scholarly journals In silico recombinant plasmid design of pHA171 with phdABCD insertion for ethidium bromide degradation

2021 ◽  
pp. 7
Author(s):  
Muhammad Ilham Fahri ◽  
Rabiah Musfira Alatiffa ◽  
Sania Isma Yanti ◽  
Indira Prakoso ◽  
Alysha Naomi Mashitah
Keyword(s):  
Ethidium Bromide ◽  
Active Site ◽  
In Silico ◽  
Recombinant Plasmid ◽  
In Silico Analysis ◽  
Protein Library ◽  
Enzyme Improvement ◽  
Plasmid Design ◽  
Low Solubility ◽  
Protein Molecular Weight

Background: Ethidium bromide is a common reagent that is used in nucleic acid staining. However, ethidium bromide has toxic and carcinogenic properties that are harmful to the environment. Phenanthrene dioxygenase (encoded by phdA, phdB, phdC, and phdD genes) in Nocardioides sp. KP7 can oxidize the phenanthridine structure aim to eliminate carcinogenic properties. Objective: This study aims to visualize and predict the structure, active site, and characteristics of the phenanthrene dioxygenase using bioinformatics tools. Methods: Plasmid design were prepared by inserting genes of interest phdA, phdB, phdC, and phdD from the NCBI database. Furthermore, several protein analysis tools were used for structure visualization, active site enzyme improvement, and protein characteristic of phenanthrene dioxygenase. Results: The prediction results found that phenanthrene dioxygenase reacts with the ethidium bromide substrate through the interaction of Fe3+ ions with water. The solubility level of phenanthrene dioxygenase protein is 0.404, suggesting that the protein has low solubility. The protein isoelectric point (pI) is between 5.17 to 5.36, and the protein molecular weight is 121.143 kDa. Conclusion: In silico analysis has supported that recombinant plasmid met characteristics for the construct which consists of gene interest and protein library.

scholarly journals Molecular docking and pharmacokinetic screening of eucalyptol (1,8 cineole) from eucalyptus essential oil against SARS-CoV-2

2020 ◽  
Vol 12 (3) ◽  
pp. 536-545
Author(s):  
Arun D. SHARMA ◽  
Inderjeet KAUR
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Active Site ◽  
In Silico ◽  
Hydrophobic Interactions ◽  
Rna Virus ◽  
In Silico Analysis ◽  
Active Site Residues ◽  
Virus Family

SARS-CoV-2 (COVID-19), member of corona virus family, is a positive single stranded RNA virus. Due to lack of drugs it is spreading its tentacles across the world. Being associated with cough, fever, and respiratory distress, this disease caused more than 15% mortality worldwide. Mpro/3CLpro has recently been regarded as a suitable target for drug design due to its vital role in virus replication. The current study focused on the inhibitory activity of eucalyptol (1,8 cineole), an essential oil component from eucalyptus oil, against Mpro/3CLprofrom SARS-CoV-2. Till date there is no work is undertaken on in-silico analysis of this compound against Mpro/3CLproof SARS-CoV-2. Molecular docking studies were conducted by using 1-click dock tool and Patchdock analysis. In-silico absorption, distribution, metabolism, excretion and toxicity (ADMET) profile were also studied. The calculated parameters such as docking score indicated effective binding of eucalyptol to COVID-19 Mpro protein. Active site prediction revealed the involvement of active site residues in ligand binding. Interactions results indicated that, Mpro/3CLpro/eucalyptol complexes forms hydrophobic interactions. ADMET studies provided guidelines and mechanistic scope for identification of potent anti-COVID 19 drug. Therefore, eucalyptol may represent potential herbal treatment to act as COVID-19 Mpro/3CLproinhibitor, a finding which must be validated in vivo.

scholarly journals Analisis In-Silico Protein Tiol-Disulfida Isomerase Bacillus sp. RP1

2012 ◽  
Vol 12 (1) ◽  
pp. 43 ◽  
Author(s):  
Vanda S Kamu ◽  
Jemmy Abidjulu ◽  
Maureen Kumaunang
Keyword(s):  
Protein Folding ◽  
Gene Product ◽  
Active Site ◽  
In Silico ◽  
In Silico Analysis ◽  
Bacillus Sp ◽  
Disulfide Isomerase ◽  
Disulfide Oxidoreductase ◽  
Silico Analysis ◽  
Bonding Site

ANALISIS IN-SILICO PROTEIN TIOL-DISULFIDA ISOMERASE Bacillus sp. RP1 ABSTRAK Pelipatan protein membutuhkan bantuan molekul chaperone serta katalis pelipatan. Penelitian ini bertujuan untuk mengkarakterisasi produk gen tiol-disulfida oksidoreduktase dari sumber organisme termofilik Bacillus sp. RP1. Metode yang dilaksanakan untuk mencapai tujuan tersebut, adalah mengkarakterisasi produk gen yang dihasilkan dengan menggunakan analisis in-silico. Dari hasil penelitian diperoleh bahwa karakterisasi terhadap produk gen yang dihasilkan menunjukkan adanya tiga protein, yaitu Bdbdred, Bdbdox, dan Etda, yang memiliki motif tioredoksin dan DsbA, serta sisi aktif dan sisi pengikatan dengan atom Zn. Prediksi struktur ketiga protein tersebut menunjukkan kemiripan satu sama lain. Kata kunci: Bdbd, chaperone, DsbA, tiol-disulfida oksidoreduktase, tioredoksin ANALYSIS OF IN-SILICO TIOL DISULFIDE ISOMERASE PROTEIN Bacillus sp. RP1 ABSTRACT Protein folding is facilitated by chaperone molecule as well as folding catalysts. The aim of this research was to characterize the gene product of thiol-disulfide oxidoreductase gene from thermophylic organism Bacillus sp. RP1, by using in-silico analysis. The characteristic of the gene product indicated three proteins, i.e. Bdbdred, Bdbdox, and Etda, which have thioredoxin motif, DsbA motif, active site and bonding site with Zn. The structure predicted of these three proteins showed similarity among them. Keywords: Bdbd, chaperone, DsbA, thiol-disulfide oxidoreductase, thioredoxin

In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes

2011 ◽  
Vol 18 (5) ◽  
pp. 2013-2019 ◽  
Author(s):  
Nirmal K. Prasad ◽  
Vaibhav Vindal ◽  
Siva Lakshmi Narayana ◽  
Ramakrishna V. ◽  
Swaraj Priyaranjan Kunal ◽  
...  
Keyword(s):  
Active Site ◽  
In Silico ◽  
In Silico Analysis ◽  
Pycnoporus Cinnabarinus ◽  
Silico Analysis

scholarly journals Functional in silico analysis of human tyrosinase and OCA1 associated mutations

2020 ◽  
Vol 9 (3) ◽  
pp. 81-92
Author(s):  
Yuri Sergeev ◽  
Milan Patel
Keyword(s):  
Active Site ◽  
In Silico ◽  
In Silico Analysis ◽  
Autosomal Recessive Disorder ◽  
Oculocutaneous Albinism ◽  
General Mechanism ◽  
Site Mutation ◽  
Tyrosinase Gene ◽  
Severity Of The Disease ◽  
Human Tyrosinase

Oculocutaneous albinism type 1 (OCA1) is an autosomal recessive disorder caused by mutations in the tyrosinase gene. OCA1 exists in two forms: OCA1A and OCA1B. OCA1A is caused by a full loss of the human tyrosinase protein (Tyr), leading to an absence of pigment in skin, hair, and eyes, while OCA1B has reduced Tyr catalytic activity and pigment. The current understanding of the disease is hampered by the absence of information regarding the alterations of protein structure and the effects leading to either form of OCA1. Here, we used computational methods to find a general mechanism for establishing this link. Tyr and mutant variants were built through homology modeling, glycosylated in silico, minimized, and simulated using 100 ns molecular dynamics in water. For OCA1B mutants, cavity size is linked to DDG values for mutants, suggesting that partial loss of Tyr is associated with the destabilizing effect of the EGF-like domain movement. In OCA1A, active site mutation simulations indicate that the absence of O2 leads to protein instability. OCA1B mutants are described in severity by the size of the cavity within the EGF–Tyr interface, while active site OCA1A mutants are unable to fully coordinate copper, leading to an absence of O2 and Tyr instability. In patients with known genotypes, free energy changes may help identify the severity of the disease by assessing either the allosteric effect of the EGF-Tyr cavity in OCA1B or the active site instability in OCA1A.

scholarly journals COMPUTATIONAL DOCKING AND IN SILICO ANALYSIS OF POTENTIAL EFFLUX PUMP INHIBITOR PUNIGRATANE

2018 ◽  
Vol 10 (3) ◽  
pp. 27 ◽  
Author(s):  
Zumaana Rafiq ◽  
Saranya Sivaraj ◽  
Rama Vaidyanathan
Keyword(s):  
Bile Acid ◽  
Active Site ◽  
In Silico ◽  
Efflux Pump ◽  
Hydrophobic Interactions ◽  
In Silico Analysis ◽  
Drug Candidate ◽  
Potential Drug ◽  
Computational Docking ◽  
Silico Analysis

Objective: Efflux-mediated resistance is a growing therapeutic complication as it reduces the efficacy of antibiotics. In gram-negative bacteria like E. coli and K. pneumoniae, this can be overcome with the help of efflux pump inhibitors (EPI) targeted at the transporter protein AcrB that plays a key role in binding to antibiotics. Our study focuses on the potential EPI Punigratane isolated from the rind of Punica granatum. Using computational docking analysis and in silico analysis, our aim is to determine whether Punigratane has the ability to interact and inhibit the AcrB pump and whether it has drug viability.Materials: Computational docking analyses were carried out using the online platforms Mcule and PatchDock. Drug-likeness and classification of Punigratane was predicted using online tools PreADMET and SuperPred. Admet SAR and Toxicity Checker at Mcule were used to predict ADME (absorption, distribution, metabolism, and excretion) and overt toxicity properties.Results: Punigratane was computationally docked with 57 AcrB crystal structures available at the PDB database to determine whether it could bind to the active site regions. It was found to bind in the periplasmic region close to the substrate bile acid where it is thought to bring about inhibition by steric hindrances. When docked with AcrB mutant (AcrB N109A), it was found to bind in the same periplasmic site as the substrates (EtBr, Rhodamine 6G, Ciprofloxacin, Bile acid) as well as the inhibitor (phenylalanine-arginine β-naphthylamide-PaβN). When docked in the active site of the inhibitor MBX2319, it was found to have a comparable docking score as well as the same hydrophobic interactions as the inhibitor. In silico analysis showed that Punigratane exhibited a drug-likeness to the inhibitor MBX2319 and that its drug classification is similar to antimicrobial agents. It was also found be a potential drug due to its intestinal absorption, increased bioavailability and non-toxic nature.Conclusion: Therefore our report shows that Punigratane could be a potential drug candidate that inhibits efflux activity by interacting and inhibiting the AcrB efflux pump. 

scholarly journals IN-SILICO ANALYSIS

2016 ◽  
Vol 23 (02) ◽  
pp. 217-222
Author(s):  
Hammad Tufail Chaudhary ◽  
Shahida Hasnain
Keyword(s):  
Hydrogen Bonds ◽  
Active Site ◽  
In Silico ◽  
Active Sites ◽  
In Silico Analysis ◽  
Data Bank ◽  
Protein Data Bank Code ◽  
In Silico Study ◽  
Study Setting ◽  
Silico Analysis

ntroduction: Different pathogen reducing technologies are being implementedwhich includes S-303. CD-61 is important receptor for clotting. Pathogen reducing agents arebeing studied extensively to probe its effects. Objective: We conducted this study to reviewthe docking of S-303 at CD-61, to look into the effect of S-303 on function of platelets. StudyDesign: This was an observational study. Setting: In-silico study. Period: March 2015 toAugust 2015. Method: The study was carried out in-silico. PDB (Protein data bank) code ofTirofiban bound to CD-61 was 2vdm. CD-61 was docked with Tirofiban using online dockingtools i.e. Patchdock and Firedock. Then, S-303 and CD-61 were also docked. Best dockingposes to active sites of 2vdm were found. Interactions of ligands and CD-61 were obtained.Then comparison of Hydrogen Bonds, Hydrogen Bond Lengths, Hydrophobic bonds of 2vdmmolecule and best poses of docking results were done. Patchdock and Firdock results of bestposes were also analyzed using SPSS-16. Results: The Hydrogen bonds and Hydrogen bondlength and hydrophobic bonds of docking results were compared to 2vdm. 2 best poses wereobtained for docking of tirofiban to CD-61. No docking to active site was observed in Patchdockand firedock for S-303to CD-61. Conclusion: S-303 did not bind to the active site of CD-61. Wecan assume that S-303 doe

A systematic review with in silico analysis on transcriptomic profile of gallbladder carcinoma

2020 ◽  
Vol 47 (6) ◽  
pp. 398-408
Author(s):  
Sonam Tulsyan ◽  
Showket Hussain ◽  
Balraj Mittal ◽  
Sundeep Singh Saluja ◽  
Pranay Tanwar ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gallbladder Carcinoma ◽  
In Silico ◽  
In Silico Analysis ◽  
Transcriptomic Profile ◽  
Silico Analysis
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