An in silico study on plant-derived inhibitors against a prognostic Biomarker, Jab1

Cancer kills millions of people worldwide every year. The main form of treatment at this point is chemotherapy, which comprises of systemic drug delivery so that they can kill the cancerous cells more effectively. But most of these drugs cause severe side effects in patients and, therefore there is a strong need to focus on identifying natural compounds as a potent phytoinhibitors using various in silico and in vitro approaches. Natural compounds pose low toxicity, hence render them to be an excellent alternative to the basis for the development of new anti-cancerous drugs. Our study considers an effective therapeutic target, Jab1 (c-Jun activation domain-binding protein-1) or a c-Jun coactivator, which has been implicated in multiple protein interactions that play a significant role in various stages of carcinogenesis. Hence we have performed screening of 1500 natural compounds having anticancerous activity by applying various in silico approaches including Lipinski rule of five, ADME, and various Molecular Docking tools. In this study, we have identified two potent phytoinhibitors against Jab1 which needs to be further validated through in vitro approaches.

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Screening of natural compounds for identification of novel inhibitors against β-lactamase CTX-M-152 reported among Kluyvera georgiana isolates: An in vitro and in silico study

Microbial Pathogenesis ◽

10.1016/j.micpath.2020.104688 ◽

2021 ◽

Vol 150 ◽

pp. 104688

Author(s):

Hemlata ◽

Mujtaba Aamir Bhat ◽

Vijay Kumar ◽

Mohammad Z. Ahmed ◽

Ali S. Alqahtani ◽

...

Keyword(s):

In Silico ◽

Natural Compounds ◽

In Silico Study

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

10.26434/chemrxiv.7591202 ◽

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.

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C0135 In vitro and in silico study of the effect of crocin and safranal on human plasma coagulation

Thrombosis Research ◽

10.1016/j.thromres.2012.08.174 ◽

2012 ◽

Vol 130 ◽

pp. S167

Author(s):

Maria Ditsa ◽

George Geromihalos ◽

Eleftheria Tragoulia ◽

Dimitra Markala ◽

Chrisa Meleti ◽

...

Keyword(s):

Human Plasma ◽

In Silico ◽

Plasma Coagulation ◽

In Silico Study

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Synthesis, in vitro anticancer activity and in silico study of new disubstituted thiazolidinedione derivatives

Medicinal Chemistry Research ◽

10.1007/s00044-013-0902-z ◽

2014 ◽

Vol 23 (6) ◽

pp. 3220-3226 ◽

Cited By ~ 10

Author(s):

Moacyr Jesus Barreto de Melo Rêgo ◽

Marina Rocha Galdino-Pitta ◽

Daniel Tarciso Martins Pereira ◽

Juliana Cruz da Silva ◽

Marcelo Montenegro Rabello ◽

...

Keyword(s):

Anticancer Activity ◽

In Silico ◽

In Silico Study

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In Silico and In Vitro Studies on the Protein-Protein Interactions between Brugia malayi Immunomodulatory Protein Calreticulin and Human C1q

PLoS ONE ◽

10.1371/journal.pone.0106413 ◽

2014 ◽

Vol 9 (9) ◽

pp. e106413 ◽

Cited By ~ 21

Author(s):

Sunita Yadav ◽

Smita Gupta ◽

Chandrabose Selvaraj ◽

Pawan Kumar Doharey ◽

Anita Verma ◽

...

Keyword(s):

Protein Interactions ◽

In Silico ◽

Brugia Malayi ◽

In Vitro Studies ◽

Protein Protein Interactions ◽

Immunomodulatory Protein

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High Throughput in Silico Identification of Novel Phytochemical Inhibitors for the Master Regulator of Inflammation (TNFα)

10.26434/chemrxiv.14178212.v2 ◽

2021 ◽

Author(s):

Pratap Kumar Parida ◽

Dipak Paul ◽

Debamitra Chakravorty

Keyword(s):

Small Molecule ◽

High Throughput ◽

In Silico ◽

Small Molecule Inhibitors ◽

Binding Free Energy ◽

Natural Compounds ◽

Free Energy Calculations ◽

Compound Libraries ◽

Relative Binding

<a>The over expression of Tumor necrosis factor-α (TNFα) has been implicated in a variety of disease and is classified as a therapeutic target for inflammatory diseases (Crohn disease, psoriasis, psoriatic arthritis, rheumatoid arthritis).Commercially available therapeutics are biologics which are associated with several risks and limitations. Small molecule inhibitors and natural compounds (saponins) were identified by researchers as lead molecules against TNFα, however, </a>they were often associated with high IC50 values which can lead to their failure in clinical trials. This warrants research related to identification of better small molecule inhibitors by screening of large compound libraries. Recent developments have demonstrated power of natural compounds as safe therapeutics, hence, in this work, we have identified TNFα phytochemical inhibitors using high throughput in silico screening approaches of 6000 phytochemicals followed by 200 ns molecular dynamics simulations and relative binding free energy calculations. The work yielded potent hits that bind to TNFα at its dimer interface. The mechanism targeted was inhibition of oligomerization of TNFα upon phytochemical binding to restrict its interaction with TNF-R1 receptor. MD simulation analysis resulted in identification of two phytochemicals that showed stable protein-ligand conformations over time. The two compounds were triterpenoids: Momordicilin and Nimbolin A with relative binding energy- calculated by MM/PBSA to be -190.5 kJ/Mol and -188.03 kJ/Mol respectively. Therefore, through this work it is being suggested that these phytochemicals can be used for further in vitro analysis to confirm their inhibitory action against TNFα or can be used as scaffolds to arrive at better drug candidates.

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IN SILICO STUDY OF THE ANTIMICROBIAL PROFILE OF β-CITRONELLOL: POTENTIAL AS AN ANTIFUNGAL

Periódico Tchê Química ◽

10.52571/ptq.v16.n32.2019.912_periodico32_pgs_894_898.pdf ◽

2019 ◽

Vol 16 (32) ◽

pp. 894-898

Author(s):

D. F. SILVA ◽

H. D. NETO ◽

M. D. L. FERREIRA ◽

A. A. O. FILHO ◽

E. O. LIMA

Keyword(s):

In Silico ◽

Fungal Infections ◽

In Silico Analysis ◽

Fungal Species ◽

In Silico Study ◽

Pass Online ◽

Therapeutic Alternatives ◽

Bioactivity Profile ◽

Silico Analysis

β-citronellol (3,7-dimethyl-6-octen-1-ol) has been exhibiting a number of pharmacological effects that creates interest about its antimicrobial potential, since several substances of the monoterpene class have already demonstrated to possess activity in this profile. In addition, the emergence of fungal species resistant to current pharmacotherapy poses a serious challenge to health systems, making it necessary to search for new effective therapeutic alternatives to deal with this problem. In this study, the antimicrobial profile of β-citronellol was analyzed. The Prediction of Activity Spectra for Substances (PASS) online software was used to study the antimicrobial activity of the β-citronellol molecule by the use of in silico analysis. In contrast, an in vitro antifungal study of this monoterpene was carried out. For this purpose, the Minimum Inhibitory Concentration (MIC) was determined by the microdilution technique in 96-well plates in Saboraud Dextrose Broth/RPMI against sensitive strains of Candida albicans, and this assay was performed in duplicate. In the in silico analysis of the antimicrobial profile, it was revealed that the monoterpene β-citronellol had a diverse antimicrobial bioactivity profile. For the antifungal activity, it presented a percentage value with Pa: 58.4% (predominant) and its MIC of 128 μg/mL, which was equivalent for all strains tested. The in silico study of the β-citronellol molecule allowed us to consider that the monoterpenoid is very likely to be bioactive against agents that cause fungal infections.

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Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study

Interface Focus ◽

10.1098/rsfs.2019.0126 ◽

2020 ◽

Vol 11 (1) ◽

pp. 20190126 ◽

Cited By ~ 1

Author(s):

B. J. M. van Rooij ◽

G. Závodszky ◽

A. G. Hoekstra ◽

D. N. Ku

Keyword(s):

Platelet Aggregation ◽

In Silico ◽

Platelet Rich Plasma ◽

High Shear ◽

Shear Rates ◽

Flow Simulations ◽

In Silico Study ◽

Platelet Aggregates

The influence of the flow environment on platelet aggregation is not fully understood in high-shear thrombosis. The objective of this study is to investigate the role of a high shear rate in initial platelet aggregation. The haemodynamic conditions in a microfluidic device are studied using cell-based blood flow simulations. The results are compared with in vitro platelet aggregation experiments performed with porcine whole blood (WB) and platelet-rich-plasma (PRP). We studied whether the cell-depleted layer in combination with high shear and high platelet flux can account for the distribution of platelet aggregates. High platelet fluxes at the wall were found in silico . In WB, the platelet flux was about twice as high as in PRP. Additionally, initial platelet aggregation and occlusion were observed in vitro in the stenotic region. In PRP, the position of the occlusive thrombus was located more downstream than in WB. Furthermore, the shear rates and stresses in cell-based and continuum simulations were studied. We found that a continuum simulation is a good approximation for PRP. For WB, it cannot predict the correct values near the wall.

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