Plasma Protein Binding Affinity and Its Relationship to Molecular Structure:  An In-silico Analysis

2007 ◽  
Vol 50 (1) ◽  
pp. 101-112 ◽  
Author(s):  
M. Paul Gleeson
Keyword(s):  
Molecular Structure ◽  
Protein Binding ◽  
Binding Affinity ◽  
Plasma Protein Binding ◽  
Plasma Protein ◽  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis

Prediction Mechanism of Nevadensin as Antibacterial Agent against S. sanguinis: In vitro and In silico Studies

2021 ◽  
Vol 24 ◽  
Author(s):  
Aldina Amalia Nur Shadrina ◽  
Yetty Herdiyati ◽  
Ika Wiani ◽  
Mieke Hemiawati Satari ◽  
Dikdik Kurnia
Keyword(s):  
Antibacterial Activity ◽  
Molecular Docking ◽  
Dental Caries ◽  
Binding Affinity ◽  
In Silico ◽  
Antibacterial Agent ◽  
In Silico Analysis ◽  
Dna Gyrase ◽  
Silico Analysis

Background: Streptococcus sanguinis can contribute to tooth demineralization, which can lead to dental caries. Antibiotics used indefinitely to treat dental caries can lead to bacterial resistance. Discovering new antibacterial agents from natural products like Ocimum basilicum will help combat antibiotic resistance. In silico analysis (molecular docking) can help determine the lead compound by studying the molecular interaction between the drug and the target receptor (MurA enzyme and DNA gyrase). It is a potential candidate for antibacterial drug development. Objective: The research objective is to isolate the secondary metabolite of O. basilicum extract that has activity against S. sanguinis through in vitro and in silico analysis. Methods: n-Hexane extract of O. basilicum was purified by combining column chromatography with bioactivity-guided. The in vitro antibacterial activity against S. sanguinis was determined using the disc diffusion and microdilution method, while molecular docking simulation of nevadensin (1) with MurA enzyme and DNA gyrase was performed used PyRx 0.8 program. Results: Nevadensin from O. basilicum was successfully isolated and characterized by spectroscopic methods. This compound showed antibacterial activity against S. sanguinis with MIC and MBC values of 3750 and 15000 μg/mL, respectively. In silico analysis showed that the binding affinity to MurA was -8.5 Kcal/mol, and the binding affinity to DNA gyrase was -6.7 Kcal/mol. The binding of nevadensin-MurA is greater than fosfomycin-MurA. Otherwise, Nevadensin-DNA gyrase has a weaker binding affinity than fluoroquinolone-DNA gyrase and chlorhexidine-DNA gyrase. Conclusion: Nevadensin showed potential as a new natural antibacterial agent by inhibiting the MurA enzyme rather than DNA gyrase.

scholarly journals Design, Molecular Docking And In Silico Analysis Of Analogues Of Chloroquine And Hydroxychloroquine Against SARs-COV-2 Target (6w63.pdb)

2020 ◽  
Author(s):  
Naruka Solomon Yakubu ◽  
Olanike Catherine Poyi ◽  
Ezikiel Olabisi Afolabi
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
Target Prediction ◽  
In Silico Analysis ◽  
Docking Studies ◽  
Biologically Active ◽  
Dynamic Simulations ◽  
Comparable Activity ◽  
Silico Analysis

Abstract Computer-aided drug design has been an effective strategy and approach to discover, develop, analyze, accelerate and economize design and development of drugs and biologically active molecules. A total of twelve analogues of chloroquine (CQ) and hydroxychloroquine (HCQ) were designed and virtually analyzed using PyRx software, Molinspiration, Swiss ADME, Swiss-Target Prediction software and ProTox-II-Prediction of toxicity platform. Based on the docking studies carried out using Autodock vina, five analogues; H-368 (-6.0 Kcal/mol), H-372 (--6.0 Kcal/mol), H-156 (-5.9 Kcal/mol), H-139 (-5.7 Kcal/mol), C-136 (-5.7 Kcal/mol) exhibited higher binding affinity compared to HCQ(-5.5 Kcal/mol), while all twelve analogues exhibited higher binding affinity compared to CQ (-4.5Kcal/mol). In silico analysis of toxicity profile of this analogues shows a lower potential to toxicity and a comparable activity on some major isoforms of cytochrome P450. But unlike the parent molecules, both H-139 and H-156 are substrates of P-glycoproteins (P-gp) which implies that these analogues possess high clearance and less pharmacokinetic-related drug-drug interactions compared to the parent molecules. Herein we propose these analogues as potential inhibitors or lead compounds against the coronavirus with a view of conducting more molecular dynamic simulations, synthesizing and conducting in vitro studies on them.

Pleurotus ostreatus heme peroxidases: An in silico analysis from the genome sequence to the enzyme molecular structure

2011 ◽  
Vol 334 (11) ◽  
pp. 795-805 ◽  
Author(s):  
Francisco J. Ruiz-Dueñas ◽  
Elena Fernández ◽  
María Jesús Martínez ◽  
Angel T. Martínez
Keyword(s):  
Molecular Structure ◽  
Genome Sequence ◽  
Pleurotus Ostreatus ◽  
In Silico ◽  
In Silico Analysis ◽  
Heme Peroxidases ◽  
Silico Analysis

Molecular and Nano Structures of Chiral PEDOT Derivatives Influence the Enantiorecognition of Biomolecules. In Silico Analysis of Chiral Recognition

The Analyst ◽  
2021 ◽  
Author(s):  
Jayakrishnan Aerathupalathu Janardhanan ◽  
Anusha Valaboju ◽  
Udesh Dhawan ◽  
Tharwat Hassan Mansoure ◽  
Ching-Cher Sanders Yan ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Surface Morphology ◽  
In Silico ◽  
Chiral Recognition ◽  
Synergistic Effects ◽  
In Silico Analysis ◽  
Nano Structures ◽  
Sensing Platform ◽  
Silico Analysis

In this study we investigated the synergistic effects of the chirality (molecular structure) and surface morphology (nanostructure) of a newly designed sensing platform for the stereoselective recognition of biomolecules. We...

scholarly journals Ayurvedic Medicinal Plants Against COVID-19: An In Silico Analysis

2021 ◽  
Vol 16 (11) ◽  
pp. 1934578X2110567
Author(s):  
Bharat Krushna Khuntia ◽  
Vandna Sharma ◽  
Sahar Qazi ◽  
Soumi Das ◽  
Shruti Sharma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Medicinal Plants ◽  
Binding Affinity ◽  
In Silico ◽  
In Silico Analysis ◽  
Cyperus Rotundus ◽  
Effective Control ◽  
Picrorhiza Kurroa ◽  
Silico Analysis

Even after one and a half years since the outbreak of COVID-19, its complete and effective control is still far from being achieved despite vaccination drives, symptomatic management with available drugs, and wider lockdowns. This has inspired researchers to screen potential phytochemicals from medicinal plants against SARS-CoV-2, adopting a bio-informatics approach. The current study aimed to assess anti-viral activity of the phytochemicals derived from Ayurvedic medicinal plants against SARS-CoV-2 drug targets [3-chymotrypsin-like protease (3CLpro) and RNA dependent RNA polymerase (RdRp)] using validated in silico methods.3D Structures of 196 phytochemicals from three Ayurvedic plants were retrieved from PubChem and KNApSAcK databases and screened for Absorption Distribution Metabolism Excretion and Toxicity(ADMET) to predict drug-likeness. The phytochemicals were subjected to molecular docking and only three showed promise: Acetovanillonewith a binding affinity of −4.7Kcal/mol with RdRp and −4.1 Kcal/mol with 3CL pro; myrtenol with equivalent values of −4.3 Kcal/mol with RdRP and −3.2 Kcal/mol with 3CLpro; and nimbochalcin with equivalent values of −5.0Kcal/mol with RdRp and −4.9 Kcal/mol with 3CLpro. Molecular dynamics simulation (50ns) analysis was made of 3CLpro and RdRp using Autodock Vina 1.1.2 software and VMD software. After ADMET analysis, 78 phytochemicals were found suitable for molecular docking. Three, namely acetovanillone, myrtenol and nimbochalcin from Picrorhiza kurroa, Azadirachta indica and Cyperus rotundus,respectively,exhibited good binding affinity with 3CLproand RdRp of SARS-CoV-2. Interaction analysis, molecular dynamics simulations and MM-PBSA calculations were executed for two complexes, acetovanillone_RdRp and myrtenol_3CL pro.Acetovanillone_RdRpcomplex did not display any structural change after MD simulation as compared to myrtenol_3CL pro. The overall stability of acetovanillone_6NUR was 154.7 kJ/mol, and for myrtenol_1UJ1 90.5 kJ/mol. In silico analysis revealed that acetovanillone ( Picrorhiza kurroa) and myrtenol ( Cyperus rotundus) possess anti SARS-CoV-2 activity. Further studies are needed to validate their efficacy in biological models.

Sign in / Sign up

Export Citation Format

Share Document