Molecular Modeling Research Articles

An alternative conformation of the N-terminal loop of human dihydroorotate dehydrogenase drives binding to a potent antiproliferative agent.

Over the years, human dihydroorotate dehydrogenase (hDHODH), which is a key player in the de novo pyrimidine-biosynthesis pathway, has been targeted in the treatment of several conditions, including autoimmune disorders and acute myelogenous leukaemia, as well as in host-targeted antiviral therapy. A molecular exploration of its inhibitor-binding behaviours yielded promising candidates for innovative drug design. A detailed description of the enzymatic pharmacophore drove the decoration of well-established inhibitory scaffolds, thus gaining further in vitro and in vivo efficacy. In the present work, using X-ray crystallography, an atypical rearrangement was identified in the binding pose of a potent inhibitor characterized by a polar pyridine-based moiety (compound 18). The crystal structure shows that upon binding compound 18 the dynamics of a protein loop involved in a gating mechanism at the cofactor-binding site is modulated by the presence of three water molecules, thus fine-tuning the polarity/hydrophobicity of the binding pocket. These solvent molecules are engaged in the formation of a hydrogen-bond mesh in which one of them establishes a direct contact with the pyridine moiety of compound 18, thus paving the way for a reappraisal of the inhibition of hDHODH. Using an integrated approach, the thermodynamics of such a modulation is described by means of isothermal titration calorimetry coupled with molecular modelling. These structural insights will guide future drug design to obtain a finer Kd/logD7.4 balance and identify membrane-permeable molecules with a drug-like profile in terms of water solubility.

A Hessian Recovery Based Linear Finite Element Method for Molecular Beam Epitaxy Growth Model with Slope Selection

A Hessian Recovery Based Linear Finite Element Method for Molecular Beam Epitaxy Growth Model with Slope Selection

Identification of Cancer Stem Cell-related Gene by Single-cell and Machine Learning Predicts Immune Status, Chemotherapy Drug, and Prognosis in Lung Adenocarcinoma.

This study aimed to identify the molecular type and prognostic model of lung adenocarcinoma (LUAD) based on cancer stem cell-related genes. Studies have shown that cancer stem cells (CSC) are involved in the development, recurrence, metastasis, and drug resistance of tumors. The clinical information and RNA-seq of LUAD were obtained from the TCGA database. scRNA dataset GSE131907 and 5 GSE datasets were downloaded from the GEO database. Molecular subtypes were identified by ConsensusClusterPlus. A CSC-related prognostic signature was then constructed via univariate Cox and LASSO Cox-regression analysis. A scRNA-seq GSE131907 dataset was employed to obtain 11 cell clusters, among which, 173 differentially expressed genes in CSC were identified. Moreover, the CSC score and mRNAsi were higher in tumor samples. 18 of 173 genes were survival time-associated genes in both the TCGA-LUDA dataset and the GSE dataset. Next, two molecular subtypes (namely, CSC1 and CSC2) were identified based on 18 survival-related CSC genes with distinct immune profiles and noticeably different prognoses as well as differences in the sensitivity of chemotherapy drugs. 8 genes were used to build a prognostic model in the TCGA-LUAD dataset. High-risk patients faced worse survival than those with a low risk. The robust predictive ability of the risk score was validated by the time-dependent ROC curve revealed as well as the GSE dataset. TIDE analysis showed a higher sensitivity of patients in the low group to immunotherapy. This study has revealed the effect of CSC on the heterogeneity of LUAD, and created an 8 genes prognosis model that can be potentially valuable for predicting the prognosis of LUAD and response to immunotherapy.

Unravelling the effect of molecular interactions on macroscale properties in Sustainion anion exchange membrane (AEM) under hydrated conditions using MD simulations

Sustainion is an anion exchange water electrolyser membrane that has exhibited a scalable performance. In this work, we present a molecular model for the Sustainion membrane incorporating functionalization of the polymer in order to better mimic experimental conditions. Here in, we present a comprehensive exploration of its structural and transport properties like density, diffusivity and conductivity at various operating hydration levels using molecular dynamics simulations. The density exhibits a non-monotonic trend while the diffusivity showcases a non-linear behavior with hydration. Furthermore, diffusion exhibits an Arrhenius-like dependence on temperature with the activation energies exhibiting a non-monotonic relationship akin to the density. It is concluded that the afore-mentioned properties of the Sustainion membrane are due to the counteracting influence of the enhancement in coordination number, and a reduction in the potentials of mean force of the different atomic pairs in the system. The effect of added salt on Sustainion properties is also determined and collated with experiments. Based on comparison with experiment, we deduce that vehicular diffusion is the predominant mechanism in the diffusion of the chloride ion, while it contributes approximately 15% to the diffusivity of the hydroxide ion.

Computational protein design - where it goes?

Proteins have been playing a critical role in the regulation of diverse biological processes related to human life. With the increasing demand, functional proteins are sparse in this immense sequence space. Therefore, protein design has become an important task in various fields, including medicine, food, energy, materials, etc. Directed evolution has recently led to significant achievements. Molecular modification of proteins through directed evolution technology has significantly advanced the fields of enzyme engineering, metabolic engineering, medicine, and beyond. However, it is impossible to identify desirable sequences from a large number of synthetic sequences alone. As a result, computational methods, including data-driven machine learning and physics-based molecular modeling, have been introduced to protein engineering to produce more functional proteins. This review focuses on recent advances in computational protein design, highlighting the applicability of different approaches as well as their limitations.

Influence of compatibilization methods on the compatibility between asphalt and DCLR components with molecular dynamics (MD) method

This study aims to investigate the effect of compatibilization methods on the compatibility between asphalt and direct coal liquefaction residue (DCLR) components to identify the key components in DCLR and asphalt that affect their compatibility. In this article, three types of compatibilizers, including benzyl alcohol (BA), dioctyl phthalate (DOP), and BA/DOP, were selected and acted on asphalt's components and DCLR's components, respectively. The molecular models of asphalt components, asphalt components with compatibilizers, DCLR components, and DCLR components with compatibilizers were established. The compatibility between DCLR and asphalt's four components, as well as between asphalt and DCLR's three components, were evaluated by solubility parameter difference (SPD) and interaction energy (IE). The compatibility between DCLR and asphalt was analyzed by Segregation test and Scanning Electron Microscope. Results indicate that the SPD and IE values between DCLR and asphalt components declined after adding compatibilizers, which implies that the repulsion decreased and the attraction increased between asphalt components and DCLR and the compatibility between asphalt components and DCLR improved. The IE values between DCLR components and asphalt increased after adding compatibilizers, which indicates that the compatibility was reduced between DCLR components and asphalt. The SPD values between DCLR components and asphalt increased after adding the BA/DOP. The SPD values between pre-asphaltene and asphalt decreased after adding the BA and DOP. The SPD value between asphaltene in DCLR and asphalt increased after adding the BA and decreased after adding the DOP. Moreover, the storage stability and homogeneity of DCLR-modified asphalt improved after adding compatibilizers, indicating that the compatibilizers enhanced compatibility between DCLR and asphalt. Finally, comparing the results of the tests, it could be found that compatibilizers preferentially acted on the asphalt components and mainly affected the aromatics in asphalt, thereby improving the compatibility between asphalt and DCLR. The effect of BA/DOP on improving the compatibility between asphalt and DCLR was better than that of BA and DOP.

Design, Synthesis, Evaluation and Toxicity Studies of Novel Acridine Derivatives in Zebra Fish Larvae

Background: Alzheimer’s disease (AD) is a complex neurodegenerative condition for which a single protein-targeting medication is not enough to provide a cure. All the medications now available for AD are palliative. FDA has approved five medications for the treatment of AD, i.e., tacrine, donepezil, galantamine, rivastigmine, and memantine. Due to hepatotoxicity, tacrine is no longer utilized in clinical practice. Due to the lack of therapeutic efficiency of single-target medications and the multifaceted etiology of AD, multitarget-directed ligands have been developed. Objectives: The present research focused on incorporating a flavone nucleus into the amino group of 9-amino acridine nucleus to make it an acetylcholinesterase (AChE) and butyryl cholinesterase inhibitor (BuChE) with less toxicity Methods: We designed and synthesized ten flavone-substituted acridine derivatives and evaluated them for in vitro AChE and BuChE inhibitory activity. Molecular modeling studies were conducted using AutoDock Vina with hAChE (PDB ID: 4EY7) and hBuChE (PDB ID: 4TPK). The toxicity profile of the most active novel compound tested on zebrafish larvae for determining the liver and cardiac toxicity and LD50 value of the compound were determined. Results: In vitro AChE and BuChE inhibitory study by Ellman assay showed acceptable results. The compound AF2 showed the highest activity with an IC50 value of 0.99 ± 0.1 µM for AChE and 1.78 ± 0.19 for BuChE. The in vivo acute toxicity studies conducted on zebra fish larvae did not show cardiac and hepatotoxicity, and the LD50 value was found to be 1000 µL Conclusion: The results highlighted the AChE and BuChE inhibitory effects of the novel acridine-flavone hybrids, and they can be promising multitarget-directed ligands for AD.

Regiodivergent biosynthesis of bridged bicyclononanes

Medicinal compounds from plants include bicyclo[3.3.1]nonane derivatives, the majority of which are polycyclic polyprenylated acylphloroglucinols (PPAPs). Prototype molecules are hyperforin, the antidepressant constituent of St. John’s wort, and garcinol, a potential anticancer compound. Their complex structures have inspired innovative chemical syntheses, however, their biosynthesis in plants is still enigmatic. PPAPs are divided into two subclasses, named type A and B. Here we identify both types in Hypericum sampsonii plants and isolate two enzymes that regiodivergently convert a common precursor to pivotal type A and B products. Molecular modelling and substrate docking studies reveal inverted substrate binding modes in the two active site cavities. We identify amino acids that stabilize these alternative binding scenarios and use reciprocal mutagenesis to interconvert the enzymatic activities. Our studies elucidate the unique biochemistry that yields type A and B bicyclo[3.3.1]nonane cores in plants, thereby providing key building blocks for biotechnological efforts to sustainably produce these complex compounds for preclinical development.

Dissecting cell membrane tension dynamics and its effect on Piezo1-mediated cellular mechanosensitivity using force-controlled nanopipettes.

The dynamics of cellular membrane tension and its role in mechanosensing, which is the ability of cells to respond to physical stimuli, remain incompletely understood, mainly due to the lack of appropriate tools. Here, we report a force-controlled nanopipette-based method that combines fluidic force microscopy with fluorescence imaging for precise manipulation of the cellular membrane tension while monitoring the impact on single-cell mechanosensitivity. The force-controlled nanopipette enables control of the indentation force imposed on the cell cortex as well as of the aspiration pressure applied to the plasma membrane. We show that this setup can be used to concurrently monitor the activation of Piezo1 mechanosensitive ion channels via calcium imaging. Moreover, the spatiotemporal behavior of the tension propagation is assessed with the fluorescent membrane tension probe Flipper-TR, and further dissected using molecular dynamics modeling. Finally, we demonstrate that aspiration and indentation act independently on the cellular mechanobiological machinery, that indentation induces a local pre-tension in the membrane, and that membrane tension stays confined by links to the cytoskeleton.

TEMPLATE-ENGINEERED TRIVALENT IRON AND CHROMIUM CONTAINING MACROCYCLIC COMPLEXES: CHARACTERIZATION AND IN VITRO STUDIES

A novel series of tetraaza macrocyclic complexes of biological importance was synthesized by “in situ” template reaction between triethylenetetramine and dibenzoylmethane in the presence of trivalent Fe and Cr metal salts in 1:1:1 molar ratio. These complexes are represented by molecular formula [M(C[Formula: see text]H[Formula: see text]N[Formula: see text]X]X2; [Formula: see text](III) and Cr(III); [Formula: see text], NO[Formula: see text], −OAc; C[Formula: see text]H[Formula: see text]N[Formula: see text] ligand. The reported complexes were characterized by using various physicochemical and spectroscopic techniques including elemental analyses, molar conductance, thermo-gravimetric analysis, FTIR, UV–Visible and mass spectral studies. The results obtained from analytical techniques and spectroscopic techniques together suggested the complexes have a square pyramidal geometry. Various computational studies were performed including molecular docking and modeling. Further, macrocyclic complexes were also screened for their “in vitro” antimicrobial activity against selected bacterial and fungal strains. The antioxidant activity of these complexes was also evaluated. Some of the complexes were found to possess remarkable antimicrobial activity and antioxidant activity. However, complex [Fe(C[Formula: see text]H[Formula: see text]N[Formula: see text](NO[Formula: see text]](NO[Formula: see text] was found to be most potent against selected bacterial and fungal strains. On the other hand, complex [Cr(C[Formula: see text]H[Formula: see text]N[Formula: see text](NO[Formula: see text]](NO[Formula: see text] was found to show best antioxidant activity with lowest value of IC[Formula: see text].

Current analytical methods and applications used in the insight of serum proteins interactions with various food additives, pesticides, and contaminants

In recent years, many societies have expressed increasing apprehension regarding the potential negative impacts of food additives, pesticides, and environmental contaminants on human health. Environmental or occupational exposure to these compounds can cause significant adverse effects on human health by causing temporary or permanent changes in the immune system. There is supporting evidence linking pesticides/food ingredients/contaminants-induced immune alterations to the prevalence of diseases associated with changes in immune responses. Hence, it is essential to comprehensively understand the key mechanisms contributing to immune dysregulation induced by these substances, including direct immunotoxicity, endocrine disruption, and antigenicity. The impact of pesticides/food ingredients and contaminants on the human body ranges from mild to severe, depending on their affinity for blood components. These compounds form complexes with blood serum proteins, influencing their metabolism, transport, absorption, and overall toxicity. Numerous studies in the literature have explored the interactions between serum proteins and various molecules, including pesticides, drugs, and food dyes. These investigations employed a range of techniques, including spectroscopy, electrochemical and chromatographic methods as well as molecular modeling and molecular dynamics simulations analyses. This recent review, spanning from 2020 to the present, has been employed to investigate the binding characteristics, mechanisms, and attributes of different food additives, pesticides, and contaminants with serum proteins by using various techniques such as steady-state fluorescence, circular dichroism and ultra-violet spectroscopies, and computational docking methods. The review provides insights into these compounds’ positions and affinities to proteins and possible effects on human health through detailed research studies.

In silico prospective analysis of the medicinal plants activity on the CagA oncoprotein from Helicobacter pylori

BACKGROUND Colonization with Helicobacter pylori (H. pylori ) has a strong correlation with gastric cancer, and the virulence factor CagA is implicated in carcinogenesis. Studies have been conducted using medicinal plants with the aim of eliminating the pathogen; however, the possibility of blocking H. pylori -induced cell differentiation to prevent the onset and/or progression of tumors has not been addressed. This type of study is expensive and time-consuming, requiring in vitro and/or in vivo tests, which can be solved using bioinformatics. Therefore, prospective computational analyses were conducted to assess the feasibility of interaction between phenolic compounds from medicinal plants and the CagA oncoprotein. AIM To perform a computational prospecting of the interactions between phenolic compounds from medicinal plants and the CagA oncoprotein of H. pylori . METHODS In this in silico study, the structures of the phenolic compounds (ligands) kaempferol, myricetin, quercetin, ponciretin (flavonoids), and chlorogenic acid (phenolic acid) were selected from the PubChem database. These phenolic compounds were chosen based on previous studies that suggested medicinal plants as non-drug treatments to eliminate H. pylori infection. The three-dimensional structure model of the CagA oncoprotein of H. pylori (receptor) was obtained through molecular modeling using computational tools from the I-Tasser platform, employing the threading methodology. The primary sequence of CagA was sourced from GenBank (BAK52797.1). A screening was conducted to identify binding sites in the structure of the CagA oncoprotein that could potentially interact with the ligands, utilizing the GRaSP online platform. Both the ligands and receptor were prepared for molecular docking using AutoDock Tools 4 (ADT) software, and the simulations were carried out using a combination of ADT and AutoDock Vina v.1.2.0 software. Two sets of simulations were performed: One involving the central region of CagA with phenolic compounds, and another involving the carboxy-terminus region of CagA with phenolic compounds. The receptor-ligand complexes were then analyzed using PyMol and BIOVIA Discovery Studio software. RESULTS The structure model obtained for the CagA oncoprotein exhibited high quality (C-score = 0.09) and was validated using parameters from the MolProbity platform. The GRaSP online platform identified 24 residues (phenylalanine and leucine) as potential binding sites on the CagA oncoprotein. Molecular docking simulations were conducted with the three-dimensional model of the CagA oncoprotein. No complexes were observed in the simulations between the carboxy-terminus region of CagA and the phenolic compounds; however, all phenolic compounds interacted with the central region of the oncoprotein. Phenolic compounds and CagA exhibited significant affinity energy (-7.9 to -9.1 kcal/mol): CagA/kaempferol formed 28 chemical bonds, CagA/myricetin formed 18 chemical bonds, CagA/quercetin formed 16 chemical bonds, CagA/ponciretin formed 13 chemical bonds, and CagA/chlorogenic acid formed 17 chemical bonds. Although none of the phenolic compounds directly bound to the amino acid residues of the K-Xn-R-X-R membrane binding motif, all of them bound to residues, mostly positively or negatively charged, located near this region. CONCLUSION In silico , the tested phenolic compounds formed stable complexes with CagA. Therefore, they could be tested in vitro and/or in vivo to validate the findings, and to assess interference in CagA/cellular target interactions and in the oncogenic differentiation of gastric cells.

Plastid phylogenomics clarifies broad-level relationships in Bulbophyllum (Orchidaceae) and provides insights into range evolution of Australasian section Adelopetalum

The hyperdiverse orchid genus Bulbophyllum is the second largest genus of flowering plants and exhibits a pantropical distribution with a center of diversity in tropical Asia. The only Bulbophyllum section with a center of diversity in Australasia is sect. Adelopetalum. However, the phylogenetic placement, interspecific relationships, and spatio-temporal evolution of this section remain largely unclear. To infer broad-level relationships within Bulbophyllum, and interspecific relationships within sect. Adelopetalum, a genome skimming dataset was generated for 89 samples, which yielded 70 plastid coding regions and a nuclear ribosomal DNA cistron. For 18 additional samples, Sanger data from two plastid loci (matK and ycf1) and nuclear ITS were added using a supermatrix approach. The study provided new insights into broad-level relationships in Bulbophyllum, including phylogenetic evidence for the non-monophyly of sections Beccariana, Brachyantha, Brachypus, Cirrhopetaloides, Cirrhopetalum, Desmosanthes, Minutissima, Oxysepala, Polymeres, and Sestochilos. Section Adelopetalum and sect. Minutissima s.s. formed a highly supported clade that was resolved as a sister group to the remainder of the genus. Divergence time estimations based on a relaxed molecular clock model placed the origin of Bulbophyllum in the Early Oligocene (ca. 33.2 Ma) and sect. Adelopetalum in the Late Oligocene (ca. 23.6 Ma). Ancestral range estimations based on a BAYAREALIKE model identified the Australian continent as the ancestral area of the sect. Adelopetalum. The section underwent crown diversification from the mid-Miocene to the late Pleistocene, predominantly in continental Australia. At least two independent long-distance dispersal events were inferred eastward from the Australian continent to New Zealand and to New Caledonia from the early Pliocene onwards, likely mediated by predominantly westerly winds of the Southern hemisphere. Retraction and fragmentation of the eastern Australian rainforests from the early Miocene onwards are likely drivers of lineage divergence within sect. Adelopetalum facilitating allopatric speciation.

Molecular fingerprint-aided prediction of organic solute rejection in reverse osmosis and nanofiltration

Reverse osmosis and nanofiltration are used to purify feedwaters that contain a range of harmful organic solutes. The rejection of many of these solutes is poorly understood due to our limited ability to experimentally measure removal of any given compound. In this work, we present a machine learning approach that predicts organic solute rejection using molecular fingerprints that encode chemical structure features, such as functional groups and rings, into simple binary vectors. We trained machine learning models on a database of 1906 membrane rejection measurements including 228 organic compounds and 39 types of reverse osmosis and nanofiltration membranes. Three types of molecular fingerprint models (structural key, circular, and path based) were compared, and we observed that the Molecular Access System (MACCS) structural key had high performance (coefficient of determination of 0.87 with the testing set), fast calculation time due to its short bit-length, and easy interpretability. In addition to evaluating prediction performance, Shapley Additive Explanations (SHAP) analysis was implemented to gain a better molecular-scale understanding of membrane rejection, identifying molecular substructures that are important in determining their rejection. Overall, this work presents a method to predict the rejection of compounds that uses readily available molecular structure information and improves our ability to understand rejection mechanisms.

In Silico Repurposing of a Novel Inhibitor (drug) of EGFR and VEGFR-2 Kinases of Cancer by Pharmacokinetics, Toxicity, Molecular Docking, and Molecular Dynamics Simulation.

Vascular endothelial growth factor is an angiogenic that promotes the development and metastasis of tumors (VEGF). The epidermal growth factor receptor, or EGFR, controls the division, growth, and death of cells via several signaling pathways. It has been found that most of the tyrosine kinase EGFR/VEGFR-2 inhibited by drugs that the FDA has approved are so far. The main objective of the present study was to identify an efficacious and selective dual inhibitor of VEGFR-2/EGFR for the treatment of cancer. Out of the 400 ligands tested against the kinases, 12 compounds demonstrated the best docking scores through molecular docking for the two kinases. Of these, only compound SCHEMBL2435814 inhibited the kinases with the highest score values when compared to a reference, vandetanib, as a dual inhibitor of EGFR/VEGFR-2 kinases through interaction with the identified active sites pocket. Following drug-likeness score toxicity and pharmacokinetic testing, the two compounds, SCHEMBL2435814 and vandetanib, were analyzed to determine how the two kinases interacted with each other. The results of calculations of π-cation interactions, hydrogen bonds, and hydrophobic interactions demonstrated a strong interaction between the two kinases and SCHEMBL2435814. Eventually, molecular dynamic modeling was used to assess the stability of complexes. This demonstrated many characteristics, including RMSF, RMSD, SASA, RG, and H-bond analysis, which demonstrated that SCHEMBL2435814 with the two kinases was more stable than vandetanib over a 100ns simulation period. By suppressing EGFR/VEGFR-2, chemical SCHEMBL2435814 may be able to postpone the signaling pathway of proteins that are essential to the advancement of cancer.

Porous Organic Polymers for Efficient and Selective SO2 Capture from CO2‐rich Flue Gas

AbstractThe quest for effective technologies to reduce SO2 pollution is crucial due to its adverse effects on the environment and human health. Markedly, removing a ppm level of SO2 from CO2‐containing waste gas is a persistent challenge, and current technologies suffer from low SO2/CO2 selectivity and energy‐intensive regeneration processes. Here using the molecular building blocks approach and theoretical calculation, we constructed two porous organic polymers (POPs) encompassing pocket‐like structures with exposed imidazole groups, promoting preferential interactions with SO2 from CO2‐containing streams. Markedly, the evaluated POPs offer outstanding SO2/CO2 selectivity, high SO2 capacity, and an easy regeneration process, making it one of the best materials for SO2 capture. To gain better structural insights into the notable SO2 selectivity of the POPs, we used dynamic nuclear polarization NMR spectroscopy (DNP) and molecular modelling to probe the interactions between SO2 and POP adsorbents. The newly developed materials are poised to offer an energy‐efficient and environment‐friendly SO2 separation process while we are obliged to use fossil fuels for our energy needs.

Crystal Structures, Molecular Docking and In Vitro Investigations of Two 4-Substituted 2-(5,5-dimethyl-3-styrylcyclohex-2-enylidene)malononitrile Derivatives as Potential Topoisomerase II Inhibitors

Type II topoisomerases (TOP2s) play a key role in altering the DNA topology by transiently cleaving both strands of a DNA duplex. Therefore, increased TOP2 activity is associated with many cancers. Herein, we present the synthesis, structural characterization, virtual screening, and structural exploration, as well as evaluation of the antiproliferative effects of two new 4-substituted 2-(5,5-dimethyl-3-styrylcyclohex-2-enylidene)malononitrile derivatives with potential application in the drug design of isoform-specific TOP2 inhibitors. Both compounds 1 and 2 were verified by ESI-TOF-MS, NMR, and single-crystal X-ray diffraction (SCXRD) analysis. Furthermore, we applied our recently proposed SCXRD/HYdrogen DEsolvation (HYDE) technology platform in order to perform molecular modeling, virtual screening, and structural exploration with 1 and 2. For this purpose, we used the crystal structure of human TOP2β complexed to DNA and the anticancer drug etoposide. Moreover, we further evaluated the antiproliferative activity of 1 and 2 on human hepatocarcinoma HepG2 cells and compared the observed effects with those of the reference hTOP2β inhibitor etoposide. Based on the obtained results, compounds 1 and 2 showed a virtually higher binding affinity (Ki HYDE values) over etoposide towards hTOP2β but lower antiproliferative activity compared to those of etoposide.

GR.6 Meningioma molecular classification predicts response to surgery and adjuvant radiotherapy: an integrated clinicomolecular analysis & prospective validation

Background: Meningiomas are the most common intracranial tumor with surgery, dural margin treatment, and radiotherapy as cornerstones of therapy. Response to treatment continues to be highly heterogeneous even across tumors of the same grade. Methods: Using a cohort of 2490 meningiomas in addition to 100 cases from the prospective RTOG-0539 phase II clinical trial, we define molecular biomarkers of response across multiple different, recently defined molecular classifications and use propensity score matching to mimic a randomized controlled trial to evaluate the role of extent of resection, dural marginal resection, and adjuvant radiotherapy on clinical outcome. Results: Gross tumor resection led to improved progression-free-survival (PFS) across all molecular groups (MG) and improved overall survival in proliferative meningiomas (HR 0.52, 95%CI 0.30-0.93). Dural margin treatment (Simpson grade 1/2) improved PFS versus complete tumor removal alone (Simpson 3). MG reliably predicted response to radiotherapy, including in the RTOG-0539 cohort. A molecular model developed using clinical trial cases discriminated response to radiotherapy better than standard of care grading in multiple cohorts (ΔAUC 0.12, 95%CI 0.10-0.14). Conclusions: We elucidate biological and molecular classifications of meningioma that influence response to surgery and radiotherapy in addition to introducing a novel molecular-based prediction model of response to radiation to guide treatment decisions.

Non-Flammable Epoxy Composition Based on Epoxy Resin DER-331 and 4-(β-Carboxyethenyl)phenoxy-phenoxycyclotriphosphazenes with Increased Adhesion to Metals

Functional cyclophosphazenes have proven to be effective modifiers of polymer materials, significantly improving their performance properties, such as adhesive characteristics, mechanical strength, thermal stability, fire resistance, etc. In this study, 4-(β-carboxyethenyl)phenoxy-phenoxycyclotriphosphazenes (CPPP) were obtained by the condensation of 4-formylphenoxy-phenoxycyclotriphosphazene with malonic acid. Its structure was studied using 31P, 1H, and 13C NMR spectroscopy and MALDI-TOF mass spectrometry, and the thermal properties were determined by DSC and TGA methods. Molecular modeling using the MM2 method showed that CPPPs are nanosized with diameters of spheres described around the molecules in the range of 1.34–1.93 nm, which allows them to be classified as nanosized structures. The epoxy resin DER-331 was cured with CPPP, and the conversion of epoxy groups was assessed using IR spectroscopy. Using optical interferometry, it was shown that CPPPs are well compatible with epoxy resin in the temperature range from 80 to 130 °C. It was established that the cured epoxy composition was fire resistant, as it successfully passed the UL-94 vertical combustion test due to the formation of porous coke during the combustion process and also had high heat resistance and thermal stability (decomposition onset temperature about 300 °C, glass transition temperature 230 °C). The composition has low water absorption, high resistance to fresh and salt water, fire resistance, and adhesive strength to steel and aluminum (11 ± 0.2 MPa), which makes it promising for use as an adhesive composition for gluing parts in the shipbuilding and automotive industries, the aviation industry, and radio electronics.

Utilization of Peptidoglycans from Lactic Acid Bacterial Cell Walls for the Mitigation of Acrylamide and 5-Hydroxymethylfurfural

Acrylamide (AA) and 5-hydroxymethylfurfural (HMF), which are potentially carcinogenic to humans, are often produced during the hot processing of foods. This study first used a molecular docking model to simulate the binding behavior of four lactic acid bacteria peptidoglycans (PGNs) to AA/HMF, and the binding rate of LAB-based PGNs to AA/HMF was evaluated in vitro. In silico results show that interaction energy is the driving force responsible for the adsorption of LAB-derived PGNs to AA/HMF. In vitro results showed that the PGN of B. lactis B1-04 bound the most AA (28.7%) and HMF (48.0%), followed by L. acidophilus NCFM, B. breve CICC 6079, and L. plantarum CICC 22135. Moreover, an AA/HMF-bound layer on the cell surface of B. lactis B1-04 was observed via AFM and SEM due to adsorption. XPS analysis indicated the removal rate of AA/HMF by selected strains was positively correlated with the proportion of C-O, C=O, and N-H groups of PGNs. The atoms O1, O2, O3, O4, N1, N2, N3, H1, and H2 are involved in the adsorption of LAB-based PGNs to AA/HMF. Thus, the PGNs derived from these four Lactobacillus strains can be regarded as natural adsorbents for the binding of AA/HMF.