scholarly journals A Comprehensive in vitro and in silico Analysis of Nematicidal Action of Essential Oils

2021 ◽  
Vol 11 ◽  
Author(s):  
Aditi Kundu ◽  
Anirban Dutta ◽  
Abhishek Mandal ◽  
Lalit Negi ◽  
Monika Malik ◽  
...  
Keyword(s):  
Essential Oils ◽  
Binding Affinity ◽  
Protein Interactions ◽  
In Silico ◽  
In Silico Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Acorus Calamus ◽  
Artemisia Absinthium ◽  
Pogostemon Cablin

Nematicidal potential of essential oils (EOs) has been widely reported. Terpenoids present in most of the essential oils have been reported responsible for their bioactivity though very less is known about their modes of action. In the present study, an in vitro screening of nine Eos, namely, Citrus sinensis (OEO), Myrtus communis (MTEO), Eucalyptus citriodora (CEO), Melaleuca alternifolia (TEO), Acorus calamus (AEO), Commiphora myrrha (MREO), Cymbopogon nardus (CNEO), Artemisia absinthium (WEO), and Pogostemon cablin (PEO) against Meloidogyne incognita revealed OEO, CNEO, and TEO as most effective with LC50 39.37, 43.22, and 76.28 μg ml–1 respectively. EOs had varying compositions of mono- and sesquiterpenes determined by gas chromatography-mass spectrometry (GC-MS) analysis. The in silico molecular interactions screening of major EO constituents and the seven selected target proteins of the nematode indicated highest binding affinity of geraniol-ODR1 (odorant response gene 1) complex (ΔG = -36.9 kcal mol–1), due to extensive H-bonding, hydrophobic and π-alkyl interactions. The relative binding affinity followed the order: geraniol-ODR1 > β-terpineol-ODR1 > citronellal-ODR1 > l-limonene-ODR1 > γ-terpinene-ODR1. Taken together, the cumulative in vitro and computational bioefficacy analysis related to the chemoprofiles of EOs provides useful leads on harnessing the potential of EOs as bionematicides. The insight on biochemical ligand–target protein interactions described in the present work will be helpful in logical selection of biomolecules and essential oils for development of practically viable bionematicidal products.

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 Chemical Profile, Antioxidant and Alpha-Amylase Inhibitory Activity of Leaves Extracts of Annona muricata: A Combined In vitro and In silico Study

2021 ◽  
Vol 11 (2) ◽  
pp. 3470-3479
Keyword(s):  
Molecular Docking ◽  
Inhibitory Activity ◽  
In Silico ◽  
Molecular Mechanisms ◽  
Hydrophobic Interactions ◽  
In Silico Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Annona Muricata ◽  
Butanol Extract

Leaves of Annona muricata are commonly used for treating diabetes. This study was conducted to investigate the molecular mechanisms involved in the antidiabetic properties of leaves of Annona muricata. Leaves of Annona muricata were extracted separately with H2O, hydromethanol (50% methanol), methanol, ethylacetate, and n-butanol. Chemical characterization of the extracts was performed by spectrophotometry and Gas chromatography-Mass Spectrometry (GC-MS) techniques. Biological activity was determined by α-amylase inhibition assays and molecular docking. The hydromethanol extract had a total phenolics concentration of 117.00±0.59 µg GAE/mg extract whereas; flavonoids were most abundant in the n-butanol extract accounting for 29.34±8.87 µg QE/mg extract. The n-butanol extract had the best FRAP value of 41.17±0.57 Vit C eqv mM, which was significantly higher than the value of the vitamin C reference. Estimated IC50 for all the extracts did not differ significantly but was significantly higher than the reference compound quercetin. All extracts inhibited α-amylase in vitro albeit significantly lower than acarbose. The hydromethanol extract had the highest inhibitory activity (53.31 ± 0.33%). Furthermore, chemical profiling of the hydromethanol extract revealed the presence of a variety of bioactive compounds. In silico analysis by molecular docking of the compounds identified by GC-MS on α-amylase revealed that the compounds had robust molecular interactions orchestrated by H-bonding and hydrophobic interactions. From the results, it can be concluded that extracts of Annona muricata possess antioxidant phytochemicals that inhibit α-amylase. Therefore, the results justify the use of the plant for the treatment of diabetes.

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.

scholarly journals In Silico Mining of Terpenes from Red-Sea Invertebrates for SARS-CoV-2 Main Protease (Mpro) Inhibitors

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 2082
Author(s):  
Mahmoud A. A. Ibrahim ◽  
Alaa H. M. Abdelrahman ◽  
Tarik A. Mohamed ◽  
Mohamed A. M. Atia ◽  
Montaser A. M. Al-Hammady ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Binding Affinity ◽  
Red Sea ◽  
Protein Interactions ◽  
In Silico ◽  
Target Function ◽  
Pathway Enrichment Analysis ◽  
Main Protease

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19 pandemic, which generated more than 1.82 million deaths in 2020 alone, in addition to 83.8 million infections. Currently, there is no antiviral medication to treat COVID-19. In the search for drug leads, marine-derived metabolites are reported here as prospective SARS-CoV-2 inhibitors. Two hundred and twenty-seven terpene natural products isolated from the biodiverse Red-Sea ecosystem were screened for inhibitor activity against the SARS-CoV-2 main protease (Mpro) using molecular docking and molecular dynamics (MD) simulations combined with molecular mechanics/generalized Born surface area binding energy calculations. On the basis of in silico analyses, six terpenes demonstrated high potency as Mpro inhibitors with ΔGbinding ≤ −40.0 kcal/mol. The stability and binding affinity of the most potent metabolite, erylosides B, were compared to the human immunodeficiency virus protease inhibitor, lopinavir. Erylosides B showed greater binding affinity towards SARS-CoV-2 Mpro than lopinavir over 100 ns with ΔGbinding values of −51.9 vs. −33.6 kcal/mol, respectively. Protein–protein interactions indicate that erylosides B biochemical signaling shares gene components that mediate severe acute respiratory syndrome diseases, including the cytokine- and immune-signaling components BCL2L1, IL2, and PRKC. Pathway enrichment analysis and Boolean network modeling were performed towards a deep dissection and mining of the erylosides B target–function interactions. The current study identifies erylosides B as a promising anti-COVID-19 drug lead that warrants further in vitro and in vivo testing.

scholarly journals The Antiviral Effect of Indonesian Medicinal Plant Extracts Against Dengue Virus In Vitro and In Silico

Pathogens ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 85 ◽  
Author(s):  
Rosmalena Rosmalena ◽  
Berna Elya ◽  
Beti E. Dewi ◽  
Fithriyah Fithriyah ◽  
Hidayati Desti ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Plant Extracts ◽  
In Silico ◽  
In Silico Analysis ◽  
Acorus Calamus ◽  
Methanolic Extracts ◽  
Free Energy Of Binding ◽  
Dose Dependent ◽  
Silico Analysis

Dengue infections are still a worldwide burden, especially in Indonesia. There is no specific medication against the dengue virus. Recently, many types of research have been conducted to discover a new drug for dengue virus using natural resource extracts. Indonesia, as a tropical country, has a wide biodiversity. There are several medicinal plants in Indonesia that are believed to possess anti-dengue activity, such as Myristica fatua, Cymbopogon citratus, and Acorus calamus plants. We conducted an in vitro laboratory experiment of several extracts from Indonesian herbs combined with in silico analysis. The extracts were evaluated for safety and antiviral activity in Huh7it-1 cell lines, using a single dose of 20 µg/mL and dose-dependent (5, 10, 20, 40, 80 and 160 µg/mL) of plant extracts against dengue virus serotype 2 (DENV-2) NGC strain. The DMSO 0.1% was used as a negative control. The cytotoxic aspect was assessed by counting the cell viability, while the antiviral activity was calculated by counting the average inhibition. The selectivity index (SI) of plant extracts were performed from a ratio of CC50/EC50 value. In silico analysis was conducted to determine the free energy of binding between NS5 of dengue virus with bioactive compounds contained in Myristica fatua, Cymbopogon citratus and Acorus calamus extract plants. We determined that all extracts were not toxic against Huh7it-1 cell lines. The methanolic extracts of A. calamus, C. citratus, and M. fatua showed inhibition of DENV-2 at a dose of 20 µg/mL to 96.5%, 98.9%, and 122.7%, respectively. The dose-dependent effects showed that M. fatua has the best inhibition activity towards DENV-2. Molecular docking result showed that artesunic acid within M. fatua has the best free energy of binding (−7.2 kcal/mol), followed by homoegonol (−7.1 kcal/mol) which was slightly different from artesunic acid among others. The methanolic extracts of A. calamus, C. citratus, and M. fatua showed prospective anti-dengue activities both in vitro and in silico. Future research should be conducted to find the pure extracts of all useful herbs as a new candidate of antiviral drug.

scholarly journals Target related in silico analysis of Bergenin and tuberculosis management

Biomedicine ◽  
2021 ◽  
Vol 40 (4) ◽  
pp. 474-481
Author(s):  
Virupaksha A. Bastikar ◽  
Alpana Bastikar ◽  
Pramodkumar P. Gupta ◽  
Sandeep R. Pai ◽  
Santosh S. Chhajed
Keyword(s):  
Protein Interactions ◽  
In Silico ◽  
Biological Process ◽  
In Silico Analysis ◽  
Enrichment Analysis ◽  
Binding Mode ◽  
Health Concern ◽  
Silico Analysis

Introduction and Aim: Tuberculosis (TB) is a global health concern, claiming two million lives every year. Although an oldest known human infectious disease, researcher is falling short of giving out an effective and reliable vaccine or therapy. The current antimycobacterial drugs include Isoniazid, Ethambutol, Rifampicin and Pyrazinemamide available in market, but most of these are known to have certain adverse effects. Hence there is an increase in demand for natural products with anti-tuberculosis activity with no or limited side effects. Indian traditional systems of medicine have a plethora of promising plants for treatment of tuberculosis, of which Bergenin is the most well established and extensively used compound. The main aim of this research was to investigate the role of Bergenin as an anti-tuberculosis agent with the help of in-silico analysis and protein interaction studies. Materials and Methods: In the present study 04 known 3-dimensional crystallized anti-tubercular drug target is considered and retrieved from PDB. Drug Isoniazid, Ethambutol, Rifampicin, Pyrazineamide and phytochemical Bergenin were retrieved, sketched and geometrically optimized. Molecular docking is carried to understand the binding mode and its core interactions. ADMET properties were calculated in assessment of the toxicity. Protein-protein interactions and enrichment analysis is carried out to understand the biological process involved with rpsA protein. Results: In the present study other than Rifampicin, Bergenin reported with better binding energy and similar pharmacophoric interaction pattern as compared to all the 04 indigenous inhibitors. The PPI network and enrichment analysis predicts the plausible biological process involved with rpsA protein and can be further targeted in treatment of tuberculosis. Conclusion: The results showed that Bergenin was better than and competent with the existing drugs and can be used as an anti-tuberculosis agent if studied in-vitro and in-vivo for its activity.

Discovery of New AKT1 Inhibitors by Combination of In silico Structure Based Virtual Screening Approaches and Biological Evaluations

2019 ◽  
Author(s):  
Filip Fratev ◽  
Denisse A. Gutierrez ◽  
Renato J. Aguilera ◽  
suman sirimulla
Keyword(s):  
Virtual Screening ◽  
Success Rate ◽  
Protein Interactions ◽  
In Silico ◽  
Biological Data ◽  
In Vitro Binding ◽  
Vitro Binding ◽  
Screening Protocol ◽  
Screening Approaches

AKT1 is emerging as a useful target for treating cancer. Herein, we discovered a new set of ligands that inhibit the AKT1, as shown by in vitro binding and cell line studies, using a newly designed virtual screening protocol that combines structure-based pharmacophore and docking screens. Taking together with the biological data, the combination of structure based pharamcophore and docking methods demonstrated reasonable success rate in identifying new inhibitors (60-70%) proving the success of aforementioned approach. A detail analysis of the ligand-protein interactions was performed explaining observed activities.<br>

In Silico Study of Potential Cross-Kingdom Plant MicroRNA Based Regulation in Chronic Myeloid Leukemia

2020 ◽  
Vol 17 (2) ◽  
pp. 125-132
Author(s):  
Marjanu Hikmah Elias ◽  
Noraziah Nordin ◽  
Nazefah Abdul Hamid
Keyword(s):  
Targeted Therapy ◽  
In Silico ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Target Prediction ◽  
In Silico Analysis ◽  
Microrna Target ◽  
Good Target

Background: Chronic Myeloid Leukaemia (CML) is associated with the BCRABL1 gene, which plays a central role in the pathogenesis of CML. Thus, it is crucial to suppress the expression of BCR-ABL1 in the treatment of CML. MicroRNA is known to be a gene expression regulator and is thus a good candidate for molecularly targeted therapy for CML. Objective: This study aims to identify the microRNAs from edible plants targeting the 3’ Untranslated Region (3’UTR) of BCR-ABL1. Methods: In this in silico analysis, the sequence of 3’UTR of BCR-ABL1 was obtained from Ensembl Genome Browser. PsRNATarget Analysis Server and MicroRNA Target Prediction (miRTar) Server were used to identify miRNAs that have binding conformity with 3’UTR of BCR-ABL1. The MiRBase database was used to validate the species of plants expressing the miRNAs. The RNAfold web server and RNA COMPOSER were used for secondary and tertiary structure prediction, respectively. Results: In silico analyses revealed that cpa-miR8154, csi-miR3952, gma-miR4414-5p, mdm-miR482c, osa-miR1858a and osa-miR1858b show binding conformity with strong molecular interaction towards 3’UTR region of BCR-ABL1. However, only cpa-miR- 8154, osa-miR-1858a and osa-miR-1858b showed good target site accessibility. Conclusion: It is predicted that these microRNAs post-transcriptionally inhibit the BCRABL1 gene and thus could be a potential molecular targeted therapy for CML. However, further studies involving in vitro, in vivo and functional analyses need to be carried out to determine the ability of these miRNAs to form the basis for targeted therapy for CML.

In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

2019 ◽  
Vol 13 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Vishal Ahuja ◽  
Aashima Sharma ◽  
Ranju Kumari Rathour ◽  
Vaishali Sharma ◽  
Nidhi Rana ◽  
...  
Keyword(s):  
Production Process ◽  
In Silico ◽  
Xylose Reductase ◽  
In Silico Analysis ◽  
Emericella Nidulans ◽  
Higher Temperature ◽  
In Silico Characterization ◽  
Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

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