scholarly journals In Vitro and In Silico Evaluation of Biological Properties of Some 1, 3, 4-Oxadiazole Derivatives Against Streptococcus mutans and Their Interaction With Gbp-C by Molecular Docking

2021 ◽  
Vol 13 (4) ◽  
pp. 142-147
Author(s):  
Behin Omidi ◽  
Yasin SarveAhrabi
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Hydrogen Bonds ◽  
Streptococcus Mutans ◽  
In Silico ◽  
Antibacterial Properties ◽  
Inhibition Zone ◽  
Biological Properties ◽  
High Concentrations

Background: The need to replace new drug structures for the treatment of resistant strains has become essential. Streptococcus mutans is one of the most important factors in causing tooth decay. Glucan binding protein-C (Gbp-C) is a crucial mobileular floor protein that is worried in biofilm formation, and 1, 3, 4-oxadiazoles are new antibacterial structures. Accordingly, this study focused on assessing in vitro and in silico activity of our previously synthesized compounds of 1, 3, 4-oxadiazole against S. mutans. Methods: To this end, our previously synthesized derivatives were re-synthesized and prepared, and then antibacterial susceptibility tests were used for inhibition zone, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) test values. The molecular docking method was also applied to confirm the effect of compounds in interaction with the Gbp-C of S. mutans. Results: All compounds showed different effects against the bacterial sample. Among these, the most effective ones were related to naphthalene (4d), fluorophenyl (4e), and dimethoxyphenyl (4h) derivatives against S. mutans, respectively. Other compounds also had antibacterial properties but to a lesser extent. In the molecular part, compounds 4d and 4h had the highest affinity to inhibit the GbpC-protein. compound 4d with amino acids ASP and GLN established 402 and 391 hydrogen bonds, respectively, and compound 4h with amino acids SER, GLU, THR, and TRP established 347, 360, 449, and 451 hydrogen bonds, respectively. Conclusions: In general, 1, 3, 4-oxadiazoles containing naphthalene and dimethoxy phenyl functional groups in high concentrations can be good alternatives to the existing drugs for eliminating caries-causing tooth mutants that have drug resistance. It seems that more inhibitory effects can be observed on clinical specimens by adding different purposeful groups and increasing the destructive power of oxadiazole-based compounds.

scholarly journals An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Pankaj Jain ◽  
Amit Joshi ◽  
Nahid Akhtar ◽  
Sunil Krishnan ◽  
Vikas Kaushik
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Docking ◽  
In Silico ◽  
Cell Epitope ◽  
Cost Effective ◽  
Dynamics Simulation ◽  
Cloning And Expression

Abstract Background Canine circovirus is a deadly pathogen of dogs and causes vasculitis and hemorrhagic enteritis. It causes lethal gastroenteritis in pigs, fox, and dogs. Canine circovirus genome contains two main (and opposite) transcription units which encode two open reading frames (ORFs), a replicase-associated protein (Rep) and the capsid (Cap) protein. The replicase protein and capsid protein consist of 303 amino acids and 270 amino acids respectively. Several immuno-informatics methods such as epitope screening, molecular docking, and molecular-dynamics simulations were used to craft peptide-based vaccine construct against canine circovirus. Results The vaccine construct was designed by joining the selected epitopes with adjuvants by suitable linker. The cloning and expression of the vaccine construct was also performed using in silico methods. Screening of epitopes was conducted by NetMHC server that uses ANN (Artificial neural networking) algorithm. These methods are fast and cost-effective for screening epitopes that can interact with dog leukocyte antigens (DLA) and initiate an immune response. Overall, 5 epitopes, YQHLPPFRF, YIRAKWINW, ALYRRLTLI, HLQGFVNLK, and GTMNFVARR, were selected and used to design a vaccine construct. The molecular docking and molecular dynamics simulation studies show that these epitopes can bind with DLA molecules with stability. The codon adaptation and in silico cloning studies show that the vaccine can be expressed by Escherichia coli K12 strain. Conclusion The results suggest that the vaccine construct can be useful in preventing the dogs from canine circovirus infections. However, the results need further validation by performing other in vitro and in vivo experiments.

scholarly journals Antibacterial Activity and Cytotoxic Effect of Pelargonium peltatum (Geranium) against Streptococcus mutans and Streptococcus sanguinis

2018 ◽  
Vol 2018 ◽  
pp. 1-5 ◽  
Author(s):  
Samantha Coronado-López ◽  
Stefany Caballero-García ◽  
Miguel Angel Aguilar-Luis ◽  
Fernando Mazulis ◽  
Juana del Valle-Mendoza
Keyword(s):  
Minimum Inhibitory Concentration ◽  
Streptococcus Mutans ◽  
Inhibitory Concentration ◽  
Antibacterial Properties ◽  
Diffusion Method ◽  
Root Extract ◽  
Streptococcus Sanguinis ◽  
Pelargonium Peltatum ◽  
High Concentrations

Objective. To evaluate the in vitro antibacterial and cytotoxic properties of the methanolic extract of Pelargonium peltatum (geranium) against Streptococcus mutans (ATCC 25175) and Streptococcus sanguinis (ATCC 10556). Methods. Three extracts of P. peltatum were prepared using the leaf, stem, and root. Nine independent assays were prepared for each type of extract with chlorhexidine at 0.12% as the positive control. The agar diffusion method was performed to determine the antibacterial properties of each extract. The minimum inhibitory concentration (MIC) was determined using the microdilution method, and the cytotoxicity was analyzed by means of the MTT reduction test using a MDCK cell line. Results. The root extract had the highest antibacterial effect with a mean result of (27.68 ± 0.97) mm and (30.80 ± 0.55) mm against S. mutans and S. sanguinis, respectively. The minimum inhibitory concentration for the leaf and root extracts was 250 mg/mL for S. mutans and 125 mg/mL for S. sanguinis. Cytotoxicity assays showed that both extracts had a low cytotoxicity at high concentrations. The cellular viability was highest for the root extract at 95.3% followed by the stem extract at 80.8% and finally the leaf extract with 75.4%. Conclusions. These findings show the antibacterial properties of the methanolic extracts of P. pelargonium against S. mutans and S. sanguinis. These extracts were not cytotoxic at high concentrations.

scholarly journals In Vitro Antimicrobial Activity of Aqueous-Methanolic Extract of Populus sp. Leaves

2019 ◽  
Vol 31 (2) ◽  
pp. 53-64
Author(s):  
Husein A. Husein ◽  
Dhurgham A.H. Alhasan ◽  
Majid A.Z. Albadry
Keyword(s):  
Amino Acids ◽  
Staphylococcus Aureus ◽  
Antimicrobial Activity ◽  
Candida Albicans ◽  
Streptococcus Mutans ◽  
Antimicrobial Agents ◽  
Methanolic Extract ◽  
Inhibition Zone ◽  
Microbial Pathogens

Plants are a rich source of giving benefit natural products, including antimicrobial agents. The current study was designed to evaluate the antimicrobial activity of Populus sp. leaves that the aqueous methanolic extract (200 mg.ml-1) of the leaves revealed antimicrobial effects against some microbial pathogens in which the highest inhibition zone was recorded against Candida albicans followed by Staphylococcus aureus but no effects on the growth of both Streptococcus mutans and Klebsiella sp. The chemical tests appeared that the extract contains sterols, terpenoids, carbohydrates, glycosides, flavonoids, tannins, proteins, amino acids, and saponins glycosides while alkaloids were not detected. GC-MS analysis detected the aqueous methanolic extract has four compounds are {2-Pyridineacetaldehyde,[2-(2-pyridinyl) ethylidene]hydrazone}, {n-Propylamine, N-acetyl-3-[2-acetyl-3,4,5-trimethoxyphenyl]-},{1-(Methyl propyl)-4-(1’,1’,2’-trichloro-3’-ethyl allyl)benzene} and {1H-Indole, 5- methyl-2-phenyl-}.

The Antiviral and Antimalarial Drug Repurposing in Quest of Chemotherapeutics to Combat COVID-19 Utilizing Structure-Based Molecular Docking

2020 ◽  
Vol 23 ◽  
Author(s):  
Sisir Nandi ◽  
Mohit Kumar ◽  
Mridula Saxena ◽  
Anil Kumar Saxena
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Drug Repurposing ◽  
Clinical Settings ◽  
The Novel ◽  
In Silico Docking ◽  
Biochemical Mechanisms ◽  
Novel Coronavirus ◽  
In Silico Molecular Docking

Background: The novel coronavirus disease (COVID-19) is caused by a new strain (SARS-CoV-2) erupted in 2019. Nowadays, it is a great threat that claims uncountable lives worldwide. There is no specific chemotherapeutics developed yet to combat COVID-19. Therefore, scientists have been devoted in the quest of the medicine that can cure COVID- 19. Objective: Existing antivirals such as ASC09/ritonavir, lopinavir/ritonavir with or without umifenovir in combination with antimalarial chloroquine or hydroxychloroquine have been repurposed to fight the current coronavirus epidemic. But exact biochemical mechanisms of these drugs towards COVID-19 have not been discovered to date. Method: In-silico molecular docking can predict the mode of binding to sort out the existing chemotherapeutics having a potential affinity towards inhibition of the COVID-19 target. An attempt has been made in the present work to carry out docking analyses of 34 drugs including antivirals and antimalarials to explain explicitly the mode of interactions of these ligands towards the COVID-19protease target. Results: 13 compounds having good binding affinity have been predicted towards protease binding inhibition of COVID-19. Conclusion: Our in silico docking results have been confirmed by current reports from clinical settings through the citation of suitable experimental in vitro data available in the published literature.

Antimyotoxic Activity of Synthetic Peptides Derived from Bothrops atrox Snake Gamma Phospholipase A2 Inhibitor Selected by Virtual Screening

2019 ◽  
Vol 19 (22) ◽  
pp. 1952-1961 ◽  
Author(s):  
J.C. Sobrinho ◽  
A.F. Francisco ◽  
R. Simões-Silva ◽  
A.M. Kayano ◽  
J.J. Alfonso Ruiz Diaz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Synthetic Peptides ◽  
Cell Damage ◽  
Neutralization Assay ◽  
Phospholipase Activity ◽  
Phospholipases A2 ◽  
Catalytically Active ◽  
Bothrops Atrox

Background: Several studies have aimed to identify molecules that inhibit the toxic actions of snake venom phospholipases A2 (PLA2s). Studies carried out with PLA2 inhibitors (PLIs) have been shown to be efficient in this assignment. Objective: This work aimed to analyze the interaction of peptides derived from Bothrops atrox PLIγ (atPLIγ) with a PLA2 and to evaluate the ability of these peptides to reduce phospholipase and myotoxic activities. Methods: Peptides were subjected to molecular docking with a homologous Lys49 PLA2 from B. atrox venom modeled by homology. Phospholipase activity neutralization assay was performed with BthTX-II and different ratios of the peptides. A catalytically active and an inactive PLA2 were purified from the B. atrox venom and used together in the in vitro myotoxic activity neutralization experiments with the peptides. Results: The peptides interacted with amino acids near the PLA2 hydrophobic channel and the loop that would be bound to calcium in Asp49 PLA2. They were able to reduce phospholipase activity and peptides DFCHNV and ATHEE reached the highest reduction levels, being these two peptides the best that also interacted in the in silico experiments. The peptides reduced the myotubes cell damage with a highlight for the DFCHNV peptide, which reduced by about 65%. It has been suggested that myotoxic activity reduction is related to the sites occupied in the PLA2 structure, which could corroborate the results observed in molecular docking. Conclusion: This study should contribute to the investigation of the potential of PLIs to inhibit the toxic effects of PLA2s.

In Silico Appraisal, Synthesis, Antibacterial Screening and DNA Cleavage for 1,2,5-thiadiazole Derivative

2019 ◽  
Vol 15 (5) ◽  
pp. 445-455 ◽  
Author(s):  
Suraj N. Mali ◽  
Sudhir Sawant ◽  
Hemchandra K. Chaudhari ◽  
Mustapha C. Mandewale
Keyword(s):  
Molecular Docking ◽  
Dna Cleavage ◽  
In Silico ◽  
Oral Absorption ◽  
Inhibition Mechanism ◽  
Hydrogen Binding ◽  
Docking Score ◽  
Antibacterial Screening ◽  
Mycobacteria Tuberculosis

Background: : Thiadiazole not only acts as “hydrogen binding domain” and “two-electron donor system” but also as constrained pharmacophore. Methods:: The maleate salt of 2-((2-hydroxy-3-((4-morpholino-1, 2,5-thiadiazol-3-yl) oxy) propyl) amino)- 2-methylpropan-1-ol (TML-Hydroxy)(4) has been synthesized. This methodology involves preparation of 4-morpholino-1, 2,5-thiadiazol-3-ol by hydroxylation of 4-(4-chloro-1, 2,5-thiadiazol-3-yl) morpholine followed by condensation with 2-(chloromethyl) oxirane to afford 4-(4-(oxiran-2-ylmethoxy)-1,2,5-thiadiazol- 3-yl) morpholine. Oxirane ring of this compound was opened by treating with 2-amino-2-methyl propan-1- ol to afford the target compound TML-Hydroxy. Structures of the synthesized compounds have been elucidated by NMR, MASS, FTIR spectroscopy. Results: : The DSC study clearly showed that the compound 4-maleate salt is crystalline in nature. In vitro antibacterial inhibition and little potential for DNA cleavage of the compound 4 were explored. We extended our study to explore the inhibition mechanism by conducting molecular docking, ADMET and molecular dynamics analysis by using Schrödinger. The molecular docking for compound 4 showed better interactions with target 3IVX with docking score of -8.508 kcal/mol with respect to standard ciprofloxacin (docking score= -3.879 kcal/mol). TML-Hydroxy was obtained in silico as non-carcinogenic and non-AMES toxic with good percent human oral absorption profile (69.639%). TML-Hydroxy showed the moderate inhibition against Mycobacteria tuberculosis with MIC 25.00 μg/mL as well as moderate inhibition against S. aureus, Bacillus sps, K. Pneumoniae and E. coli species. Conclusion: : In view of the importance of the 1,2,5-thiadiazole moiety involved, this study would pave the way for future development of more effective analogs for applications in medicinal field.

Virtual Screening, Molecular docking and in-silico ADME-Tox analysis for identification of potential main protease (Mpro) enzyme inhibitors

2020 ◽  
Vol 18 ◽  
Author(s):  
Debadash Panigrahi ◽  
Ganesh Prasad Mishra
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
Data Bank ◽  
Future Research ◽  
Reference Compound ◽  
Unexpected Death ◽  
Main Protease ◽  
In Silico Admet

Objective:: Recent pandemic caused by SARS-CoV-2 described in Wuhan China in December-2019 spread widely almost all the countries of the world. Corona virus (COVID-19) is causing the unexpected death of many peoples and severe economic loss in several countries. Virtual screening based on molecular docking, drug-likeness prediction, and in silico ADMET study has become an effective tool for the identification of small molecules as novel antiviral drugs to treat diseases. Methods:: In the current study, virtual screening was performed through molecular docking for identifying potent inhibitors against Mpro enzyme from the ZINC library for the possible treatment of COVID-19 pandemic. Interestingly, some compounds are identified as possible anti-covid-19 agents for future research. 350 compounds were screened based on their similarity score with reference compound X77 from ZINC data bank and were subjected to docking with crystal structure available of Mpro enzyme. These compounds were then filtered by their in silico ADME-Tox and drug-likeness prediction values. Result:: Out of these 350 screened compounds, 10 compounds were selected based on their docking score and best docked pose in comparison to the reference compound X77. In silico ADME-Tox and drug likeliness predictions of the top compounds were performed and found to be excellent results. All the 10 screened compounds showed significant binding pose with the target enzyme main protease (Mpro) enzyme and satisfactory pharmacokinetic and toxicological properties. Conclusion:: Based on results we can suggest that the identified compounds may be considered for therapeutic development against the COVID-19 virus and can be further evaluated for in vitro activity, preclinical, clinical studies and formulated in a suitable dosage form to maximize their bioavailability.

scholarly journals Synthesis, Characterization, Antibacterial Properties, and In Vitro Studies of Selenium and Strontium Co-Substituted Hydroxyapatite

2021 ◽  
Vol 22 (8) ◽  
pp. 4246
Author(s):  
Muhammad Maqbool ◽  
Qaisar Nawaz ◽  
Muhammad Atiq Ur Atiq Ur Rehman ◽  
Mark Cresswell ◽  
Phil Jackson ◽  
...  
Keyword(s):  
Negative Impact ◽  
Antibacterial Properties ◽  
Biological Properties ◽  
Ion Concentration ◽  
Charge Composition ◽  
Bacterial Strains ◽  
X Ray Diffraction ◽  
Molar Ratios ◽  
Human Osteosarcoma Cells

In this study, as a measure to enhance the antimicrobial activity of biomaterials, the selenium ions have been substituted into hydroxyapatite (HA) at different concentration levels. To balance the potential cytotoxic effects of selenite ions (SeO32−) in HA, strontium (Sr2+) was co-substituted at the same concentration. Selenium and strontium-substituted hydroxyapatites (Se-Sr-HA) at equal molar ratios of x Se/(Se + P) and x Sr/(Sr + Ca) at (x = 0, 0.01, 0.03, 0.05, 0.1, and 0.2) were synthesized via the wet precipitation route and sintered at 900 °C. The effect of the two-ion concentration on morphology, surface charge, composition, antibacterial ability, and cell viability were studied. X-ray diffraction verified the phase purity and confirmed the substitution of selenium and strontium ions. Acellular in vitro bioactivity tests revealed that Se-Sr-HA was highly bioactive compared to pure HA. Se-Sr-HA samples showed excellent antibacterial activity against both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus carnosus) bacterial strains. In vitro cell–material interaction, using human osteosarcoma cells MG-63 studied by WST-8 assay, showed that Se-HA has a cytotoxic effect; however, the co-substitution of strontium in Se-HA offsets the negative impact of selenium and enhanced the biological properties of HA. Hence, the prepared samples are a suitable choice for antibacterial coatings and bone filler applications.

scholarly journals In silico molecular docking and in vitro antimicrobial efficacy of phytochemicals against multi-drug-resistant enteroaggregative Escherichia coli and non-typhoidal Salmonella spp.

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Padikkamannil Abishad ◽  
Pollumahanti Niveditha ◽  
Varsha Unni ◽  
Jess Vergis ◽  
Nitin Vasantrao Kurkure ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Docking ◽  
In Silico ◽  
Docking Studies ◽  
Antimicrobial Efficacy ◽  
Drug Resistant ◽  
Protein Motifs ◽  
Phytochemical Compounds ◽  
In Silico Molecular Docking

Abstract Background In the wake of emergence of antimicrobial resistance, bioactive phytochemical compounds are proving to be important therapeutic agents. The present study envisaged in silico molecular docking as well as in vitro antimicrobial efficacy screening of identified phytochemical ligands to the dispersin (aap) and outer membrane osmoporin (OmpC) domains of enteroaggregative Escherichia coli (EAEC) and non-typhoidal Salmonella spp. (NTS), respectively. Materials and methods The evaluation of drug-likeness, molecular properties, and bioactivity of the identified phytocompounds (thymol, carvacrol, and cinnamaldehyde) was carried out using Swiss ADME, while Protox-II and StopTox servers were used to identify its toxicity. The in silico molecular docking of the phytochemical ligands with the protein motifs of dispersin (PDB ID: 2jvu) and outer membrane osmoporin (PDB ID: 3uu2) were carried out using AutoDock v.4.20. Further, the antimicrobial efficacy of these compounds against multi-drug resistant EAEC and NTS strains was determined by estimating the minimum inhibitory concentrations and minimum bactericidal concentrations. Subsequently, these phytochemicals were subjected to their safety (sheep and human erythrocytic haemolysis) as well as stability (cationic salts, and pH) assays. Results All the three identified phytochemicals ligands were found to be zero violators of Lipinski’s rule of five and exhibited drug-likeness. The compounds tested were categorized as toxicity class-4 by Protox-II and were found to be non- cardiotoxic by StopTox. The docking studies employing 3D model of dispersin and ompC motifs with the identified phytochemical ligands exhibited good binding affinity. The identified phytochemical compounds were observed to be comparatively stable at different conditions (cationic salts, and pH); however, a concentration-dependent increase in the haemolytic assay was observed against sheep as well as human erythrocytes. Conclusions In silico molecular docking studies provided useful insights to understand the interaction of phytochemical ligands with protein motifs of pathogen and should be used routinely before the wet screening of any phytochemicals for their antibacterial, stability, and safety aspects.

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