Optimal Binding Research Articles

Fabrication and evaluation of chitosan-coated nanostructured lipid carriers for co-delivery of paclitaxel and PD-L1 siRNA

This study aimed to develop a nanostructured lipid carrier (NLC) capable of co-delivering paclitaxel (PTX) and programmed death-ligand 1 (PD-L1) small interfering RNA (siRNA) to enhance PTX bioavailability and bolster immunity through PD-L1 knockdown. We prepared a PTX-loaded NLC (P-NLC) and coated it with positively charged chitosan (Chi) to create P-NLC-Chi, which was subsequently conjugated to siRNA (P-NLC-Chi-siRNA). The P-NLC-Chi formulation was optimized using the Box–Behnken design. P-NLC-Chi measured 123.8 ± 0.52 nm (zeta potential, 22.71 ± 0.49 mV). By verifying the gel retardation assay and observing changes in the zeta potential, the optimal binding ratio of NLC to PD-L1 siRNA was identified as 50:1. The P-NLC-Chi-siRNA particle size was 181.97 ± 0.67 nm, with a zeta potential of 18.66 ± 0.23 mV. siRNA stability was observed in serum over a 24-h period. Enhanced cytotoxicity and intracellular uptake of the complex were evident in breast cancer cells and breast cancer-resistant cells (MCF-7 and MCF-7/ADR cells, respectively). Evaluation of P-glycoprotein-mediated efflux demonstrated that NLC mitigated drug efflux in MCF-7/ADR cells. Subcutaneous injection of P-NLC-Chi-siRNA into tumor-bearing BALB/c nude mice injected with MCF-7/ADR cells revealed a reduction in tumor size. In vitro and in vivo experiments indicated a significant reduction in PD-L1 mRNA expression levels. Additionally, an in vivo study revealed tumor-specific CD4 + and CD8 + T cell responses within the tumor tissue following the injection of P-NLC-Chi-siRNA. Our findings suggest that Chi-coated NLC for the co-delivery of PTX and PD-L1 siRNA has great potential as an innovative delivery system for chemoimmunotherapy.

A newly NH2-UiO-66 composite functionalized by molecularly imprinted polymer for selective and rapid removal of sulfamethoxazole

Metal–organic frameworks (MOFs) are used as novel adsorption materials owing to their large surface area and tunable pore size. However, the lack of selectivity considerably limits their application. Consequently, designing functionalized MOFs with specific recognition abilities is essential for enhancing their adsorption performance. Herein, we synthesized a functionalized NH2-UiO-66 composite modified by molecularly imprinted polymers (MIP@NH2-UiO-66) via a one-step polymerization process in which NH2-UiO-66 and MIP were formed simultaneously. Results demonstrate that MIP@NH2-UiO-66 effectively recognized sulfamethoxazole (SMX) in complex matrices. The adsorption equilibrium was reached in only 30 min, and this fast SMX adsorption on MIP@NH2-UiO-66 was described by the Avrami kinetic model, which indicates a spontaneous and exothermic adsorption process. Within the pH range of 3.0–10.0, MIP@NH2-UiO-66 exhibited an optimal binding capacity for SMX, and the maximum adsorption of SMX was 68.36 mg g−1 at 25°C, which exceeded those of existing adsorption materials (< 60.10 mg g−1). Additionally, MIP@NH2-UiO-66 was regenerated for ∼17 cycles compared to less than eight cycles for the other adsorbents. MIP@NH2-UiO-66 effectively removed 90.58%–99.60% of SMX from river water, rainwater, soil, sediment, chicken, pork, and milk samples, with a relative standard deviation of less than 4.43%. The superior adsorption of SMX on MIP@NH2-UiO-66 was primarily driven by the synergistic effects of the imprinting sites, hydrogen bonding, and electrostatic forces. The one-step polymerization method substantially simplified the synthesis process and reduced the costs, which are promising factors for the synthesis of MOFs with high selectivity.

Vibrio cholerae CsrA controls ToxR levels by increasing the stability and translation of toxR mRNA

ABSTRACT Intestinal colonization and virulence factor production in response to environmental cues is mediated through several regulatory factors in Vibrio cholerae , including the highly conserved RNA-binding global regulatory protein CsrA. We have shown previously that CsrA increases synthesis of the virulence-associated transcription factor ToxR in response to specific amino acids (NRES) and is required for the virulence of V. cholerae in the infant mouse model of cholera. In this study, we mapped the 5′ untranslated region (5′ UTR) of toxR and showed that CsrA can bind directly to an RNA sequence encompassing the 5′ UTR, indicating that the regulation of ToxR levels by CsrA is direct. Consistent with this observation, the 5′ UTR of toxR contains multiple putative CsrA binding sequences (GGA motifs), and mutating these motifs disrupted the CsrA-mediated increase in ToxR. Optimal binding of CsrA to a defined RNA oligonucleotide required the bridging of two GGA motifs within a single RNA strand. To determine the mechanism of regulation by CsrA, we assayed toxR transcript levels, stability, and efficiency of translation. Both the amount of toxR mRNA in NRES and the stability of the toxR transcript were increased by CsrA. Using an in vitro translation assay, we further showed that synthesis of ToxR was greatly enhanced in the presence of purified CsrA, suggesting a direct role for CsrA in the translation of toxR mRNA. We propose a model in which CsrA binding to the 5′ UTR of the toxR transcript promotes ribosomal access while precluding interactions with RNA-degrading enzymes. IMPORTANCE Vibrio cholerae is uniquely adapted to marine environments as well as the human intestinal tract. Global regulators, such as CsrA, which help translate environmental cues into an appropriate cellular response, are critical for switching between these distinct environments. Understanding the pathways involved in relaying environmental signals is essential for understanding both the environmental persistence and the intestinal pathogenesis of this devastating human pathogen. In this study, we demonstrate that CsrA directly regulates the synthesis of ToxR, a key virulence factor of V. cholerae . Under conditions favoring high levels of active CsrA in the cell, such as in the presence of particular amino acids, CsrA increases ToxR protein levels by binding to the toxR transcript and enhancing both its stability and translation. By responding to nutrient availability, CsrA is perfectly poised to activate the virulence gene regulatory cascade at the preferred site of colonization in the human host, the nutrient-rich small intestinal mucosa.

In Silico Efficacy of Oleic Acid, n-Hexanoic acid, and Epiglobulol Obtained from Conocarpus Lancifolius against Class D β-lactamases

Introduction: Antimicrobial resistance poses an escalating global challenge, compounded by the sluggish pace of new antibiotic discovery. Objectives: This study undertook an in silico analysis of phytochemicals derived from Conocarpus lancifolius, a local plant in the Jazan region of Saudi Arabia, to investigate potential antibacterial agents. Methods: The 3D crystallographic structure of OXA-48 was sourced from the RCSB protein databank (PDBID: 3HBR) and pre-processed. The Lib Dock algorithm facilitated the analysis of optimal binding orientations and potential interactions between compounds and the 3HBR. Results: The docking analysis outcome revealed Oleic acid as the most active compound and the binding mode exhibited that the -OH group of the terminal carboxylic acid moiety formed hydrogen bonds with Thr197 and Ala207, and the oxygen atom showed bonding with Lys116. Moreover, N-hexanoic acid also demonstrated promising binding interactions with the 3HBR, displaying hydrogen bond interactions with Lys208, Tyr211, and Ser70, along with hydrophobic alkyl interactions with Lys208 and Met115 at the protein's active sites. Unfavourable donor-donor and acceptor-acceptor bindings were also observed with Ser70 and Arg250 residues. Conclusions: The OXA-48 and NDM-1 predominate in countries of the Arabian Peninsula. Our findings suggest oleic acid as a promising candidate for combating OXA-48 β-lactamase, pending further assessment of its atomic structure via X-ray crystallography.

Unconventional Hexagonal Close-Packed High-Entropy Alloy Surfaces Synergistically Accelerate Alkaline Hydrogen Evolution.

Accelerating the alkaline hydrogen evolution reaction (HER), which involves the slow cleavage of HO-H bonds and the adsorption/desorption of hydrogen (H*) and hydroxyl (OH*) intermediates, requires developing catalysts with optimal binding strengths for these intermediates. Here, the unconventional hexagonal close-packed (HCP) high-entropy alloy (HEA) atomic layers are prepared composed of five platinum-group metals to enhance the alkaline HER synergistically. The breakthrough is made by layer-by-layer heteroepitaxial deposition of subnanometer RuRhPdPtIr HEA layers on the HCP Ru seeds, despite the thermodynamic stability of Rh, Pd, Pt, and Ir in a face-centered cubic (FCC) structure except for Ru. The synchrotron X-ray absorption spectroscopy (XAS) confirms the atomic mixing and coordination environment of HCP RuRhPdPtIr HEA. Most importantly, they exhibit notable improvements in both electrocatalytic activity and durability for the HER in an alkaline environment, as compared to their FCC RuRhPdPtIr counterparts. Electrochemical measurements, operando XAS analysis, and density functional theory unveil that the binding strengths of H* and OH* intermediates on the active Pt and Ir sites can be weakened and strengthened to a moderate level, respectively, by mixing non-active Ru, Rh, and Pd atoms with Pt and Ir atoms within the HCP HEA with strong synergistic electronic effects.

PGE2 Binding Affinity of Hemocyte Membrane Preparations of Manduca sexta and Identification of the Receptor-Associated G Proteins in Two Lepidopteran Species.

Prostaglandin E2 (PGE2) is an eicosanoid that mediates a range of physiological actions in vertebrates and invertebrates, including reproduction and immunity. The PGE2 receptor was identified and functionally assessed in two lepidopteran insects, Manduca sexta and Spodoptera exigua. However, its binding affinity to the receptor has not been reported. The PGE2 receptor is a G-protein coupled receptor (GPCR) although its corresponding G-protein is not identified. PGE2 binding assays were performed with membrane preparations from hemocytes of M. sexta larvae. We recorded an optimal binding in 4 h reactions conducted at pH 7.5 with 12 nM tritium-labeled PGE2. We found that hemocytes express a single population of PGE2 binding sites with a high affinity (Kd = 35 pmol/mg protein), which are specific and saturable. The outcomes of experiments on the influence of purine nucleotides suggested these are functional GPCRs. A bioinformatics analysis led to a proposed trimeric G-protein in the S. exigua transcriptome, in which the Gα subunit is classified into five different types: Gα(o), Gα(q), Gα(s), Gα(12), and Gα(f). After confirming expressions of these five types in S. exigua, individual RNA interference (RNAi) treatments were applied to the larvae using gene-specific double-stranded RNAs. RNAi treatments specific to Gα(s) or Gα(12) gene expression significantly suppressed the cellular immune responses although the RNAi treatments specific to other three Gα components did not. While PGE2 treatments led to elevated hemocyte cAMP or Ca2+ levels, the RNAi treatments specific to Gα(s) or Gα(12) genes led to significantly reduced second messenger levels under PGE2, although the RNAi treatments specific to the other three Gα components did not. These results showed that the PGE2 receptor has high PGE2 affinity in the nanomolar range and binds G-proteins containing a Gα(s) or Gα(12) trimeric component in S. exigua and M. sexta, and likely, all lepidopteran insects.

Reversible Multi‐Complexation of CO2 to Alkaline Earth Metal Ion‐Pair at 400 ppm and 298 K

AbstractThe efficient capture of low‐pressure CO2 remains a significant challenge due to the lack of established multi‐complexation of CO2 to active sites in microporous materials. In this study, we introduce a novel concept of reversible multi‐complexation of CO2 to alkaline earth metal (AEM) ion pairs, utilizing a host site in ferrierite‐type zeolite (FER). This unique site constrains two AEM ions in proximity, thereby enhancing and isotopically spreading their electrostatic potentials within the zeolite cavity. This electrostatic potential‐engineered micropore can trap up to four CO2 molecules, forming M2+−(CO2)n−M2+ (n=0–4, M=Ca, Sr, Ba) complexes, where each CO2 molecule is stabilized by interactions between terminal oxygen (Ot) in CO2 and the AEM ions. Notably, the Ba2+ pair site exhibits higher thermodynamic stability for multiple adsorptions due to the optimal binding mode of Ba2+−Ot−Ba2+. Through high‐accuracy energy calculations, we have established the relationship among structure, CO2 uptake, and operating temperature/pressure, demonstrating that the Ba2+ pair site can capture four CO2 molecules even at concentrations as low as 400 ppm and at 298 K. Three of the four molecules of CO2 trapped were removable at room temperature and under vacuum. The findings in the present study provide a new direction for developing efficient CO2 adsorbents.

Regulating transport efficiency through the nuclear pore complex: The role of binding affinity with FG-Nups.

Macromolecules are transported through the nuclear pore complex (NPC) via a series of transient binding and unbinding events with FG-Nups, which are intrinsically disordered proteins anchored to the pore's inner wall. Prior studies suggest that the weak and transient nature of this binding is crucial for maintaining the transported molecules' diffusivity. In this study, we explored the relationship between binding kinetics and transport efficiency using Brownian dynamics simulations. Our results indicate that the duration of binding is a critical factor in regulating transport efficiency. Specifically, excessively short binding durations insufficiently facilitate transport, while overly long durations impede molecular movement. We calculated the optimal binding duration for efficient molecular transport and found that it aligns with other theoretical predictions. Additionally, the calculated value is comparable to experimental measurements of the association timescale between nuclear transport receptors and FG-Nups at a single binding site. Our study provides a quantitative framework that bridges local molecular interactions with overall transport dynamics through the NPC, offering valuable insights into the mechanisms governing selective molecular transport.

De novo design of mIDH1 inhibitors by integrating deep learning and molecular modeling.

Mutations in the IDH1 gene have been shown to be an important driver in the development of acute myeloid leukemia, gliomas and certain solid tumors, which is a promising target for cancer therapy. Bidirectional recurrent neural network (BRNN) and scaffold hopping methods were used to generate new compounds, which were evaluated by principal components analysis, quantitative estimate of drug-likeness, synthetic accessibility analysis and molecular docking. ADME prediction, molecular docking and molecular dynamics simulations were used to screen candidate compounds and assess their binding affinity and binding stability with mutant IDH1 (mIDH1). BRNN and scaffold hopping methods generated 3890 and 3680 new compounds, respectively. The molecules generated by the BRNN performed better in terms of molecular diversity, druggability, synthetic accessibility and docking score. From the 3890 compounds generated by the BRNN model, 10 structurally diverse drug candidates with great docking score were preserved. Molecular dynamics simulations showed that the RMSD of the four systems, M1, M2, M3 and M6, remained stable, with local flexibility and compactness similar to the positive drug. The binding free energy results indicated that compound M1 exhibited the best binding properties in all energy aspects and was the best candidate molecule among the 10 compounds. In present study, compounds M1, M2, M3 and M6 generated by BRNN exhibited optimal binding properties. This study is the first attempt to use deep learning to design mIDH1 inhibitors, which provides theoretical guidance for the design of mIDH1 inhibitors.

New acetophenone scaffolds: Synthesis, antifungal activities, biocompatibility, molecular docking, ADMET analysis and dynamic simulations

In this work, the chemical reactivity of 2-cyano-N′-(1-phenylethylidene)acetohydrazide (3) towards different aldehydes is utilized to synthesize binary and fused heterocyclic compounds, including arylidenes 6, 7, 12, 13, 14, 18a-c, 19a,b, 20, chromone 23, and chromene derivatives 24, 26a-c, 29, and 30. The capability of newly synthesized compounds to inhibit fungal growth of Aspergillus niger ATCC 16404, A. flavus ATCC 9643, Penicillium chrysogenum ATCC 10106, and Rhizopus oryazae ATCC 96382 are assessed. It is observed that compound 29 had strong antifungal activity against all fungi with MFIC values varying from 250 to 1000 µg/ml, while compound 18a demonstrated potent antifungal effect against A. niger and A. flavus. In addition, it is found that compound 29 was cytotoxic to Vero cells at doses of 1000–500 µg/ml; however, no discernible variation was observed between the concentrations of 250–31.25 µg/ml. Moreover, the interactions between the promising compounds 18a, 19b, and 29 and antifungal target proteins are assessed using molecular docking. The results of the docking simulations demonstrated that these compounds demonstrated optimal binding energies and effectively engaged with the active sites of FDC1 protein in A. niger, UDP-N-acetylglucosamine in A. fumigatus, Adenosine 5′-phosphosulfate kinase in P. chrysogenum, and protease in Rhizopus oryazae. These interactions involved various types of molecular interactions, indicating that these compounds have the ability to impede enzymes and exhibit strong antimicrobial effects. Furthermore, the in-silico ADMET profiles of compounds 18a, 19b, and 29 reveal that they adhere to the Lipinski rules, suggesting favorable physicochemical properties. Also, MD simulations revealed stable complexes of 29 with anti-fungal receptors including fdc1, UDP-N-acetylglucosamine, APS kinase, and protease with RMSD (0.1–0.8, 0.19–0.25, 0.20–0.30, and 0.20–0.35 nm), RMSF (0.1–0.8 nm), SASA (140–155, 130–140, 135–145, and 120–130 nm2), and Rg (1.90–2.00, 1.80–1.90, 2.40–2.50, and 2.10–2.20 nm) respectively. Our results provide potential and promising compounds for fungal infection diseases.

The homeodomain regulates stable DNA binding of prostate cancer target ONECUT2.

The CUT and homeodomain are ubiquitous DNA binding elements often tandemly arranged in multiple transcription factor families. However, how the CUT and homeodomain work concertedly to bind DNA remains unknown. Using ONECUT2, a driver and therapeutic target of advanced prostate cancer, we show that while the CUT initiates DNA binding, the homeodomain thermodynamically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT. We identify an arginine pair in the ONECUT family homeodomain that can adapt to DNA sequence variations. Base interactions by this ONECUT family-specific arginine pair as well as the evolutionarily conserved residues are critical for optimal DNA binding and ONECUT2 transcriptional activity in a prostate cancer model. The evolutionarily conserved base interactions additionally determine the ONECUT2-DNA binding energetics. These findings provide insights into the cooperative DNA binding by CUT-homeodomain proteins.

Identification of Novel PPARγ Partial Agonists Based on Virtual Screening Strategy: In Silico and In Vitro Experimental Validation.

Thiazolidinediones (TZDs) including rosiglitazone and pioglitazone function as peroxisome proliferator-activated receptor gamma (PPARγ) full agonists, which have been known as a class to be among the most effective drugs for the treatment of type 2 diabetes mellitus (T2DM). However, side effects of TZDs such as fluid retention and weight gain are associated with their full agonistic activities toward PPARγ induced by the AF-2 helix-involved "locked" mechanism. Thereby, this study aimed to obtain novel PPARγ partial agonists without direct interaction with the AF-2 helix. Through performing virtual screening of the Targetmol L6000 Natural Product Library and utilizing molecular dynamics (MD) simulation, as well as molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis, four compounds including tubuloside b, podophyllotoxone, endomorphin 1 and paliperidone were identified as potential PPARγ partial agonists. An in vitro TR-FRET competitive binding assay showed podophyllotoxone displayed the optimal binding affinity toward PPARγ among the screened compounds, exhibiting IC50 and ki values of 27.43 µM and 9.86 µM, respectively. Further cell-based transcription assays were conducted and demonstrated podophyllotoxone's weak agonistic activity against PPARγ compared to that of the PPARγ full agonist rosiglitazone. These results collectively demonstrated that podophyllotoxone could serve as a PPARγ partial agonist and might provide a novel candidate for the treatment of various diseases such as T2DM.

Exploring the Mechanisms of Self-made Kuiyu Pingchang Recipe for the Treatment of Ulcerative Colitis and Irritable Bowel Syndrome using a Network Pharmacology-based Approach and Molecular Docking.

Ulcerative colitis (UC) and irritable bowel syndrome (IBS) are common intestinal diseases. According to the clinical experience and curative effect, the authors formulated Kuiyu Pingchang Decoction (KYPCD) comprised of Paeoniae radix alba, Aurantii Fructus, Herba euphorbiae humifusae, Lasiosphaera seu Calvatia, Angelicae sinensis radix, Panax ginseng C.A. Mey., Platycodon grandiforus and Allium azureum Ledeb. The aim of the present study was to explore the mechanisms of KYPCD in the treatment of UC and IBS following the Traditional Chinese Medicine (TCM) theory of "Treating different diseases with the same treatment". The chemical ingredients and targets of KYPCD were obtained using the Traditional Chinese Medicine Systems Pharmacology database and analysis platform (TCMSP). The targets of UC and IBS were extracted using the DisGeNET, GeneCards, DrugBANK, OMIM and TTD databases. The "TCM-component-target" network and the "TCM-shared target-disease" network were imaged using Cytoscape software. The protein-protein interaction (PPI) network was built using the STRING database. The DAVID platform was used to analyze the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Using Autodock Tools software, the main active components of KYPCD were molecularly docked with their targets and visualized using PyMOL. A total of 46 active ingredients of KYPCD corresponding to 243 potential targets, 1,565 targets of UC and 1,062 targets of IBS, and 70 targets among active ingredients and two diseases were screened. Core targets in the PPI network included IL6, TNF, AKT1, IL1B, TP53, EGFR and VEGFA. GO and KEGG enrichment analysis demonstrated 563 biological processes, 48 cellular components, 82 molecular functions and 144 signaling pathways. KEGG enrichment results revealed that the regulated pathways were mainly related to the PI3K-AKT, MAPK, HIF-1 and IL-17 pathways. The results of molecular docking analysis indicated that the core active ingredients of KYPCD had optimal binding activity to their corresponding targets. KYPCD may use IL6, TNF, AKT1, IL1B, TP53, EGFR and VEGFA as the key targets to achieve the treatment of UC and IBS through the PI3K-AKT, MAPK, HIF-1 and IL-17 pathways.

Screening Transition-Metal-Incorporated β-AgVO3 for Augmented Oxygen Reduction Activity.

Exploring cost-effective alternatives to Pt-based catalysts for the oxygen reduction reaction (ORR) in fuel cells is crucial for their large-scale deployment in green energy applications. Silver vanadate (AgVO3) is a well-studied material for photocatalytic applications. Here, we investigate the electrocatalytic ORR activity of the thermodynamically stable β phase of AgVO3 through computational modeling based on DFT. It is found that β-AgVO3 exhibits weak catalytic activity for the ORR, with vanadium being the preferable active site. Incorporating single atoms of transition metals at surface-level vacancies in β-AgVO3 significantly modifies the ORR activity. We study the scaling of free energy changes for the ORR intermediates *OOH, *OH, and *O for various transition metals incorporated, which leads to an optimal overpotential for the system. The optimal overpotential thus obtained is remarkably lower than that of pristine β-AgVO3. For the transition metal atoms we consider here, Co-incorporated β-AgVO3 exhibits the best ORR catalytic activity due to its optimal binding of ORR species to the vanadium site. It is also observed that some of the transition metals considered like Re, Rh, Os, or Mn show weak activity, either due to strong or weak binding. Analysis of the electronic structure of the adsorbate-catalyst interface shows a strong correlation between optimal activity and evolution of midgap states in β-AgVO3, due to transition metal incorporation. Our study concludes that the ORR activity of a stable mixed transition metal oxide like β-AgVO3 can be enhanced with a minimal loading of transition metals, which could help in developing a novel series of ORR catalysts.

Generating globin-like reactivities in [human serum albumin-FeII(heme)] complex through N-donor ligand addition

Human serum albumin (HSA) has a strong binding affinity for heme b, forming a complex in a 1:1 ratio with the co-factor ([HSA-FeIIIheme]). This system displays spectroscopic and functional properties comparable to globins when chemical derivatives mimicking them are incorporated into the protein matrix. The aim of this study is to generate globin-like systems using [HSA-FeIIIheme] as a protein template and binding N-donor ligands (imidazole, Im; and 1-methylimidazole, 1-MeIm) to construct artificial [HSA-Fe(heme)-(N-donor)] complexes. Their electronic structure and binding thermodynamics are investigated using UV–vis and (synchronous) fluorescence spectroscopies, while ligand-protein interactions are visualized using docking simulations. The imidazole derivatives have a strong affinity for [HSA-FeIIIheme] (K ~ 104–106), where the spontaneous binding of Im and 1-MeIm are dominated by entropic and enthalpic effects, respectively. The reduced form of the [HSA-Fe(heme)-(N-donor)] complexes demonstrate nitrite reductase (NiR) activity similar to that observed in globins, but with significant differences in their rates. [HSA-FeIIheme-(1-MeIm)] reduces nitrite ~4× faster than the Im analogue, and ~ 30× faster than myoglobin (Mb). The enhanced NiR activity of [HSA-FeIIheme-(1-MeIm)] is a cumulative effect of several factors including a slightly expanded and more optimal heme binding pocket, nearby residues as possible proton sources, and a H-bonding interaction between 1-MeIm and residues Arg160 and Lys181 that may have a long-distance influence on the heme π electron density.

Exploration of modified β-cyclodextrin compounds as enhanced eco-friendly and easily accessible corrosion inhibitors for carbon steel in hydrochloric acid

β-CD was esterified independently with two distinct ionic liquids to evaluate their potential as corrosion inhibitors for carbon steel in a 1.0 M HCl solution. Experimental and computational methods were used to assess the inhibitors’ efficiency regarding temperature and concentration effects and to elucidate the adsorption mechanism. Both inhibitors acted as barriers, with a maximum inhibition efficiency of about 94 % at 200 ppm. There was a direct relationship between the inhibitor's concentration and their efficiency, while increasing the temperature reduced the inhibitors’ effectiveness. The thermodynamic and kinetic parameters were evaluated and studied. DFT calculation revealed the electronic structure and reactivity of the inhibitors. Molecular dynamic simulation provided insight into the optimal configuration and binding energies of inhibitors on the Fe (110) surface.

Reversible Multi-Complexation of CO2 to Alkaline Earth Metal Ion-Pair at 400 ppm and 298 K.

The efficient capture of low-pressure CO2 remains a significant challenge due to the lack of established multi-complexation of CO2 to active sites in microporous materials. In this study, we introduce a novel concept of reversible multi-complexation of CO2 to alkaline earth metal (AEM) ion pairs, utilizing a host site in ferrierite-type zeolite (FER). This unique site constrains two AEM ions in proximity, thereby enhancing and isotopically spreading their electrostatic potentials within the zeolite cavity. This electrostatic potential-engineered micropore can trap up to four CO2 molecules, forming M2+-(CO2)n-M2+ (n = 0-4, M = Ca, Sr, Ba) complexes, where each CO2 molecule is stabilized by interactions between terminal oxygen (Ot) in CO2 and the AEM ions. Notably, the Ba2+ pair site exhibits higher thermodynamic stability for multiple adsorptions due to the optimal binding mode of Ba2+-Ot-Ba2+. Through high-accuracy energy calculations, we established the relationship among structure, CO2 uptake, and operating temperature/pressure, demonstrating that the Ba2+ pair site can reversibly capture four CO2 molecules even at concentrations as low as 400 ppm and at 298 K. The findings in the present study provide a new direction for developing efficient CO2 adsorbents.

Orbital coupling of Pt single crystal via decoration of hetero-diatomic nickel-cobalt for efficient hydrogen evolution

Loading active metals in forms of single atoms or nanocluster is considered as an effective approach for designing catalysts with high atomic utilization efficiency. However, synthesis single atoms or clusters precisely in large quantities is a challenge. In this work, the isolated diatomic sites (Ni, Co) decorated single crystal Pt cluster were synthesized as efficient catalyst for hydrogen evolution. Adjacent Ni and Co atoms optimize the electronic structure of Pt single crystal, effectively lowering the water dissociation barrier and ensuring optimal binding strength of intermediates throughout the reaction process. As results, the mass activity of 2.087 A mg−1 was achieved under 200 mA cm−2, approximately 3 times than that of Pt/C. Theoretical calculations reveal that diatomic Ni, Co decorated Pt cluster reduces the energy barrier for breaking the OH-H bond, as well as facilitating the preferential adsorption and dissociation of H*. This work provides an opportunity for regulation electronic structure of catalytic via decoration single crystal cluster with diatomic sites and provides guidance for designing high efficiency electrocatalysts for promising applications.

Basics of the reaction kinetics on metallic alloys.

Kinetics of heterogeneous catalytic reactions are often complicated by various factors, and from the perspective of statistical physics the development of the corresponding models is frequently challenging especially in the case of practically important alloy catalysts. To extend the basics in this area, I use a generic kinetic model of N_{2} formation inthe NO reaction with such species as CO or H_{2}. The focus is onthe reaction on the surface of a bimetallic alloy with low integral fraction of one of the metals so that the alloy is formed only at the surface. The main goal is to illustrate the specifics of the reaction kinetics and to clarify the accuracy of various approximations which are often inevitable for the analysis of such systems. The key results are as follows. (i) In the baseline one-metal case with the Langmuir-type equations, the model predicts the existence of the optimal adsorbate binding energy corresponding to the maximal reaction rate. (ii) With suitable substitution of the symbols, the equations employed for a uniform surface [item (i)] can be used for the mean-field description of reaction on the surface of a random alloy. In particular, the maximum in the dependence of the reaction rate on the binding energy is converted to the maximum with respect to the alloy composition. (iii) The reaction kinetics on the random-alloy surface have been described exactly. The corresponding maximum in the reaction rate is lower and somewhat smeared compared to that predicted in the mean-field approximation for an alloy or for the optimal monometallic catalyst. (iv) The reaction kinetics have been scrutinized also in the case of two-dimensional (2D) segregation of metal atoms at the surface in the limits of slow and rapid adsorbate diffusion between the spots. The kinetics are shown to be qualitatively different in these limits and also compared to the random-alloy case. (v) The thermodynamic criteria for 2D segregation of metal atoms at the surface have been derived as well.

Gardenin B, A Natural Inhibitor for USP7: In vitro Evaluation and In silico Identification

Background: Ubiquitin-specific protease 7 (USP7) is one of the most widely studied deubiquitin enzymes (DUBs). The protein level of USP7 is highly expressed in a variety of malignant cancers, which suggests that it is a prognostic marker of cancers and a potential drug target for oncotherapy. Objective: The aim of this study was to identify natural and effective USP7 inhibitors, in order to understand the activation of the USP7/p53 pathway by natural inhibitors. Methods: In this study, USP7 enzyme activity screening assay system and p53 luciferase reporter assay system have been applied for the discovery of natural USP7 inhibitors targeting the catalytic active site. Molecular docking and molecular dynamics (MD) simulation revealed the combined mechanism between USP7 with gardenin B. Results: The gardenin B was screened from our home-lab natural products (160 flavonoids) and had cytotoxicity in HCT116 cells (IC50 = 46.28 ± 2.16 μM). Preliminary in vitro studies disclosed its antiproliferative activity and activated p53 signaling pathway in HCT116 cells. We found that the complex formed by gardenin B and 5vsk (Ledock score = -6.86, MM/GBSA score = -53.35) had the optimal binding conformation. Moreover, the MD simulation showed that the π-π interactions between gardenin B with His461 and Phe409, and the hydrogen bonds interaction between gardenin B with Leu406 played an important role in maintaining the close binding of the complexes. Conclusion: In conclusion, gardenin B could be used as a natural product inhibitor of USP7 for further optimized design and development potential.