scholarly journals Multi-dimensional computational pipeline for large-scale deep screening of compound effect assessment: an in silico case study on ageing-related compounds

2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Vipul Gupta ◽  
Alina Crudu ◽  
Yukiko Matsuoka ◽  
Samik Ghosh ◽  
Roger Rozot ◽  
...  
Keyword(s):  
Large Scale ◽  
Network Effects ◽  
Chemical Compounds ◽  
Structural Similarity ◽  
Computational Pipeline ◽  
In Vivo Experiments ◽  
Cell Vitality ◽  
Alternative Means ◽  
Related Compounds

AbstractDesigning alternative approaches to efficiently screen chemicals on the efficacy landscape is a challenging yet indispensable task in the current compound profiling methods. Particularly, increasing regulatory restrictions underscore the need to develop advanced computational pipelines for efficacy assessment of chemical compounds as alternative means to reduce and/or replace in vivo experiments. Here, we present an innovative computational pipeline for large-scale assessment of chemical compounds by analysing and clustering chemical compounds on the basis of multiple dimensions—structural similarity, binding profiles and their network effects across pathways and molecular interaction maps—to generate testable hypotheses on the pharmacological landscapes as well as identify potential mechanisms of efficacy on phenomenological processes. Further, we elucidate the application of the pipeline on a screen of anti-ageing-related compounds to cluster the candidates based on their structure, docking profile and network effects on fundamental metabolic/molecular pathways associated with the cell vitality, highlighting emergent insights on compounds activities based on the multi-dimensional deep screen pipeline.

scholarly journals A mm-Sized Free-Floating Wireless Implantable Opto-Electro Stimulation Device

Micromachines ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 621
Author(s):  
Yaoyao Jia ◽  
Yan Gong ◽  
Arthur Weber ◽  
Wen Li ◽  
Maysam Ghovanloo
Keyword(s):  
Electrical Stimulation ◽  
Large Scale ◽  
Electrode Array ◽  
Cmos Process ◽  
Optical Stimulation ◽  
In Vivo Experiments ◽  
Stimulation Mode ◽  
Shift Keying ◽  
On Chip

Towards a distributed neural interface, consisting of multiple miniaturized implants, for interfacing with large-scale neuronal ensembles over large brain areas, this paper presents a mm-sized free-floating wirelessly-powered implantable opto-electro stimulation (FF-WIOS2) device equipped with 16-ch optical and 4-ch electrical stimulation for reconfigurable neuromodulation. The FF-WIOS2 is wirelessly powered and controlled through a 3-coil inductive link at 60 MHz. The FF-WIOS2 receives stimulation parameters via on-off keying (OOK) while sending its rectified voltage information to an external headstage for closed-loop power control (CLPC) via load-shift-keying (LSK). The FF-WIOS2 system-on-chip (SoC), fabricated in a 0.35-µm standard CMOS process, employs switched-capacitor-based stimulation (SCS) architecture to provide large instantaneous current needed for surpassing the optical stimulation threshold. The SCS charger charges an off-chip capacitor up to 5 V at 37% efficiency. At the onset of stimulation, the capacitor delivers charge with peak current in 1.7–12 mA range to a micro-LED (µLED) array for optical stimulation or 100–700 μA range to a micro-electrode array (MEA) for biphasic electrical stimulation. Active and passive charge balancing circuits are activated in electrical stimulation mode to ensure stimulation safety. In vivo experiments conducted on three anesthetized rats verified the efficacy of the two stimulation mechanisms. The proposed FF-WIOS2 is potentially a reconfigurable tool for performing untethered neuromodulation.

Deep Learning in Drug Target Interaction Prediction: Current and Future Perspective

2020 ◽  
Vol 27 ◽  
Author(s):  
Karim Abbasi ◽  
Parvin Razzaghi ◽  
Antti Poso ◽  
Saber Ghanbari-Ara ◽  
Ali Masoudi-Nejad
Keyword(s):  
Deep Learning ◽  
Drug Target ◽  
Large Scale ◽  
Future Perspective ◽  
Multiple Perspectives ◽  
Comprehensive Overview ◽  
In Vivo Experiments ◽  
Drug Compound

Drug-target Interactions (DTIs) prediction plays a central role in drug discovery. Computational methods in DTIs prediction have gotten more attention because carrying out in vitro and in vivo experiments on a large scale is costly and time-consuming. Machine learning methods, especially deep learning, are widely applied to DTIs prediction. In this study, the main goal is to provide a comprehensive overview of deep learning-based DTIs prediction approaches. Here, we investigate the existing approaches from multiple perspectives. We explore these approaches to find out which deep network architectures are utilized to extract features from drug compound and protein sequences. Also, the advantages and limitations of each architecture are analyzed and compared. Moreover, we explore the process of how to combine descriptors for drug and protein features. Likewise, a list of datasets that are commonly used in DTIs prediction is investigated. Finally, current challenges are discussed and a short future outlook of deep learning in DTI prediction is given.

Potential Papain-like Protease Inhibitors against COVID-19: A Comprehensive In Silico Based Review

2021 ◽  
Vol 25 ◽  
Author(s):  
Neetu Agrawal ◽  
Shilpi Pathak ◽  
Ahsas Goyal
Keyword(s):  
In Silico ◽  
Chemical Compounds ◽  
Potential Candidate ◽  
In Vivo Experiments ◽  
Drug Databases ◽  
In Silico Studies ◽  
Approved Drugs ◽  
Fda Approved Drugs

: The entire world has been in a battle against the COVID-19 pandemic since its first appearance in December 2019. Thus researchers are desperately working to find an effective and safe therapeutic agent for its treatment. The multifunctional coronavirus enzyme papain-like protease (PLpro) is a potential target for drug discovery to combat the ongoing pandemic responsible for cleavage of the polypeptide, deISGylation, and suppression of host immune response. The present review collates the in silico studies performed on various FDA-approved drugs, chemical compounds, and phytochemicals from various drug databases and represents the compounds possessing the potential to inhibit PLpro. Thus this review can provide quick access to a potential candidate to medicinal chemists to perform in vitro and in vivo experiments who are thriving to find the effective agents for the treatment of COVID-19.

scholarly journals Hypoglycemic and Anti-Inflammatory Effects of Triterpene Glycoside Fractions from Aeculus hippocastanum Seeds

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3784
Author(s):  
Avez Sharipov ◽  
Khurshid Tursunov ◽  
Sunnatullo Fazliev ◽  
Bahtigul Azimova ◽  
Jamoliddin Razzokov
Keyword(s):  
Triterpene Glycoside ◽  
Biomedical Applications ◽  
Chemical Compounds ◽  
Chemical Components ◽  
Horse Chestnut ◽  
Pharmaceutical Drugs ◽  
Triterpene Saponins ◽  
In Vivo Experiments ◽  
Anti Inflammatory

Horse chestnut (Aesculus hippocastanum L.)-derived drugs have shown their potential in biomedical applications. The seed of A. hippocastanum contains various kinds of chemical compounds including phenolics, flavonoids, coumarins, and triterpene saponins. Here, we investigated the chemical components in A. hippocastanum L. grown in Uzbekistan, which has not yet been studied in detail. We identified 30 kinds of triterpene saponins in an extract of A. hippocastanum L. Classifying extracted saponins into eight fractions, we next studied the hypoglycemic and the anti-inflammatory activities of escin and its derivatives through in vivo experiments. We came by data indicating the highest (SF-1 and SF-2) and the lowest (SF-5 and SF-8) antidiabetic and anti-inflammatory effects of those eight fractions. These results imply the prospective use of A. hippocastanum L. grown in Uzbekistan in the production of pharmaceutical drugs to treat diabetes and inflammation.

scholarly journals Development of an Oral Salmonella-Based Vaccine Platform against SARS-CoV-2

Vaccines ◽  
2022 ◽  
Vol 10 (1) ◽  
pp. 67
Author(s):  
Wonsuck Yoon ◽  
Yongsung Park ◽  
Seunghyun Kim ◽  
Iel Soo Bang
Keyword(s):  
Large Scale ◽  
Vaccine Development ◽  
Oral Vaccine ◽  
Oral Bacteria ◽  
Expression Vectors ◽  
Effective Vaccine ◽  
Vaccine Platform ◽  
In Vivo Experiments

Effective vaccine development for global outbreaks, such as the coronavirus disease 2019 (COVID-19), has been successful in the short run. However, the currently available vaccines have been associated with a higher frequency of adverse effects compared with other general vaccines. In this study, the possibility of an oral bacteria-based vaccine that can be safely used as a platform for large-scale, long-term immunization was evaluated. A well-known Salmonella strain that was previously considered as a vaccine delivery candidate was used. Recombinant Salmonella cells expressing engineered viral proteins related with COVID-19 pathogenesis were engineered, and the formulation of the oral vaccine candidate strain was evaluated by in vitro and in vivo experiments. First, engineered S proteins were synthesized and cloned into expression vectors, which were than transformed into Salmonella cells. In addition, when orally administrated to mice, the vaccine promoted antigen-specific antibody production and cellular immunity was induced with no significant toxicity effects. These results suggest that Salmonella strains may represent a valuable platform for the development of an oral vaccine for COVID-19 as an alternative to tackle the outbreak of various mutated coronavirus strains and new infectious diseases in the future.

scholarly journals The ectodomains determine ligand function in vivo and selectivity of DLL1 and DLL4 toward NOTCH1 and NOTCH2 in vitro

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Lena Tveriakhina ◽  
Karin Schuster-Gossler ◽  
Sanchez M Jarrett ◽  
Marie B Andrawes ◽  
Meike Rohrbach ◽  
...  
Keyword(s):  
Functional Divergence ◽  
Structural Similarity ◽  
In Vivo Experiments ◽  
Binding Interface ◽  
Functional Differences ◽  
High Structural Similarity ◽  
Selective Ligand ◽  
Notch Ligands

DLL1 and DLL4 are Notch ligands with high structural similarity but context-dependent functional differences. Here, we analyze their functional divergence using cellular co-culture assays, biochemical studies, and in vivo experiments. DLL1 and DLL4 activate NOTCH1 and NOTCH2 differently in cell-based assays and this discriminating potential lies in the region between the N-terminus and EGF repeat three. Mice expressing chimeric ligands indicate that the ectodomains dictate ligand function during somitogenesis, and that during myogenesis even regions C-terminal to EGF3 are interchangeable. Substitution of NOTCH1-interface residues in the MNNL and DSL domains of DLL1 with the corresponding amino acids of DLL4, however, does not disrupt DLL1 function in vivo. Collectively, our data show that DLL4 preferentially activates NOTCH1 over NOTCH2, whereas DLL1 is equally effective in activating NOTCH1 and NOTCH2, establishing that the ectodomains dictate selective ligand function in vivo, and that features outside the known binding interface contribute to their differences.

scholarly journals Poly-L-lysine as an Effective and Safe Desquamation Inducer of Urinary Bladder Epithelium

Polymers ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 1506 ◽  
Author(s):  
Mojca Kerec Kos ◽  
Peter Veranič ◽  
Andreja Erman
Keyword(s):  
Urinary Bladder ◽  
Large Scale ◽  
Structural Changes ◽  
Structural Integrity ◽  
Ex Vivo ◽  
Urothelial Cells ◽  
Bladder Epithelium ◽  
Epithelial Regeneration ◽  
In Vivo Experiments

Induced desquamation of urinary bladder epithelial cells, also called urothelial cells, is frequently used in studies of bladder epithelial regeneration and also in treating recurrent bacterial cystitis. Positively charged polymer chitosan is known to cause large-scale desquamation of terminally differentiated urothelial cells called umbrella cells. Aiming to compare the desquamation ability of another polycation poly-L-lysine, we studied the effect of this polymer on the functional and structural integrity of the urothelium in ex vivo and in vivo experiments. The urothelium was analyzed by measuring transepithelial electrical resistance, and the structural changes of its luminal surface were analyzed with scanning electron microscopy. The results revealed a selective and concentration-dependent desquamation effect of poly-L-lysine on superficial urothelial cells followed by quick regeneration of the urothelium, which functionally and structurally recovers in 2 to 3 h after poly-L-lysine–induced injury. Poly-L-lysine was thus proven to be a promising polymer to be used when desquamation of urothelial cells is required in basic and potentially clinical studies.

Purification of the Antihemophilic Factor by Gel Filtration on Agarose

1969 ◽  
Vol 22 (03) ◽  
pp. 577-583 ◽  
Author(s):  
M.M.P Paulssen ◽  
A.C.M.G.B Wouterlood ◽  
H.L.M.A Scheffers
Keyword(s):  
Factor Viii ◽  
Plasma Proteins ◽  
Large Scale ◽  
Gel Filtration ◽  
Large Scale Preparation ◽  
Scale Preparation ◽  
Antihemophilic Factor

SummaryFactor VIII can be isolated from plasma proteins, including fibrinogen by chromatography on agarose. The best results were obtained with Sepharose 6B. Large scale preparation is also possible when cryoprecipitate is separated by chromatography. In most fractions containing factor VIII a turbidity is observed which may be due to the presence of chylomicrons.The purified factor VIII was active in vivo as well as in vitro.

The Effect of Active Site-inhibited Factor VIIa on Tissue Factor-initiated Coagulation Using Platelets before and after Aspirin Administration

1997 ◽  
Vol 78 (04) ◽  
pp. 1202-1208 ◽  
Author(s):  
Marianne Kjalke ◽  
Julie A Oliver ◽  
Dougald M Monroe ◽  
Maureane Hoffman ◽  
Mirella Ezban ◽  
...  
Keyword(s):  
Tissue Factor ◽  
Active Site ◽  
Large Scale ◽  
Thrombin Generation ◽  
Factor Viia ◽  
Dependent Manner ◽  
Antithrombotic Agent ◽  
Before And After ◽  
Ic50 Values

SummaryActive site-inactivated factor VIIa has potential as an antithrombotic agent. The effects of D-Phe-L-Phe-L-Arg-chloromethyl ketone-treated factor VIla (FFR-FVIIa) were evaluated in a cell-based system mimicking in vivo initiation of coagulation. FFR-FVIIa inhibited platelet activation (as measured by expression of P-selectin) and subsequent large-scale thrombin generation in a dose-dependent manner with IC50 values of 1.4 ± 0.8 nM (n = 8) and 0.9 ± 0.7 nM (n = 7), respectively. Kd for factor VIIa binding to monocytes ki for FFR-FVIIa competing with factor VIIa were similar (11.4 ± 0.8 pM and 10.6 ± 1.1 pM, respectively), showing that FFR-FVIIa binds to tissue factor in the tenase complex with the same affinity as factor VIIa. Using platelets from volunteers before and after ingestion of aspirin (1.3 g), there were no significant differences in the IC50 values of FFR-FVIIa [after aspirin ingestion, the IC50 values were 1.7 ± 0.9 nM (n = 8) for P-selectin expression, p = 0.37, and 1.4 ± 1.3 nM (n = 7) for thrombin generation, p = 0.38]. This shows that aspirin treatment of platelets does not influence the inhibition of tissue factor-initiated coagulation by FFR-FVIIa, probably because thrombin activation of platelets is not entirely dependent upon expression of thromboxane A2.

Sign in / Sign up

Export Citation Format

Share Document