In-Silico Analysis to Identify Potent Quinoline Analogues Against Multi-Targets of SARS-CoV-2

2021 ◽  
Vol 6 (4) ◽  
pp. 25-37
Author(s):  
Shahanas Naisam ◽  
Viji V.S. ◽  
Suvanish Kumar ◽  
Nidhin Sreekumar
Keyword(s):  
Interaction Analysis ◽  
In Silico Analysis ◽  
Preventive Treatment ◽  
Drug Molecule ◽  
Current Outbreak ◽  
In Vivo Analysis ◽  
Effective Drugs ◽  
Silico Analysis

In the current outbreak of COVID-19, various studies have been conducted all over the world to develop effective drugs against the virus. Recent studies have shown that hydroxychloroquine, chloroquine (antimalarial drugs), isoflavones, flavonoids, etc. have potent antiviral properties, and few have been proven as effective drugs for the preventive treatment of COVID-19. But their exact action against SARS-CoV-2 is still unknown. The strategy of this study is the virtual screening of quinoline analogues, design new ligand molecules, perform molecular interaction analysis, their MD validation against multi targets (Spike-ACE2, TMPRSS2, and Spike Protein) of SARS-CoV-2, and to suggest the most promising and effective drug molecule. Hydroxychloroquine and chloroquine were considered as the reference molecules in this study. A ligand N-[4-(3-Benzylideneazetidine-1-carbonyl)phenyl]quinoline-8-sulfonamide interacting with TMPRSS2 shows better interaction among the list even after MD validation. Further in-vitro and in-vivo analysis of this study is needed for future validation.

In-Silico Analysis to Identify Potential Inhibitors Against the Protein NSP12 of SARS-CoV-2

2021 ◽  
Vol 6 (3) ◽  
pp. 48-60
Author(s):  
Hima Vyshnavi ◽  
Gayathri S. S. ◽  
Shahanas Naisam ◽  
Suvanish Kumar ◽  
Nidhin Sreekumar
Keyword(s):  
In Silico ◽  
Interaction Analysis ◽  
In Silico Analysis ◽  
Drug Efficacy ◽  
Drug Candidate ◽  
In Vivo Analysis ◽  
The Stability ◽  
Potential Inhibitors ◽  
Silico Analysis

In this pandemic condition, a drug candidate which is effective against COVID-19 is very much desired. This study initiates an in silico analysis to screen small molecules such as phytochemicals, drug metabolites, and natural metabolites against Nsp12 (a catalytic unit for RNA transcription and replication). Molecular interaction analysis of 6M71 was carried out against 2,860 ligands using Schrodinger Glide software. After docking analysis, the top 10 molecules (Glide score) were subjected to MD simulation for validating the stability. It resulted in top 10 compounds with high binding affinities with the target molecule NSP 12. Out of these, top 3 compounds including PSID_08_LIG3 (HMDB0133544), PSID_08_LIG4 (HMDB0132898), and PSID_08_LIG9 (HMDB0128199) show better Glide scores, better H-bond interaction, better MMGBSA value and stability on dynamic simulation after analysis of the results. The suggested ligands can be postulated as effective antiviral drugs against COVID-19. Further in vivo analysis is needed for validating the drug efficacy.

Investigation of indole functionalized pyrazoles and oxadiazoles as anti-inflammatory agents: synthesis, in-vivo, in-vitro and in-silico analysis

2021 ◽  
pp. 105068
Author(s):  
Devendra Kumar ◽  
Ravi Ranjan Kumar ◽  
Shelly Pathania ◽  
Pankaj Kumar Singh ◽  
Sourav Kalra ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Anti Inflammatory ◽  
Silico Analysis

scholarly journals Predicting In Vivo Responses to Biomaterials via Combined In Vitro and In Silico Analysis

2015 ◽  
Vol 21 (2) ◽  
pp. 148-159 ◽  
Author(s):  
Matthew T. Wolf ◽  
Yoram Vodovotz ◽  
Stephen Tottey ◽  
Bryan N. Brown ◽  
Stephen F. Badylak
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis

scholarly journals Evolutionary Origin of Insulin-Degrading Enzyme and Its Subcellular Localization and Secretion Mechanism: A Study in Microglial Cells

Cells ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 227
Author(s):  
Miriam Corraliza-Gómez ◽  
Concepción Lillo ◽  
Irene Cózar-Castellano ◽  
Eduardo Arranz ◽  
Diego Sanchez ◽  
...  
Keyword(s):  
Subcellular Localization ◽  
Phylogenetic Analyses ◽  
In Silico Analysis ◽  
Insulin Degrading Enzyme ◽  
Degrading Enzyme ◽  
Raft Domains ◽  
The Brain ◽  
Silico Analysis

The insulin-degrading enzyme (IDE) is a zinc-dependent metalloendopeptidase that belongs to the M16A metalloprotease family. IDE is markedly expressed in the brain, where it is particularly relevant due to its in vitro amyloid beta (Aβ)-degrading activity. The subcellular localization of IDE, a paramount aspect to understand how this enzyme can perform its proteolytic functions in vivo, remains highly controversial. In this work, we addressed IDE subcellular localization from an evolutionary perspective. Phylogenetic analyses based on protein sequence and gene and protein structure were performed. An in silico analysis of IDE signal peptide suggests an evolutionary shift in IDE exportation at the prokaryote/eukaryote divide. Subcellular localization experiments in microglia revealed that IDE is mostly cytosolic. Furthermore, IDE associates to membranes by their cytoplasmatic side and further partitions between raft and non-raft domains. When stimulated, microglia change into a secretory active state, produces numerous multivesicular bodies and IDE associates with their membranes. The subsequent inward budding of such membranes internalizes IDE in intraluminal vesicles, which later allows IDE to be exported outside the cells in small extracellular vesicles. We further demonstrate that such an IDE exportation mechanism is regulated by stimuli relevant for microglia in physiological conditions and upon aging and neurodegeneration.

In Vitro, In Vivo and In Silico Analysis of the Anticancer and Estrogen-like Activity of Guava Leaf Extracts

2014 ◽  
Vol 21 (20) ◽  
pp. 2322-2330 ◽  
Author(s):  
L.Y. Rizzo ◽  
G.B. Longato ◽  
A.LT.G. Ruiz ◽  
S.V. Tinti ◽  
A. Possenti ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Leaf Extracts ◽  
Guava Leaf ◽  
Silico Analysis

scholarly journals In vivo, in vitro, and in silico analysis of methylation of the HIV-1 provirus

Methods ◽  
2011 ◽  
Vol 53 (1) ◽  
pp. 47-53 ◽  
Author(s):  
Leonard Chávez ◽  
Steven Kauder ◽  
Eric Verdin
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis ◽  
Hiv 1

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.

scholarly journals A Report on Multi-Target Anti-Inflammatory Properties of Phytoconstituents from Monochoria hastata (Family: Pontederiaceae)

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7397
Author(s):  
Md Mazedul Haq ◽  
Md Arifur Rahman Chowdhury ◽  
Hilal Tayara ◽  
Ibrahim Abdelbaky ◽  
Md Shariful Islam ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Control Group ◽  
Dependent Manner ◽  
In Vivo Experiments ◽  
Microbial Infections ◽  
Anti Inflammatory ◽  
Silico Analysis

This study aims to investigate the potential analgesic properties of the crude extract of Monochoria hastata (MH) leaves using in vivo experiments and in silico analysis. The extract, in a dose-dependent manner, exhibited a moderate analgesic property (~54% pain inhibition in acetic acid-induced writhing test), which is significant (** p < 0.001) as compared to the control group. The complex inflammatory mechanism involves diverse pathways and they are inter-connected. Therefore, multiple inflammatory modulator proteins were selected as the target for in silico analysis. Computational analysis suggests that all the selected targets had different degrees of interaction with the phytochemicals from the extract. Rutin (RU), protocatechuic acid (PA), vanillic acid (VA), and ferulic acid (FA) could regulate multiple targets with a robust efficiency. None of the compounds showed selectivity to Cyclooxygenase-2 (COX-2). However, regulation of COX and lipoxygenase (LOX) cascade by PA can reduce non-steroidal analgesic drugs (NSAIDs)-related side effects, including asthma. RU showed robust regulation of cytokine-mediated pathways like RAS/MAPK and PI3K/NF-kB by inhibition of EGFR and IKBα (IKK), which may prevent multi-organ failure due to cytokine storm in several microbial infections, for example, SARS-CoV-2. Further investigation, using in vivo and in vitro experiments, can be conducted to develop multi-target anti-inflammatory drugs using the isolated compounds from the extract.

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.

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