scholarly journals Utilization Of Nano Ethanolic Extract Combination Chamber Bitter (Phyllanthus Niruri L.) And Garlic (Allium Sativum L.) As A Natural Immunomodulator In Nanoherbal Development, In Silico And In Vitro Study

2017 ◽  
Vol 2 (02) ◽  
pp. 110
Author(s):  
Kadek Hendra Darmawan
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Allium Sativum ◽  
In Vitro Study ◽  
Ethanolic Extract ◽  
Phagocytic Index ◽  
Phyllanthus Niruri ◽  
The Right ◽  
Phagocytosis Activity

The Filantin compounds in chamber bitter (<em>Phyllanthus niruri</em> L.) and lectin in garlic (<em>Allium sativum</em> L.) was proven as immunomudulatory agents through interaction with <em>Toll-Like Reseptors</em> (TLR) which have role in innate immune responds. Immunomodulators drug available on the market still have many shortcomings such as the low potential. Drug developing by nanotechnology is the right solution to increase the potential of the drug by increasing the absorption and minimize the dose. This research aimed to know the interaction of filantin and lectin with TLR2-TLR1 receptors through <em>molecular docking</em> and produce the nanoemulsion combination of chamber bitter and garlic ethanolic extracts that have phagocytosis activity. <em>In silico </em>assay through <em>molecular docking</em> showed that filantin has affinity for binding to TLR2-TLR1, docking score of lectin (-33,5389) was lower than the filantin (-31.5112). That means lectin has higher affinity for binding to TLR2-TLR1. Nanoemulsion was formulated by SNEDDS methods with composition of co-surfactant: surfactant: oil is 1: 5,25: 1. The nanoemulsion stable at 0,414% (w/v). <em>In vitro</em> assay of phagocytic index (5,03) and ratio (95%) showed that the formulation with nanoemulsion of the combination has higher phagocyte index and ratio than the formulation without nanoemulsion or even the positive controls.

scholarly journals In silico and in vitro Study of the Inhibitory Effect of Antiinflammatory Drug Betamethasone on Two Lipases

2020 ◽  
Vol 19 (4) ◽  
pp. 387-392
Author(s):  
Nia Samira ◽  
Benarous Khedidja ◽  
Abdelalim Fatima Zahra ◽  
Chellali Khadidja Nour Elyakine ◽  
Yousfi Mohamed
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Candida Rugosa ◽  
In Vitro Study ◽  
Antiinflammatory Drug ◽  
Inhibitory Effect ◽  
Vitro Study ◽  
Inflammatory Drug ◽  
Anti Inflammatory

Background: For the first time, the anti-inflammatory drug betamethasone is investigated for its inhibitory activity against lipase. Objective: This work aims to demonstrate the in vitro and in silico inhibitory effect of the anti-inflammatory drug betamethasone on the enzymatic activity of two lipases. Methods: In vitro study using p-nitrophenyllaurate as lipase substrate is used to determine inhibition potency. Molecular Docking is performed using the Autodock Vina for drug molecule and two enzymes Candida rugosa lipase and human pancreatic lipase. Results: Betamethasone represents a moderate inhibition effect with a value of IC50 of 0.36±0.01 mg/ml. Molecular docking allowed us to understand inhibitory – enzyme interactions and to confirm in vitro obtained results. Conclusion: These experiments showed that betamethasone can be used in the treatment of diseases related to lipase activity.

scholarly journals Syzygium aromaticum Extracts as a Potential Antibacterial Inhibitors against Clinical Isolates of Acinetobacter baumannii: An In-Silico-Supported In-Vitro Study

Antibiotics ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1062
Author(s):  
Abdelhamed Mahmoud ◽  
Magdy M. Afifi ◽  
Fareed El Shenawy ◽  
Wesam Salem ◽  
Basem H. Elesawy
Keyword(s):  
Acinetobacter Baumannii ◽  
In Silico ◽  
In Vitro Study ◽  
Ethanolic Extract ◽  
Vitro Study ◽  
Clinical Samples ◽  
Syzygium Aromaticum ◽  
Molecular Docking Study ◽  
Spectra Analysis

Imipenem is the most efficient antibiotic against Acinetobacter baumannii infection, but new research has shown that the organism has also developed resistance to this agent. A. baumannii isolates from a total of 110 clinical samples were identified by multiplex PCR. The antibacterial activity of Syzygium aromaticum multiple extracts was assessed following the GC-Mass spectra analysis. The molecular docking study was performed to investigate the binding mode of interactions of guanosine (Ethanolic extract compound) against Penicillin- binding proteins 1 and 3 of A. baumannii. Ten isolates of A. baumannii were confirmed to carry recA and iutA genes. Isolates were multidrug-resistant containing blaTEM and BlaSHV. The concentrations (0.04 to 0.125 mg mL−1) of S. aromaticum ethanolic extract were very promising against A. baumannii isolates. Even though imipenem (0.02 mg mL−1) individually showed a great bactericidal efficacy against all isolates, the in-silico study of guanosine, apioline, eugenol, and elemicin showed acceptable fitting to the binding site of the A. baumannii PBP1 and/or PBP3 with highest binding energy for guanosine between −7.1 and −8.1 kcal/mol respectively. Moreover, it formed π-stacked interactions with the residue ARG76 at 4.14 and 5.6, Å respectively. These findings might support the in vitro study and show a substantial increase in binding affinity and enhanced physicochemical characteristics compared to imipenem.

scholarly journals Cleroda-4(18),13-dien-15,16-olide as novel xanthine oxidase inhibitors: An integrated in silico and in vitro study

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253572
Author(s):  
Ha Thi Nguyen ◽  
Thien-Y Vu ◽  
Tikam Chand Dakal ◽  
Bhanupriya Dhabhai ◽  
Xuan Hong Quan Nguyen ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Xanthine Oxidase ◽  
In Silico ◽  
Hydrophobic Interactions ◽  
Target Prediction ◽  
Docking Simulation ◽  
In Vitro Study ◽  
Inhibitory Effect ◽  
Reference Drug

In the present study, in silico predictions and molecular docking were performed on five clerodane diterpenes (1–5) from Polyalthia longifolia seeds to evaluate their potential as xanthine oxidase (XO) inhibitors. The initial screening was conducted by target prediction using TargetNet web server application and only compounds 3 and 4 showed a potential interaction with XO. Compounds 3 and 4 were subsequently subjected to in silico analyses on XO protein structure (PDB: 1N5X) using Schrödinger Release 2020–3 followed by structural modeling & molecular simulation studies to confirm the initial prediction result and identify the binding mode of these compounds to the XO. Molecular docking results revealed that compounds 3 (-37.3 kcal/mol) and 4 (-32.0 kcal/mol) binds more stably to XO than the reference drug allopurinol (-27.0 kcal/mol). Interestingly, two residues Glu 802 and Thr 1010 were observed as the two main H-bond binding sites for both tested compounds and the allopurinol. The center scaffold of allopurinol was positioned by some π-π stacking with Phe 914 and Phe 1009, while that of compounds 3 and 4 were supported by many hydrophobic interactions mainly with Leu 648, Phe 649, Phe 1013, and Leu 1014. Additionally, the docking simulation predicted that the inhibitory effect of compounds 3 and 4 was mediated by creating H-bond with particularly Glu 802, which is a key amino acid for XO enzyme inhibition. Altogether, in vitro studies showed that compounds 3 and 4 had better inhibitory capacity against XO enzyme with IC50 values significantly (p < 0.001) lower than that of allopurinol. In short, the present study identified cleroda-4(18),13-dien-15,16-olide as novel potential XO inhibitors, which can be potentially used for the treatment of gout.

scholarly journals SKRINING IN SILICO POTENSI SENYAWA ALLICIN DARI ALLIUM SATIVUM SEBAGAI ANTIPLASMODIUM

2015 ◽  
Vol 17 (2) ◽  
pp. 175-184
Author(s):  
Fatmawaty Fatmawaty ◽  
Muhammad Hanafi ◽  
Rosmalena Rosmalena ◽  
Vivitri Dewi Prasasty
Keyword(s):  
Molecular Docking ◽  
Inhibitory Activity ◽  
In Silico ◽  
Allium Sativum ◽  
Specific Interaction ◽  
Docking Analysis ◽  
Drug Candidates ◽  
In Silico Identification ◽  
Activity Mechanism

Allicin compound (2-propene-1- sulphinothioat acid S-2-propenyl ester) is known to have potential as antiplasmodium in vitro. However, the inhibitory activity mechanism of Allicin to plasmodium is still unknown. In this research, we determined the inhibitory activity of Allicin in silico. Identification of physicochemical properties of Allicin compound and two Allicin derivatives, Alc1, Alc2 and Ac2Alc3 were also conducted.. Furthermore, analysis of drug-likeness and adsorption-distribution-metabolism-excretion (ADME) were carried out on the Allicin compound and its derivatives to find the potential of these compounds as drug candidates. In determining the specific interaction, we utilized molecular docking analysis between Allicin and its derivatives against a protein target Cysteine Protease (SP). Molecular  docking results showed that Allicin derivative, Alc2 (S-prop-2-en-1-yl 3-methylbut-2-ene-1-sulfinothioate, C10H18OS2) has better potential as inhibitors than Allicin, based on the lower bond energies and the inhibition constants, thus Alc2 can be used as an antiplasmodium agent candidate.Keywords: Allicin, Allicin derivatives, drug likeness, ADME, molecular docking

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.

Acetate Kinase (AcK) is Essential for Microbial Growth and Betel-derived Compounds Potentially Target AcK, PhoP and MDR Proteins in M. tuberculosis, V. cholerae and Pathogenic E. coli: An in silico and in vitro Study

2019 ◽  
Vol 18 (31) ◽  
pp. 2731-2740 ◽  
Author(s):  
Sandeep Tiwari ◽  
Debmalya Barh ◽  
M. Imchen ◽  
Eswar Rao ◽  
Ranjith K. Kumavath ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
In Silico ◽  
Pathogenic Bacteria ◽  
In Vitro Study ◽  
Docking Studies ◽  
Acetate Kinase ◽  
E Coli ◽  
Pathogenic Escherichia Coli ◽  
Novel Target

Background: Mycobacterium tuberculosis, Vibrio cholerae, and pathogenic Escherichia coli are global concerns for public health. The emergence of multi-drug resistant (MDR) strains of these pathogens is creating additional challenges in controlling infections caused by these deadly bacteria. Recently, we reported that Acetate kinase (AcK) could be a broad-spectrum novel target in several bacteria including these pathogens. Methods: Here, using in silico and in vitro approaches we show that (i) AcK is an essential protein in pathogenic bacteria; (ii) natural compounds Chlorogenic acid and Pinoresinol from Piper betel and Piperidine derivative compound 6-oxopiperidine-3-carboxylic acid inhibit the growth of pathogenic E. coli and M. tuberculosis by targeting AcK with equal or higher efficacy than the currently used antibiotics; (iii) molecular modeling and docking studies show interactions between inhibitors and AcK that correlate with the experimental results; (iv) these compounds are highly effective even on MDR strains of these pathogens; (v) further, the compounds may also target bacterial two-component system proteins that help bacteria in expressing the genes related to drug resistance and virulence; and (vi) finally, all the tested compounds are predicted to have drug-like properties. Results and Conclusion: Suggesting that, these Piper betel derived compounds may be further tested for developing a novel class of broad-spectrum drugs against various common and MDR pathogens.

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.

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