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

scholarly journals IN SILICO STUDY OF THE ANTIMICROBIAL PROFILE OF β-CITRONELLOL: POTENTIAL AS AN ANTIFUNGAL

2019 ◽  
Vol 16 (32) ◽  
pp. 894-898
Author(s):  
D. F. SILVA ◽  
H. D. NETO ◽  
M. D. L. FERREIRA ◽  
A. A. O. FILHO ◽  
E. O. LIMA
Keyword(s):  
In Silico ◽  
Fungal Infections ◽  
In Silico Analysis ◽  
Fungal Species ◽  
In Silico Study ◽  
Pass Online ◽  
Therapeutic Alternatives ◽  
Bioactivity Profile ◽  
Silico Analysis

β-citronellol (3,7-dimethyl-6-octen-1-ol) has been exhibiting a number of pharmacological effects that creates interest about its antimicrobial potential, since several substances of the monoterpene class have already demonstrated to possess activity in this profile. In addition, the emergence of fungal species resistant to current pharmacotherapy poses a serious challenge to health systems, making it necessary to search for new effective therapeutic alternatives to deal with this problem. In this study, the antimicrobial profile of β-citronellol was analyzed. The Prediction of Activity Spectra for Substances (PASS) online software was used to study the antimicrobial activity of the β-citronellol molecule by the use of in silico analysis. In contrast, an in vitro antifungal study of this monoterpene was carried out. For this purpose, the Minimum Inhibitory Concentration (MIC) was determined by the microdilution technique in 96-well plates in Saboraud Dextrose Broth/RPMI against sensitive strains of Candida albicans, and this assay was performed in duplicate. In the in silico analysis of the antimicrobial profile, it was revealed that the monoterpene β-citronellol had a diverse antimicrobial bioactivity profile. For the antifungal activity, it presented a percentage value with Pa: 58.4% (predominant) and its MIC of 128 μg/mL, which was equivalent for all strains tested. The in silico study of the β-citronellol molecule allowed us to consider that the monoterpenoid is very likely to be bioactive against agents that cause fungal infections.

scholarly journals Short hydrogen bonds in the catalytic mechanism of serine proteases

2008 ◽  
Vol 73 (4) ◽  
pp. 393-403 ◽  
Author(s):  
Vladimir Leskovac ◽  
Svetlana Trivic ◽  
Draginja Pericin ◽  
Mira Popovic ◽  
Julijan Kandrac
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Active Site ◽  
Serine Proteases ◽  
Active Sites ◽  
Catalytic Mechanism ◽  
Data Bank ◽  
Ground State Structure ◽  
Low Barrier Hydrogen Bonds ◽  
Short Hydrogen Bonds

The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 ? revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 ? long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short "low-barrier" hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the "low-barrier hydrogen bond" hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 ? long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the "low-barrier hydrogen bond" hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.

scholarly journals Influence of cantilever position and implant connection in a zirconia custom implant-supported fixed partial prosthesis: in silico analysis

2018 ◽  
Vol 47 (4) ◽  
pp. 223-229
Author(s):  
Juliana Maria Coutinho BASTOS ◽  
Dimorvan BORDIN ◽  
Andréa Araújo de VASCONCELLOS ◽  
Milton Edson MIRANDA
Keyword(s):  
In Silico ◽  
Maximum Stress ◽  
In Silico Analysis ◽  
Compression Stress ◽  
Vertical Load ◽  
Occlusal Force ◽  
Tension Distribution ◽  
Custom Implant ◽  
In Silico Study ◽  
Silico Analysis

Abstract Introduction A better tension distribution on implants and abutments in implant-supported fixed partial prosthesis is essential in the rehabilitation of posterior mandible area. Objective: To evaluate the influence of cantilever position and implant connection in a zircônia custom implant-supported fixed partial prosthesis using the 3-D finite element method. Material and method: Four models were made based on tomographic slices of the posterior mandible with a zirconia custom three-fixed screw-retained partial prosthesis. The investigated factors of the in silico study were: cantilever position (mesial or distal) and implant connection (external hexagon or morse taper). 100 N vertical load to premolar and 300 N to molar were used to simulate the occlusal force in each model to evaluate the distribution of stresses in implants, abutments, screws and cortical and cancellous bone. Result: The external hexagon (EH) connection showed higher cortical compression stress when compared to the morse taper (MT). For both connections, the molar cantilever position had the highest cortical compression. The maximum stress peak concentration was located at the cervical bone in contact with the threads of the first implant. The prosthetic and abutment screws associated with the molar cantilevers showed the highest stress concentration, especially with the EH connection. Conclusion: Morse taper implant connetions associated with a mesial cantilever showed a more favorable treatment option for posterior mandible rehabilitation.

scholarly journals Inhibitory Effect of Phytochemicals from Azadirachta indica A Juss. and Tinospora cordifolia (Thunb.) Miers against SARS-CoV-2 M pro and Spike Protease- An In Silico Analysis

2020 ◽  
Author(s):  
RAMÀKRISHNAMACHARYA CH ◽  
VANITHA MURALIKUMAR ◽  
CHANDRASEKAR SESHACHALAM
Keyword(s):  
Medicinal Plants ◽  
Azadirachta Indica ◽  
In Silico ◽  
Viral Infections ◽  
In Silico Analysis ◽  
Inhibitory Effect ◽  
Tinospora Cordifolia ◽  
Reference Drug ◽  
In Silico Study ◽  
Silico Analysis

COVID 19 caused by SARS-CoV-2 is spreading worldwide and affected 10 million people with a mortality rate between 0.5 % to 5%. Medicinal plants from China, Morocco, Algeria, Africa and India were tested for antiviral efficacy in SARS-CoV-2. Ayurveda Medicine described many medicinal plants. The Nimba ( Azadirachta indica A. Juss) is used in fever, bacterial and viral infections, and Amrita ( Tinospora cordifolia (Thunb.) Miers) is used as antiviral, antipyretic, and anti-inflammatory purposes. The combination of both these plants is called Nimbamritam, and it is widely used in pyrexia, dermatitis, viral infections, etc. Spike protease (PDB ID 6VXX) and M pro (PDB ID 6LU) were retrieved from RCSB and 16 ligands from A. indica and 6 ligands from T. cordifolia were obtained from IMPPAT and PubChem. AutoDock Vina embedded PyRx was used for docking. Remdesivir was taken as a reference drug. In silico study of Cordifolide A of T cordifolia showed the highest scores with -8.2 Kcal/mol and -10.3Kcal/mol with M pro protease and Spike protease respectively. Cordifolide A had 4 H bonds and Kaempferol had 7 non-conventional bonds, including van der Waal with M pro (6LU7) protease. The interactions with 6VXX had 5 H bonds in each ligand Cordifolide A and Azadirachtin B. The prevention of virus entry by targeting spike protease host receptor ACE2 and restricting replication of the viral genome by targeting M pro residues were identified in our study. A. indica and T. cordifolia are promising therapeutic agents in COVID 19.

In silico analysis of interaction pattern switching in ligand⋯receptor binding in Golgi α-mannosidase II induced by the protonated states of inhibitors

2017 ◽  
Vol 19 (19) ◽  
pp. 12527-12537 ◽  
Author(s):  
V. Sladek ◽  
J. Kóňa ◽  
H. Tokiwa
Keyword(s):  
Receptor Binding ◽  
In Silico ◽  
Active Sites ◽  
Biological Activities ◽  
In Silico Analysis ◽  
Interaction Pattern ◽  
Binding Modes ◽  
Silico Analysis

Different binding modes for charge-neutral and protonated inhibitor forms in Golgi α-mannosidase II active sites may influence their biological activities.

scholarly journals The Expression Patterns of BECN1, LAMP2, and PINK1 Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study

2020 ◽  
Vol 9 (12) ◽  
pp. 4020
Author(s):  
Martyna Bednarczyk ◽  
Edyta Fatyga ◽  
Sylwia Dzięgielewska-Gęsiak ◽  
Dariusz Waniczek ◽  
Beniamin Grabarek ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
In Silico ◽  
Expression Patterns ◽  
Cpg Islands ◽  
In Silico Analysis ◽  
Epigenetic Changes ◽  
Grid Infrastructure ◽  
In Silico Study ◽  
Silico Analysis

Background: Autophagy plays a dual role of tumor suppression and tumor promotion in colorectal cancer. The study aimed to find those microRNAs (miRNAs) important in BECN1, LAMP2, and PINK1 regulation and to determine the possible role of the epigenetic changes in examined colorectal cancer using an in silico approach. Methods: A total of 44 pairs of surgically removed tumors at clinical stages I‒IV and healthy samples (marginal tissues) from patients’ guts were analyzed. Analysis of the obtained results was conducted using the PL-Grid Infrastructure and Statistica 12.0 program. The miRNAs and CpG islands were estimated using the microrna.org database and MethPrimer program. Results: The autophagy-related genes were shown to be able to be regulated by miRNAs (BECN1—49 mRNA, LAMP2—62 mRNA, PINK1—6 mRNA). It was observed that promotion regions containing at least one CpG region were present in the sequence of each gene. Conclusions: The in silico analysis performed allowed us to determine the possible role of epigenetic mechanisms of regulation gene expression, which may be an interesting therapeutic target in the treatment of colorectal cancer.

scholarly journals Proapoptosis Effect of Root of Eurycoma longifolia (Pasak Bumi) on the Prostate Cancer: In Silico Analysis

2020 ◽  
Vol 20 ◽  
pp. 03003
Author(s):  
Eka Yudha Rahman ◽  
Mulyohadi Ali ◽  
Basuki Bambang Purnomo ◽  
Nia Kania
Keyword(s):  
Prostate Cancer ◽  
In Silico ◽  
Caspase 3 ◽  
In Silico Analysis ◽  
Data Bank ◽  
Active Ingredients ◽  
Caspase 9 ◽  
Active Compounds ◽  
Eurycoma Longifolia ◽  
Silico Analysis

This study aimed to predict the proapoptosis effect of E. longifolia active compounds on prostate cancer by in silico analysis. Protein data such as BCL-2 (GI: 2506216), Caspase 3 (GI: 6978605), Caspase 8(GI: 11560103), data quassinoid (ID: 5459060 and chantin (ID: 97176) were collected from GenBank of NCBI. Protein BCL-2 collected from NCBI compare with Protein Data Bank (PDB) and UNIPROT. The docking process was carried out using software HEX 8.0. to compute the binding affinity between ligands (active compounds of Pasak Bumi) and protein target. The interaction between quassinoid and chantin was strongest and stable against caspase-9, indicating that the active ingredient in E. longifolia triggered caspase-9 activity after activation of BH3 domains in Bcl-2 in prostate cancer. The low energy binding between quassinoid and chantin with caspase-3 indicates the interaction between the active ingredients is not strong with caspase-3. E. longifolia active ingredients that are potentially used in the treatment of prostate cancer are quassinoid and chantin by inducing apoptotic mechanisms via both extrinsic and intrinsic pathways. The combination of active ingredients of E. longifolia that is quassinoid and chantin can be used as a strategy of prostate cancer therapy both through extrinsic and intrinsic pathways.

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

scholarly journals In silico Analysis of Copper Nanoparticles Synthesizing Bacteria Contributing Towards Big Data Bank

2019 ◽  
Vol 8 (01) ◽  
pp. 3078-3083
Author(s):  
Priyanka Kashyap ◽  
Poonam Shirkot ◽  
Praveen Khatri ◽  
Pooja Thakur ◽  
Vikrant Gautam
Keyword(s):  
Big Data ◽  
Copper Nanoparticles ◽  
In Silico ◽  
In Silico Analysis ◽  
Data Bank ◽  
Silico Analysis

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
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