Interaction Sites Research Articles

Abstract 4641: Preclinical evaluation of the novel curcumin Analogue AKT-100 demonstrates therapeutic effectiveness in p53-mutated cancer cells

Abstract Among the myriad of molecular alterations associated with cancer, loss of the normal tumor suppressive functions of p53, the “guardian of the genome,” is the most consistent. Thus, the possibility of targeting oncogenic, mutant p53 proteins has long been a therapeutic goal. However, that aspiration has not been fully realized, leaving patients vulnerable to aggressive disease that is resistant to chemotherapy and to targeted agents such as PARP inhibitors and immunotherapy owing to the loss of wild type p53 functionality and the gain of new oncogenic functions when mutant p53 is expressed. An effective therapeutic strategy is urgently needed for p53 mutant cancers, and our team is developing novel analogues of curcumin with the potential to convert mutant p53 to a wild type conformation and restore its tumor suppressive functions. In this study, we investigated the effects of AKT-100, which was developed from the parent molecule and curcumin analogue HO-3867. Effects were compared to another drug believed to reactivate p53 functionality, APR-246, using CyQUANT IC50 cell proliferation assays and bulk and single cell RNA sequencing. Structural analyses are underway investigating the specific sites of interaction of AKT-100 with various mutant forms of p53. Our findings indicate that, first, AKT-100 exhibits impressive cell killing in multiple ovarian and serous endometrial cancer cells at concentrations ranging from 100-300 nM and is synergistic with the PARP inhibitor olaparib. Second, RNA sequencing demonstrates the reactivation of wild type p53 genes associated with normal cell cycle regulation (induction of CDKN1A encoding p21 and GADD45A), apoptosis (induction of PMAIP1 encoding Noxa and DR5 encoding Death Receptor 5), and the inhibition of DNA replication and multiple alternative mechanisms of DNA repair employed by malignant cells. Third, RNA sequencing indicates that AKT-100 acts through both p53-dependent and independent pathways to inhibit cancer cell proliferation. Gene expression is impacted in ways that portend a therapeutic effect as well as highlight potential resistance pathways (e.g. significant induction of PLK5 encoding polo like kinase 5) that can be further targeted to create synthetic lethal drug combinations with AKT-100 chosen specifically to target the various mutant forms of p53. Taken together, these results identify novel curcumin analogues in early development with the potential to improve therapy for p53 mutant cancers. Through this strategy it is also possible to identify and block resistance pathways that are activated by different forms of mutant p53 in response to AKT-100 and to create synthetic lethal precision drug combinations. Citation Format: Kimberly K. Leslie, Jamie L. Padilla, Geneva L. Williams, Hua-Ying Fan, Cristian G. Bologa, Eric R. Prossnitz, Jun-Yong Choe, Lane E. Smith, Alexander Goss, Robert J. Lake, Avinash D. Sahu. Preclinical evaluation of the novel curcumin Analogue AKT-100 demonstrates therapeutic effectiveness in p53-mutated cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4641.

Screening ionic liquids based on COSMO-SAC model for extracting organic sulfur from coal and mechanism study

Screening suitable ionic liquids（ILs） for removing organic sulfur compounds from coal and discovering new, effective and environmentally friendly coal desulfurization additives is crucial. The solubility properties (SP) of six organic sulfur model compounds (OSMCs) in imidazole ILs were calculated based on the COSMO-SAC model. The results showed that 2-thiophenecarboxylic acid and 2-aminophenyl phenyl sulfone exhibited favorable solubility properties in certain ILs. The solubility properties of partial imidazole ILs consisting of [Cl]- were significantly better than other anions. Through the σ -profiles analysis of ILs anions, cations and OSMCs, it showed that [Cl]- had a higher tendency to be hydrogen bond acceptor than other anions. The polar groups in OSMCs increased the hydrogen bond donor or acceptor sites for interactions with ILs, while extended the optional range of ILs for hydrogen bond interactions with OSMCs. The extraction efficiencies of 2-thiophenecarboxylic acid by ILs were above 25%, with [DMIM][Cl] displaying the highest efficiency at 47.5%. Meanwhile, [DMIM][Cl] was the most effective extractant for removing all OSMCs except benzothiophene, which was basically consistent with the calculation results. Electrostatic potential analysis was used to obtain the sites where OSMCs are the most likely to form hydrogen bond interactions with [DMIM][Cl]. And characterization of hydrogen bond formation between ILs and OSMCs was obtained by FTIR analysis. The hydrogen bond formed by p-thiocresol with [DMIM][Cl] is weak, and the hydrogen bonds formed by 2-thiophenecarboxylic acid, 2-aminophenyl phenyl sulfone with [DMIM][Cl] are relatively strong. The analysis of intermolecular hydrogen bond interactions verified the mechanism underlying the excellent extraction performance for specific OSMCs by the selected ILs.

Abstract 3388: Targeting liver specific βII-Spectrin to prevent the development of metabolic dysfunction associated steatohepatitis (MASH) through CEACAM1 axis

Abstract Background: Obesity and pro-inflammatory alteration of the gut microbiome are risk factors for gastrointestinal (GI) cancers, including liver cancer (HCC). Dysregulated TGF-β signaling and loss of CEACAM1 activity are implicated in fatty liver disease. Clinically, 40% of human liver and GI cancers have genetic alterations in the TGF-β pathway members. CEACAM1 expression is significantly decreased in the liver of patients with Metabolic dysfunction-associated steatohepatitis (MASH). In contrast, in hepatocellular carcinoma (HCC), high CEACAM1 is associated with invasion, metastasis and poor prognosis. We hypothesized that TGF-β signaling and βII-Spectrin modulate MASH and HCC through CEACAM1. Methods: Wild type and the liver-specific βII-Spectrin (Sptbn1) knockout (LSKO) mice fed a high-fat diet (HFD) or Western diet (WD) and analyzed for Ceacam1 expression, changes in immune cell population, liver inflammation, and cancer. We used Alphafold and molecular modeling to identify the CEACAM1 and SPTBN1 interaction sites. Results: Single cell sequencing analysis of MASH mice liver revealed that Ceacam1 expression is significantly decreased in hepatocytes. Interestingly, we found that CEACAM1 levels are restored to normal in tissues from liver-specific βII-Spectrin knockout (LSKO) mice. Transcriptomic and multiplex imaging analysis suggest that proinflammatory TGF-β signaling is activated and infiltration of CD11b+ cells is increased in MASH liver. These phenotypes are blocked in LSKO mice. Furthermore, siRNA-knockdown of βII-Spectrin blocks diet-induced obesity, fibrosis, lipid accumulation, tissue damage, and cancer susceptibility. We have also found that CEACAM1 interacts with the Smad3 adaptor, βII-Spectrin. Furthermore, structural analysis of CECAM1 and βII-Spectrin revealed critical residues involved in the interaction. Conclusion: These data suggest that βII-Spectrin regulates CEACAM1 expression in the liver and is a potential target for therapeutic intervention to treat MASH and prevent progression to HCC. Citation Format: Krishanu Bhowmick, Kazufumi Ohshiro, Xiyan Xiang, Sahara John, Xiaochun Yang, Nicole Beauchemin, Mohammad I. Hassan, Taj Mohammad, Lopa Mishra. Targeting liver specific βII-Spectrin to prevent the development of metabolic dysfunction associated steatohepatitis (MASH) through CEACAM1 axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3388.

Abstract 6239: Human computer interface guided approach to accelerate anticancer drug discovery: Application to human estrogen receptor interactome

Abstract Structure-based drug discovery of target specific drugs greatly rely on the existence of high resolution X-ray crystal structure of the target proteins. Flexible and dynamic regions including hinges and loops which constitute major protein-protein interaction sites as well as allosteric sites are often beyond the scope of current tools and techniques available for protein folding and modeling. Human ability in recognizing patterns and to solve complex puzzles are far superior to any existing computer program at folding these atypical regions of proteins. We have utilized an unconventional combination of using dynamic three-dimensional protein models as physical human computer interface (HCI) devices and integrated proteomics data to predict flexible and dynamic protein-protein interfaces and allosteric pockets of key regulatory proteins to accelerate compound discovery. To this end, we have successfully utilized 1) Flexible HCI devices to generate an ensemble of dynamic three dimensional structures which includes a subset of biologically active conformations among others (thereby exploring the viable chemical space) and 2) Structure refinement and efficient filtering of biologically active conformations can be accomplished by integrating protein-protein interface and fold proteomics data. Here we present AI ready, HCI guided exploration of human estrogen receptor interactome and early in vitro confirmatory analyses. AI approachs to predict 3D protein structures from amino acid sequences like AlphaFold are often on par with experimentally generated structures and AI-guided structure prediction or docking approaches have been reported to significantly reduce computer time utilization. Streamlining of HCIguided tools to enable access to dynamic druggable pockets in protein targets will accelerate drug discovery. Citation Format: Rajendram V. Rajnarayanan, Aya Alsabagh. Human computer interface guided approach to accelerate anticancer drug discovery: Application to human estrogen receptor interactome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6239.

Abstract 753: CEACAM1 induces microbiome and metabolite driven diversion of TGF-β signaling to promote colon cancer

Abstract Background: Colon cancer is rising in younger individuals in the United States. Potential causal factors are altered diets and gut microbiomes. Yet key signaling pathways, host-microbe interactions, and metabolites such as ammonia in cancer remain unclear. CEACAM1 responds to pathogenic microbes, interacts with the TGF-β/SPTBN1 and levels are raised in invasive colon cancer. Alterations in the TGF-β pathway occur ~40% of human GI cancers, and mouse models with disrupted TGF-β signaling (Tgfbr2−/−, Smad4+/−Sptbn1+/−, and Tgfb1−/−) develop colorectal cancer (CRC) that is dependent upon an altered gut microbiome. Our previous studies indicate the lipid metabolites (reactive aldehydes) form toxic adducts with cleaved SPTBN1 and divert TGF-β signaling to pro-oncogenic process. Poor prognosis CRC is associated with raised levels of microbial metabolites, such as ammonia. Thus, we hypothesized that “the intricate relationships among pathogen-binding CEACAM1, the gut microbiome, metabolites such as ammonia, and βII-Spectrin drive colon cancer development”. Methods: We examined gut microbiota composition, immune cell population, inflammation, and cancers in Smad4+/−Sptbn1+/− and Sptbn1LSKO mice fed a normal chow diet or a high-fat diet (HFD). We evaluated CEACAM1 and TGF-β member alterations in in CRCs using TCGA datasets. Alphafold-based molecular modeling predicted interaction sites between βII-Spectrin and CEACAM1 was followed by functional studies. Results: Increased CEACAM1 levels with alterations in TGF-β members were associated with lower survival (TCGA). Mice with disrupted TGF-β signaling (Smad4+/−Sptbn1+/−) develop CRC, have high CEACAM1 levels, and an altered gut microbiome signature. CEACAM1 interacts with βII-Spectrin, and levels are restored to normal in βII-Spectrin LSKO which restores the gut microbiome and blocks inflammation and cancer. Ammonia induces CASPASE-3 mediated cleavage of βII-Spectrin, forms toxic adducts and divert TGF-β signaling to pathological pro-oncogenic signaling, triggering CRC. Conclusion: We have found a critical role for CEACAMs in CRC cancer development, through diverting the TGF-β signaling pathway to a pro-oncogenic phenotype. CEACAM1 and βII-Spectrin are attractive therapeutic targets for CRC. Citation Format: Krishanu Bhowmick, Kazufumi Ohshiro, Xiyan Xiang, Sahara John, Xiaochun Yang, Kevin Idicula, Nicole Beauchemin, Raja Mazumder, Keith A. Crandall, Mohammad I. Hassan, Taj Mohammad, Lopa Mishra. CEACAM1 induces microbiome and metabolite driven diversion of TGF-β signaling to promote colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 753.

A1CF Binding to the p65 Interaction Site on NKRF Decreased IFN-β Expression and p65 Phosphorylation (Ser536) in Renal Carcinoma Cells.

Apobec-1 complementation factor (A1CF) functions as an RNA-binding cofactor for APO-BEC1-mediated C-to-U conversion during RNA editing and as a hepatocyte-specific regulator in the alternative pre-mRNA splicing of metabolic enzymes. Its role in RNA editing has not been clearly established. Western blot, co-immunoprecipitation (Co-IP), immunofluorescence (IF), methyl thiazolyl tetrazolium (MTT), and 5-ethynyl-2'-deoxyuridine (EdU) assays were used to examine the role of A1CF beyond RNA editing in renal carcinoma cells. We demonstrated that A1CF interacts with NKRF, independent of RNA and DNA, without affecting its expression or nuclear translocation; however, it modulates p65(Ser536) phosphorylation and IFN-β levels. Truncation of A1CF or deletion on NKRF revealed that the RRM1 domain of A1CF and the p65 binding motif of NKRF are required for their interaction. Deletion of RRM1 on A1CF abrogates NKRF binding, and the decrease in IFN-β expression and p65(Ser536) phosphorylation was induced by A1CF. Moreover, full-length A1CF, but not an RRM1 deletion mutant, promoted cell proliferation in renal carcinoma cells. Perturbation of A1CF levels in renal carcinoma cells altered anchorage-independent growth and tumor progression in nude mice. Moreover, p65(Ser536) phosphorylation and IFN-β expression were lower, but ki67 was higher in A1CF-overexpressing tumor tissues of a xenograft mouse model. Notably, primary and metastatic samples from renal cancer patients exhibited high A1CF expression, low p65(Ser536) phosphorylation, and decreased IFN-β levels in renal carcinoma tissues compared with the corresponding paracancerous tissues. Our results indicate that A1CF-decreased p65(Ser536) phosphorylation and IFN-β levels may be caused by A1CF competitive binding to the p65-combined site on NKRF and demonstrate the direct binding of A1CF independent of RNA or DNA in signal pathway regulation and tumor promotion in renal carcinoma cells.

Abstract 4327: Development of bioluminescent biosensors to monitor the interaction betweenGSDMD and caspase-1 in living cells

Abstract Gasdermin D (GSDMD) is the key executioner of pyroptosis, an inflammatory form of programmed cell death implicated in various inflammation-driven diseases, including cancer, heart failure and strokes. The interaction between GSDMD and caspase-1 (CASP1) orchestrates the critical pathway of GSDMD-mediated pyroptosis. During pyroptosis, pyroptosis stimuli activate CASP1, which subsequently binds to and cleave GSDMD between GSDMD’s N- and C-terminal domains. The free N-terminal domains oligomerize and translocate to the cell membrane, forming pores and releasing proinflammatory cytokines and causing cellular lysis. Key interaction sites have been identified for GSDMD recognition and engagement by CASP1; therefore, blocking functionally significant residues presents a new therapeutic strategy for inhibiting CASP1-induced GSDMD cleavage and pyroptosis. Currently, there is no small molecule capable of specifically disrupting the GSDMD and CASP1 interaction. In response, the ongoing pursuit of identifying potential inhibitors is a driving force for developing a biosensor capable of monitoring this interaction and their roles in downstream pyroptotic effects. In this study, we utilized the NanoLuc Binary Technology (NanoBiT) to construct several bioluminescent biosensors comprising two NanoLuc luciferase enzyme fragments (LgBiT and SmBiT) fused to GSDMD and CASP1, respectively, in various combinations. Further validation of these biosensors by luciferase assays in living cells identified a GSDMD-CASP1 biosensor with highest luciferase activity. This newly developed biosensor paves the way for high-throughput screens to identify novel small molecule inhibitors disrupting the GSDMD-CASP1 interplay. These small molecule inhibitors will effectively impede GSDMD-mediated pyroptosis, holding promise for novel therapies of various human diseases. Citation Format: Tynan Kelly. Development of bioluminescent biosensors to monitor the interaction betweenGSDMD and caspase-1 in living cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4327.

Effect of caffeine on the aggregation of amyloid-β-A 3D RISM study.

Alzheimer's disease is a detrimental neurological disorder caused by the formation of amyloid fibrils due to the aggregation of amyloid-β peptide. The primary therapeutic approaches for treating Alzheimer's disease are targeted to prevent this amyloid fibril formation using potential inhibitor molecules. The discovery of such inhibitor molecules poses a formidable challenge to the design of anti-amyloid drugs. This study investigates the effect of caffeine on dimer formation of the full-length amyloid-β using a combined approach of all-atom, explicit water molecular dynamics simulations and the three-dimensional reference interaction site model theory. The change in the hydration free energy of amyloid-β dimer, with and without the inhibitor molecules, is calculated with respect to the monomeric amyloid-β, where the hydration free energy is decomposed into energetic and entropic components, respectively. Dimerization is accompanied by a positive change in the partial molar volume. Dimer formation is spontaneous, which implies a decrease in the hydration free energy. However, a reverse trend is observed for the dimer with inhibitor molecules. It is observed that the negatively charged residues primarily contribute for the formation of the amyloid-β dimer. A residue-wise decomposition reveals that hydration/dehydration of the side-chain atoms of the charged amino acid residues primarily contribute to dimerization.

Weed Species’ Diversity and Composition as Shaped by the Interaction of Management, Site, and Soil Variables in Olive Groves of Southern Greece

Gaining a comprehensive understanding of how weed communities respond to both environmental and human-induced factors is of paramount importance in developing effective and ecologically sound weed control strategies. The objectives of the current research were to (1) assess the effect of the main weed management practices used in Greek olive groves on weed species’ diversity; (2) explore the filtering effect of management, site, and soil variables in determining weed species’ composition; and (3) shed light on the association between weed species’ composition and the diversity of the understory vegetation of olive groves. To accomplish these objectives, winter weed species’ coverage was assessed in 116 olive groves, both conventional and organic, distributed across three provinces in southern Greece. The investigation encompassed 29 explanatory variables, categorized into three groups: soil (22), management practices (6), and site conditions (1). It was confirmed that glyphosate use may lower biodiversity and species richness; however, this trend was not universal. In fact, the negative influence of the presence of Oxalis pes-caprae L. on species richness and diversity far outweighed the effect of spraying glyphosate. Redundancy analysis (RDA) revealed that among the 29 variables used to describe the ecological niche, eight (i.e., Mn, Mg, chemical spraying, mowing, rotary tiller, grazing, irrigation, and elevation) were significant and explained 21.5% of the total variation in weed species’ data. Interestingly, the soil Mn concentration was identified as the most influential one, highlighting the importance of soil micronutrients in determining weed species’ composition. The variation partitioning procedure demonstrated that the effect of the management variables on weed species’ composition accounted for 2.2 times the variance of soil variables and 4.5 times the variance of elevation. The present findings might help to enhance optimal management in olive groves that can sustain the biodiversity of flora and, in turn, provide various ecosystem services to agro-ecosystems.

CRISPR du-HITI an attractive approach to targeting Long Noncoding RNA HCP5 as inhibitory factor for proliferation of ovarian cancer cell.

This research provides a glimmer of hope that the knockout of HCP5 leads to a therapy response to considerably prolong the life of patients with OC. RT-PCR evaluated the expression of lncRNA HCP5 in the ovarian cancer OVCAR-3 cell line. CRISPR knockout cell lines validated by western blot. Small genomic deletions at the targeted locus were induced. CCK-8 colony formation assays were used to analyze the effect of HCP5 knockout on the proliferation capacity of OVCAR-3 cells. Transwell migration and invasion assayed. Furthermore, the Sphere-formation assay isolated the most aggressive population of cancer stem cells. Bioinformatic analysis showed a significant correlation between lncRNA HCP5 up-regulation and OVCAR-3 cell proliferation. The ChIP technique assesses specific sites of interaction between transcription factors and DNA. Real-time PCR assays explored the relationship between HCP5, Hsa-miR-9-5p, CXCR4, CDH1, caspase-3, p53, bcl2 and survivin. PCR carried out amplification of the 448-bp band for sgRNA1 and sgRNA2 after the use of particular primers for HCP5. the number of breast cancer cells that moved to the bottom chamber reduced considerably after transfection with PX461-sgRNA1/2 vectors compared to the Blank control groups (P < 0.05). MTT assay designated growth curves that showed the rate of OVCAR-3 growth was significantly repressed (***P < 0.001) when compared with control OVCAR-3 cells after HCP5 knockdown. Also, the survival results of W.T cells in 24, 48 and 72 h showed 92%, 87% and 85%, respectively. This is while the cells of the CRISPR/Cas9 group in which LncRNA HCP5 was knocked out had 42% (*P < 0.05), 23%(**P < 0.01) and 14% (**P < 0.01) survival, respectively. The expression levels of caspase-3, Hsa-miR-9-5p, P53 genes in the HCP5 deletion of CRISPR/Cas9 group significantly increased than the W.T. control group; the deletion group showed a considerable reduction in HCP5 expression compared to the blank control group (3.6-fold, p < 0.01). Whereas BCL2, SURVIVIN, CXCR4, CDH1 genes expression markedly increased than in HCP5 knockout cells (5.8-fold, p < 0.05). These results indicate that CRISPR/Cas9-mediated HCP5 disruption on OVCAR-3 cell lines promotes anti-tumor biomarkers, suppressing ovarian cancer progression. Consistent with these results, HCP5 is one of the most critical lnc for the efficient proliferation and migration of OVCAR-3 cell lines.

LiViT-Net: A U-Net-like, lightweight Transformer network for retinal vessel segmentation

The intricate task of precisely segmenting retinal vessels from images, which is critical for diagnosing various eye diseases, presents significant challenges for models due to factors such as scale variation, complex anatomical patterns, low contrast, and limitations in training data. Building on these challenges, we offer novel contributions spanning model architecture, loss function design, robustness, and real-time efficacy. To comprehensively address these challenges, a new U-Net-like, lightweight Transformer network for retinal vessel segmentation is presented. By integrating MobileViT+ and a novel local representation in the encoder, our design emphasizes lightweight processing while capturing intricate image structures, enhancing vessel edge precision. A novel joint loss is designed, leveraging the characteristics of weighted cross-entropy and Dice loss to effectively guide the model through the task's challenges, such as foreground-background imbalance and intricate vascular structures. Exhaustive experiments were performed on three prominent retinal image databases. The results underscore the robustness and generalizability of the proposed LiViT-Net, which outperforms other methods in complex scenarios, especially in intricate environments with fine vessels or vessel edges. Importantly, optimized for efficiency, LiViT-Net excels on devices with constrained computational power, as evidenced by its fast performance. To demonstrate the model proposed in this study, a freely accessible and interactive website was established (https://hz-t3.matpool.com:28765?token=aQjYR4hqMI), revealing real-time performance with no login requirements.

A triazine-based covalent organic framework decorated with cadmium sulfide for efficient photocatalytic hydrogen evolution from water

Construction of inorganic/organic heterostructures has been proven to be a very promising strategy to design highly efficient photocatalysts for solar driven hydrogen evolution from water. Herein, we report the preparation of a direct Z-scheme heterojunction photocatalyst by in situ growth of cadmium sulfide on a triazine-based covalent organic framework (COF). The triazine based-COF was synthesized by condensation reaction of precursors 1,3,5-tris-(4-formyl-phenyl) triazine (TFPT) and 2,5-bis-(3-hydroxypropoxy) terephthalohydrazide (DHTH), termed as TFPT-DHTH-COF. Widely distributed nitrogen atoms throughout TFPT-DHTH-COF skeletons serve as anchoring sites for strong interfacial interactions with CdS. The CdS/TFPT-DHTH-COF composite showed a hydrogen evolution rate of 15.75 mmol h−1 g−1, which is about 75 times higher than that of TFPT-DHTH-COF (0.21 mmol h−1 g−1) and 3.4 times higher than that of CdS (4.57 mmol h−1 g−1). With the properly staggered band alignment and strong interfacial interaction between TFPT-DHTH-COF and CdS, a Z-scheme charge transfer pathway is achieved. The mechanism has been systematically analyzed by steady state and time-resolved photoluminescence measurements as well as in situ irradiated X-ray photoelectron spectroscopy.

Lagrangian of extended multiconfigurational self-consistent field second-order quasidegenerate perturbation theory combined with reference interaction site model self-consistent field constraint spatial electron density.

Lagrangians of the state-averaged multiconfigurational self-consistent field (SA-MCSCF) and multistate extended second-order quasidegenerate perturbation theory (MS-XMCQDPT2) coupled with the reference interaction site model self-consistent field constraint spatial electron density are defined. In addition, variational equations were derived to calculate the excitation energies of the target molecules dissolved in various solvents. The theory was applied to a phenol molecule in various solutions, and the gradients and Hessian matrices were calculated to evaluate the absorption spectral lines, including the broadening bandwidth. Numerical calculations revealed fine structures in any solvent surroundings. The main intramolecular vibrational modes related to such fine structures were stretching vibrations of the aromatic ring and the oxygen atom of the phenol molecule. The present theory plays an important role in predicting the structure of potential energy surfaces, such as Hessian matrices for various solvent types, during the photoexcitation process.

High-entropy engineering with regulated defect structure and electron interaction tuning active sites for trifunctional electrocatalysis

High-entropy alloy nanoparticles (HEANs) possessing regulated defect structure and electron interaction exhibit a guideline for constructing multifunctional catalysts. However, the microstructure-activity relationship between active sites of HEANs for multifunctional electrocatalysts is rarely reported. In this work, HEANs distributed on multi-walled carbon nanotubes (HEAN/CNT) are prepared by Joule heating as an example to explain the mechanism of trifunctional electrocatalysis for oxygen reduction, oxygen evolution, and hydrogen evolution reaction. HEAN/CNT excels with unmatched stability, maintaining a 0.8V voltage window for 220 h in zinc-air batteries. Even after 20 h of water electrolysis, its performance remains undiminished, highlighting exceptional endurance and reliability. Moreover, the intrinsic characteristics of the defect structure and electron interaction for HEAN/CNT are investigated in detail. The electrocatalytic mechanism of trifunctional electrocatalysis of HEAN/CNT under different conditions is identified by in situ monitoring and theoretical calculation. Meanwhile, the electron interaction and adaptive regulation of active sites in the trifunctional electrocatalysis of HEANs were further verified by density functional theory. These findings could provide unique ideas for designing inexpensive multifunctional high-entropy electrocatalysts.

MD investigation on the differences in the dynamic interactions between the specific ligand azamulin and two CYP3A isoforms, 3A4 and 3A5

The unmarked potential drug molecule azamulin has been found to be a specific inhibitor of CYP3A4 and CYP3A5 in recent years, but this molecule also shows different binding ability and affinity to the two CYP3A isoforms. In order to explore the microscopic mechanism, conventional molecular dynamics (MD) simulation methods were performed to study the dynamic interactions between two isoforms and azamulin. The simulation results show that the binding of the ligand leads to different structural properties of two CYP3A proteins. First of all, compared with apo-CYP3A4, the binding of the ligand azamulin can lead to changes in the structural flexibility of CYP3A4, i.e., holo-CYP3A4 is more flexible than apo-CYP3A4. The structural changes of CYP3A5 are just the opposite. The ligand binding increases the rigidity of CYP3A5. Furthermore, the representative structures of the production phase in the MD simulation were in details analyzed to obtain the microscopic interactions between the ligand azamulin and two CYP3A isoforms at the atomic level. It is speculated that the difference of composition and interaction of the active sites is the fundamental cause of the change of structural properties of the two proteins. Communicated by Ramaswamy H. Sarma

Crystal structure, hydrogen bonding interactions, Hirshfeld surfaces, energy frameworks, and DFT calculation of Diethyl 3-(4-substitutedbenzoyl)indolizine-1,2-dicarboxylates

The diethyl 3-(4-substitutedbenzoyl)indolizine-1,2-dicarboxylates have been synthesized by reacting the electron-deficient diethyl but-2-ynedioate with 1-(2-(4-substitutedphenyl)-2-oxoethyl)pyridin-1-ium bromide, the intermediates obtained from the reaction of pyridine and 4-substituted phenacyl bromides. The synthesized compounds were investigated by FT-IR, NMR (1H and 13C), LC-MS, and elemental analysis spectroscopic methods along with PXRD. The molecular structures were determined using the single crystal X-ray diffraction technique which revealed that 5a and 5c crystallize in triclinic space group P1¯. The crystal structures of 5a and 5c preferred the C-H···O hydrogen-bonded dimeric ring motifs, resembling those observed in the earlier reported 5b. Furthermore, various computational analyzes such as Hirshfeld surface, Energy framework, and MEP analysis predicted the interaction site and inter-molecular interactions in these molecules. The FMOs analysis was carried out to obtain global reactivity parameters for the synthesized compounds (5a-c). The NCI and QTAIM studies revealed the nature as well as qualitative and quantitative description of intra and inter-molecular hydrogen bonding interactions present in these molecules and their crystal packing.

Novel manganese and nitrogen co-doped biochar based on sodium bicarbonate activation for efficient removal of bisphenol A: Mechanism insight and role analysis of manganese and nitrogen by combination of characterizations, experiments and density functional theory calculations

A novel porous manganese and nitrogen co-doped biochar (Mn-N@SBC) was synthesized via one-step pyrolysis, utilizing loofah agricultural waste as the precursor and NaHCO3 as the activator. The behavior of bisphenol A adsorbed on Mn-N@SBC was evaluated using static batch adsorption experiments. Compared to direct manganese-nitrogen co-doping, co-doping based on NaHCO3 activation significantly increased the specific surface area (231 to 1027 m2·g−1) and adsorption capacity (15 to 351 mg·g−1). Wide pH (2–10) and good resistance to cation/anion, humic acid and actual water demonstrated the robust adaptability of Mn-N@SBC to environmental factors. The significantly reduced specific surface area after adsorption, adverse effects of ethanol and phenanthrene on the removal of bisphenol A, and theoretically predicted interaction sites indicated the primary adsorption mechanisms involved pore filling, hydrophobicity, and π-π-electron-donor–acceptor interaction. This work presented an approach to create high-efficiency adsorbents from agricultural waste, offering theoretical and practical guidance for the removal of pollutants.

Functionalization of porous silica with graphene oxide and polyethyleneimine, containing zinc copper ferrite nanoparticles for water treatment and antibacterial application

The article discusses the removal of methylene blue (MB) dye, a common cationic dye used in the textile industry, from aqueous solutions through an adsorption process. The use of porous components as adsorbents are shown to facilitate complete separation after the process is completed. The substrate was synthesized by connecting zinc copper ferrite (ZnCuFe2O4), polyethyleneimine (PEI), and Graphene Oxide (GO) sheets to MCM-48, which is a mesoporous material. The surface of MCM-48 was modified using CPTMS, which created an O–Si–Cl bridge, thereby improving the adsorption rate. The substrate was shown to have suitable sites for electrostatic interactions and creating hydrogen bonds with MB. The adsorption process from the Freundlich isotherm (R2 = 0.9224) and the pseudo-second-order diagram (R2 = 0.9927) demonstrates the adsorption of several layers of dye on the heterogeneous surface of the substrate. The synthesized substrate was also shown to have good bactericidal activity against E. coli and S. aureus bacterial strain. Furthermore, the substrate maintained its initial ability to adsorb MB dye for four consecutive cycles. The research resulted that ZnCuFe2O4@MCM-48/PEI-GO substrate has the potential for efficient and economical removal of MB dye from aqueous solutions (R = 88.82%) (qmax = 294.1176 mg. g−1), making it a promising solution for the disposal of harmful industrial waste.

Identification of PS1/gamma-secretase and glutamate transporter GLT-1 interaction sites

The recently discovered interaction between Presenilin 1 (PS1), a catalytic subunit of γ-secretase responsible for generating amyloid-β (Aβ) peptides, and GLT-1, a major glutamate transporter in the brain (EAAT2) provides a mechanistic link between these two key factors involved in Alzheimer’s disease (AD) pathology. Modulating this interaction can be crucial to understand the consequence of such crosstalk in AD context and beyond. However, the interaction sites between these two proteins are unknown. Herein, we utilized an alanine scanning approach coupled with FRET-based fluorescence lifetime imaging microscopy (FLIM) to identify the interaction sites between PS1 and GLT-1 in their native environment within intact cells. We found that GLT-1 residues at position 276 to 279 (TM5) and PS1 residues at position 249 to 252 (TM6) are crucial for GLT-1/PS1 interaction. These results have been cross validated using AlphaFold Multimer prediction. To further investigate whether this interaction of endogenously expressed GLT-1 and PS1 can be prevented in primary neurons, we designed PS1/GLT-1 cell-permeable peptides (CPPs) targeting the PS1 or GLT-1 binding site. We used HIV TAT domain to allow for cell penetration which was assayed in neurons. First, we assessed the toxicity and penetration of CPPs by confocal microscopy. Next, to ensure the efficiency of CPPs, we monitored the modulation of GLT-1/PS1 interaction in intact neurons by FLIM. We saw significantly less interaction between PS1 and GLT-1 with both CPPs. Our study establishes a new tool to study the functional aspect of GLT-1/PS1 interaction and its relevance in normal physiology and AD models.

Marine particle microbiomes during a spring diatom bloom contain active sulfate-reducing bacteria.

Phytoplankton blooms fuel marine food webs with labile dissolved carbon and also lead to the formation of particulate organic matter composed of living and dead algal cells. These particles contribute to carbon sequestration and are sites of intense algal-bacterial interactions, providing diverse niches for microbes to thrive. We analyzed 16S and 18S ribosomal RNA gene amplicon sequences obtained from 51 time points and metaproteomes from 3 time points during a spring phytoplankton bloom in a shallow location (6-10m depth) in the North Sea. Particulate fractions larger than 10µm diameter were collected at near daily intervals between early March and late May in 2018. Network analysis identified two major modules representing bacteria co-occurring with diatoms and with dinoflagellates, respectively. The diatom network module included known sulfate-reducing Desulfobacterota as well as potentially sulfur-oxidizing Ectothiorhodospiraceae. Metaproteome analyses confirmed presence of key enzymes involved in dissimilatory sulfate reduction, a process known to occur in sinking particles at greater depths and in sediments. Our results indicate the presence of sufficiently anoxic niches in the particle fraction of an active phytoplankton bloom to sustain sulfate reduction, and an important role of benthic-pelagic coupling for microbiomes in shallow environments. Our findings may have implications for the understanding of algal-bacterial interactions and carbon export during blooms in shallow-water coastal areas.