Rearrangement of vinyl allene oxide geometric isomers to cyclopentenones. Further computational insights with biologically relevant model systems

2017 ◽  
Vol 15 (13) ◽  
pp. 2846-2855 ◽  
Author(s):  
Adán B. González-Pérez ◽  
Alexander Grechkin ◽  
Ángel R. de Lera
Keyword(s):  
Computational Study ◽  
Model Systems ◽  
Allene Oxide ◽  
Geometric Isomers ◽  
Relevant Model ◽  
Biologically Relevant ◽  
Biological Relevance ◽  
Naturally Occurring ◽  
Allene Oxides

A computational study of the rearrangement of vinyl allene oxides of biological relevance, which include alkyl (methyl, propyl) or unsaturated groups (allyl, crotyl) attached to the Csp3 atom has revealed interesting insights into the formation of naturally occurring cyclopentenones.

scholarly journals Organoids in image-based phenotypic chemical screens

2021 ◽  
Author(s):  
Ilya Lukonin ◽  
Marietta Zinner ◽  
Prisca Liberali
Keyword(s):  
Small Molecule ◽  
High Throughput ◽  
Model Systems ◽  
High Content Screening ◽  
Phenotypic Screening ◽  
Relevant Model ◽  
Practical Advice ◽  
Biologically Relevant ◽  
Technical Advances ◽  
Cells Cultured

AbstractImage-based phenotypic screening relies on the extraction of multivariate information from cells cultured under a large variety of conditions. Technical advances in high-throughput microscopy enable screening in increasingly complex and biologically relevant model systems. To this end, organoids hold great potential for high-content screening because they recapitulate many aspects of parent tissues and can be derived from patient material. However, screening is substantially more difficult in organoids than in classical cell lines from both technical and analytical standpoints. In this review, we present an overview of studies employing organoids for screening applications. We discuss the promises and challenges of small-molecule treatments in organoids and give practical advice on designing, running, and analyzing high-content organoid-based phenotypic screens.

A unifying mechanism for the rearrangement of vinyl allene oxide geometric isomers to cyclopentenones

2014 ◽  
Vol 12 (39) ◽  
pp. 7694-7701 ◽  
Author(s):  
Adán B. González-Pérez ◽  
Alexander Grechkin ◽  
Ángel R. de Lera
Keyword(s):  
High Fidelity ◽  
Allene Oxide ◽  
Geometric Isomers ◽  
Allene Oxides

Z-Vinyl allene oxides are predicted to rearrange with high fidelity to stereodefined cyclopentenones through intermediate cyclopropanones.

On the Rearrangements of Biologically-Relevant Vinyl Allene Oxides to cis-Cyclopentenones, Ketols, Cyclopropylcarbinols and Favorskii-type Carboxylic Acids

2021 ◽  
Author(s):  
Pedro Villar ◽  
Alexander Grechkin ◽  
Adán B Gónzalez Pérez ◽  
Angel R. de LERA
Keyword(s):  
Carboxylic Acids ◽  
Biologically Relevant ◽  
Dft Computations ◽  
Naturally Occurring ◽  
Allene Oxides ◽  
Acetic Acids

In addition to stereodefined cis-cyclopentenones, the rearrangement of naturally-occurring vinyl allene oxides can provide ketols, cyclopropylcarbinols, and Favorskii-type bis-(Z)-but-2-en-1-yl acetic acids. These processes have been studied by DFT computations using...

scholarly journals Regulation of Cytochrome c Oxidase by Natural Compounds Resveratrol, (–)-Epicatechin, and Betaine

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1346
Author(s):  
Icksoo Lee
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Model Systems ◽  
Health Improvement ◽  
Published Data ◽  
Mitochondrial Electron Transport Chain ◽  
Naturally Occurring ◽  
Transport Chain ◽  
Wide Range ◽  
Experimental Model Systems

Numerous naturally occurring molecules have been studied for their beneficial health effects. Many compounds have received considerable attention for their potential medical uses. Among them, several substances have been found to improve mitochondrial function. This review focuses on resveratrol, (–)-epicatechin, and betaine and summarizes the published data pertaining to their effects on cytochrome c oxidase (COX) which is the terminal enzyme of the mitochondrial electron transport chain and is considered to play an important role in the regulation of mitochondrial respiration. In a variety of experimental model systems, these compounds have been shown to improve mitochondrial biogenesis in addition to increased COX amount and/or its enzymatic activity. Given that they are inexpensive, safe in a wide range of concentrations, and effectively improve mitochondrial and COX function, these compounds could be attractive enough for possible therapeutic or health improvement strategies.

scholarly journals Photoprotective Properties of Eumelanin: Computational Insights into the Photophysics of a Catechol:Quinone Heterodimer Model System

Photochem ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 26-37
Author(s):  
Victoria C. Frederick ◽  
Thomas A. Ashy ◽  
Barbara Marchetti ◽  
Michael N. R. Ashfold ◽  
Tolga N. V. Karsili
Keyword(s):  
Ground State ◽  
Sandwich Structure ◽  
Computational Study ◽  
Minimum Energy ◽  
Carbonyl Oxygen ◽  
Model System ◽  
Molecular Structures ◽  
Uv Damage ◽  
Chromosomal Dna ◽  
Relevant Model

Melanins are skin-centered molecular structures that block harmful UV radiation from the sun and help protect chromosomal DNA from UV damage. Understanding the photodynamics of the chromophores that make up eumelanin is therefore paramount. This manuscript presents a multi-reference computational study of the mechanisms responsible for the experimentally observed photostability of a melanin-relevant model heterodimer comprising a catechol (C)–benzoquinone (Q) pair. The present results validate a recently proposed photoinduced intermolecular transfer of an H atom from an OH moiety of C to a carbonyl-oxygen atom of the Q. Photoexcitation of the ground state C:Q heterodimer (which has a π-stacked “sandwich” structure) results in population of a locally excited ππ* state (on Q), which develops increasing charge-transfer (biradical) character as it evolves to a “hinged” minimum energy geometry and drives proton transfer (i.e., net H atom transfer) from C to Q. The study provides further insights into excited state decay mechanisms that could contribute to the photostability afforded by the bulk polymeric structure of eumelanin.

scholarly journals Single amino acid mutations effect Zika virus replication in vitro and virulence in vivo

2020 ◽  
Author(s):  
Nicole M. Collette ◽  
Victoria H.I. Lao ◽  
Dina R. Weilhammer ◽  
Barbara Zingg ◽  
Shoshana D. Cohen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Zika Virus ◽  
Model Systems ◽  
Single Amino Acid ◽  
Replication Rate ◽  
Adult Mice ◽  
Naturally Occurring ◽  
Viral Virulence

AbstractThe 2014-2016 Zika virus (ZIKV) epidemic in the Americas resulted in large deposits of next-generation sequencing data from clinical samples. This resource was mined to identify emerging mutations and trends in mutations as the outbreak progressed over time. Information on transmission dynamics, prevalence and persistence of intra-host mutants, and the position of a mutation on a protein were then used to prioritize 544 reported mutations based on their ability to impact ZIKV phenotype. Using this criteria, six mutants (representing naturally occurring mutations) were generated as synthetic infectious clones using a 2015 Puerto Rican epidemic strain PRVABC59 as the parental backbone. The phenotypes of these naturally occurring variants were examined using both cell culture and murine model systems. Mutants had distinct phenotypes, including changes in replication rate, embryo death, and decreased head size. In particular, a NS2B mutant previously detected during in vivo studies in rhesus macaques was found to cause lethal infections in adult mice, abortions in pregnant females, and increased viral genome copies in both brain tissue and blood of female mice. Additionally, mutants with changes in the region of NS3 that interfaces with NS5 during replication displayed reduced replication in the blood of adult mice. This analytical pathway, integrating both bioinformatic and wet lab experiments, provides a foundation for understanding how naturally occurring single mutations affect disease outcome and can be used to predict the of severity of future ZIKV outbreaks.Author summaryTo determine if naturally occurring individual mutations in the Zika virus epidemic genotype effect viral virulence or replication rate in vitro or in vivo, we generated an infectious clone representing the epidemic genotype of stain Puerto Rico, 2015. Using this clone, six mutants were created by changing nucleotides in the genome to cause one to two amino acid substitutions in the encoded proteins. The six mutants we generated represent mutations that differentiated the early epidemic genotype from genotypes that were either ancestral or that occurred later in the epidemic. We assayed each mutant for changes in growth rate, and for virulence in adult mice and pregnant mice. Three of the mutants caused catastrophic embryo effects including increased embryonic death or significant decrease in head diameter. Three other mutants that had mutations in a genome region associated with replication resulted in changes in in vitro and in vivo replication rates. These results illustrate the potential impact of individual mutations in viral phenotype.

scholarly journals Crystallographic and computational study of t-butyl N-[3-hydroxy-1-phenyl-4-(pyridin- 2-ylsulfanyl)butan-2-yl]carbamate and its pyrimidin-2-yl analogue

2016 ◽  
Vol 231 (11) ◽  
Author(s):  
Walcimar T. Vellasco Junior ◽  
Claudia R.B. Gomes ◽  
Thatyana R.A. Vasconcelos ◽  
James L. Wardell ◽  
Alberto Otero-de-la-Roza ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Analysis ◽  
Title Compound ◽  
Computational Study ◽  
Crystal Structure Analysis ◽  
Biologically Relevant

AbstractThe crystal structure analysis of the biologically-relevant title compound (

scholarly journals A computational study on how structure influences the optical properties in model crystal structures of amyloid fibrils

2017 ◽  
Vol 19 (5) ◽  
pp. 4030-4040 ◽  
Author(s):  
Luca Grisanti ◽  
Dorothea Pinotsi ◽  
Ralph Gebauer ◽  
Gabriele S. Kaminski Schierle ◽  
Ali A. Hassanali
Keyword(s):  
Optical Properties ◽  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Crystal Structures ◽  
Amyloid Fibrils ◽  
Computational Study ◽  
Model Systems ◽  
Hydrogen Bonding Interactions ◽  
Model Crystal ◽  
Different Types

Different types of hydrogen bonding interactions that occur in amyloids model systems and molecular factors that control the susceptibility of the protons to undergo proton transfer and how this couples to the optical properties.

scholarly journals N6-Furfuryladenine is protective in Huntington’s disease models by signaling huntingtin phosphorylation

2018 ◽  
Vol 115 (30) ◽  
pp. E7081-E7090 ◽  
Author(s):  
Laura E. Bowie ◽  
Tamara Maiuri ◽  
Melanie Alpaugh ◽  
Michelle Gabriel ◽  
Nicolas Arbez ◽  
...  
Keyword(s):  
Dna Damage ◽  
Huntington's Disease ◽  
Huntington’S Disease ◽  
Oxidative Dna Damage ◽  
Model Systems ◽  
Protective Effects ◽  
Mutant Huntingtin ◽  
Naturally Occurring ◽  
Phosphate Donor ◽  
High Content Analysis

The huntingtin N17 domain is a modulator of mutant huntingtin toxicity and is hypophosphorylated in Huntington’s disease (HD). We conducted high-content analysis to find compounds that could restore N17 phosphorylation. One lead compound from this screen was N6-furfuryladenine (N6FFA). N6FFA was protective in HD model neurons, and N6FFA treatment of an HD mouse model corrects HD phenotypes and eliminates cortical mutant huntingtin inclusions. We show that N6FFA restores N17 phosphorylation levels by being salvaged to a triphosphate form by adenine phosphoribosyltransferase (APRT) and used as a phosphate donor by casein kinase 2 (CK2). N6FFA is a naturally occurring product of oxidative DNA damage. Phosphorylated huntingtin functionally redistributes and colocalizes with CK2, APRT, and N6FFA DNA adducts at sites of induced DNA damage. We present a model in which this natural product compound is salvaged to provide a triphosphate substrate to signal huntingtin phosphorylation via CK2 during low-ATP stress under conditions of DNA damage, with protective effects in HD model systems.

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