Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Routescore: Punching the Ticket to More Efficient Materials Development.

ABSTRACT: Self-driving laboratories, in the form of automated experimentation platforms guided by machine learning algorithms, have emerged as a potential solution to the need for accelerated science. While new tools for automated analysis and characterization are being developed at a steady rate, automated synthesis remains the bottleneck in the chemical space accessible to self-driving laboratories. Combining automated and manual synthesis efforts immediately significantly expands the explorable chemical space. To effectively direct the different capabilities of automated (higher throughput and less labor) and manual synthesis (greater chemical versatility), we describe a protocol, the RouteScore, that quantifies the cost of combined synthetic routes. In this work, the RouteScore is used to determine the most efficient synthetic route to a well-known pharmaceutical (structure-oriented optimization) and to simulate a self-driving laboratory that finds the most easily synthesizable organic laser molecule with specific photophysical properties from a space of ∼3500 possible molecules (property-oriented optimization). These two examples demonstrate the power and flexibility of our approach in mixed synthetic planning and optimization and especially in downselecting promising candidates from a large chemical space via an a priori estimation of the synthetic costs.

SUBMITTER: Seifrid M

PROVIDER: S-EPMC8796309 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Development of noncytotoxic chitosan-gold nanocomposites as efficient antibacterial materials.

Project description:This work describes the synthesis and characterization of noncytotoxic nanocomposites either colloidal or as films exhibiting high antibacterial activity. The biocompatible and biodegradable polymer chitosan was used as reducing and stabilizing agent for the synthesis of gold nanoparticles embedded in it. Herein, for the first time, three different chitosan grades varying in the average molecular weight and deacetylation degree (DD) were used with an optimized gold precursor concentration. Several factors were analyzed in order to obtain antimicrobial but not cytotoxic nanocomposite materials. Films based on chitosan with medium molecular weight and the highest DD exhibited the highest antibacterial activity against biofilm forming strains of Staphylococcus aureus and Pseudomonas aeruginosa. The resulting nanocomposites did not show any cytotoxicity against mammalian somatic and tumoral cells. They produced a disruptive effect on the bacteria wall while their internalization was hindered on the eukaryotic cells. This selectivity and safety make them potentially applicable as antimicrobial coatings in the biomedical field.

| S-EPMC4326049 | biostudies-literature

More than just a ticket canceller: the mitochondrial processing peptidase tailors complex precursor proteins at internal cleavage sites.

Project description:Most mitochondrial proteins are synthesized as precursors that carry N-terminal presequences. After they are imported into mitochondria, these targeting signals are cleaved off by the mitochondrial processing peptidase (MPP). Using the mitochondrial tandem protein Arg5,6 as a model substrate, we demonstrate that MPP has an additional role in preprotein maturation, beyond the removal of presequences. Arg5,6 is synthesized as a polyprotein precursor that is imported into mitochondria and subsequently separated into two distinct enzymes. This internal processing is performed by MPP, which cleaves the Arg5,6 precursor at its N-terminus and at an internal site. The peculiar organization of Arg5,6 is conserved across fungi and reflects the polycistronic arginine operon in prokaryotes. MPP cleavage sites are also present in other mitochondrial fusion proteins from fungi, plants, and animals. Hence, besides its role as a "ticket canceller" for removal of presequences, MPP exhibits a second conserved activity as an internal processing peptidase for complex mitochondrial precursor proteins.

| S-EPMC8734313 | biostudies-literature

Mechanism of a prototypical synthetic membrane-active antimicrobial: Efficient hole-punching via interaction with negative intrinsic curvature lipids.

Project description:Phenylene ethynylenes comprise a prototypical class of synthetic antimicrobial compounds that mimic antimicrobial peptides produced by eukaryotes and have broad-spectrum antimicrobial activity. We show unambiguously that bacterial membrane permeation by these antimicrobials depends on the presence of negative intrinsic curvature lipids, such as phosphatidylethanolamine (PE) lipids, found in high concentrations within bacterial membranes. Plate-killing assays indicate that a PE-knockout mutant strain of Escherichia coli drastically out-survives the wild type against the membrane-active phenylene ethynylene antimicrobials, whereas the opposite is true when challenged with traditional metabolic antibiotics. That the PE deletion is a lethal mutation in normative environments suggests that resistant bacterial strains do not evolve because a lethal mutation is required to gain immunity. PE lipids allow efficient generation of negative curvature required for the circumferential barrel of an induced membrane pore; an inverted hexagonal H(II) phase, which consists of arrays of water channels, is induced by a small number of antimicrobial molecules. The estimated antimicrobial occupation in these water channels is nonlinear and jumps from approximately 1 to 3 per 4 nm of induced water channel length as the global antimicrobial concentration is increased. By comparing to exactly solvable 1D spin models for magnetic systems, we quantify the cooperativity of these antimicrobials.

| S-EPMC2634941 | biostudies-literature

Efficient Triazine Derivatives for Collagenous Materials Stabilization.

Project description:Nowadays, the need to reduce plastic waste and scantly biodegradable fossil-based products is of great importance. The use of leather as an alternative to synthetic materials is gaining renewed interest, but it is fundamental that any alternative to plastic-based materials should not generate an additional environmental burden. In the present work, a simple protocol for collagen stabilization mediated by 2-chloro-4,6-diethoxy-1,3,5-triazine (CDET) and a tert-amine has been described. Different tert-amines were tested in combination with CDET in a standard amidation reaction between 2-phenylethylamine and benzoic acid. Best performing condensation systems have been further tested for the cross-linking of both collagen powder and calf hides. The best results were achieved with CDET/NMM giving high-quality leather with improved environmental performances.

| S-EPMC8200008 | biostudies-literature

Development of Efficient One-Pot Methods for the Synthesis of Luminescent Dyes and Sol-Gel Hybrid Materials.

Project description:This paper presents a comparison of the simultaneous preparation of di-O-alkylated and ether-ester derivatives of fluorescein using different methods (conventional or microwave heating). Shortening of the reaction time and increased efficiency were observed when using a microwave reactor. Moreover, described here for the first time is the application of a fast, simple, and eco-friendly ball-assisted method to exclusively obtain ether-ester derivatives. We also demonstrate that fluorescein can be effectively functionalized by O-alkylation carried out under microwave or ball-milling conditions, saving time and energy and affording the desired products with good yields and minimal byproduct formation. All the synthesized products as well as pH-dependent (prototropic) forms trapped in the SiO2 matrix were examined using UV-Vis and fluorescence spectroscopy.

| S-EPMC8746091 | biostudies-literature

Efficient prion disease transmission through common environmental materials.

Project description:Prion diseases are a group of fatal neurodegenerative diseases associated with a protein-based infectious agent, termed prion. Compelling evidence suggests that natural transmission of prion diseases is mediated by environmental contamination with infectious prions. We hypothesized that several natural and man-made materials, commonly found in the environments of wild and captive animals, can bind prions and may act as vectors for disease transmission. To test our hypothesis, we exposed surfaces composed of various common environmental materials (i.e. wood, rocks, plastic, glass, cement, stainless steel, aluminum, and brass) to hamster-adapted 263K scrapie prions and studied their attachment and retention of infectivity in vitro and in vivo Our results indicated that these surfaces, with the sole exception of brass, efficiently bind, retain, and release prions. Prion replication was studied in vitro using the protein misfolding cyclic amplification technology, and infectivity of surface-bound prions was analyzed by intracerebrally challenging hamsters with contaminated implants. Our results revealed that virtually all prion-contaminated materials transmitted the disease at high rates. To investigate a more natural form of exposure to environmental contamination, we simply housed animals with large contaminated spheres made of the different materials under study. Strikingly, most of the hamsters developed classical clinical signs of prion disease and typical disease-associated brain changes. Our findings suggest that prion contamination of surfaces commonly present in the environment can be a source of disease transmission, thus expanding our understanding of the mechanisms for prion spreading in nature.

| S-EPMC5836136 | biostudies-literature

Ticket to divide: m6A reader YTHDC1 drives acute myeloid leukemia proliferation.

Project description: Not available

| S-EPMC8718629 | biostudies-literature

Efficient Persistent Luminescence Tuning Using a Cyclodextrin Inclusion Complex as Efficient Light Conversion Materials.

Project description:Developing an appropriate method to broaden the color of long persistent luminescence materials has important scientific significance and practical value but remains a great challenge. Herein, we have developed a unique strategy to fine-tune the persistent luminescence using the inclusion complex of rhodamine 6G with (2-hydroxypropyl)-β-cyclodextrin as efficient light conversion materials. The emitting color of the novel persistent luminescence material could be tuned from green to orange by changing the concentration of the light conversion agent. Furthermore, afterglow decay measurements showed that the initial afterglow brightness is 9.65 cd/m2, and the initial afterglow brightness gradually decreased as the cyclodextrin inclusion compound coating increased. This design concept introduces a new perspective for broadening the luminescence color of afterglow phosphors, which may open up new opportunities for persistent luminescence materials toward many emerging applications.

| S-EPMC8495874 | biostudies-literature

Efficient strain modulation of 2D materials via polymer encapsulation.

Project description:Strain engineering is a promising method to manipulate the electronic and optical properties of two-dimensional (2D) materials. However, with weak van der Waals interaction, severe slippage between 2D material and substrate could dominate the bending or stretching processes, leading to inefficiency strain transfer. To overcome this limitation, we report a simple strain engineering method by encapsulating the monolayer 2D material in the flexible PVA substrate through spin-coating approach. The strong interaction force between spin-coated PVA and 2D material ensures the mechanical strain can be effectively transferred with negligible slippage or decoupling. By applying uniaxial strain to monolayer MoS2, we observe a higher bandgap modulation up to ~300?meV and a highest modulation rate of ~136?meV/%, which is approximate two times improvement compared to previous results achieved. Moreover, this simple strategy could be well extended to other 2D materials such as WS2 or WSe2, leading to enhanced bandgap modulation.

| S-EPMC7052151 | biostudies-literature

Ticagrelor - toward more efficient platelet inhibition and beyond.

Project description:Novel antiplatelet drugs, including ticagrelor, are being successively introduced into the therapy of atherothrombotic conditions due to their superiority over a standard combination of clopidogrel with acetylsalicylic acid in patients with acute coronary syndromes (ACS). A P2Y12 receptor antagonist, ticagrelor, is unique among antiplatelet drugs, because ticagrelor inhibits the platelet P2Y12 receptor in a reversible manner, and because it demonstrates a wide palette of advantageous pleiotropic effects associated with the increased concentration of adenosine. The pleiotropic effects of ticagrelor comprise cardioprotection, restoration of the myocardium after an ischemic event, promotion of the release of anticoagulative factors and, eventually, anti-inflammatory effects. Beyond the advantageous effects, the increased concentration of adenosine is responsible for some of ticagrelor's adverse effects, including dyspnea and bradycardia. Large-scale clinical trials demonstrated that both standard 12-month therapy and long-term use of ticagrelor reduce the risk of cardiovascular events in patients with ACS, but at the expense of a higher risk of major bleeding. Further trials focused on the use of ticagrelor in conditions other than ACS, including ischemic stroke, peripheral artery disease and status after coronary artery bypass grafting. The results of these trials suggest comparable efficacy and safety of ticagrelor and clopidogrel in extra-coronary indications, but firm conclusions are anticipated from currently ongoing studies. Here, we summarize current evidence on the superiority of ticagrelor over other P2Y12 antagonists in ACS, discuss the mechanism underlying the drug-drug interactions and pleiotropic effects of ticagrelor, and present future perspectives of non-coronary indications for ticagrelor.

| S-EPMC5775739 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data