Temperature dependence of dielectric properties of some biomolecules with and without irradiation.
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Acetylcholine↗
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FusionTarget: Computational framework for drug repurposing against modeled fusion protein structures from genomic breakpoints.
Many fusion genes have been recognized as biomarkers and therapeutic targets. However, the lack of knowledge on protein structures and targeting approaches made it challenging to develop effective targeting therapeutics. To fill this, we developed a computational pipeline, FusionTarget, which annotates the genomic DNA breakage to RNA and protein sequences, predicts the 3D structures of fusion proteins, and performs comparative virtual screening, comparative molecular dynamics simulation, and quantitative analyses to identify the fusion protein-selective small molecules by selecting drugs with consistent high-fold binding affinity between fusion and wild-type proteins in multiple isoforms. We applied our pipeline to EWSR1::FLI1 in Ewing sarcoma and KMT2A::AFF1 in infant acute lymphoblastic leukemia. Further cell assay experiments confirmed that cells expressing individual fusion genes were more sensitive to the suggested drugs, and the key downstream genes were affected by our drugs. FusionTarget provides a unique foundation for developing therapeutics targeting fusion proteins.
applied computing in medical science↗
RAD51 separation of function mutation disables replication fork maintenance but preserves DSB repair.
Homologous recombination (HR) protects replication forks (RFs) and repairs DNA double-strand breaks (DSBs). Within HR, BRCA2 regulates RAD51 via two interaction regions: the BRC repeats to form filaments on single-stranded DNA and exon 27 (Ex27) to stabilize the filament. Here, we identified a RAD51 S181P mutant that selectively disrupted the RAD51-Ex27 association while maintaining interaction with BRC repeat and proficiently forming filaments capable of DNA binding and strand invasion. Interestingly, RAD51 S181P was defective for RF protection/restart but proficient for DSB repair. Our data suggest that Ex27-mediated stabilization of RAD51 filaments is required for the protection of RFs, while it seems dispensable for the repair of DSBs.
Genetics↗
Conjecture on the role of dry charges in radiosensitization.
A model of cellular radiation damage that involves dry electrons and holes is proposed and the implications of this model to hypoxic radiosenstization are discussed. The transport and reaction properties of dry charges in the structured water surrounding polar biomolecules are considered and a solvation time of 600 picoseconds in this medium is derived. Pre-solvation charge migration, attachment and recombination and the relevance of these processes to sensitization are discussed. DNA damage by physico-chemical interactions with dry holes is proposed and is shown to be modified by oxygen and other electron affinic sensitizers.
DNA↗
Microalgae-Mediated Synthesis of Gold Nanoparticles from Indonesian Chlorella vulgaris InaCC M205 with Potential Anticancer Properties for Biomedical Application.
Sustainable nanomaterial synthesis has emerged as a critical strategy to reduce the environmental burden associated with conventional chemical synthesis method. Microalgae-derived biomolecules offer a promising platform for the green production of metal nanoparticles due to their rich bioactive compounds capable of acting as natural reducing and stabilizing agents. Here, we report the eco-friendly synthesis of gold nanoparticles (AuNPs) using extract of Indonesian microalga Chlorella vulgaris extract. To optimize the synthesis process, the effects of precursor-to-extract ratio, temperature, and incubation time were evaluated. Optimal synthesis of C5-AuNPs was obtained at 37 °C for 20 h with precursor to extract ratio of 6:4, resulting in moderately stable C5-AuNPs characterized by a surface plasmon resonance (SPR) peak at 541 nm. Furthermore, Fourier-transmission infra-red (FT-IR) analysis revealed the involvement of functional groups of C. vulgaris extract in the interaction with Au+ during the production of C5-AuNPs. Transmission electron microscopy (TEM) demonstrated the formation of uniformly spherical nanoparticles with an average diameter of approximately 8.8 nm. Biological evaluation showed that the synthesized C5-AuNPs exerted pronounced dose-dependent cytotoxicity against MCF-7 breast cancer cells with an IC50 threshold of 21.17 ppm, while no toxicity appears in normal HEK293 cells. Mechanistically, the C5-AuNPs induced early apoptosis and inhibit cell-cycle progression at the stage of G0/G1. Collectively, these findings demonstrate that C. vulgaris-mediated AuNPs represent a promising preliminary in vitro findings for cancer therapy candidate.
Gold↗
Tumor specimen cold ischemia time impacts molecular cancer drug target discovery.
Tumor tissue collections are used to uncover pathways associated with disease outcomes that can also serve as targets for cancer treatment, ideally by comparing the molecular properties of cancer tissues to matching normal tissues. The quality of such collections determines the value of the data and information generated from their analyses including expression and modifications of nucleic acids and proteins. These biomolecules are dysregulated upon ischemia and decompose once the living cells start to decay into inanimate matter. Therefore, ischemia time before final tissue preservation is the most important determinant of the quality of a tissue collection. Here we show the impact of ischemia time on tumor and matching adjacent normal tissue samples for mRNAs in 1664, proteins in 1818, and phosphosites in 1800 cases (tumor and matching normal samples) of four solid tumor types (CRC, HCC, LUAD, and LUSC NSCLC subtypes). In CRC, ischemia times exceeding 15 min impacted 12.5% (mRNA), 25% (protein), and 50% (phosphosites) of differentially expressed molecules in tumor versus normal tissues. This hypoxia- and decay-induced dysregulation increased with longer ischemia times and was observed across tumor types. Interestingly, the proteomics analysis revealed that specimen ischemia time above 15 min is mostly associated with a dysregulation of proteins in the immune-response pathway and less so with metabolic processes. We conclude that ischemia time is a crucial quality parameter for tissue collections used for target discovery and validation in cancer research.
Humans↗
A benchmarking study of feature screening approaches across type 1 diabetes omics studies classification settings.
In recent years, high dimensional omics analyses have become more commonplace for investigating complex biological systems. Typically, these studies attempt to identify key biomolecules associated with a particular biological process. Often, machine learning (ML) is used to identify these biomolecules, typically by learning which biomolecules are highly predictive of a treatment, biological outcome, or phenotype. A major challenge of applying ML to high throughput omics is overcoming noise when sample size is limited and unbalanced with respect to tens of thousands of biomolecules measured. Thus, feature selection (the process of reducing the number of predictors) is both a critical and common step in the ML analysis pipeline. While much attention has been given to embedding and wrapping techniques for feature selection in the omics space, filter-based methods for model-free feature selection have appealing theoretical properties. This manuscript evaluates sure screening, a class of filter-based feature selection methods which provide analytical guarantees for true feature set retention. Here, we cover existing feature screening methods based on the sure screening principal, available software, methods to improve feature screening, and contextualize feature screening in the larger discussion of feature selection for omics data analysis. Additionally, a suite of model-free sure screening approaches is applied and compared for several omics biomedical applications in a ML classification context. We identified BcorSIS as the most effective and computationally efficient screening method across various omics datasets, consistently outperforming others like CSIS and DCSIS in runtime.
Humans↗
Drug-biomolecule interactions: interactions of mononucleotides and polybasic amino acids.
Histones and ribosomal proteins are basic proteins that participate in gene regulation and protein synthesis, respectively. How these proteins interact with nucleic acids is not yet clear, although specificities in these interactions have been observed. Study of the interaction of mononucleotides with basic polyamino acids is one approach to understanding such interactions. The results of studies with the mononucleotides can help elucidate the normal molecular processes in biological systems and also shed light on some effects of drugs, such as puromycin and tubericidin, that are nucleotide derivatives. A review of studies on the interaction of mononucleotides and basic polyamino acids such as polylysine and polyarginine is presented. In addition, a short review of the self-associative properties of mononucleotides is given. Studies of the mononucleotide-polyamino acid interaction have involved a wide variety of techniques including equilibrium dialysis, NMR, optical rotatory dispersion, circular dichroism, and precipitate analysis.
Amino Acids↗
Micro- and nanoplastics-induced neurotoxicity: a CNS-centered, evidence-graded adverse outcome pathway framework based on systematic weight-of-evidence assessment.
Micro- and nanoplastics (MPs/NPs) are ubiquitous anthropogenic particulate pollutants posing emerging threats to human neurological health. Severe heterogeneity in particle physicochemical properties, environmental aging status, exposure paradigms and experimental platforms has created persistent mechanistic uncertainties in MP/NP neurotoxicology, hindering reliable hazard characterization and risk translation. Here, we systematically consolidate empirical toxicological evidence and construct a dedicated central nervous system (CNS)-targeted adverse outcome pathway (AOP) network integrated with rigorous weight-of-evidence (WoE) grading to elucidate the hierarchical, particle-specific toxic cascades underlying MP/NP-induced neural injury. Our synthesis overturns the conventional linear toxicity paradigm, demonstrating that MPs/NPs trigger neurotoxicity via a complex multi-input mechanistic network. We definitively establish oxidative stress as a robust early convergent key event-rather than a universal molecular initiating event-orchestrating ROS overproduction, lipid peroxidation, mitochondrial dysfunction, and neuroinflammation to propagate neuronal damage. This core module is driven by five distinct particulate upstream triggers: particle-biomolecule interfacial perturbation, corona-facilitated cellular internalization, plastic-associated chemical leaching, aging-derived free radical reactivity, and gut-borne systemic neurotoxic signaling. Downstream pathogenic outcomes encompass glial overactivation, neurotransmitter dyshomeostasis, autophagy-lysosome dysfunction, metabolic reprogramming, regulated neuronal cell death, and behavioral impairments. Tiered WoE analysis confirms strong validation for early oxidative/inflammatory cascades, moderate support for gut-brain axis crosstalk and intracellular trafficking disruption, and nascent evidence for synaptic dysfunction and neurodegeneration-linked proteostatic defects. Extrapolation to human health risk remains constrained by the frequent use of high-dose exposure paradigms, limited validated data on internal dosimetry in the human brain, discrepancies between effective concentrations in experimental models and environmentally relevant human tissue burdens, and insufficient causal validation of distal adverse outcomes. We highlight key research priorities including aged mixed-particle exposure systems, leachate-controlled assays, quantitative internal dose evaluation, and mechanistic intervention verification. This evidence-stratified AOP framework resolves longstanding mechanistic ambiguities in particulate neurotoxicity, providing a standardized, causality-based foundation for future mechanistic exploration and health risk assessment of global plastic pollution.
Adverse outcome pathway↗
Biological autoxidation. I. Decontrolled iron: an ultimate carcinogen and toxicant: an hypothesis.
Ionic iron at physiological pH hydrolyzes into insoluble aggregates, which disperse on slight acidification. Uncontrolled ionic iron promotes autoxidation, which crosslinks biomolecules and produces destructive activated oxygen. Defenses against autoxidative crosslinking include: 1. ferritin, the macromolecular scavenger of iron; 2. metabolic turnover, which prevents irreversible crosslinking through early catabolic degradation and replacement; and 3. enzymatic deactivation of oxygen. I am proposing that the anticrosslinking defenses are defeated by transient actions of metabolic perturbations, toxicants, oxidants and "foreign bodies", which cause oxidative crosslinking of proteins and lipids into irreversible tissue imprint: indigestible bodies containing porous limited-access spaces (LASs). The pores exclude the macromolecular ferritin and the digestive and antiautoxidation enzymes but admit ionic iron which, sheltered from ferritin, accumulates into decontrolled-iron pathogen (DIP). DIP utilizes the energy of ambient pH fluctuations to erupt from the LAS, swamp the available ferritin, poison the surroundings, catalyze autoxidation and crosslink cell components into additional LAS carriers. With time and sufficient promotion by pH fluctuations or metal-complexing agents, DIP and LAS expand. DIP injures through heavy-metal inhibition of life processes and catalysis of autoxidation. Typically, carcinogenic initiators are protein denaturants, cell poisons, "foreign bodies" and autoxidation catalysts. These are DIP-initiating properties, and DIP may be a preneoplastic stage of carcinogenesis. A DIP-model interpretation is given for the growth of asbestos bodies. DIP is an inorganic parasite. It may envelope and attack phagocytized particles.
Animals↗
Mass spectrometry-based top-down proteomics for proteoform profiling of protein coronas.
The protein corona is a layer of biomolecules-primarily proteins-that adsorbs to nanoparticle (NP) surfaces in biological fluids. If the purpose of the NP is therapeutic, this can have a profound effect on its biological activity and function in vivo. Protein corona formation can also be exploited for diagnostic purposes and to differentially enrich proteins for biomarker discovery. For all of these applications, it is useful to determine which proteins, and which specific proteoforms, bind to different types of NP. The traditional mass spectrometry (MS)-based bottom-up proteomics does not accurately identify specific proteoforms within the protein corona. This limitation impedes the nanomedicine field's ability to precisely predict the biological fate and pharmacokinetics of nanomedicines and their effectiveness in early-stage biomarker discovery and disease detection because many different proteoforms of the same gene could exist in the corona, and they have divergent biological functions. Here, we describe how to use capillary zone electrophoresis (CZE)-MS-based top-down proteomics to characterize the proteoform landscape of the protein corona. Our procedures detail the recovery of intact proteoforms from NP surfaces by using detergent-assisted proteoform elution and the measurement of these proteoforms by using CZE-tandem MS (MS/MS) and CZE-high-field asymmetric waveform ion mobility spectrometry (FAIMS)-MS/MS. The entire workflow is completed within 3-4 d. Using this protocol, hundreds of proteoforms from the protein corona of polystyrene NPs can be identified. Distinct protein corona proteoform profiles were observed from NPs with different physicochemical properties. The addition of FAIMS is beneficial for more in-depth proteoform characterization.
Proteomics↗
Drug-biomolecule interactions: interaction of gentamicin with lipid monomolecular films.
The interaction of gentamicin with monomolecular films of a series of biologically important lipids spread on an aqueous buffered subphase was studied. The surface pressure, pi, of these films was determined by the Wilhelmy plate method as a function of surface area, A, and pi-A curves were constructed. Changes in the pi-A characteristics in the presence of gentamicin were used as a measure of antibiotic-film interaction. No interaction was observed between gentamicin and films of cholesterol, egg lecithin, dipalmitoyl lecithin, phosphatidyl ethanolamine, stearyl alcohol, and bovine ceramides at all pH values studied. Stearic acid films showed no interaction with gentamicin at pH 5. At pH 7 and 8, a small increase in pressure (approximately 3 dynes/cm) was noted. A dramatic increase in surface pressure was observed in the presence of stearyl aldehyde films ranging from approximately 9 dynes/cm at pH 7,2 to 23 dynes/cm at pH 8.4. This effect was attributed to a Schiff-base reaction between the nonprotonated primary amino groups on the gentamicin molecule and the stearyl aldehyde. Further evidence was reported by the fact that the addition of glucose (which has been reported to participate in Schiff-base formation with amines) to the subphase inhibited the stearyl aldehyde-gentamicin interaction. Sucrose did not show a corresponding effect. The addition of sodium bisulfite, which reacts with aldehydes to form alpha-hydroxysulfonic acid, also inhibited the gentamicin-stearyl aldehyde interaction. It is postulated that Schiff-base formation is a step in the in vivo transport of gentamicin across the membrane of sensitive organisms.
Chemical Phenomena↗