scholarly journals In silico study of PEI-PEG-squalene-dsDNA polyplex formation: The delicate role of PEG length to the binding of PEI to DNA

2021 ◽  
Author(s):  
Tudor Vasiliu ◽  
Bogdan Florin Florin Craciun ◽  
Andrei Neamtu ◽  
Lilia Clima ◽  
Dragos Lucian Isac ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Polyethylene Glycol ◽  
Gene Delivery ◽  
In Silico ◽  
Biomedical Applications ◽  
Experimental Studies ◽  
Biomedical Devices ◽  
In Silico Study ◽  
Or Gene

The biocompatible hydrophilic polyethylene glycol (PEG) is widely used in biomedical applications, such as drug or gene delivery, tissue engineering or as antifouling in biomedical devices. Experimental studies have shown...

Graphene and Graphene-Based Materials in Biomedical Applications

2019 ◽  
Vol 26 (38) ◽  
pp. 6834-6850 ◽  
Author(s):  
Mohammad Omaish Ansari ◽  
Kalamegam Gauthaman ◽  
Abdurahman Essa ◽  
Sidi A. Bencherif ◽  
Adnan Memic
Keyword(s):  
Tissue Engineering ◽  
Thermal Properties ◽  
Gene Delivery ◽  
Regenerative Medicine ◽  
Biomedical Research ◽  
Biomedical Applications ◽  
Biomedical Application ◽  
Two Dimensional ◽  
Drug And Gene Delivery ◽  
Biomedical Fields

: Nanobiotechnology has huge potential in the field of regenerative medicine. One of the main drivers has been the development of novel nanomaterials. One developing class of materials is graphene and its derivatives recognized for their novel properties present on the nanoscale. In particular, graphene and graphene-based nanomaterials have been shown to have excellent electrical, mechanical, optical and thermal properties. Due to these unique properties coupled with the ability to tune their biocompatibility, these nanomaterials have been propelled for various applications. Most recently, these two-dimensional nanomaterials have been widely recognized for their utility in biomedical research. In this review, a brief overview of the strategies to synthesize graphene and its derivatives are discussed. Next, the biocompatibility profile of these nanomaterials as a precursor to their biomedical application is reviewed. Finally, recent applications of graphene-based nanomaterials in various biomedical fields including tissue engineering, drug and gene delivery, biosensing and bioimaging as well as other biorelated studies are highlighted.

scholarly journals Combining experiments and in silico modeling to infer the role of adhesion and proliferation on the collective dynamics of cells

2021 ◽  
Author(s):  
Hygor P. M. Melo ◽  
F. Raquel Maia ◽  
André S. Nunes ◽  
Rui L. Reis ◽  
Joaquim M. Oliveira ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Cell Adhesion ◽  
Glioblastoma Multiforme ◽  
In Silico ◽  
Relative Importance ◽  
Collective Dynamics ◽  
Surfaces And Interfaces ◽  
In Silico Modeling ◽  
Cell Cell

ABSTRACTThe collective dynamics of cells on surfaces and interfaces poses technological and theoretical challenges in the study of morphogenesis, tissue engineering, and cancer. Different mechanisms are at play, including, cell-cell adhesion, cell motility, and proliferation. However, the relative importance of each one is elusive. Here, experiments with a culture of glioblastoma multiforme cells on a substrate are combined with in silico modeling to infer the rate of each mechanism. By parametrizing these rates, the time-dependence of the spatial correlation observed experimentally is reproduced. The obtained results suggest a reduction in cell-cell adhesion with the density of cells. The reason for such reduction and possible implications for the collective dynamics of cancer cells are discussed.

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

2020 ◽  
Vol 11 (1) ◽  
pp. 20190126 ◽  
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.

scholarly journals In Silico Investigation of Mitragynine and 7-Hydroxymitragynine Metabolism

2019 ◽  
Author(s):  
Taweetham Limpanuparb ◽  
Rattha Noorat ◽  
Yuthana Tantirungrotechai
Keyword(s):  
Gas Phase ◽  
In Silico ◽  
Metabolic Pathways ◽  
Experimental Studies ◽  
Medicinal Uses ◽  
Detection Techniques ◽  
Mass Spectrom ◽  
Gibbs Energies ◽  
In Silico Study

Abstract Objective: Mitragynine is the main active compound of Mitragyna speciose (Kratom in Thai). The understanding of mitragynine derivative metabolism in human body is required to develop effective detection techniques in case of drug abuse or establish an appropriate dosage in case of medicinal uses. This in silico study is based upon in vivo results in rat and human by Philipp et al. (J. Mass Spectrom., 2009, 44, 1249.) Results: The gas-phase structures of mitragynine, 7-hydroxymitragynine and their metabolites were obtained by quantum chemical method at B3LYP/6-311++G(d,p) level. Results in terms of standard Gibbs energies of reaction for all metabolic pathways are reported with solvation energy from SMD model. We found that 7-hydroxy substitution leads to changes in reactivity in comparison to mitragynine: position 17 is more reactive towards demethylation and conjugation to a glucuronide and position 9 is less reactive towards conjugation to a glucuronide. Despite the changes, position 9 is the most reactive for demethylation and position 17 is the most reactive for conjugation to a glucuronide for both mitragynine and 7-hydroxymitragynine. Our results suggest that 7-hydroxy substitution could lead to different metabolic pathways and raise an important question for further experimental studies of this more potent derivative.

scholarly journals Understanding the Role of R266K Mutation in Cystathionine β-Synthase (CBS) Enzyme: An in Silico Study

2021 ◽  
Author(s):  
Aashish Bhatt ◽  
Md. Ehesan Ali
Keyword(s):  
Hydrogen Bonding ◽  
In Silico ◽  
Density Functional ◽  
Experimental Studies ◽  
Salt Bridge ◽  
Md Simulations ◽  
Enzymatic Activities ◽  
Wild Type ◽  
Long Distance

<div>Human cystathionine β-synthase (hCBS) is a unique pyridoxal 5’-phosphate (PLP) dependent enzyme that catalyses the condensation reactions in the transsulfuration pathways. The specific role of Heme in the enzymatic activities has not yet been established, however, several experimental studies indicated the bi-directional communications between the Heme and PLP. Performing classical molecular dynamics (MD) simulations upon developing the necessary force field parameters for the cysteine and histidine bound hexa-coordinated Heme, we have investigated <i>In Silico</i> dynamical aspects of the bi-directional communications. Furthermore, we have investigated the comparative aspects of electron density overlap across the communicating pathways adopting the density functional theory (DFT) in conjunction with the hybrid exchange correlation functional for the CSB<sup>WT</sup> (wild-type) and CBS<sup>R266K</sup> (mutated) case. The atomistic dynamical simulations and subsequent explorations of the electronic structure not only confirm the reported observations but provide an in-depth mechanistic understating of how the non-covalent hydrogen bonding interactions with Cys52 control the such long-distance communication. Our study also provides a convincing answer to the reduced enzymatic activities in the R266K hCBS in comparison to the wild-type enzymes. We further realized that the difference in hydrogen-bonding patterns as well as salt-bridge interactions play the pivotal role in such long distant bi-directional communications.</div>

scholarly journals In silico Study of the Interactions between Schiff Base Polyphenols and HPV 16 E6/E6AP/p53 complex

2021 ◽  
pp. 3973-3980
Author(s):  
Jeremiah I. Ogah ◽  
Olatunji M. Kolawole ◽  
Steven O. Oguntoye ◽  
Muhammed Mustapha Suleiman
Keyword(s):  
Molecular Docking ◽  
Anticancer Agents ◽  
In Silico ◽  
In Silico Analysis ◽  
Docking Study ◽  
Hydrogen Atoms ◽  
Molecular Docking Study ◽  
Hpv 16 ◽  
In Silico Study

The rise in the incidence of cervical cancer globally has accentuate attention to the potential role of polyphenols as anticancer agents. Different studies have demonstrated the role of some polyphenols in altering Human Papillomavirus (HPV) carcinogenesis. Thus, this study was aimed at establishing the potentials of Schiff-based polyphenols from imesatin and satin as anticancer agents through in silico analysis. The polyphenols were synthesized and characterized using elemental analyses, spectroscopic analyses, UV-visible, Infrared, and Nuclear Magnetic Resonance (1H NMR and 13C, NMR). Molecular docking study of the polyphenols was carried out using Auto Dock Vina. The oncogenic E6 protein structure of HPV 16 was obtained from the protein bank (ID: 4XR8). The E6 proteins were prepared using AutoDock tools. Water molecules were removed from the protein molecules while hydrogen atoms were added. Also, the structures of Curcumin and Isomericitrin were obtained from PubChem. Results showed that three different Schiff based polyphenols were obtained from the synthesis; 3-(2’,4’-dimethoxy benzylidene hydrazono) indoline-2-one (DMBH), 3-(2’-hydroxy-4’-methoxy benzylidene hydrazono) indoline-2-one (HMBD), and 3-((4-4’-((2’’, 4’’-dimethoxy benzylidene amino) benzyl)phenyl)imino) indoline-2-one (DMBP). Higher ability of the docked polyphenols to bind to the E6/E6AP/p53 complex when compared to Curcumin was revealed. Also, results showed that the binding energy of Curcumin and Isomericitrin were -7.1kcal/mol and -8.4kcal/mol respectively while that of the polyphenols ranged from -7.4kcal/mol to -7.9kcal/mol. The molecular docking results of the polyphenols used in this study further confirm their potentials as strong anti-cancer agents.

scholarly journals In silico study to examine the role of amino acids in Jasmonate induced plant defense process

2018 ◽  
Vol 5 (10) ◽  
pp. 289-301
Author(s):  
Ruma Ganguly ◽  
Sailesh K. Mehta
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Jasmonic Acid ◽  
Plant Defense ◽  
In Silico ◽  
Induced Plant Defense ◽  
In Silico Study

The role of amino acid is important to Jasmonate induce plant defense process. Jasmonic acid and amino acid Isoleucine conjugate (JA-Ile) has been found to be necessary to achieve such process effectively. We have examined the origin of such process computationally and showed that Isoleucine is more active compared to other Jasmonic acid conjugates. The epimerization process revealed that Isoleucine conjugated Jasmonic acid is energetically a favoured process compared to JA-Leu and JA-Val. Water has functioned as a catalyst in the whole epimerization process. This study would unravel the importance of Isoleucine in the Jasmonic acid induced plant defense process.

scholarly journals In-silico study of antituberculous activity of Zn-pyrazinamide in pyrazinamidase

2020 ◽  
Author(s):  
Jesus Antonio Alvarado-Huayhuaz ◽  
Wilmar Puma-Zamora ◽  
Ana Cecilia Valderrama-Negrón
Keyword(s):  
In Silico ◽  
Chemical Reactivity ◽  
Experimental Studies ◽  
New Drugs ◽  
In Silico Study ◽  
Three Stages ◽  
Dynamics Simulations ◽  
Antituberculous Activity ◽  
Tuberculosis Activity ◽  
Pyrazinoic Acid

Tuberculosis is caused by Mycobacterium tuberculosis and is one of the leading causes of death. Treatment with pyrazinamide depends on the formation of the bioactive species, pyrazinoic acid (POA), catalyzed by the enzyme pyrazinamidase (PZAse). New mutant strains show resistance to PZA, therefore, it is necessary to search for new drugs. Metallodrugs can offer a synergistic effect on the biological activity of the metal and the drug. Recent studies by our group show anti-tuberculosis activity of pyrazinamide coordinated with Zn, however, the mechanism of action is unknown. In this work, an in-silico study was carried out in three stages: Quantum mechanical, molecular docking and molecular dynamics simulations. ZnPZA (Egap = 4.12 eV) presented greater chemical reactivity than PZA (Egap = 4.97 eV). Greater binding energy was found in ZnPZA-PZAse (-6.98 kcal/mol) than in PZA-PZAse (-6.48 kcal/mol). RMSD and RMSF show stability in PZA-PZAse and ZnPZA-PZAse dockings. Hydrogen bonds interaction of ZnPZA with the catalytic amino acids Asp8 and Lys96 occurs for 83 and 40 ns, respectively. It is concluded that ZnPZA could serve as a transporter of PZA to the active site of PZAse, to promote the production of POA and the antituberculous effect; however, further experimental studies are needed.

Synthesis and Applications of Hydrogels in Cancer Therapy

2020 ◽  
Vol 20 (12) ◽  
pp. 1431-1446
Author(s):  
Anchal Singhal ◽  
Niharika Sinha ◽  
Pratibha Kumari ◽  
Manoushikha Purkayastha
Keyword(s):  
Drug Delivery ◽  
Tissue Engineering ◽  
Cancer Therapy ◽  
Mechanical Strength ◽  
Biomedical Applications ◽  
Three Dimensional ◽  
Polymer Chains ◽  
Human Tissues ◽  
Methods Of Synthesis

: Hydrogels are water-insoluble, hydrophilic, cross-linked, three-dimensional networks of polymer chains having the ability to swell and absorb water but do not dissolve in it, that comprise the major difference between gels and hydrogels. The mechanical strength, physical integrity and solubility are offered by the crosslinks. The different applications of hydrogels can be derived based on the methods of their synthesis, response to different stimuli, and their different kinds. Hydrogels are highly biocompatible and have properties similar to human tissues that make it suitable to be used in various biomedical applications, including drug delivery and tissue engineering. The role of hydrogels in cancer therapy is highly emerging in recent years. In the present review, we highlighted different methods of synthesis of hydrogels and their classification based on different parameters. Distinctive applications of hydrogels in the treatment of cancer are also discussed.

Nanomaterials for bioprinting: functionalization of tissue-specific bioinks

2021 ◽  
Author(s):  
Andrea S. Theus ◽  
Liqun Ning ◽  
Linqi Jin ◽  
Ryan K. Roeder ◽  
Jianyi Zhang ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Tissue Engineering ◽  
Regenerative Medicine ◽  
Biomedical Applications ◽  
Disease Modeling ◽  
Three Dimensional ◽  
3D Bioprinting ◽  
Significant Step ◽  
Printing Processes

Abstract Three-dimensional (3D) bioprinting is rapidly evolving, offering great potential for manufacturing functional tissue analogs for use in diverse biomedical applications, including regenerative medicine, drug delivery, and disease modeling. Biomaterials used as bioinks in printing processes must meet strict physiochemical and biomechanical requirements to ensure adequate printing fidelity, while closely mimicking the characteristics of the native tissue. To achieve this goal, nanomaterials are increasingly being investigated as a robust tool to functionalize bioink materials. In this review, we discuss the growing role of different nano-biomaterials in engineering functional bioinks for a variety of tissue engineering applications. The development and commercialization of these nanomaterial solutions for 3D bioprinting would be a significant step towards clinical translation of biofabrication.

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