Distinct Species-Specific and Toxigenic Metabolic Profiles for 6PPD and 6PPD Quinone by P450 Enzymes: Insights from In Vitro and In Silico Studies.

The tire rubber antioxidant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) and its quinone product (6PPDQ) are prevalent emerging contaminants, yet their biotransformation profiles remain poorly understood, hampering the assessment of environmental and health risks. This study investigated the phase-I metabolism of 6PPD and 6PPDQ across aquatic and mammalian species through in vitro liver microsome (LM) incubations and in silico simulations. A total of 40 metabolites from seven pathways were identified using the highly sensitive nano-electrospray ionization mass spectrometry. Notably, 6PPDQ was consistently detected as a 6PPD metabolite with an approximate 2% yield, highlighting biotransformation as a neglected indirect exposure pathway for 6PPDQ in organisms. 6PPDQ was calculated to form through a facile two-step phenyl hydroxylation of 6PPD, catalyzed by cytochrome P450 enzymes. Distinct species-specific metabolic kinetics were observed, with fish LM demonstrating retarded biotransformation rates for 6PPD and 6PPDQ compared to mammalian LM, suggesting the vulnerability of aquatic vertebrates to these contaminants. Intriguingly, two novel coupled metabolites were identified for 6PPD, which were predicted to exhibit elevated toxicity compared to 6PPDQ and result from C-N oxidative coupling by P450s. These unveiled metabolic profiles offer valuable insights for the risk assessment of 6PPD and 6PPDQ, which may inform future studies and regulatory actions.

Phytochemical Targeting of Nerve Growth Factor by Thymoquinone and Cuscutin: A Molecular Dynamics Simulation Study.

Background Nerve growth factor (NGF) is a novel target of pain therapeutics for oral cancer, and it plays a main role in the nociception of chronic pain. Surgery, along with chemotherapy or radiotherapy, is the gold standard for treating patients, but the side effects are significant as well. Newer effective interventions with natural phytochemicals could improve patient compliance and enhance the quality of life among patients with oral cancer. A literature search revealed a positive correlation between NGF and oral cancer pain. Nigella sativa (N. sativa) and Cuscuta reflexa (C. reflexa) have proven anticancer effects, but their activity with NGF is unexplored. Aims and objectives We aimed to identify the potential phytochemicals in N. sativa and C. reflexa. We also checked the NGF-blocking activity of the phytochemicals. Molecular docking and molecular dynamic (MD) simulations evaluated the binding energy and stability between the NGF protein and selected phytochemical ligands. Materials and methods We obtained protein NGF structure from UniProt (ID: 4EDX, P01138, Beta-nerve growth factor), ligand (thymoquinone) structure using PubChem ID: 10281, and ligand (cuscutin) structure using PubChem ID: 66065. Maestro protein (Schrödinger Inc., Mannheim, Germany) was used for molecular docking. Desmond Simulation Package (Schrödinger Inc., Mannheim, Germany) was used to model MD for 100 nanoseconds (ns). We have assessed the interaction between the protein and ligands by root mean square deviation (RMSD) values.  Results The interaction of thymoquinone and cuscutin with NGF was assessed. While interacting with thymoquinone, there was mild fluctuation from 0.6 Å to 2.5 Å up to 80 ns and ended up at 4.8 Å up to 100 ns. While interacting with cuscutin, mild fluctuation was seen from 0.8 Å to 4.8 Å till 90 ns and ended at 6.4 Å up to 100 ns. We found a stable interaction between our drug combination and the NGF receptor. Conclusion We have identified a stable interaction between thymoquinone, cuscutin, and NGF by our MD simulations. Hence, it could be used as an NGF inhibitor for pain relief and to control tumor progression. Further in vitro and in vivo evaluations of this novel drug combination with phytochemicals will help us understand their biological activities and potential clinical applications in oral cancer therapeutics.

Unveiling a Hidden Pocket in HIV-1 Protease: New Insights Into Retroviral Protease Cantilever-Tip Region Characteristics.

The HIV-1 protease is critical for the process of viral maturation and as such, it is one of the most well characterized proteins in the Protein Data Bank. There is some evidence to suggest that the HIV-1 protease is capable of accommodating small molecule fragments at several locations on its surface outside of the active site. However, some pockets on the surface of proteins remain unformed in the apo structure and are termed "cryptic sites." To date, no cryptic sites have been identified in the structure of HIV-1 protease. Here, we characterize a novel cryptic cantilever pocket on the surface of the HIV-1 protease through mixed-solvent molecular dynamics simulations using several probes. Interestingly, we noted that several homologous retroviral proteases exhibit evolutionarily conserved dynamics in the cantilever region and possess a conserved pocket in the cantilever region. Immobilization of the cantilever region of the HIV-1 protease via disulfide cross-linking resulted in curling-in of the flap tips and the propensity for the protease to adopt a semi-open flap conformation. Structure-based analysis and fragment-based screening of the cryptic cantilever pocket suggested that the pocket may be capable of accommodating ligand structures. Furthermore, molecular dynamics simulations of a top scoring fragment bound to the cryptic pocket illustrated altered flap dynamics of the fragment-bound enzyme. Together, these results suggest that the mobility of the cantilever region plays a key role in the global dynamics of retroviral proteases. Therefore, the cryptic cantilever pocket of the HIV-1 protease may represent an interesting target for future in vitro studies.

Surface Structure of Lecithin-Capped Cesium Lead Halide Perovskite Nanocrystals Using Solid-State and Dynamic Nuclear Polarization NMR Spectroscopy.

Inorganic colloidal cesium lead halide perovskite nanocrystals (NCs) encapsulated by surface capping ligands exhibit tremendous potential in optoelectronic applications, with their surface structure playing a pivotal role in enhancing their photophysical properties. Soy lecithin, a tightly binding zwitterionic surface-capping ligand, has recently facilitated the high-yield synthesis of stable ultraconcentrated and ultradilute colloids of CsPbX3 NCs, unlocking a myriad of potential device applications. However, the atomic-level understanding of the ligand-terminated surface structure remains uncertain. Herein, we use a versatile solid-state nuclear magnetic resonance (NMR) spectroscopic approach, in combination with dynamic nuclear polarization (DNP) and atomistic molecular dynamics (MD) simulations, to explore the effect of lecithin on the core-to-surface structures of CsPbX3 (X = Cl or Br) perovskites, sized from micron to nanoscale. Surface-selective (cross-polarization, CP) solid-state and DNP NMR (133Cs and 207Pb) methods were used to differentiate the unique surface and core chemical environments, while the head-groups {trimethylammonium [-N(CH3)3+] and phosphate (-PO4-)} of lecithin were assigned via 1H, 13C, and 31P NMR spectroscopy. A direct approach to determining the surface structure by capitalizing on the unique heteronuclear dipolar couplings between the lecithin ligand (1H and 31P) and the surface of the CsPbCl3 NCs (133Cs and 207Pb) is demonstrated. The 1H-133Cs heteronuclear correlation (HETCOR) DNP NMR indicates an abundance of Cs on the NC surface and an intimate proximity of the -N(CH3)3+ groups to the surface and subsurface 133Cs atoms, supported by 1H{133Cs} rotational-echo double-resonance (REDOR) NMR spectroscopy. Moreover, the 1H-31P{207Pb} CP REDOR dephasing curve provides average internuclear distance information that allows assessment of -PO4- groups binding to the subsurface Pb atoms. Atomistic MD simulations of ligand-capped CsPbCl3 surfaces aid in the interpretation of this information and suggest that ligand -N(CH3)3+ and -PO4- head-groups substitute Cs+ and Cl- ions, respectively, at the CsCl-terminated surface of the NCs. These detailed atomistic insights into surface structures can further guide the engineering of various relevant surface-capping zwitterionic ligands for diverse metal halide perovskite NCs.

Regulating the electronic structure of Pt SAs-Ni2P for enhanced hydrogen evolution reaction.

The single atom catalysts (SACs) show immense promise as catalytic materials. By doping the single atoms (SAs) of precious metals onto substrates, the atomic utilization of these metals can be maximized, thereby reducing catalyst costs. The electronic structure of precious metal SAs is significantly influenced by compositions of doped substrates. Therefore, optimizing the electronic structure through appropriate doping of substrates can further enhance catalytic activity. Here, Pt single atoms (Pt SAs) are doped onto transition metal sulfide substrate NiS2 (Pt SAs-NiS2) and phosphide substrate Ni2P (Pt SAs-Ni2P) to design and prepare catalysts. Compared to the Pt SAs-NiS2 catalyst, the Pt SAs-Ni2P catalyst exhibits better hydrogen evolution catalytic performance and stability. Under 1 M KOH conditions, the hydrogen evolution mass activity current density of the Pt SAs-Ni2P catalyst reaches 0.225 A mgPt-1 at 50 mV, which is 33 times higher than that of commercial Pt/C catalysts. It requires only 44.9 mV to achieve a current density of 10 mA cm-2. In contrast, for the Pt SAs-NiS2 catalyst, the hydrogen evolution mass activity current density is 0.178 A mgPt-1, requiring 77.8 mV to achieve a current density of 10 mA cm-2. Theoretical calculations indicate that in Pt SAs-Ni2P, the interaction between Pt SAs and the Ni2P substrate causes the Pt d-band center to shift downward, enhancing the H2O desorption and providing optimal H binding sites. Additionally, the hollow octahedral morphology of Ni2P provides a larger surface area, exposing more reactive sites and improving reaction kinetics. This study presents an effective pathway for preparing high-performance hydrogen evolution electrocatalysts by selecting appropriate doped substrates to control the electronic structure of Pt SAs.

MLgrating: a program for simulating multilayer gratings for tender X-ray applications.

Multilayer gratings are increasingly popular optical elements at X-ray beamlines, as they can provide much higher photon flux in the tender X-ray range compared with traditional single-layer coated gratings. While there are several proprietary software tools that provide the functionality to simulate the efficiencies of such gratings, until now the X-ray community has lacked an open-source alternative. Here MLgrating is presented, a program for simulating the efficiencies of both multilayer gratings and single-layer coated gratings for X-ray applications. MLgrating is benchmarked by comparing its output with that of other software tools and plans are discussed for how the program could be extended in the future.

Dissecting molecular mechanisms underlying the inhibition of ß-glucuronidase by alkaloids from Hibiscus trionum: Integrating in vitro and in silico perspectives.

ß-Glucuronidase, a crucial enzyme in drug metabolism and detoxification, represents a promising target for therapeutic intervention due to its potential to modulate drug pharmacokinetics and enhance therapeutic efficacy. Herein, we assessed the inhibitory potential of phytochemicals from Hibiscus trionum against ß-glucuronidase. Grossamide and grossamide K emerged as the most potent ß-glucuronidase inhibitors with IC50 values of 0.73 ± 0.03 and 1.24 ± 0.03 µM, respectively. The investigated alkaloids effectively inhibited ß-glucuronidase-catalyzed PNPG hydrolysis through a noncompetitive inhibition mode, whereas steppogenin displayed a mixed inhibition mechanism. Molecular docking analyses highlighted grossamide and grossamide K as inhibitors with the lowest binding free energy, all compounds successfully docked into the same main binding site occupied by the reference drug Epigallocatechin gallate (EGCG). We explored the interaction dynamics of isolated compounds with ß-glucuronidase through a 200 ns molecular dynamics (MD) simulation. Analysis of various MD parameters revealed that grossamide and grossamide K maintained stable trajectories and demonstrated significant energy stabilization upon binding to ß-glucuronidase. Additionally, these compounds exhibited the lowest average interaction energies with the target enzyme. The MM/PBSA calculations further supported these findings, showing the lowest binding free energies for grossamide and grossamide K. These computational results are consistent with experimental data, suggesting that grossamide and grossamide K could be potent inhibitors of ß-glucuronidase.

Intrinsic dynamics of emulsions: Experiments in microgravity on the International Space Station.

HYPOTHESIS: In order to understand the basic mechanisms affecting emulsion stability, the intrinsic dynamics of the drop population must be investigated. We hypothesize that transient ballistic motion can serve as a marker of interactions between drops. In 1G conditions, buoyancy-induced drop motion obscures these interactions. The microgravity condition onboard the International Space Station enable this investigation. EXPERIMENTS: We performed Diffusing Wave Spectroscopy (DWS) experiments in the ESA Soft Matter Dynamics (SMD) facility. We used Monte Carlo simulations of photon trajectory to support data analysis. The analysis framework was validated by ground-based characterizations of the initial drop size distribution (DSD) and the properties of the oil/water interface in the presence of surfactant. FINDINGS: We characterized the drop size distribution and found to be bi-disperse. Drop dynamics shows transient ballistic features at early times, reaching a stationary regime of primarily diffusion-dominated motion. This suggests different ageing mechanisms: immediately after emulsification, the main mechanism is coalescence or aggregation between small drops. However at later times, ageing proceeds via coalescence or aggregation of small with large drops in some emulsions. Our results elucidate new processes relevant to emulsion stability with potential impact on industrial processes on Earth, as well as enabling technologies for space exploration.

Exploration of dynamic interaction between ß-lactoglobulin and casein micelles during UHT milk process.

The protein aggregation induced by UHT treatment shortens the shelf life of UHT milk. However, the mechanism of ß-Lg induced casein micelle aggregation remains unclear. Herein, the dynamic interaction between ß-Lg and casein micelles during UHT processing was investigated by experimental techniques and molecular dynamics simulations. Results showed that ß-Lg decreased the stability of casein micelles, increased their size and zeta potential. Raman and FTIR spectra analysis suggested that hydrogen and disulfide bonds facilitated their interaction. Cryo-TEM showed that the formation of the casein micelle/ß-Lg complex involved rigid binding, flexible linking, and severe cross-linking aggregation during UHT processing. SAXS and MST demonstrated ß-Lg bound to κ-casein on micelle surfaces with a dissociation constant (Kd) of 3.84 ± 1.14 µm. Molecular docking and dynamic simulations identified the interacting amino acid residues and clarified that electrostatic and van der Waals forces drove the interaction. UHT treatment increased hydrogen bonds and decreased total binding energy. The non-covalent binding promoted the formation of disulfide bonds between ß-Lg and casein micelles under heat treatment. Ultimately, it was concluded that non-covalent interaction and disulfide bonding resulted in casein micelle/ß-Lg aggregates. These findings provided scientific insights into protein aggregation in UHT milk.

Structure based computational RNA design towards MafA transcriptional repressor implicated in multiple myeloma.

Multiple myeloma is recognized as the second most common hematological cancer. MafA transcriptional repressor is an established mediator of myelomagenesis. While there are multitude of drugs available for targeting various effectors in multiple myeloma, current literature lacks a candidate RNA based MafA modulator. Thus, using the structure of MafA homodimer-consensus target DNA, a computational effort was implemented to design a novel RNA based chemical modulator against MafA. First, available MafA-consensus DNA structure was employed to generate an RNA library. This library was further subjected to global docking to select the most plausible RNA candidates, preferring to bind DNA binding region of MafA. Following global docking, MD-ready complexes that were prepared via local docking program, were subjected to 500 ns of MD simulations. First, each of these MD simulations were analyzed for relative binding free energy through MM-PBSA method, which pointed towards a strong RNA based MafA binder, RNA1. Second, through a detailed MD analysis, RNA1 was shown to prefer binding to a single monomer of the dimeric DNA binding domain of MafA using higher number of hydrophobic interactions compared with positive control MafA-DNA complex. At the final phase, a principal component analyses was conducted, which led us to identify the actual interaction region of RNA1 and MafA monomer. Overall, to our knowledge, this is the first computational study that presents an RNA molecule capable of potentially targeting MafA protein. Furthermore, limitations of our study together with possible future implications of RNA1 in multiple myeloma were also discussed.

Enhancement of the degradation capacity of IsPETase by acidic amino acids insertion and carbohydrate-binding module fusion.

The biocatalytic degradation of poly(ethylene terephthalate) (PET) through enzymatic methods has garnered considerable attention due to its environmentally friendly and non-polluting nature, as well as its high specificity. While previous efforts in enhancing IsPETase performance have focused on amino acid substitutions in protein engineering, we introduced an amino acid insertion strategy in this work. By inserting a negatively charged acidic amino acid, Glu, at the right-angle bend of IsPETase, the binding capability between the enzyme's active pocket and PET was improved. The resulted mutant IsPETase9394insE exhibited enhanced hydrolytic activity towards PET at various temperatures ranging from 30 to 45 ℃ compared with the wild-type IsPETase. Notably, a 10.04-fold increase was observed at 45 ℃. To further enhance PET hydrolysis, different carbohydrate-binding modules (CBMs) were incorporated at the C-terminus of IsPETase9394insE. Among these, the fusion of CBM from Verrucosispora sioxanthis exhibited the highest enhancement, resulting in a 1.82-fold increase in PET hydrolytic activity at 37 ℃ compared with the IsPETase9394insE. Finally, the engineered variant was successfully employed for the degradation of polyester filter cloth, demonstrating its promising hydrolytic capacity. In conclusion, this research presents an alternative enzyme engineering strategy for modifying PETases and enriches the pool of potential candidates for industrial PET degradation.

Assessing Heterogeneity Effects on Points A, B, and Organs at Risk Doses in High-dose-Rate Brachytherapy for Cervical Cancer - A Comparison of 192Ir and 60Co Sources Using Monte Carlo N-Particle 5.

Purpose: The present article deals with investigating the effects of tissue heterogeneity consideration on the dose distribution of 192Ir and 60Co sources in high-dose-rate brachytherapy (HDR-BT). Materials and Methods: A Monte Carlo N-Particle 5 (MCNP5) code was developed for the simulation of the dose distribution in homogeneous and heterogeneous phantoms for cervical cancer patients. The phantoms represented water-equivalent and human body-equivalent tissues. Treatment data for a patient undergoing HDR-BT with a 192Ir source were used as a reference for validation, and for 60Co, AAPM Task Group 43 methodology was also applied. The dose values were calculated for both source types in the phantoms. Results: The results showed a good agreement between the calculated dose in the homogeneous phantom and the real patient's treatment data, with a relative difference of less than 5% for both sources. However, when comparing the absorbed doses at critical points such as Point A right, Point A left, Point B right, Point B left, bladder International Commission on Radiation Units and Measurement (ICRU) point, and recto-vaginal ICRU point, the study revealed significant percentage differences (approximately 5.85% to 12.02%) between the homogeneous and heterogeneous setups for both 192Ir and 60Co sources. The analysis of dose-volume histograms (DVH) indicated that organs at risk, notably the rectum and bladder, still received doses within recommended limits. Conclusions: The study concludes that 60Co and 192Ir sources can be effectively used in HDR-BT, provided that careful consideration is given to tissue heterogeneity effects during treatment planning to ensure optimal therapeutic outcomes.

Sound-mediated nucleation and growth of amyloid fibrils.

Mechanical energy, specifically in the form of ultrasound, can induce pressure variations and temperature fluctuations when applied to an aqueous media. These conditions can both positively and negatively affect protein complexes, consequently altering their stability, folding patterns, and self-assembling behavior. Despite much scientific progress, our current understanding of the effects of ultrasound on the self-assembly of amyloidogenic proteins remains limited. In the present study, we demonstrate that when the amplitude of the delivered ultrasonic energy is sufficiently low, it can induce refolding of specific motifs in protein monomers, which is sufficient for primary nucleation; this has been revealed by MD. These ultrasound-induced structural changes are initiated by pressure perturbations and are accelerated by a temperature factor. Furthermore, the prolonged action of low-amplitude ultrasound enables the elongation of amyloid protein nanofibrils directly from natively folded monomeric lysozyme protein, in a controlled manner, until it reaches a critical length. Using solution X-ray scattering, we determined that nanofibrillar assemblies, formed either under the action of sound or from natively fibrillated lysozyme, share identical structural characteristics. Thus, these results provide insights into the effects of ultrasound on fibrillar protein self-assembly and lay the foundation for the potential use of sound energy in protein chemistry.

Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling.

Understanding the intracellular dynamics of brain cells entails performing three-dimensional molecular simulations incorporating ultrastructural models that can capture cellular membrane geometries at nanometer scales. While there is an abundance of neuronal morphologies available online, e.g. from NeuroMorpho.Org, converting those fairly abstract point-and-diameter representations into geometrically realistic and simulation-ready, i.e. watertight, manifolds is challenging. Many neuronal mesh reconstruction methods have been proposed; however, their resulting meshes are either biologically unplausible or non-watertight. We present an effective and unconditionally robust method capable of generating geometrically realistic and watertight surface manifolds of spiny cortical neurons from their morphological descriptions. The robustness of our method is assessed based on a mixed dataset of cortical neurons with a wide variety of morphological classes. The implementation is seamlessly extended and applied to synthetic astrocytic morphologies that are also plausibly biological in detail. Resulting meshes are ultimately used to create volumetric meshes with tetrahedral domains to perform scalable in silico reaction-diffusion simulations for revealing cellular structure-function relationships. Availability and implementation: Our method is implemented in NeuroMorphoVis, a neuroscience-specific open source Blender add-on, making it freely accessible for neuroscience researchers.

Dynamical modelling of lipid droplet formation suggests a key function of membrane phospholipids.

Cells store triacylglycerol (TAG) within lipid droplets (LDs). A dynamic model describing complete LD formation at the endoplasmic reticulum (ER) membrane does not yet exist. A biochemical-biophysical model of LD synthesis is proposed. It describes the time-dependent accumulation of TAG in the ER membrane as the formation of a potential LD (pLD) bounded by spherical caps of the inner and outer monolayers of the membrane. The expansion rate of the pLD depends on the TAG supply, the elastic properties of the ER membrane, and the recruitment of phospholipids (PLs) to the cap-covering monolayers. Model simulations provided the following insights: (a) Marginal differences in the surface tension of the cap monolayers are sufficient to fully drive the expansion of the pLD towards the cytosol or lumen. (b) Selective reduction of PL supply to the luminal monolayer ensures stable formation of cytosolic LDs, irrespective of variations in the elasto-mechanical properties of the ER membrane. (c) The rate of TAG supply to the cytosolic monolayer has a major effect on the size and maturation time of LDs but has no significant effect on the TAG export per individual LD. The recruitment of additional PLs to the cap monolayers of pLDs critically controls the budding direction, size, and maturation time of LDs. The ability of cells to acquire additional LD initiation sites appears to be key to coping with acutely high levels of potentially toxic free fatty acids.

Integrative network pharmacology, molecular docking, and dynamic simulation analysis of a polyherbal formulation for potential therapeutic impact on prostate cancer.

Background: Prostate cancer (PCa) remains a significant health concern globally, prompting a continual search for novel therapeutic strategies. In this study, we employed a comprehensive approach combining network pharmacology, molecular docking and dynamic simulation to explore the potential impact of a polyherbal formulation on PCa. Methods: Utilizing comprehensive network pharmacology approaches, we elucidated the complex interactions between the bioactive compounds within the polyherbal formulation and key targets associated with PCa progression, highlighting their multitarget mechanisms through integrated protein‒protein interaction and KEGG pathway analyses. Molecular docking simulation studies were performed to predict the binding affinities and modes of interaction between the identified bioactive compounds and their respective protein targets. Results: Complex connections comprising 486 nodes and 845 edges were found by the compound-target network analysis. Significant interactions were observed, and the average node degree was 4.23. KEGG research revealed that PCa and the PI3K-Akt signalling pathway are implicated in modulating prostate cancer. The Quercetin docking investigations revealed that the binding energies for AR and PIK3R1 were -9 and -9.5 kcal/mol, respectively. Based on the results of the MD simulations, it appears that tiny molecules and proteins have formed stable complexes with low fluctuations. Conclusion: In conclusion, this comprehensive method emphasises the value of network pharmacology in conjunction with molecular docking and dynamic simulation in revealing the anti-PCa therapeutic potential of polyherbal formulations, opening up new possibilities for the creation of efficient anti-cancer medicines.

Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method.

Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for the determination of structures of complex biological molecules. The accurate characterisation of the dynamics of such systems, however, remains a challenge. To address this problem, we introduce cryoENsemble, a method that applies Bayesian reweighting to conformational ensembles derived from molecular dynamics simulations to improve their agreement with cryo-EM data, thus enabling the extraction of dynamics information. We illustrate the use of cryoENsemble to determine the dynamics of the ribosome-bound state of the co-translational chaperone trigger factor (TF). We also show that cryoENsemble can assist with the interpretation of low-resolution, noisy or unaccounted regions of cryo-EM maps. Notably, we are able to link an unaccounted part of the cryo-EM map to the presence of another protein (methionine aminopeptidase, or MetAP), rather than to the dynamics of TF, and model its TF-bound state. Based on these results, we anticipate that cryoENsemble will find use for challenging heterogeneous cryo-EM maps for biomolecular systems encompassing dynamic components.

Selective detection of food contaminants using engineered gallium-organic frameworks with MD and metadynamics simulations.

The exclusion mechanism of food contaminants such as bisphenol A (BPA), Flavonoids (FLA), and Goitrin (GOI) onto the novel gallium-metal organic framework (MOF) and functionalized MOF with oxalamide group (MOF-OX) is evaluated by utilizing molecular dynamics (MD) and Metadynamics simulations. The atoms in molecules (AIM) analysis detected different types of atomic interactions between contaminant molecules and substrates. To assess this procedure, a range of descriptors including interaction energies, root mean square displacement, radial distribution function (RDF), density, hydrogen bond count (HB), and contact numbers are examined across the simulation trajectories. The most important elements in the stability of the systems under examination are found to be stacking π-π and HB interactions. It was confirmed by a significant value of total interaction energy for BPA/MOF-OX (- 338.21 kJ mol-1) and BPA/MOF (- 389.95 kJ mol-1) complexes. Evaluation of interaction energies reveals that L-J interaction plays an essential role in the adsorption of food contaminants on the substrates. The free energy values for the stability systems of BPA/MOF and BPA/MOF-OX complexes at their global minima reached about BPA/MOF = - 254.29 kJ mol-1 and BPA/MOF-OX = - 187.62 kJ mol-1, respectively. Nevertheless, this work provides a new strategy for the preparation of a new hierarchical tree-dimensional of the Ga-MOF hybrid material for the adsorption and exclusion of food contaminates and their effect on human health.

Dispersion Influence of Electroacoustic Transducer Parameters in the Design Process of Miniature Loudspeaker Arrays and Omnidirectional Sound Sources.

Electroacoustic transducers represent one of the crucial materials used in the construction of loudspeaker arrays. The dispersion in their parameters may influence the performance of a speaker set. Parametric loudspeaker arrays and omnidirectional sound sources have been used for years. However, the possible influence of transducer manufacturing tolerances on the arrays' performance has not been investigated. In previous research, the sources of possible dispersion in acoustic measurements carried out with omnidirectional sources were studied, pointing out that the problems with sound sources may be a significant reason behind the small measurement repeatability in standards. This paper investigated the measurement of several common types of miniature speakers, using 10 pieces of each type and investigating the influence of their parameter dispersion in electric and acoustic ways. Numerical simulations of omnidirectional sound sources were performed to investigate the drivers' dispersion influence sensitivity. The results provided proof of the small-signal parameter dispersion reaching 20% of the variation. The acoustic measurements show that the loudspeakers may differ in sensitivity parameters by up to 4 dB in 10 transducer tests. The analysis of an example multitransducer array indicated that a dispersion of a sensitivity higher than 1 dB might lead to significant misperformance in constructed arrays and measurement deviations with this type of array.

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.