-Terminal Kinase (JNK)AbstractJNK is one of gene that has a role in T2DM condition. To curve T2DM use JNK as potential healing using natural compounds. Eight-shogaol which found in ginger has function as a antioxidant.. The aim of the research is to investigate and analyze role 8-shogaol againts JNK. Protein JNK (ID: 464Y) was taken from Protein Data Bank and ligand 8-shogaol (CID:6442560 ) acquired from pubchem. Ligand and protein model were docked using Hex 8.0.0 software. Visualization and analysis molecular interactions by the Discovery Studio Client 4.1 software. Interaction ligand-protein showed one hydrogen bond in amino acid residue LYS93 and formed van der Waals in eighteen amino acid residues which energy binding -289.68cal/mol. This interaction has a potential to inhibit JNK role and lead to therapy T2DM.

scholarly journals POTENSI SENYAWA BIOAKTIF TANAMAN GENUS Phyllanthus SEBAGAI INHIBITOR REPLIKASI VIRUS HEPATITIS B

2017 ◽  
Vol 4 (2) ◽  
pp. 85
Author(s):  
. Firdayani ◽  
Susi Kusumaningrum ◽  
Yosephine Ria Miranti
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Hepatitis B ◽  
Protein Data Bank ◽  
Bioactive Compounds ◽  
Core Protein ◽  
Data Bank ◽  
Amino Acid Residues ◽  
Virus Hepatitis ◽  
Molegro Virtual Docker

Potency of Plant Bioactive Compounds from the Genus Phyllanthus as Hepatitis B Virus Replication InhibitorIn this research, simulations of molecular docking of Phyllanthus bioactive compounds were performed into the core protein of HBV. This simulation aimed to predict the interaction between compounds with virus core protein causing disruption of capsid formation and inhibiting its replication. The docking simulation was completed by Molegro Virtual Docker 6.0. The 3D stable conformation of molecule structures were docked into HBV core protein downloaded from Protein Data Bank, then the results were analyzed to view the minimum energy and interactions that occurred. The coordinate docking was done at the same coordinate as the previously docked reference ligand position and was validated. From the results it was known that repandusinic acid formed the most stable affinity bond with amino acid residues of viral core proteins. Interaction of B chain forming hydrogen bonds with the amino acid residues of Thr 33, Trp 102, Phe 23, Leu 140, Tyr 118 and Ser 141, and C chain with Thr 128, Val 124 and Glu 117.These compounds can be used as marker for anti HBV.Keyword: Bioactive compounds, core protein, HBV , molecular docking, Phyllanthus ABSTRAKPada penelitian ini dilakukan simulasi penambatan molekul senyawa-senyawa bioaktif Phyllanthus ke dalam protein inti virus hepatitis B. Simulasi ini bertujuan untuk memprediksi interaksi terbentuk antara senyawa dengan protein yang menyebabkan terganggunya pembentukan kapsid virus dan menghambat replikasinya. Simulasi penambatan molekul dilakukan menggunakan program Molegro Virtual Docker 6.0. Sebagai reseptor target digunakan struktur 3D protein inti yang diunduh dari Protein Data Bank. Posisi penambatan dilakukan pada koordinat yang sama dengan posisi ligan referensi yang sudah tertambat sebelumnya dan tervalidasi. Dari hasil simulasi diketahui bahwa asam repandusinat membentuk komplek dengan energi afinitas ikatan yang paling kecil dengan residu asam amino protein inti virus. Interaksi terjadi dengan rantai B yang membentuk ikatan hidrogen dengan asam amino Thr 33, Trp 102, Phe 23, Leu 140, Tyr 118 dan Ser 141, dan rantai C dengan asam amino Thr 128, Val 124 dan Glu 117. Senyawa ini dapat dijadikan sebagai marka untuk anti VHB.Kata kunci: Penambatan molekul, Phyllanthus, protein inti, senyawa bioaktif, VHBReceived: 11 December 2017                 Accepted: 27 December 2017           Published: 31 December 2017 

scholarly journals Analysis of molecular interactions of 8-gingerol compounds in Ginger (Zingiber officinale) as ACE Inhibitor

BIOEDUSCIENCE ◽  
2020 ◽  
Vol 4 (2) ◽  
pp. 183-187
Author(s):  
Yohanes Bare ◽  
Mansur S ◽  
Aprianus Pani Pili ◽  
Maria Helvina
Keyword(s):  
Amino Acid ◽  
Hydrogen Bonds ◽  
Ace Inhibitor ◽  
Van Der Waals ◽  
Zingiber Officinale ◽  
Van Der Waals Forces ◽  
Amino Acid Residues ◽  
Protein Database ◽  
Discovery Studio ◽  
Software Analysis

Background: Hypertension is a disease with increasing characteristics of blood pressure. The ACE gene has a role in the conversion of ATI to ATII in hypertensive conditions. Healing is done by using the 8-gingerol content contained in ginger. The purpose of this study is to analyze the molecular interaction that occurs between 8-gingerol and ACE. Method: ACE model proteins (ID: 3bkk) were obtained from the Bank Data Protein database (PDB) through 8-gingerol ligands (CID: 168114) obtained from the PubChem database. ACE and 8-gingerol were docked by Discovery Study Client 4.1 software. Analysis of amino acid residues, binding energy, Van der Waals forces, and hydrogen bonds formed using Discovery Studio Client 4.1. Results: The interaction between 8-gingerol and ACE showed that there were seven amino acid residues that interacted with 8-gingerol, also found hydrogen bonds, hydrophobic and Van der Waals forces that strengthen and stabilize these bonds. Conclusion: the interaction of 8-ginger with the active side of ACE is determined as an ACE inhibitor, the inhibition is a significant effect on the obstruction of ACE conversion.

scholarly journals Making glycoproteins a little bit sweeter withPDB-REDO

2018 ◽  
Vol 74 (8) ◽  
pp. 463-472 ◽  
Author(s):  
Bart van Beusekom ◽  
Thomas Lütteke ◽  
Robbie P. Joosten
Keyword(s):  
Experimental Data ◽  
Amino Acid ◽  
Protein Data Bank ◽  
Model Building ◽  
Data Bank ◽  
Structure Model ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
High Quality ◽  
Glycoprotein Structure

Glycosylation is one of the most common forms of protein post-translational modification, but is also the most complex. Dealing with glycoproteins in structure model building, refinement, validation and PDB deposition is more error-prone than dealing with nonglycosylated proteins owing to limitations of the experimental data and available software tools. Also, experimentalists are typically less experienced in dealing with carbohydrate residues than with amino-acid residues. The results of the reannotation and re-refinement byPDB-REDOof 8114 glycoprotein structure models from the Protein Data Bank are analyzed. The positive aspects of 3620 reannotations and subsequent refinement, as well as the remaining challenges to obtaining consistently high-quality carbohydrate models, are discussed.

scholarly journals Alignment of Alzheimer’s Disease Amyloid-β Peptide and Herpes Simplex Virus-1 pUL15 C-Terminal Nuclease Domain

2020 ◽  
Vol 4 (1) ◽  
pp. 373-377
Author(s):  
Steven Lehrer ◽  
Peter H. Rheinstein
Keyword(s):  
Herpes Simplex Virus ◽  
Immune System ◽  
Amino Acid ◽  
Herpes Simplex ◽  
Protein Data Bank ◽  
Amyloid Β ◽  
Data Bank ◽  
Amino Acid Residues ◽  
Simplex Virus ◽  
Hsv 1

Background: The cause of Alzheimer’s disease (AD) is poorly understood. Neurotropic microbes, particularly herpesviruses, might set off chronic neuroinflammation. Amyloid-β (Aβ) has antimicrobial properties and could represent a brain defense against infection. Objective: We searched for protein sequence alignment between herpes simplex virus type I (HSV-1) HSV-2, and Aβ. Methods: Protein data bank (pdb) structures for Aβ, HSV-1, and HSV-2 were searched on the RCSB Protein Data Bank. The protein structures were superimposed and aligned on PYMOL v 2.3.4. Results: For HSV-1 and Aβ, amino acid residues ser549 – his569 of HSV-1 aligned closely with residues asp7 - asn27 of Aβ. For HSV-2 and Aβ, amino acid residues of HSV-2 aligned less closely than those of HSV-1 with residues of Aβ. Conclusion: Conjugating and binding to the same alpha helix in the HSV-1 protease, Aβ could be marking HSV-1 for attack by the immune system, providing a rapid inherited immune response to a destructive neurotropic virus that would otherwise require the more time-consuming involvement of T-cells, B-cells, and the adaptive immune system. But older people do not respond to viral infections as well as younger individuals. When HSV-1 infection advances in an old person, more and more amyloid is produced, forming an adhesive web. As the brain tries to hold the pathologic process in check, neuroinflammation increases and spreads. Progressive neurodegeneration and cognitive decline are the outcome.

scholarly journals Characteristics of Interactions at Protein Segments External to Globular Domains in the Protein Data Bank

2018 ◽  
Author(s):  
Kota Kasahara ◽  
Shintaro Minami ◽  
Yasunori Aizawa
Keyword(s):  
Amino Acid ◽  
Protein Data Bank ◽  
Protein Function ◽  
Three Dimensional ◽  
Data Bank ◽  
Side Chain ◽  
Globular Domain ◽  
Amino Acid Residues ◽  
Structural Elements

ABSTRACTThe principle of three-dimensional protein structure formation is a long-standing conundrum in structural biology. A globular domain of a soluble protein is formed by a network of atomic contacts among amino acid residues, but regions external to globular domains, like loop and linker, often do not have intramolecular contacts with globular domains. Although these regions can play key roles for protein function as interfaces for intermolecular interactions, their nature remains unclear. Here, we termed protein segments external to globular domains as floating segments and sought for them in tens of thousands of entries in the Protein Data Bank. As a result, we found that 0.72 % of residues are in floating segments. Regarding secondary structural elements, coil structures are enriched in floating segments, especially for long segments. Interactions with polypeptides and polynucleotides, but not small compounds, are enriched in floating segments. The amino acid preferences of floating segments are similar to those of surface residues, with exceptions; the small side chain amino acids, Gly and Ala, are preferred, and some charged side chains, Arg and His, are disfavored for floating segments compared to surface residues. Our comprehensive characterization of floating segments may provide insights into understanding protein sequence-structure-function relationships.

scholarly journals In Silico Analysis of rbcl Protein and D-Ribulose 1,5-bisphosphate Bond

JSMARTech ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 065-068
Author(s):  
◽  
Dewi Sari ◽  
Luchman Hakim ◽  
Catur Retnaningdyah ◽  
Estri Arumingtiyas ◽  
...  
Keyword(s):  
Amino Acid ◽  
Dna Sequences ◽  
In Silico Analysis ◽  
Rbcl Gene ◽  
Amino Acid Residues ◽  
Model Quality ◽  
Discovery Studio ◽  
Plot Analysis ◽  
Protein Model ◽  
Alignment Analysis

The aim of this study was to determine the bond between the protein rbcL and D-Ribulose 1,5-bisphosphate by insilico. DNA sequences of the Mangrove Rhizophora mucronate rbcL gene DNA sequences from 7 different sources were obtained from NCBI for further alignment analysis using BioEdit software, phylogeny analysis using Mega6 software, molecular docking using PyRx software, preparation and visualization of docking results using Biovia Discovery Studio Visualizer software and analysis of the protein model quality based on the number of amino acid residues (Ramachandran plot analysis). The results of the docking molecular analysis showed interaction of 9 hydrogen bonds namely Asp203, Thr173, His294, Glu204, His327, Ser379, His298, Arg295, and Asn123 and 2 unfavorable bonds namely Lys177 and Lys175. This ligand and protein interaction complex was of good quality because the presence of amino acid residues in the most favored regions was greater than the amino acid residues in the disallowed regions outcomes

ANÁLISE COMPUTACIONAL DA INTERAÇÃO ENTRE O CANAL IÔNICO DE α-HL E COMPOSTOS TIAZOLIDÍNICOS

2021 ◽  
Author(s):  
Maria Isabel dos Santos Cavalcanti ◽  
Débora Brígida Moura de Freitas ◽  
Dijanah Cota Machado ◽  
Cláudio Gabriel Rodrigues
Keyword(s):  
Staphylococcus Aureus ◽  
Protein Data Bank ◽  
Data Bank ◽  
Discovery Studio

Introdução: Staphylococcus aureus (S. aureus) é uma bactéria associada a diversas infecções, tanto na comunidade quanto em ambiente hospitalar, ocasionando desde infecção cutânea até septicemia(1). Um importante fator de virulência é a exotoxina alfa-hemolisina (α-HL), que oligomeriza e forma canais iônicos transmembranares nas células-alvo, permitindo o fluxo livre de várias espécies químicas, resultando na morte celular(2). Diversas cepas de S. aureus exibem multirresistência aos antibióticos, limitando as opções de tratamento. Os derivados tiazolidínicos podem ser uma boa alternativa para bloquear a α-HL, pois possuem amplas propriedades bioativas, como por exemplo a antimicrobiana para cepas multirresistentes, sendo eficazes contra o S. aureus e inibindo o seu crescimento(3). Objetivos: Dada a importância da busca de compostos com ação antibacteriana, via bloqueio da α-HL, este trabalho visa analisar, via docagem molecular, a interação de derivados tiazolidínicos 5-benzilideno com o canal iônico formado pela toxina. Métodos: A estrutura cristalográfica da α-HL de S. aureus foi obtida pelo Protein Data Bank (PDB) e utilizou-se o MolView para modelagem dos compostos denominados GQ294 e GQ443, posteriormente submetidos ao Avogadro 1.1.1 para minimização de energia molecular. A docagem foi realizada pelo DockThor e os resultados foram analisados utilizando o Discovery Studio Visualizer. Resultados: A partir dos resultados de docagem pelo DockThor, foi obtida uma classificação dos compostos de acordo com suas energias totais e scores de afinidade com a toxina. Os valores de energia total do GQ443 e GQ294 foram iguais a -15,152 KJ/ mol e -19,009 KJ/ mol, respectivamente. Enquanto o score de afinidade de GQ443 e GQ294 foi de -6,820 Kcal/ mol e -5,902 Kcal/ mol respectivamente. As análises obtidas a partir do Discovery Studio Visualizer demonstraram que os dois compostos interagem com a região de constrição do canal iônico, principalmente com os resíduos GLU 111 e LYS 147, sendo estas interações mediadas principalmente por ligações de hidrogênio, além de interações do tipo cátionpi, pi-alquila, pi-enxofre. Esses dados corroboram com outros trabalhos já encontrados na literatura(4). Conclusões: Os resultados indicam, preditivamente, que os compostos GQ443 e GQ294 interagem com o canal da α-HL na região de constrição, sugerindo um bloqueio de sua atividade. São necessários dados experimentais para elucidar os dados teóricos já obtidos.

scholarly journals ANALYSIS OF MOLECULAR DOCKING EFFICIENCY OF CLEISTANTHIN-A, AS AN ALTERNATIVE FOR NICOTINE ADDICTION

2018 ◽  
Vol 10 (4) ◽  
pp. 98
Author(s):  
A. Amala Lourthuraj ◽  
M. Masilamani Selvam ◽  
Bharathi Ravikrishnan ◽  
M. Vinoth ◽  
Waheeta Hopper
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Protein Data Bank ◽  
Acetylcholine Receptor ◽  
Nicotinic Acetylcholine Receptor ◽  
High Throughput ◽  
In Silico ◽  
Data Bank ◽  
Tobacco Consumption ◽  
Nicotinic Acetylcholine

Objective: The present research was aimed to understand the molecular docking efficiency of a plant-derived compound cleistanthin-A and a common ingredient in tobacco consumption nicotine with nicotinic acetylcholine receptor (nAChR).Methods: The 3-D structure of nAChR was retrieved from the protein data bank (ID 5AFH). Ligand was obtained from the PUBCHEM. The in silico protocol comprised of three steps: high-throughput virtual screening (HTVS), standard preci­sion (SP) and extra precision (XP). The screened molecules were ranked accordingly using glide score. Schrödinger tool was used to perform the docking analysis.Results: The binding efficiency of the nicotine and cleistanthin-A was found to be docked at the cys-cys loop of the receptor. Based upon the glide score and glide energy it can be reported that, nicotine binding can be inhibited by the binding of cleistanthin-A to the nAChR.Conclusion: The docking efficiency of cleistanthin-A was good compared to nicotine towards nAChR. Hence, cleistanthin–A was derived as a better choice as an alternative for nicotine in smoke therapy.

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