Impacts of Nutlin-3a and exercise on murine double minute 2-enriched glioma treatment

JOURNAL/nrgr/04.03/01300535-202504000-00029/figure1/v/2024-07-06T104127Z/r/image-tiff Recent research has demonstrated the impact of physical activity on the prognosis of glioma patients, with evidence suggesting exercise may reduce mortality risks and aid neural regeneration. The role of the small ubiquitin-like modifier (SUMO) protein, especially post-exercise, in cancer progression, is gaining attention, as are the potential anti-cancer effects of SUMOylation. We used machine learning to create the exercise and SUMO-related gene signature (ESLRS). This signature shows how physical activity might help improve the outlook for low-grade glioma and other cancers. We demonstrated the prognostic and immunotherapeutic significance of ESLRS markers, specifically highlighting how murine double minute 2 (MDM2), a component of the ESLRS, can be targeted by nutlin-3. This underscores the intricate relationship between natural compounds such as nutlin-3 and immune regulation. Using comprehensive CRISPR screening, we validated the effects of specific ESLRS genes on low-grade glioma progression. We also revealed insights into the effectiveness of Nutlin-3a as a potent MDM2 inhibitor through molecular docking and dynamic simulation. Nutlin-3a inhibited glioma cell proliferation and activated the p53 pathway. Its efficacy decreased with MDM2 overexpression, and this was reversed by Nutlin-3a or exercise. Experiments using a low-grade glioma mouse model highlighted the effect of physical activity on oxidative stress and molecular pathway regulation. Notably, both physical exercise and Nutlin-3a administration improved physical function in mice bearing tumors derived from MDM2-overexpressing cells. These results suggest the potential for Nutlin-3a, an MDM2 inhibitor, with physical exercise as a therapeutic approach for glioma management. Our research also supports the use of natural products for therapy and sheds light on the interaction of exercise, natural products, and immune regulation in cancer treatment.

Effect of surface species on the alcohol-acid adsorption from FTS wastewater on graphene: A structure-capacity study

Fischer-Tropsch synthesis (FTS) wastewater retaining low-carbon alcohols and acids are organic pollutants as a limiting factor for FTS industrialization. In this work, the structure-capacity relationships between alcohol-acid adsorption and surface species on graphene were reported, shedding light into their intricate interactions. The graphene oxide (GO) and reduced graphene oxide (rGO) were synthesized via improved Hummers method with flake graphite (G). The physicochemical properties of samples were characterized via SEM, XRD, XPS, FT-IR, and Raman. The alcohol-acid adsorption behaviors and adsorption quantities on G, GO, and rGO were measured via theoretical and experimental method. It was revealed that the presence of COOH, C=O and CO species on graphene occupy the adsorption sites and increase the interactions of water with graphene, which are unfavorable for alcohol-acid adsorption. The equilibrium adsorption quantities of alcohols and acids grow in pace with carbon number. The monolayer adsorption occurs on graphene was verified via model fitting. rGO has the highest FTS modeling wastewater adsorption quantity (110 mg/g) due to the reduction of oxygen species. These novel findings provide a foundation for the alcohol-acid wastewater treatment, as well as the design and development of high-performance carbon-based adsorbent materials.

Barrierless reactions of C2 Criegee intermediates with H2SO4 and their implication to oligomers and new particle formation

The formation of oligomeric hydrogen peroxide triggered by Criegee intermediate maybe contributes significantly to the formation and growth of secondary organic aerosol (SOA). However, to date, the reactivity of C2 Criegee intermediates (CH3CHOO) in areas contaminated with acidic gas remains poorly understood. Herein, high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations are used to explore the reaction of CH3CHOO and H2SO4 both in the gas phase and at the air-water interface. In the gas phase, the addition reaction of CH3CHOO with H2SO4 to generate CH3HC(OOH)OSO3H (HPES) is near-barrierless, regardless of the presence of water molecules. BOMD simulations show that the reaction at the air-water interface is even faster than that in the gas phase. Further calculations reveal that the HPES has a tendency to aggregate with sulfuric acids, ammonias, and water molecules to form stable clusters, meanwhile the oligomerization reaction of CH3CHOO with HPES in the gas phase is both thermochemically and kinetically favored. Also, it is noted that the interfacial HPES- ion can attract H2SO4, NH3, (COOH)2 and HNO3 for particle formation from the gas phase to the water surface. Thus, the results of this work not only elucidate the high atmospheric reactivity of C2 Criegee intermediates in polluted regions, but also deepen our understanding of the formation process of atmospheric SOA induced by Criegee intermediates.

Tailored design of novel Co0-Coδ+ dual phase nanoparticles for selective CO2 hydrogenation to ethanol

Catalytic hydrogenation of CO2 to ethanol is a promising solution to address the greenhouse gas (GHG) emissions, but many current catalysts face efficiency and cost challenges. Cobalt based catalysts are frequently examined due to their abundance, cost-efficiency, and effectiveness in the reaction, where managing the Co0 to Coδ+ ratio is essential. In this study, we adjusted support nature (Al2O3, MgO-MgAl2O4, and MgO) and reduction conditions to optimize this balance of Co0 to Coδ+ sites on the catalyst surface, enhancing ethanol production. The selectivity of ethanol reached 17.9% in a continuous flow fixed bed micro-reactor over 20 mol% Co@MgO-MgAl2O4 (CoMgAl) catalyst at 270 °C and 3.0 MPa, when reduced at 400 °C for 8 h. Characterisation results coupled with activity analysis confirmed that mild reduction condition (400 °C, 10% H2 balance N2, 8 h) with intermediate metal support interaction favoured the generation of partially reduced Co sites (Coδ+ and Co0 sites in single atom) over MgO-MgAl2O4 surface, which promoted ethanol synthesis by coupling of dissociative (CHx*)/non-dissociative (CHxO*) intermediates, as confirmed by density functional theory analysis. Additionally, the CoMgAl, affordably prepared through the coprecipitation method, offers a potential alternative for CO2 hydrogenation to yield valuable chemicals.

Theoretical calculation on degradation mechanism of novel copolyesters under CALB enzyme

Poly(butylene succinate-co-furandicarboxylate) (PBSF) and poly(butylene adipate-co-furandicarboxylate) (PBAF) are novel furandicarboxylic acid-based biodegradable copolyesters with great potential to replace fossil-derived terephthalic acid-based copolyesters such as poly(butylene succinate-co-terephthalate) (PBST) and poly(butylene adipate-co-terephthalate) (PBAT). In this study, quantum chemistry techniques after molecular dynamics simulations are employed to investigate the degradation mechanism of PBSF and PBAF catalyzed by Candida antarctica lipase B (CALB). Computational analysis indicates that the catalytic reaction follows a four-step mechanism resembling the ping-pong bibi mechanism, with the initial two steps being acylation reactions and the subsequent two being hydrolysis reactions. Notably, the first step of the hydrolysis is identified as the rate-determining step. Moreover, by introducing single-point mutations to expand the substrate entrance tunnel, the catalytic distance of the first acylation step decreases. Additionally, energy barrier of the rate-determining step is decreased in the PBSF system by site-directed mutations on key residues increasing hydrophobicity of the enzyme's active site. This study unprecedently show the substrate binding pocket and hydrophobicity of the enzyme's active site have the potential to be engineered to enhance the degradation of copolyesters catalyzed by CALB.

The role of sulfur cycle in new particle formation: Cycloaddition reaction of SO3 to H2S

The chemistry of sulfur cycle contributes significantly to the atmospheric nucleation process, which is the first step of new particle formation (NPF). In the present study, cycloaddition reaction mechanism of sulfur trioxide (SO3) to hydrogen sulfide (H2S) which is a typical air pollutant and toxic gas detrimental to the environment were comprehensively investigate through theoretical calculations and Atmospheric Cluster Dynamic Code simulations. Gas-phase stability and nucleation potential of the product thiosulfuric acid (H2S2O3, TSA) were further analyzed to evaluate its atmospheric impact. Without any catalysts, the H2S + SO3 reaction is infeasible with a barrier of 24.2 kcal/mol. Atmospheric nucleation precursors formic acid (FA), sulfuric acid (SA), and water (H2O) could effectively lower the reaction barriers as catalysts, even to a barrierless reaction with the efficiency of cis-SA > trans-FA > trans-SA > H2O. Subsequently, the gas-phase stability of TSA was investigated. A hydrolysis reaction barrier of up to 61.4 kcal/mol alone with an endothermic isomerization reaction barrier of 5.1 kcal/mol under the catalytic effect of SA demonstrates the sufficient stability of TSA. Furthermore, topological and kinetic analysis were conducted to determine the nucleation potential of TSA. Atmospheric clusters formed by TSA and atmospheric nucleation precursors (SA, ammonia NH3, and dimethylamine DMA) were thermodynamically stable. Moreover, the gradually decreasing evaporation coefficients for TSA-base clusters, particularly for TSA-DMA, suggests that TSA may participate in NPF where the concentration of base molecules are relatively higher. The present new reaction mechanism may contributes to a better understanding of atmospheric sulfur cycle and NPF.

Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures

JOURNAL/nrgr/04.03/01300535-202501000-00034/figure1/v/2024-05-14T021156Z/r/image-tiff Certain amino acids changes in the human Na+/K+-ATPase pump, ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1), cause Charcot-Marie-Tooth disease type 2 (CMT2) disease and refractory seizures. To develop in vivo models to study the role of Na+/K+-ATPase in these diseases, we modified the Drosophila gene homolog, Atpα, to mimic the human ATP1A1 gene mutations that cause CMT2. Mutations located within the helical linker region of human ATP1A1 (I592T, A597T, P600T, and D601F) were simultaneously introduced into endogenous DrosophilaAtpα by CRISPR/Cas9-mediated genome editing, generating the AtpαTTTF model. In addition, the same strategy was used to generate the corresponding single point mutations in flies (AtpαI571T, AtpαA576T, AtpαP579T, and AtpαD580F). Moreover, a deletion mutation (Atpαmut) that causes premature termination of translation was generated as a positive control. Of these alleles, we found two that could be maintained as homozygotes (AtpαI571T and AtpαP579T). Three alleles (AtpαA576T, AtpαP579 and AtpαD580F) can form heterozygotes with the Atpαmut allele. We found that the Atpα allele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila. Flies heterozygous for AtpαTTTF mutations have motor performance defects, a reduced lifespan, seizures, and an abnormal neuronal morphology. These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump.

Ozonolysis of ketoprofen in polluted water: Reaction pathways, kinetics, removal efficiency, and health effects

Ketoprofen (KET), as a non-steroidal anti-inflammatory drug frequently detected in aqueous environments, is a threat to human health due to its accumulation and low biodegradability, which requires the transformation and degradation of KET in aqueous environments. In this paper, the reaction process of ozone-initiated KET degradation in water was investigated using density functional theory (DFT) method at the M06-2X/6-311++g(3df,2p)//M06-2X/6-31+g(d,p) level. The detailed reaction path of KET ozonation is proposed. The thermodynamic results show that ozone-initiated KET degradation is feasible. Under ultraviolet irradiation, the reaction of ozone with water can also produce OH radicals (HO·) that can react with KET. The degradation reaction of KET caused by HO· was further studied. The kinetic calculation illustrates that the reaction rate (1.99 × 10-1 (mol/L)-1 sec-1) of KET ozonation is relatively slow, but the reaction rate of HO· reaction is relatively high, which can further improve the degradation efficiency. On this basis, the effects of pollutant concentration, ozone concentration, natural organic matter, and pH value on degradation efficiency under UV/O3 process were analyzed. The ozonolysis reaction of KET is not sensitive to pH and is basically unaffected. Finally, the toxicity prediction of oxidation compounds produced by degradation reaction indicates that most of the degradation products are harmless, and a few products containing benzene rings are still toxic and have to be concerned. This study serves as a theoretical basis for analyzing the migration and transformation process of anti-inflammatory compounds in the water environment.

Mechanism investigation of Forsythoside A against esophageal squamous cell carcinoma in vitro and in vivo

CONTEXT

Forsythoside A (FSA) was extracted from Forsythia suspensa, a traditional Chinese medicine, which has been demonstrated to exert anti-inflammatory, antibacterial, and other pharmacological effects. However, the anticancer effect of FSA in esophageal squamous cell carcinoma (ESCC) has not been documented.

OBJECTIVE

The present study aimed to elucidate the mechanism of FSA against ESCC.

MATERIALS AND METHODS

Network pharmacology and molecular docking were employed to predict the mechanism. FSA was utilized to treat ESCC cell lines KYSE450 and KYSE30, followed by CCK-8 assay, cell cloning formation assay, flow cytometry, Western blot, RNA-seq analysis, and subsequent in vivo experiments.

RESULTS

Network pharmacology and molecular docking predicted that the therapeutic effect of FSA in ESCC is mediated through proteins such as BCL2 and BAX, influencing KEGG pathways associated with apoptosis. In vitro experiments showed that FSA inhibited cell proliferation and plate clone formation, promoted cell apoptosis and impacted the cell cycle distribution of G2/M phase by regulating BCL2, BAX, and p21. Further RNA-seq in KYSE450 cells showed that FSA regulated the expression of 223 genes, specifically affecting the biological process of epidermal development. In vivo experiments showed that gastric administration of FSA resulted in notable reductions in both tumor volume and weight by regulating BCL2, BAX, and p21. 16S rRNA sequencing showed that FSA led to significant changes of beta diversity. Abundance of 11 specific bacterial taxa were considerably changed following administration of FSA.

CONCLUSIONS

This study presents a novel candidate drug against ESCC and establishes a foundation for future clinical application.

Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics

Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.

A ratiometric fluorescence method for the detection of diquat by a large Stokes shift fluorescent probe

Pesticide residues are currently a prominent concern for food safety, and the development of a rapid, convenient, and accurate method for detecting pesticide residues is crucial to ensure the quality of agricultural products. In this study, a small molecule fluorescent probe based on biphenyl disulfonic acid (BDSA) was designed and prepared, and a sensitive, specific, and rapid detection method for diquat (DQ) and paraquat (PQ) was developed. The fluorescent molecule (BDSA-NDA) was synthesized through amide reaction between BDSA and 1,8-naphthalic anhydride, which exhibited cyan fluorescence (480 nm) when excited at 305 nm in aqueous solution with a large Stokes shift (>150 nm). Diquat and paraquat were found to quench the fluorescence of the probe through internal filtration effect (IFE) and photoelectron transfer (PET). Moreover, diquat possessed a large conjugated structure that emitted fluorescence at 340 nm which was assembled into a pair of ratio fluorescence with BDSA-NDA. Under optimized experimental conditions, the developed method achieved detection limits of 0.003 mg/L for diquat and 0.202 mg/L for paraquat. Furthermore, it could identify paraquat doped in diquat formulations. Additionally, when applied to environmental water samples as well as rice and urine, this detection method demonstrated good recovery rates (water: 96.2-100.6 %, rice: 93.5-101.9 %, urine: 96-103.7 %), meeting actual sample detection requirements effectively. This work presents a novel approach for rapidly detecting diquat and paraquat residues which holds practical application value in areas such as pesticide residue analysis in foods, environmental or clinical samples.

The third-order nonlinear optical responses of zinc porphyrin oligomers: Cycles vs linear chains

Porphyrins are widely used as potential nonlinear optical (NLO) materials because of their highly delocalized π electrons and feasible synthesis and functionalization with broad biological applications. A variety of linear and cyclic porphyrin derivatives have been synthesized, and the correlation between their structures and NLO properties awaits being disclosed. In this work, the electronic structures and third-order NLO properties of linear and cyclic butadiyne-linked zinc porphyrin oligomers have been studied by quantum chemical methods and sum-over-states model. The static second hyperpolarizability (<γ0>) increases exponentially with the number of zinc porphyrin units ([<γ0>n] = 0.67[<γ0>1]n2.63, n = 2 ∼ 6) in linear π-conjugated oligomers, and the <γ0> of the linear hexamer is about 74 times that of the monomer. Such enhancement of <γ0> in linear oligomers originates from closely-lying frontier molecular orbitals available for low energy electron excitations and strong charge transfer-based excitations across porphyrins. The <γ0>s of cyclic porphyrins are lower than that of the linear hexamer, though the interaction between the ring and the ligand enhances the <γ0> of some cyclic zinc porphyrin complexes. The large two-photon absorption cross sections confer on these zinc porphyrin derivatives excellent candidates for two-photon absorption applications.

Elucidation of the hydration pattern of trifluoroacetic acid in dilute solutions: FTIR and computational study

The atmospheric partitioning of trifluoroacetic acid (TFA) in aerosol is a complex function of the size of suspended water droplets and their pH value. The unraveling of the affinity of TFA towards basic but not acidic conditions may be accomplished by providing an insight into the hydration pattern of undissociated TFA. Owing to rather scarce details on very dilute aqueous solutions of trifluoroacetic acid (TFA), we examined CF3COOD and CF3COONa solutions in D2O in the concentration range 0.001-0.1 mol dm-3 using transmission FTIR spectroscopy and computational methods. Besides detecting the signals originated from undissociated species in both CF3COOD (1787 cm-1 and 1766 cm-1 at c0 = 0.1 mol dm-3) and CF3COONa (1807 cm-1 at c0 = 0.1 mol dm-3) D2O solutions, through computational techniques we identified different TFA hydrates that contribute to the complexity of the spectral appearance. The combination of experimental and computational data suggested the concentration dependence of the predominant hydrogen bonding pattern of TFA. The results obtained in this work should help in understanding the partitioning of TFA into micron-size water droplets in the atmosphere in molecular and structural terms, i.e. the eventual stability of a hydrated complex for a particular TFA conformer.

Multiple pathways for lanthanide sensitization in self-assembled aqueous complexes

Lanthanide photoluminescence (PL) emission has attracted much attention for technological and bioimaging applications because of its particularly interesting features, such as narrow emission bands and very long PL lifetimes. However, this emission process necessitates a preceding step of energy transfer from suitable antennas. While biocompatible applications require luminophores that are stable in aqueous media, most lanthanide-based emitters are quenched by water molecules. Previously, we described a small luminophore, 8-methoxy-2-oxo-1,2,4,5-tetrahydrocyclopenta[de]quinoline-3-phosphonic acid (PAnt), which is capable of dynamically coordinating with Tb(III) and Eu(III), and its exchangeable behavior improved their performance in PL lifetime imaging microscopy (PLIM) compared with conventional lanthanide cryptate imaging agents. Herein, we report an in-depth photophysical and time-dependent density functional theory (TD-DFT) computational study that reveals different sensitization mechanisms for Eu(III) and Tb(III) in stable complexes formed in water. Understanding this unique behavior in aqueous media enables the exploration of different applications in bioimaging or novel emitting materials.

DFT studies on N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl)

In this work, molecular descriptors of N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl) halogenated benzamides (1a-h) have been computed using a quantum chemical technique through DFT. Prior work involved the synthesis of compounds (1a-h) and the assessment of their anticancer activity on breast, colon, and liver tumors: MCF-7, HCT-116, and HepG-2 cell lines respectively. Since 1a, 1b, and 1d showed the most potential anticancer impact, their ability to inhibit EGFRWT was investigated. Based on the biological data, 1b inhibited EGFRWT the most. According to the docking evaluation, an H-bond with the threonine residue was one of the main non-covalent contacts between 1b and the EGFRWT active site residues. PES, MESP, HOMOs, LUMOs, energy band gap, global reactivity indices [electron affinity (A), ionization energies (I), electrophilicity index (ω), nucleophilicity index (ε), chemical potential (μ), electronegativity (χ), hardness (η), and softness (S)], condensed Fukui functions, NBO, and NCIs are the molecular descriptors of 1a-h that were computed using DFT technique. According to the theoretical investigation results, compounds (1a-h) might have anticancer effects; these findings are consistent with the biological findings from our previous research. Compound 1b had the lowest binding energy, according to an assessment of the binding energies between the threonine and the three most active compounds (1a, 1b, and 1d). This is consistent with the outcomes of the docking study and the biological examination of the influence of 1a, 1b, and 1d on EGFRWT.

An Eu (III)-functionalized covalent organic framework fluorescent probe for specific detection of Flumequine based on pore restriction and antenna effect

The overuse of quinolone antibiotics has led to a series of health and environmental issues. Herein, we combine the distinct luminescence properties of Eu3+ with the unique structure of covalent organic frameworks (COFs) to develop a precise and sensitive fluorescent probe for detecting Flumequine (Flu) in water. Eu3+ is thoroughly anchored into the channels of COFs as recognition sites, while the synthesized probe material still maintains its intact framework structure. The unique structure of COFs provides excellent support and protection for Eu3+. Therefore, COF-Eu can rapidly bind with Flu which can transfer the absorbed energy to Eu3+ through an "antenna effect", resulting in red fluorescence. Moreover, there is a good linear relationship between Flu concentration in the range of 0-30 µM, with a detection limit of 41 nM. Simultaneously, the material maintains remarkable reproducibility, with its performance remaining almost unchanged after five cycles of use. Remarkably, the probe demonstrates excellent Flu recovery rates in real samples. This study provides a viable approach for the recognition of flumequine in the environment through a customized fluorescence detection method.

Sensing mechanism of the benzo-bodipy based fluorescent probe for Hypochlorous acid detection: Invalidity of photoinduced electron transfer

In vivo real-time detection of hypochlorous acid (HClO) in biological systems plays a crucial role in diagnosing immune-related diseases. Experimentally, a benzo-bodipy probe based on the photo-induced electron transfer (PeT) sensing mechanism has been developed for live fluorescence imaging. However, there have been no theoretical studies conducted to substantiate the precision of the sensing mechanism. This paper employs density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods to investigate the fluorescence detection mechanism of benzo-bodipy derivatives (BBy-T and BBy-TO), proposing a detection approach based on dark nπ* state quenching. The study reveals that the fluorescence quenching mechanism of BBy-T is primarily regulated by a thiomorpholine moiety, involving a dark nπ* state transition non-radiatively. Furthermore, this paper explains the fluorescence enhancement observed in BBy-TO. Theoretical investigations demonstrate, based on frontier molecular orbitals (FMOs) and hole-electron analysis, that the fluorescence enhancement for BBy-TO is not governed by the previously proposed intramolecular charge transfer (ICT) mechanism in experiments but rather follows a locally excited (LE) ππ* pattern. This work offers new insights for the design of novel fluorescence probes based on bodipy and benzo derivatives, expanding the understanding of their fluorescence properties.

Interaction of plant phenol vanillin with human hemoglobin: A spectroscopic and molecular docking study

Vanillin is a phenolic aldehyde widely used as a flavouring agent in the food industry. Vanillin has many health benefits and has gained attention in pharmacological industries also, due to its antioxidant properties and non-toxic nature. The interaction of vanillin with human hemoglobin (hHb), an abundant tetrameric heme protein, was investigated by several spectroscopic techniques and molecular modeling methods. UV-visible spectra showed that the binding of vanillin to hHb induces structural changes due to alterations in the micro-environment of hHb. Vanillin quenches the intrinsic fluorescence of hHb by the dynamic mechanism, which was confirmed by both temperature dependent and time resolved fluorescence studies. Vanillin binds spontaneously to hHb at a single site and the binding is stabilized by hydrogen bonds and hydrophobic interactions. The circular dichroism spectra showed that the binding of vanillin altered the secondary structure of hHb due to change in its alpha-helical content. Molecular docking identified the amino acids of hHb involved in binding to vanillin and also that the free energy change of the binding reaction is -5.5 kcal/mol. Thus, our results indicate that vanillin binds spontaneously to hHb at a single site and alters its secondary structure. This will help in understanding the potential use of vanillin and related antioxidants as therapeutic agents in various hematological disorders.

Theoretical study on optimizing dipeptidomimetic isocyanonaphthalene chemosensor and the fluorescence mechanism for detecting Hg2

The excited (S1) state charge distribution characteristics and fluorescence mechanism of fluorescence probes benzyl (6-cyano-2-naphthoyl)-L-valinate (NPI) and benzyl (6-amino-2-naphthoyl)-L-valinate (NPA) have been discussed using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). Further analysis by constructing a torsional potential energy curve (PEC) shows that a well-defined minimum energy conformation is observed when the C-C single bond between the valine benzyl ester and naphthalene ring in NPI rotates. For NPA, the most stable conformation is the naphthalene ring conformation with dihedral angle N2C1C2C3 of -30.60°, whose total energy is 0.17 kcal/mol lower than that of the second most stable conformer. The frontier molecular orbitals (FMOs) demonstrate that NPI exhibits a low degree of charge coupling, and the oscillator intensity is close to zero, indicating that it is not conducive to luminescence. However, in the S1 state, the oscillator strength of NPA is 1.2044, which is a bright state, resulting in the strong emitting. Additionally, fluorescence imaging is favored as a visual observation technique, and Stokes shift is an important physical parameter to measure fluorescence. According to the idea that changing the number and position of functional groups can affect the photophysical properties of fluorescent dyes, o-NPDI, p-NPDI and m-NPDI dyes were newly designed and o-NPDA, p-NPDA, m-NPDA produced after recognition of Hg2+. The spectral performance results show that the newly designed fluorescent dye (p-NPDA) can not only emit in the near infrared region after recognizing Hg2+, but also has a large Stokes shift (236 nm). This indirectly reflects that para-substitution is more conducive to Stokes shift, and has become one of the strategies for fluorescent dye design.

Uncovering the sensing mechanism of a zinc ion sensor: Fluorescence enhancement induced by the elimination of the TICT state

Precise detection of zinc ion is of fundamental importance in the fields of environment protection and food safety. A comprehensive understanding of the sensing mechanism will help to the design of such sensors. The detailed photophysical process of a zinc ion sensor as well as the sensing mechanism are uncovered with the aid of density functional theory (DFT) and time-dependent density functional theory (TDDFT). Both the ground state and first excited state potential energy surfaces (PES) of the sensor are carefully explored to reveal the photo-physical process of the sensor. Excited state intramolecular proton transfer (ESIPT) is observed on the S1 state PES. Then, the twist motion of C=N double bond is triggered after the ESIPT process, which leads to a twisted intramolecular charge transfer (TICT) state. This TICT state is found to make the sensor non-emissive. With the addition of Zn2+, the TICT state is eliminated which greatly enhances the fluorescence of the sensor and achieves zinc ion detection. The interaction of the sensor with Cd2+ and Hg2+ are also explored, which well explains the good selectivity of the sensor.

Effect of geometric isomerism on the anticancer property of new platinum complexes with glycine derivatives as asymmetric N, O donate ligands against human cancer

In this project, to fallow the anticancer ability of new Pt drugs, several new Pt complexes were synthesized with the asymmetric bidentate glycine derivatives, as named propyl- and hexyl glycine (L), in the general formula: [Pt(NH3)2(L)]NO3, and cis- and trans-[Pt(L)2]. The structure of two cis- and trans-[Pt(propylgly)2] complexes was proved by single crystallography analysis. However, all complex structures were characterized by various methods of 1H NMR, 13C NMR, 195Pt NMR, FTIR, LC-Mass, and Raman spectroscopy. To study the passage of water-soluble complexes of [Pt(NH3)2(L)]NO3 via cell membrane, their solubility, and lipophilicity were analyzed. In addition, the cytotoxic properties of these complexes were evaluated against normal and malignant cell lines (skin, breast, and lung cancer cells). The results indicated that they were either comparable to cisplatin or less damaging than carboplatin and oxaliplatin. It was expected that due to less steric effect, and the presence of length aliphatic hydrocarbon chain in the complex structure, trans-[Pt(hexylgly)2] is more toxic on cancerous cell lines than trans-[Pt(propylgly)2]. Cellular accumulation of all complexes was evaluated on A549 and MCF7 cell lines, and the amount of platinum metal (ng) was measured by the ICP method. Results showed that trans-[Pt(hexylgly)2] complex has the highest accumulation inside both mentioned cell lines and [Pt(NH3)2(L)]NO3 complexes behave like clinical Pt-drugs. Ultimately, the interaction patterns of DNA were examined using spectroscopic methods and molecular docking simulations for all substances.

Synthesis of highly sensitive and multi-response Eu-MOF, fluorescence sensing properties and anti-counterfeiting applications

A new Europium metal-organic framework (Eu-MOF), namely [Eu(dpa) (H2O)]·0.5(bpy)·4H2O}n (H4dpa = 5-(3,4-dicarboxyphenoxy) isophenic acid, bpy = protonated 4,4'-bipyridine) was synthesized and structurally characterized by elemental analyses, infrared spectroscopy, and X-ray single-crystal diffraction analyses. Eu-MOF shows a three-dimensional network structure based on EuIII ions and (dpa)4- ligands via µ4: η1, η2, η2, η2 coordination mode. Fluorescence analysis shows that Eu-MOF has excellent fluorescence sensing characteristics, which can efficiently and sensitively detect various pollutants in water: the limit of detection (LOD) of ratiometric fluorescence detection of ANI in water was 42.9 nM, which was better than the single-peak detection limit. In addition, the peak detection limits of Eu-MOF for Flu, ORN and NB were 120 nM, 27 nM and 94 nM, respectively. In addition, XPS, LUMO orbital energy level, fluorescence lifetime, ultraviolet absorption and other principles are used to explore the mechanism of fluorescence quenching. Surprisingly, Eu-MOF not only has excellent anti- counterfeiting ability and stability, can be used as anti-counterfeiting material in life, but also has good selectivity to Flu. Eu-MOF has obvious fluorescence quenching effect on Flu on paper under ultraviolet light, which can be used for rapid in situ imaging test paper of pesticide residues.

Oppositely-charged silver nanoparticles enable selective SERS molecular enhancement through electrostatic interactions

Label-free surface-enhanced Raman spectroscopy (SERS) has attracted extensive attention as an emerging technique for molecular phenotyping of biological samples. However, the selective enhancement property of SERS mediated by complicated interactions between substrates and analytes is unfavorable for molecular profiling. The electrostatic force is among the most dominating interactions that can cause selective adsorption of molecules to charged substrates. This means if only negatively- or positively-charged SERS substrates are applied, then considerable SERS information from a portion of analytes would be lost, hindering comprehensive SERS sensing. In this work, we utilize both negatively- and positively-charged colloidal silver (Ag) nanoparticles (NPs) to detect various charged molecules. The negatively-charged citrate-stabilized Ag and the positively-charged Ag prepared via a cetyltrimethyl-ammonium chloride-based charge reversal protocol have been adopted as SERS substrates. The Ag NPs are all relatively well-dispersed with good uniformity. After applying the oppositely-charged NPs to the detection of charged molecules, we find the SERS results explicitly demonstrate the electrostatically-driven SERS selective enhancement, which is further supported and clarified by molecular electrostatic potential calculations. Our work highlights the importance of developing SERS substrates modified with appropriate surface charges for various analytes, and enlightens us that potentially more molecular SERS information can be acquired from complex bio-samples using combinations of oppositely-charged substrates.

Computational insights into the underlying mechanism of zinc ion-specificity of the fluorescent probe, BDA-1

Ion specificity is crucial for developing fluorescence probes. Using a recently reported optical sensor (BDA-1) of Zn2+ as a representative, we carried out extensive quantum chemical calculations on its photophysical properties using density function theory. According to the calculated optimized geometries, excitation energies and transition oscillator strengths, the weak fluorescence of BDA-1 observed in experiments is attributed to the suppression of fluorescence emission by efficient internal conversion, rather than the previously proposed photoinduced electron transfer (PET) mechanism. With the addition of Zn2+ or Cd2+ ions, the tetradentate chelates [M:BDA-1-H+]+ (M=Zn, Cd) are produced. According to frontier molecular orbital and interfragment charge transfer analyses of these complexes, PET is preferentially confirmed to occur upon photo-excitation. Notably, as one coordination bond in the excited [Cd:BDA-1-H+]+ complex is significantly weakened in comparison to that of [Zn:BDA-1-H+]+, their molecular orbital compositions in the S1 state are completely different. As a result, absorption and radiation transitions of [Zn:BDA-1-H+]+ both have considerable oscillator strength, while fluorescence radiation from the excited [Cd:BDA-1-H+]+ is doubly suppressed. This difference causes that the fluorescence intensity of BDA-1 is sensitive to the addition of metal ions, and exhibits the zinc ion-specificity.

Extending the emission peak tail of indole cyanine for deep-near-infrared bioimaging

We propose a novel strategy for tailoring the structure of fluorescent molecules to achieve emission at the tail end of the NIR-II window. The favorable spectroscopic properties and low cytotoxicity of YNs make them powerful tools for bioimaging. Notably, YN-4 exhibits a brightness 2.5 times greater than YN-3, 6 times that of IR-783, and 5 times that of ICG. This enhanced brightness enabled high-resolution imaging of mouse thoracic and abdominal cavities, tumor vasculature, and real-time monitoring of gastrointestinal motility using YN-4. Furthermore, covalent grafting of glucose onto the YN-Glu scaffold significantly improved tumor-targeting capability and facilitated tracking of glucose metabolism. This work aims to extend the application of fluorescent molecule imaging beyond the NIR-IIa window.

Tactfully regulating the ESIPT and TICT mechanism in the AIE-active multifunctional triphenylamine Schiff-base compound (TPASB) by methyl substitution

The triphenylamine Schiff-base (TPASB) with dual proton transfer sites (N1…H1-O1 [R1] and N2…H2-O2 [R2]), which is crucial in the field of optoelectronic materials. Herein, a novel molecular design strategy for preparing of TPASB-1 and TPASB-2 via the selective methylation of the hydroxyl group at the R2 or R1 position was proposed. The analysis of electronic structures and potential energy surfaces revealed that a single excited state intramolecular proton transfer (ESIPT) process of TPASB occurs only at R1. Nevertheless, the ESIPT process of TPASB-2 was successfully turned on at R2. More noteworthy is that compared to TPASB, the methylation of hydroxyl group at the R2 position triggers the TICT process of TPASB-1, effectively reducing the potential barrier of ESIPT at the R1 position. This theoretical study explains the role of the substituent effect in regulating ESIPT behaviour, and provides valuable guidance for synthesising efficacious ESIPT-active compounds.

Multi-spectral and docking assessments to explore the combination of an antiviral drug, entecavir with bovine serum albumin

Molecular interaction of entecavir (ETV) with the transport protein, albumin from bovine serum (BSA) was explored through multispectral and molecular docking approaches. The BSA fluorescence was appreciably quenched upon ETV binding and the quenching nature was static. The ETV-BSA complexation and the static quenching process were further reiterated using UV-visible absorption spectra. The binding constant (Ka) values of the complex were found as 1.47 × 104-4.0 × 103 M-1, which depicting a modarate binding strength in the ETV-BSA complexation. The experimental outcomes verified that the stable complexation was primarily influenced by hydrophobic interactions, hydrogen bonds and van der Waals forces. Synchronous and 3-D fluorescence spectral results demonstrated that ETV had significant impact on the hydrophobicity and polarity of the molecular environment near Tyr and Trp residues. Competitive site-markers displacement (with warfarin and ketoprofen) results discovered the suitable binding locus of ETV at site I in BSA. The molecular docking assessments also revealed that ETV formed hydrogen bonds and hydrophobic interactions with BSA, predominantly binding to site I (sub-domain IIA) of BSA.

Spectroscopic study on volasertib: Highly stable complexes with albumin and encapsulation into alginate/montmorillonite bionanocomposites

In the present work, we study different physicochemical properties related to LADME processes of volasertib, a Polo-like kinase 1 inhibitor in advanced clinical trials. Firstly, the protonation equilibria, the extent of ionization at the physiological pH and pKa values of this drug are studied combining spectroscopic techniques and computational calculations. Secondly, the binding process of volasertib to the human serum albumin (HSA) protein is analyzed by fluorescence spectroscopy. We report a high binding constant to HSA (Ka = 4.10 × 106 M-1) and their pharmacokinetic implications are discussed accordingly. The negative enthalpy and entropy (ΔH0 = -54.49 kJ/mol; ΔS0 = -58.90 J K-1 mol-1) determined for the binding process suggests the implication of hydrogen bonds and van der Waals interactions in the formation of the HSA-volasertib complex. Additionally, volasertib is encapsulated in an alginate/montmorillonite bionanocomposite as a proof of concept for an oral delivery nanocarrier. The physical properties of that nanocomposite as well as volasertib delivery kinetics are analyzed.

Discovery and biochemical characterization of thermostable glycerol oxidases

Alditol oxidases are promising tools for the biocatalytic oxidation of glycerol to more valuable chemicals. By integrating in silico bioprospecting with cell-free protein synthesis and activity screening, an effective pipeline was developed to rapidly identify enzymes that are active on glycerol. Three thermostable alditol oxidases from Actinobacteria Bacterium, Streptomyces thermoviolaceus, and Thermostaphylospora chromogena active on glycerol were discovered. The characterization of these three flavoenzymes demonstrated their glycerol oxidation activities, preference for alkaline conditions, and excellent thermostabilities with melting temperatures higher than 75 °C. Structural elucidation of the alditol oxidase from Actinobacteria Bacterium highlighted a constellation of side chains that engage the substrate through several hydrogen bonds, a histidine residue covalently bound to the FAD prosthetic group, and a tunnel leading to the active site. Upon computational simulations of substrate binding, a double mutant targeting a residue pair at the tunnel entrance was created and found to display an improved thermal stability and catalytic efficiency for glycerol oxidation. The hereby described alditol oxidases form a valuable panel of oxidative biocatalysts that can perform regioselective oxidation of glycerol and other polyols. KEY POINTS: • Rapid pipeline designed to identify putative oxidases • Biochemical and structural characterization of alditol oxidases • Glycerol oxidation to more valuable derivatives.

Angelica keiskei water extract Mitigates Age-Associated Physiological Decline in Mice

OBJECTIVE

Angelica keiskei is a medicinal and edible plant that has been reported to possess potent antioxidant properties in several in vitro models, but its effectiveness on naturally aging organisms is still lacking. This study explores the antioxidant and health-promoting effects of Angelica keiskei in naturally aging mice.

METHODS

We treated 48-week-old mice with Angelica keiskei water extract (AKWE) 30 days, and measured indicators related to aging and antioxidants. In addition, we conducted network pharmacology analysis, component-target molecular docking, real-time PCR, and MTS assays to investigate relevant factors.

RESULTS

The results indicated that administration of AKWE to mice led to decrease blood glucose levels, improve muscle fiber structure, muscle strength, gait stability, and increase levels of glutathione and superoxide dismutase in serum. Additionally, it decreased pigmentation of the heart tissues. Angelica keiskei combats oxidative stress by regulating multiple redox signaling pathways, and its ingredients Coumarin and Flavonoids have the potential to bind to SIRT3 and SIRT5.

CONCLUSIONS

Our findings indicated the potential of Angelica keiskei as a safe and effective dietary supplement to combat aging and revealed the broad prospects of medicinal and edible plants for addressing aging and age-related chronic diseases.

Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions

The complex relationships between gastrointestinal (GI) nematodes and the host gut microbiota have been implicated in key aspects of helminth disease and infection outcomes. Nevertheless, the direct and indirect mechanisms governing these interactions are, thus far, largely unknown. In this proof-of-concept study, we demonstrate that the excretory-secretory products (ESPs) and extracellular vesicles (EVs) of key GI nematodes contain peptides that, when recombinantly expressed, exert antimicrobial activity in vitro against Bacillus subtilis. In particular, using time-lapse microfluidics microscopy, we demonstrate that exposure of B. subtilis to a recombinant saposin-domain containing peptide from the 'brown stomach worm', Teladorsagia circumcincta, and a metridin-like ShK toxin from the 'barber's pole worm', Haemonchus contortus, results in cell lysis and significantly reduced growth rates. Data from this study support the hypothesis that GI nematodes may modulate the composition of the vertebrate gut microbiota directly via the secretion of antimicrobial peptides, and pave the way for future investigations aimed at deciphering the impact of such changes on the pathophysiology of GI helminth infection and disease.

A multidisciplinary approach to the antioxidant and hepatoprotective activities of Arbutus pavarii Pampan fruit; in vitro and in Vivo biological evaluations, and in silico investigations

The Libyan Strawberry, Arbutus pavarii Pampan (ARB), is an endemic Jebel Akhdar plant used for traditional medicine. This study presents the antioxidant and hepatoprotective properties of ARB fruit-extract. ARB phytochemical analysis indicated the presence of 354.54 GAE and 36.2 RE of the phenolics and flavonoids. LC-MS analysis identified 35 compounds belonging to phenolic acids, procyanidins, and flavonoid glycosides. Gallic acid, procyanidin dimer B3, β-type procyanidin trimer C, and quercetin-3-O-glucoside were the major constituents of the plant extract. ARB administration to paracetamol (PAR)-intoxicated rats reduced serum ALT, AST, bilirubin, hepatic tissue MDA and proinflammatory markers; TNF-α and IL-6 with an increase in tissue GSH level and SOD activity. Histological and immunohistochemical studies revealed that ARB restored the liver histology and significantly reduced the tissue expression of caspase 3, IL-1B, and NF-KB in PAR-induced liver damage. Docking analysis disclosed good binding affinities of some compounds with XO, COX-1, 5-LOX, and PI3K.

Design, synthesis, molecular modelling and biological evaluation of novel 6-amino-5-cyano-2-thiopyrimidine derivatives as potent anticancer agents against leukemia and apoptotic inducers

Herein, a novel series of 6-amino-5-cyano-2-thiopyrimidines and condensed pyrimidines analogues were prepared. All the synthesized compounds (1a-c, 2a-c, 3a-c, 4a-r and 5a-c) were evaluated for in vitro anticancer activity by the National Cancer Institute (NCI; MD, USA) against 60 cell lines. Compound 1c showed promising anticancer activity and was selected for the five-dose testing. Results demonstrated that compound 1c possessed broad spectrum anti-cancer activity against the nine cancerous subpanels tested with selectivity ratio ranging from 0.7 to 39 at the GI50 level with high selectivity towards leukaemia. Mechanistic studies showed that Compound 1c showed comparable activity to Duvelisib against PI3Kδ (IC50 = 0.0034 and 0.0025 μM, respectively) and arrested cell cycle at the S phase and displayed significant increase in the early and late apoptosis in HL60 and leukaemia SR cells. The necrosis percentage showed a significant increase from 1.13% to 3.41% in compound 1c treated HL60 cells as well as from 1.51% to 4.72% in compound 1c treated leukaemia SR cells. Also, compound 1c triggered apoptosis by activating caspase 3, Bax, P53 and suppressing Bcl2. Moreover, 1c revealed a good safety profile against human normal lung fibroblast cell line (WI-38 cells). Molecular analysis of Duvelisib and compound 1c in PI3K was performed. Finally, these results suggest that 2-thiopyrimidine derivative 1c might serve as a model for designing novel anticancer drugs in the future.

Rational design of monomeric IL37 variants guided by stability and dynamical analyses of IL37 dimers

IL37 plays important roles in the regulation of innate immunity and its oligomeric status is critical to these roles. In its monomeric state, IL37 can effectively inhibit the inflammatory response of IL18 by binding to IL18Rα, a capacity lost in its dimeric form, underlining the pivotal role of the oligomeric status of IL37 in its anti-inflammatory action. Until now, two IL37 dimer structures have been deposited in PDB, reflecting a substantial difference in their dimer interfaces. Given this discrepancy, we analyzed the PDB structures of the IL37 dimer (PDB IDs: 6ncu, 5hn1) along with a AF2-multimer prediction by molecular dynamics (MD) simulations. Results showed that the 5hn1 and AF2-predicted dimers have the same interface and stably maintained their conformations throughout simulations, while the recent IL37 dimer (PDB ID: 6ncu) with a different interface did not, proposing a possible issue with the recent IL37 dimer structure (6ncu). Next, focusing on the stable dimer structures, we have identified five critical positions of V71/Y85/I86/E89/S114, three new positions compared to the literature, that would reduce dimer stability without affecting the monomer structure. Two quintuple mutants were tested by MD simulations and showed partial or complete dissociation of the dimer. Overall, the insights gained from this study reinforce the validity of the 5hn1 and AF2 multimer structures, while also advancing our understanding of the IL37 dimer interface through the generation of monomer-locked IL37 variants.

Helicobacter pylori East Asian type CagA hijacks more SHIP2 by its EPIYA-D motif to potentiate the oncogenicity

CagA is a significant oncogenic factor injected into host cells by Helicobacter pylori, which is divided into two subtypes: East Asian type (CagAE), characterized by the EPIYA-D motif, and western type (CagAW), harboring the EPIYA-C motif. CagAE has been reported to have higher carcinogenicity than CagAW, although the underlying reason is not fully understood. SHIP2 is an intracellular phosphatase that can be recruited by CagA to perturb the homeostasis of intracellular signaling pathways. In this study, we found that SHIP2 contributes to the higher oncogenicity of CagAE. Co-Immunoprecipitation and Pull-down assays showed that CagAE bind more SHIP2 than CagAW. Immunofluorescence staining showed that a higher amount of SHIP2 recruited by CagAE to the plasma membrane catalyzes the conversion of PI(3,4,5)P3 into PI(3,4)P2. This alteration causes higher activation of Akt signaling, which results in enhanced IL-8 secretion, migration, and invasion of the infected cells. SPR analysis showed that this stronger interaction between CagAE and SHIP2 stems from the higher affinity between the EPIYA-D motif of CagAE and the SH2 domain of SHIP2. Structural analysis revealed the crucial role of the Phe residue at the Y + 5 position in EPIYA-D. After mutating Phe of CagAE into Asp (the corresponding residue in the EPIYA-C motif) or Ala, the activation of downstream Akt signaling was reduced and the malignant transformation of infected cells was alleviated. These findings revealed that CagAE hijacks SHIP2 through its EPIYA-D motif to enhance its carcinogenicity, which provides a better understanding of the higher oncogenic risk of H. pylori CagAE.

Click estradiol dimers with novel aromatic bridging units: synthesis and anticancer evaluation

Estradiol dimers (EDs) possess significant anticancer activity by targeting tubulin dynamics. In this study, we synthesised 12 EDs variants via copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction, focusing on structural modifications within the aromatic bridge connecting two estradiol moieties. In vitro testing of these EDs revealed a marked improvement in selectivity towards cancerous cells, particularly for ED1-8. The most active compounds, ED3 (IC50 = 0.38 μM in CCRF-CEM) and ED5 (IC50 = 0.71 μM in CCRF-CEM) demonstrated cytotoxic effects superior to 2-methoxyestradiol (IC50 = 1.61 μM in CCRF-CEM) and exhibited anti-angiogenic properties in an endothelial cell tube-formation model. Cell-based experiments and in vitro assays revealed that EDs interfere with mitotic spindle assembly. Additionally, we proposed an in silico model illustrating the probable binding modes of ED3 and ED5, suggesting that dimers with a simple linker and a single substituent on the aromatic central ring possess enhanced characteristics compared to more complex dimers.

Acidic sphingomyelinase interactions with lysosomal membranes and cation amphiphilic drugs: A molecular dynamics investigation

Lysosomes are pivotal in cellular functions and disease, influencing cancer progression and therapy resistance with Acid Sphingomyelinase (ASM) governing their membrane integrity. Moreover, cation amphiphilic drugs (CADs) are known as ASM inhibitors and have anti-cancer activity, but the structural mechanisms of their interactions with the lysosomal membrane and ASM are poorly explored. Our study, leveraging all-atom explicit solvent molecular dynamics simulations, delves into the interaction of glycosylated ASM with the lysosomal membrane and the effects of CAD representatives, i.e., ebastine, hydroxyebastine and loratadine, on the membrane and ASM. Our results confirm the ASM association to the membrane through the saposin domain, previously only shown with coarse-grained models. Furthermore, we elucidated the role of specific residues and ASM-induced membrane curvature in lipid recruitment and orientation. CADs also interfere with the association of ASM with the membrane at the level of a loop in the catalytic domain engaging in membrane interactions. Our computational approach, applicable to various CADs or membrane compositions, provides insights into ASM and CAD interaction with the membrane, offering a valuable tool for future studies.

Simulation- and AI-directed optimization of 4,6-substituted 1,3,5-triazin-2(1H)-ones as inhibitors of human DNA topoisomerase IIα

The 4,6-substituted-1,3,5-triazin-2(1H)-ones are promising inhibitors of human DNA topoisomerase IIα. To further develop this chemical class targeting the enzyme´s ATP binding site, the triazin-2(1H)-one substitution position 6 was optimized. Inspired by binding of preclinical substituted 9H-purine derivative, bicyclic substituents were incorporated at position 6 and the utility of this modification was validated by a combination of molecular simulations, dynamic pharmacophores, and free energy calculations. Considering also predictions of Deepfrag, a software developed for structure-based lead optimization based on deep learning, compounds with both bicyclic and monocyclic substitutions were synthesized and investigated for their inhibitory activity. The SAR data showed that the bicyclic substituted compounds exhibited good inhibition of topo IIα, comparable to their mono-substituted counterparts. Further evaluation on a panel of human protein kinases showed selectivity for the inhibition of topo IIα. Mechanistic studies indicated that the compounds acted predominantly as catalytic inhibitors, with some exhibiting topo IIα poison effects at higher concentrations. Integration of STD NMR experiments and molecular simulations, provided insights into the binding model and highlighted the importance of the Asn120 interaction and hydrophobic interactions with substituents at positions 4 and 6. In addition, NCI-60 screening demonstrated cytotoxicity of the compounds with bicyclic substituents and identified sensitive human cancer cell lines, underlining the translational relevance of our findings for further preclinical development of this class of compounds. The study highlights the synergy between simulation and AI-based approaches in efficiently guiding molecular design for drug optimization, which has implications for further preclinical development of this class of compounds.

Investigation of in silico studies for cytochrome P450 isoforms specificity

Cytochrome P450 (CYP450) enzymes comprise a highly diverse superfamily of heme-thiolate proteins that responsible for catalyzing over 90 % of enzymatic reactions associated with xenobiotic metabolism in humans. Accurately predicting whether chemicals are substrates or inhibitors of different CYP450 isoforms can aid in pre-selecting hit compounds for the drug discovery process, chemical toxicology studies, and patients treatment planning. In this work, we investigated in silico studies on CYP450s specificity over past twenty years, categorizing these studies into structure-based and ligand-based approaches. Subsequently, we utilized 100 of the most frequently prescribed drugs to test eleven machine learning-based prediction models which were published between 2015 and 2024. We analyzed various aspects of the evaluated models, such as their datasets, algorithms, and performance. This will give readers with a comprehensive overview of these prediction models and help them choose the most suitable one to do prediction. We also provide our insights for future research trend in both structure-based and ligand-based approaches in this field.

Evaluation of N-alkyl isatins and indoles as acetylcholinesterase and butyrylcholinesterase inhibitors

Two series of N-alkyl isatins and N-alkyl indoles varying in size of the alkyl group were synthesised and evaluated for inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Among the N-alkyl isatins 4a-j, the addition of the N-alkyl group improved inhibition potency towards AChE and BChE compared to isatin. Selectivity towards inhibition of BChE was observed, and the increase in size of the N-alkyl group positively correlated to improved inhibition potency. The most potent inhibitor for BChE was 4i (IC50 = 3.77 µM, 22-fold selectivity for BChE over AChE). N-alkyl indoles 5a-j showed similar inhibition of AChE, the most potent being 5g (IC50 = 35.0 µM), but 5a-j lost activity towards BChE. This suggests an important role of the 3-oxo group on isatin for BChE inhibition, and molecular docking of 4i with human BChE indicates a key hydrogen bond between this group and Ser198 and His438 of the BChE catalytic triad.

o-Vanillin binds covalently to MAL/TIRAP Lys-210 but independently inhibits TLR2

Toll-like receptor (TLR) innate immunity signalling protects against pathogens, but excessive or prolonged signalling contributes to a range of inflammatory conditions. Structural information on the TLR cytoplasmic TIR (Toll/interleukin-1 receptor) domains and the downstream adaptor proteins can help us develop inhibitors targeting this pathway. The small molecule o-vanillin has previously been reported as an inhibitor of TLR2 signalling. To study its mechanism of action, we tested its binding to the TIR domain of the TLR adaptor MAL/TIRAP (MALTIR). We show that o-vanillin binds to MALTIR and inhibits its higher-order assembly in vitro. Using NMR approaches, we show that o-vanillin forms a covalent bond with lysine 210 of MAL. We confirm in mouse and human cells that o-vanillin inhibits TLR2 but not TLR4 signalling, independently of MAL, suggesting it may covalently modify TLR2 signalling complexes directly. Reactive aldehyde-containing small molecules such as o-vanillin may target multiple proteins in the cell.

Molecular interactions between a diphenyl scaffold and PED/PEA15: Implications for type II diabetes therapeutics targeting PED/PEA15 - Phospholipase D1 interaction

In a recent study, we have identified BPH03 as a promising scaffold for the development of compounds aimed at modulating the interaction between PED/PEA15 (Phosphoprotein Enriched in Diabetes/Phosphoprotein Enriched in Astrocytes 15) and PLD1 (phospholipase D1), with potential applications in type II diabetes therapy. PED/PEA15 is known to be overexpressed in certain forms of diabetes, where it binds to PLD1, thereby reducing insulin-stimulated glucose transport. The inhibition of this interaction reestablishes basal glucose transport, indicating PED as a potential target of ligands capable to recover glucose tolerance and insulin sensitivity. In this study, we employ computational methods to provide a detailed description of BPH03 interaction with PED, evidencing the presence of a hidden druggable pocket within its PLD1 binding surface. We also elucidate the conformational changes that occur during PED interaction with BPH03. Moreover, we report new NMR data supporting the in-silico findings and indicating that BPH03 disrupts the PED/PLD1 interface displacing PLD1 from its interaction with PED. Our study represents a significant advancement toward the development of potential therapeutics for the treatment of type II diabetes.

In-cell bioluminescence resonance energy transfer (BRET)-based assay uncovers ceritinib and CA-074 as SARS-CoV-2 papain-like protease inhibitors

Papain-like protease (PLpro) is an attractive anti-coronavirus target. The development of PLpro inhibitors, however, is hampered by the limitations of the existing PLpro assay and the scarcity of validated active compounds. We developed a novel in-cell PLpro assay based on BRET and used it to evaluate and discover SARS-CoV-2 PLpro inhibitors. The developed assay demonstrated remarkable sensitivity for detecting the reduction of intracellular PLpro activity while presenting high reliability and performance for inhibitor evaluation and high-throughput screening. Using this assay, three protease inhibitors were identified as novel PLpro inhibitors that are structurally disparate from those previously known. Subsequent enzymatic assays and ligand-protein interaction analysis based on molecular docking revealed that ceritinib directly inhibited PLpro, showing high geometric complementarity with the substrate-binding pocket in PLpro, whereas CA-074 methyl ester underwent intracellular hydrolysis, exposing a free carboxyhydroxyl group essential for hydrogen bonding with G266 in the BL2 groove, resulting in PLpro inhibition.

Comparison of two peroxidases with high potential for biotechnology applications - HRP vs. APEX2

Peroxidases are essential elements in many biotechnological applications. An especially interesting concept involves split enzymes, where the enzyme is separated into two smaller and inactive proteins that can dimerize into a fully active enzyme. Such split forms were developed for the horseradish peroxidase (HRP) and ascorbate peroxidase (APX) already. Both peroxidases have a high potential for biotechnology applications. In the present study, we performed biophysical comparisons of these two peroxidases and their split analogues. The active site availability is similar for all four structures. The split enzymes are comparable in stability with their native analogues, meaning that they can be used for further biotechnology applications. Also, the tertiary structures of the two peroxidases are similar. However, differences that might help in choosing one system over another for biotechnology applications were noticed. The main difference between the two systems is glycosylation which is not present in the case of APX/sAPEX2, while it has a high impact on the HRP/sHRP stability. Further differences are calcium ions and cysteine bridges that are present only in the case of HRP/sHRP. Finally, computational results identified sAPEX2 as the systems with the smallest structural variations during molecular dynamics simulations showing its dominant stability comparing to other simulated proteins. Taken all together, the sAPEX2 system has a high potential for biotechnological applications due to the lack of glycans and cysteines, as well as due to high stability.

A shared mechanism for TNP-ATP recognition by members of the P2X receptor family

P2X receptors (P2X1-7) are non-selective cation channels involved in many physiological activities such as synaptic transmission, immunological modulation, and cardiovascular function. These receptors share a conserved mechanism to sense extracellular ATP. TNP-ATP is an ATP derivative acting as a nonselective competitive P2X antagonist. Understanding how it occupies the orthosteric site in the absence of agonism may help reveal the key allostery during P2X gating. However, TNP-ATP/P2X complexes (TNP-ATP/human P2X3 (hP2X3) and TNP-ATP/chicken P2X7 (ckP2X7)) with distinct conformations and different mechanisms of action have been proposed. Whether these represent species and subtype variations or experimental differences remains unclear. Here, we show that a common mechanism of TNP-ATP recognition exists for the P2X family members by combining enhanced conformation sampling, engineered disulfide bond analysis, and covalent occupancy. In this model, the polar triphosphate moiety of TNP-ATP interacts with the orthosteric site, while its TNP-moiety is deeply embedded in the head and dorsal fin (DF) interface, creating a restrictive allostery in these two domains that results in a partly enlarged yet ion-impermeable pore. Similar results were obtained from multiple P2X subtypes of different species, including ckP2X7, hP2X3, rat P2X2 (rP2X2), and human P2X1 (hP2X1). Thus, TNP-ATP uses a common mechanism for P2X recognition and modulation by restricting the movements of the head and DF domains which are essential for P2X activation. This knowledge is applicable to the development of new P2X inhibitors.

Cyclodextrins: Establishing building blocks for AI-driven drug design by determining affinity constants in silico

Cyclodextrins (CDs) are cyclic carbohydrate polymers that hold significant promise for drug delivery and industrial applications. Their effectiveness depends on their ability to encapsulate target molecules with strong affinity and specificity, but quantifying affinities in these systems accurately is challenging for a variety of reasons. Computational methods represent an exceptional complement to in vitro assays because they can be employed for existing and hypothetical molecules, providing high resolution structures in addition to a mechanistic, dynamic, kinetic, and thermodynamic characterization. Here, we employ potential of mean force (PMF) calculations obtained from guided metadynamics simulations to characterize the 1:1 inclusion complexes between four different modified βCDs, with different type, number, and location of substitutions, and two sterol molecules (cholesterol and 7-ketocholesterol). Our methods, validated for reproducibility through four independent repeated simulations per system and different post processing techniques, offer new insights into the formation and stability of CD-sterol inclusion complexes. A systematic distinct orientation preference where the sterol tail projects from the CD's larger face and significant impacts of CD substitutions on binding are observed. Notably, sampling only the CD cavity's wide face during simulations yielded comparable binding energies to full-cavity sampling, but in less time and with reduced statistical uncertainty, suggesting a more efficient approach. Bridging computational methods with complex molecular interactions, our research enables predictive CD designs for diverse applications. Moreover, the high reproducibility, sensitivity, and cost-effectiveness of the studied methods pave the way for extensive studies of massive CD-ligand combinations, enabling AI algorithm training and automated molecular design.

The LysR family transcriptional regulator ORF-L16 regulates spinosad biosynthesis in Saccharopolyspora spinosa

Spinosad, a potent broad-spectrum bioinsecticide produced by Saccharopolyspora spinosa, has significant market potential. Despite its effectiveness, the regulatory mechanisms of spinosad biosynthesis remain unclear. Our investigation identified the crucial role of the LysR family transcriptional regulator ORF-L16, located upstream of spinosad biosynthetic genes, in spinosad biosynthesis. Through reverse transcription PCR (RT-PCR) and 5'-rapid amplification of cDNA ends (5'-Race), we unveiled that the spinosad biosynthetic gene cluster (BGC) contains six transcription units and seven promoters. Electrophoretic mobility shift assays (EMSAs) demonstrated that ORF-L16 bound to seven promoters within the spinosad BGC, indicating its involvement in regulating spinosad biosynthesis. Notably, deletion of ORF-L16 led to a drastic reduction in spinosad production from 1818.73 mg/L to 1.69 mg/L, accompanied by decreased transcription levels of spinosad biosynthetic genes, confirming its positive regulatory function. Additionally, isothermal titration calorimetry (ITC) and EMSA confirmed that spinosyn A, the main product of the spinosad BGC, served as an effector of ORF-L16. Specifically, it decreased the binding affinity between ORF-L16 and spinosad BGC promoters, thus exerting negative feedback regulation on spinosad biosynthesis. This research enhances our comprehension of spinosad biosynthesis regulation and lays the groundwork for future investigations on transcriptional regulators in S. spinosa.

DeepSP: Deep learning-based spatial properties to predict monoclonal antibody stability

Therapeutic antibody development faces challenges due to high viscosities and aggregation tendencies. The spatial charge map (SCM) and spatial aggregation propensity (SAP) are computational techniques that aid in predicting viscosity and aggregation, respectively. These methods rely on structural data derived from molecular dynamics (MD) simulations, which are computationally demanding. DeepSCM, a deep learning surrogate model based on sequence information to predict SCM, was recently developed to screen high-concentration antibody viscosity. This study further utilized a dataset of 20,530 antibody sequences to train a convolutional neural network deep learning surrogate model called Deep Spatial Properties (DeepSP). DeepSP directly predicts SAP and SCM scores in different domains of antibody variable regions based solely on their sequences without performing MD simulations. The linear correlation coefficient between DeepSP scores and MD-derived scores for 30 properties achieved values between 0.76 and 0.96 with an average of 0.87. DeepSP descriptors were employed as features to build machine learning models to predict the aggregation rate of 21 antibodies, and the performance is similar to the results obtained from the previous study using MD simulations. This result demonstrates that the DeepSP approach significantly reduces the computational time required compared to MD simulations. The DeepSP model enables the rapid generation of 30 structural properties that can also be used as features in other research to train machine learning models for predicting various antibody stability using sequences only. DeepSP is freely available as an online tool via https://deepspwebapp.onrender.com and the codes and parameters are freely available at https://github.com/Lailabcode/DeepSP.

Unlocking the specificity of antimicrobial peptide interactions for membrane-targeted therapies

Antimicrobial peptides (AMPs) are increasingly recognized as potent therapeutic agents, with their selective affinity for pathological membranes, low toxicity profile, and minimal resistance development making them particularly attractive in the pharmaceutical landscape. This study offers a comprehensive analysis of the interaction between specific AMPs, including magainin-2, pleurocidin, CM15, LL37, and clavanin, with lipid bilayer models of very different compositions that have been ordinarily used as biological membrane models of healthy mammal, cancerous, and bacterial cells. Employing unbiased molecular dynamics simulations and metadynamics techniques, we have deciphered the intricate mechanisms by which these peptides recognize pathogenic and pathologic lipid patterns and integrate into lipid assemblies. Our findings reveal that the transverse component of the peptide's hydrophobic dipole moment is critical for membrane interaction, decisively influencing the molecule's orientation and expected therapeutic efficacy. Our approach also provides insight on the kinetic and dynamic dependence on the peptide orientation in the axial and azimuthal angles when coming close to the membrane. The aim is to establish a robust framework for the rational design of peptide-based, membrane-targeted therapies, as well as effective quantitative descriptors that can facilitate the automated design of novel AMPs for these therapies using machine learning methods.

CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform

The study of cyclic peptides (CPs) and self-assembling cyclic peptide nanotubes (SCPNs) is pivotal in advancing applications in diverse fields such as biomedicine, nanoelectronics, and catalysis. Recognizing the limitations in the experimental study of these molecules, this article introduces CYCLOPEp Builder, a comprehensive web-based application designed to facilitate the design, simulation, and visualization of CPs and SCPNs. The tool is engineered to generate molecular topologies, essential for conducting Molecular Dynamics simulations that span All-Atom to Coarse-Grain resolutions. CYCLOPEp Builder's user-friendly interface simplifies the complex process of molecular modeling, providing researchers with the ability to readily construct CPs and SCPNs. The platform is versatile, equipped with various force fields, and capable of producing structures ranging from individual CPs to complex SCPNs with different sequences, offering parallel and antiparallel orientations among them. By enhancing the capacity for detailed visualization of molecular assemblies, CYCLOPEp Builder improves the understanding of CP and SCPN molecular interactions. This tool is a step forward in democratizing access to sophisticated simulations, offering an invaluable resource to the scientific community engaged in the exploration of supramolecular structures. CYCLOPEp is accessible at http://cyclopep.com/.