Non-bonded force field model with advanced restrained electrostatic potential charges (RESP2)

Supramolecular assembly strategy of modified starch chains for achieving recyclable emulsion biocatalysis within a narrow pH range

Stimuli-responsive Pickering emulsions are promising in biocatalysis for their ease of product separation and emulsifier recovery. However, pH responsiveness, though simple and cost-effective, faces challenges in precise control and narrow transition ranges, limiting its use in enzymatic catalysis. Herein we introduced amorphous octenyl succinic anhydride-modified debranched starch chains (Am-OSA-St) to control emulsion properties within a pH range suitable for enzymatic catalysis. By adjusting the OSA group density and molecular weight, Am-OSA-St allowed emulsions to transition reversibly between pH 7.3 and 5.5 and enabled self-recycling through supramolecular self-assembly. Employing molecular dynamics simulations and physicochemical characterization, we elucidated the control mechanism of oil-water interfaces via the microstructure transformation of Am-OSA-St. The findings revealed that protonation of carboxylate groups disrupted the charge balance and polarity of starch chains, leading to strong electrostatic and van der Waals interactions that drove self-assembly. This entanglement caused starch chains in the aqueous phase to "drag" those at the oil-water interface, moving them into the aqueous phase and forming micelles. These micelles, with a hydrophobic interior and hydrophilic exterior, prevented re-adsorption. Testing with Candida antarctica Lipase B (CALB) and N-acetylneuraminic lyase showed that the pH-regulated emulsion system maintained excellent efficiency and cycling stability in mild conditions.

Concentration polarization induced phase rigidification in ultralow salt colloid chemistry to stabilize cryogenic Zn batteries

The breakthrough in electrolyte technology stands as a pivotal factor driving the battery revolution forward. The colloidal electrolytes, as one of the emerging electrolytes, will arise gushing research interest due to their complex colloidal behaviors and mechanistic actions at different conditions (aqueous/nonaqueous solvents, salt concentrations etc.). Herein, we show "beyond aqueous" colloidal electrolytes with ultralow salt concentration and inherent low freezing points to investigate its underlying mechanistic principles to stabilize cryogenic Zn metal batteries. Impressively, the "seemingly undesired" concentration polarization at the interface would disrupt the coalescence stability of the electrolyte, leading to a mechanically rigid interphase of colloidal particle-rich layer, positively inhibiting side reactions on either side of the electrodes. Importantly, the multi-layered pouch cells with cathode loading of 10 mg cm-2 exhibit undecayed capacity at various temperatures, and a relatively high capacity of 50 mAh g-1 could be well maintained at -80 °C.

Uncovering the Crucial Role of Chelating Structures in Cyano-Alkyl-Phosphate Electrolytes for High-Voltage Lithium Metal Batteries

The inferior oxidative stability of commercial carbonate electrolytes and overgrowth of the electrode-electrolyte interphase (EEI) have largely hindered the development of high-voltage lithium metal batteries. In this study, these challenges are addressed by designing Li+-solvent chelating solvation structures to inhibit solvent decomposition using cyano-alkyl-phosphate as a demonstration. Theoretical and experimental studies confirm that the -P═O and -C≡N groups within diethyl (2-cyanethyl) phosphonate exhibit a comparable ability to coordinate with Li+, facilitating the formation of seven-membered chelating structures. This unique solvation structure contributes to the formation of anion-derived inorganic-rich EEI with high stability and robustness, hindering the further decomposition of the electrolyte. Additionally, the cyano group has a strong complexation with the transition metal (TM) in the cathode to inhibit TM dissolution, thereby ensuring the structural stability of the cathode particle. Utilizing this special chelating structure, the designed electrolyte demonstrates favorable Li plating/stripping reversibility and promising oxidative stability in high-voltage batteries. Consequently, the LiNi0.8Co0.1Mn0.1O2 (NCM811) cathode exhibits a high capacity retention (90%) after operating 300 cycles. Under harsh testing conditions, the 4.6 V Li||NCM811 pouch cell with a capacity of 1.4 Ah (∼295 Wh kg-1 based on the total mass of the cell) retains 70% capacity after 80 cycles. This work provides new insights into the correlation between the solvation structure and oxidative stability of electrolytes, contributing significantly to the advancement of high-voltage lithium metal batteries.

Intramolecular interaction induced C-C cleavages in fructose conversion in polar aprotic solvents-origin of the formation of excess formic acid and oligomers

Understanding the mechanism of excess formic acid formation in the dehydration of fructose to HMF would be beneficial to improve HMF selectivity and carbon efficiency. The production of formic acid from keto-D-fructose in polar aprotic solvents, such as THF, DIO, and MTHF, and MIBK solvents without a catalyst was investigated via DFT calculations. It was found that in THF, DIO and MTHF solvents, fructose tended to generate formic acid directly with the catalysis of the intramolecular hydroxyls, especially C6-OH (terminal hydroxyl), while in MIBK, the solvent molecule could react with the intermediates produced in the process, making the barrier of production of acetic acid lower than that of formic acid. Molecular dynamics simulations showed that the lower dielectric polar aprotic solvents (THF, DIO and MTHF) could not destroy the intramolecular H-bonds of hydroxyls in fructose, which could promote the keto-enol tautomerization and hydration steps, facilitating the formation of six-member-ring transition states, which reduced the ring tension and decreased the activation energy greatly, leading to the overproduction of formic acid and oligomers. ETS-NOCV analysis further indicated that the donated electrons from C-O σ-bonds on the carbon chain of fructose made the intramolecular hydroxyls more basic, which could catalyse keto-enol tautomerization with a lower energy barrier than water molecules. To obtain more target products, such as HMF, suitable reaction environments, such as a higher polar aprotic solvent with a low boiling point or restriction of the activity of hydroxyls of fructose, might be selected to destroy the intramolecular interaction and then reduce the overproduction of formic acid and the formation of oligomers.

Exploring the mechanism of action of Modified Simiao Powder in the treatment of osteoarthritis: an in-silico study

Introduction

Osteoarthritis (OA) is the most common form of arthritis and the leading musculoskeletal disorders in adults. Modified Simiao Powder (MSMP) has been widely used in the treatment of OA with remarkable clinical ecaciousness.

Objective

This study aimed to elucidate underlying mechanisms of MSMP in OA by employing network pharmacology, molecular docking, and molecular dynamics simulations, due to the unclear mode of action.

Methods

Bioinformatic analysis was used to evaluate the major chemical constituents of MSMP, determine prospective target genes, and screen genes associated with OA. Network pharmacology methods were then applied to identify the crucial target genes of MSMP in OA treatment. Further analyses included gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. These key targets within the pertinent pathways was further confirmed by molecular docking, binding energy evaluation, and molecular dynamics simulations.

Results

Network pharmacology analysis identified an MSMP component-target-pathway network comprising 11 central active compounds, 25 gene targets, and 12 biological pathways.

Discussion

These findings imply that the therapeutic effects of MSMP was potentially mediated by targeting several pivotal genes, such as androgen receptor (AR), NFKB1, AKT1, MAPK1, and CASP3, and regulating some pathways, including lipid metabolism and atherosclerosis, the AGE-RAGE signaling pathway in diabetic complications, the PI3K-Akt signaling pathway, fluid shear stress, atherosclerosis, and Kaposi's sarcoma-associated herpesvirus infection. Molecular docking assessments demonstrated that these compounds of MSMP, such as berberine, kaempferol, quercetin, and luteolin, exhibit high binding anities to AR and AKT1. Molecular dynamics simulations validated the interactions between these compounds and targets.

Conclusion

The therapeutic effect of MSMP likely attributed to the modulation of multiple pathways, including lipid metabolism, atherosclerosis, the AGE-RAGE signaling pathway, and the PI3K-Akt signaling pathway, by the active components such as berberine, kaempferol, luteolin, and quercetin. Especially, their actions on target genes like AR and AKT1 contribute to the therapeutic benefits of MSMP observed in the treatment of OA.

Structural Insight into Melatonin's Influence on the Conformation of Aβ42 Dimer Studied by Molecular Dynamics Simulation

The accumulation of amyloid-beta (Aβ) oligomers is recognized as a potential culprit in Alzheimer's disease (AD). Experimental studies show that melatonin, a hormone that mainly regulates circadian rhythm and sleep, can interact with Aβ peptides and disrupt the formation of oligomers. However, how melatonin inhibits the oligomerization of soluble Aβ is unclear. Here, by computational simulations, we investigate the effect of different levels of melatonin on the conformation of the Aβ42 dimer. We find that the conformation of the Aβ42 dimer is dependent on melatonin levels. When melatonin is absent, the dimer mainly forms a parallel β-sheet in the CHC region. When one melatonin molecule is present, the overall conformation of the dimer does not change much, but the N-terminal of the dimer tends to adopt antiparallel β-sheets. When two melatoinin molecules are present, the Aβ42 dimer exhibits significant structural change, especially in its central region, resulting in a more compact conformation, and forms parallel β-sheets in the C-terminal. This conformational difference induced by different levels of melatoinin can shed light on the protective role of melatonin.

PVA-Stabilized and Coassembled Nano/Microparticles with High Payload of Dual Phytochemicals for Enhanced Antibacterial and Targeting Effect

The codelivery of multiple bioactive phytochemicals via nano/microparticles (NPs/MPs) represents a promising strategy for enhancing therapeutic efficacy. This study presents the development of novel poly(vinyl alcohol) (PVA)-stabilized hybrid particles designed for codelivery of palmatine hydrochloride (PAL) and glycyrrhizic acid (GL). Employing a straightforward coassembly method, we synthesized dual-drug particles achieving a high payload capacity of over 70%. The particles were characterized as uniform in size, within the nano/micron range, and exhibited a ζ-potential of -5.0 mV. The incorporation of PVA not only stabilized the particles but also refined the aggregation process, resulting in more uniform and finer particles approximately 1 μm in size. Spectral analysis and molecular dynamics simulations verified the presence of π-π stacking and hydrogen bonding between PAL and GL within the particles. In vitro antibacterial assays indicated that the hybrid particles had a lower minimum inhibitory concentration against Escherichia coli and Multidrug-Resistant Staphylococcus aureus than those of the pure drugs. In vivo biodistribution study in rats revealed that the PVA-stabilized particles revealed enhanced targeting to the liver, lung, and heart, demonstrating improved tissue selectivity compared with the solution group. In summary, the PVA-stabilized hybrid NPs/MPs represent an innovative and efficient platform for codelivery of multidrugs. These findings highlight the promise of coassembled particles for high loading, enhanced bioactivity, and targeted delivery, making them a strong candidate for future clinical applications.

Enzyme Tunnel Dynamics and Catalytic Mechanism of Norcoclaurine Synthase: Insights from a Combined LiGaMD and DFT Study

This study conducts a systematic investigation into the catalytic mechanism of norcoclaurine synthase (NCS), a key enzyme in the biosynthesis of tetrahydroisoquinolines (THIQs) with therapeutic applications. By integration of LiGaMD and DFT calculations, the reaction pathway of NCS is mapped, providing detailed insights into its catalytic activity and selectivity. Our findings underscore the critical role of E103 in substrate capture and reveal the hitherto unappreciated influence of nonpolar residues M183 and L76 on tunnel dynamics. A prominent discovery is the identification of a high-energy barrier (44.2 kcal/mol) associated with the aromatic electrophilic attack, which pinpoints the rate-limiting step. Moreover, we disclose the existence of dual transition states leading to different products with the energetically favored six-membered ring formation consistent with experimental evidence. These mechanistic revelations not only refine our understanding of NCS but also advocate for a renewed emphasis on enzyme tunnel engineering for optimizing THIQs biosynthesis. The research sets the stage for translating these findings into practical enzyme modifications. Our results highlight the potential of NCS as a biocatalyst to overcome the limitations of current synthetic methodologies, such as low yields and environmental impacts, and provide a theoretical contribution to the efficient, eco-friendly production of THIQs-based pharmaceuticals.

A Thin Polymer Layer Enables Peptide-Polycation Complexes with Ultrahigh Efficient Encapsulation

A monolayer encapsulation is a new opportunity for engineering a system with high drug loading, but immobilizing polymer molecules on the surface of individual peptide nanoparticles is still an ongoing challenge. Herein, an individual peptide nanoparticle encapsulation strategy is proposed via surface adsorption, in which peptide molecules undergo granulation and subsequently aggregate with polymer molecules, forming a network via electrostatic interactions. Under the water phase, surplus polymer molecules dissolve, leading to a single nanoparticle encapsulation with a core-shell structure. As expected, the dense interfacial layer on the peptide nanoparticle surface achieves a superior loading degree of up to 95.4%. What's more, once the core-shell structure is established, the peptide mass fraction in individual encapsulation always exceeds 90% even under fierce external force. Following the individual nanoparticle encapsulation, the insulin-polycation complex (InsNp@PEI) reduces the inflammation from polymer and displays an effective glycemic control in type 1 diabetes. Overall, the newly developed single surface decoration encapsulates peptides with ultrahigh efficiency and opens up the possibility for further encapsulation.

Cellulose nanocrystal-stabilized Pickering emulsion gels as vehicles for follicular delivery of minoxidil

Minoxidil (MXD) is the only topical over-the-counter medicine approved by the United States Food and Drug Administration for the treatment of androgenetic alopecia. For the purpose of targeting the delivery of MXD to dermal papilla in the hair follicle, MXD Pickering emulsion gels were fabricated based on the designability of deep eutectic solvent (DES) and the versatility of cellulose nanocrystal (CNC) and sodium carboxymethyl cellulose (CMC-Na). Structural studies and theoretical calculations results suggest that CNC can stabilize the interface between the MXD-DES and water, leading to the formation of Pickering emulsions. The rheological properties and stabilities of MXD Pickering emulsions were enhanced through gelation using CMC-Na, which highlights the good compatibility and effectiveness of natural polysaccharides in emulsion gels. Due to the particle size of emulsion droplets (679 nm) and the rheological properties of emulsion gel, the fabricated MXD formulations show in vivo hair regrowth promotion and hair follicle targeting capabilities. Interestingly, the MXD Pickering emulsion-based formulations exert therapeutic effects by upregulating the expression of hair growth factors. The proposed nanodrug strategy based on supramolecular strategies of CNC and CMC-Na provides an interesting avenue for androgenetic alopecia treatment.

MEPO-ML: a robust graph attention network model for rapid generation of partial atomic charges in metal-organic frameworks

Accurate computation of the gas adsorption properties of MOFs is usually bottlenecked by the DFT calculations required to generate partial atomic charges. Therefore, large virtual screenings of MOFs often use the QEq method which is rapid, but of limited accuracy. Recently, machine learning (ML) models have been trained to generate charges in much better agreement with DFT-derived charges compared to the QEq models. Previous ML charge models for MOFs have all used training sets with less than 3000 MOFs obtained from the CoRE MOF database, which has recently been shown to have high structural error rates. In this work, we developed a graph attention network model for predicting DFT-derived charges in MOFs where the model was developed with the ARC-MOF database that contains 279,632 MOFs and over 40 million charges. This model, which we call MEPO-ML, predicts charges with a mean absolute error of 0.025e on our test set of over 27 K MOFs. Other ML models reported in the literature were also trained using the same dataset and descriptors, and MEPO-ML was shown to give the lowest errors. The gas adsorption properties evaluated using MEPO-ML charges are found to be in significantly better agreement with the reference DFT-derived charges compared to the empirical charges, for both polar and non-polar gases. Using only a single CPU core on our benchmark computer, MEPO-ML charges can be generated in less than two seconds on average (including all computations required to apply the model) for MOFs in the test set of 27 K MOFs.

Cryo-EM structures of a mycobacterial ABC transporter that mediates rifampicin resistance

Drug-resistant Tuberculosis (TB) is a global public health problem. Resistance to rifampicin, the most effective drug for TB treatment, is a major growing concern. The etiological agent, Mycobacterium tuberculosis (Mtb), has a cluster of ATP-binding cassette (ABC) transporters which are responsible for drug resistance through active export. Here, we describe studies characterizing Mtb Rv1217c-1218c as an ABC transporter that can mediate mycobacterial resistance to rifampicin and have determined the cryo-electron microscopy structures of Rv1217c-1218c. The structures show Rv1217c-1218c has a type V exporter fold. In the absence of ATP, Rv1217c-1218c forms a periplasmic gate by two juxtaposed-membrane helices from each transmembrane domain (TMD), while the nucleotide-binding domains (NBDs) form a partially closed dimer which is held together by four salt-bridges. Adenylyl-imidodiphosphate (AMPPNP) binding induces a structural change where the NBDs become further closed to each other, which downstream translates to a closed conformation for the TMDs. AMPPNP binding results in the collapse of the outer leaflet cavity and the opening of the periplasmic gate, which was proposed to play a role in substrate export. The rifampicin-bound structure shows a hydrophobic and periplasm-facing cavity is involved in rifampicin binding. Phospholipid molecules are observed in all determined structures and form an integral part of the Rv1217c-1218c transporter system. Our results provide a structural basis for a mycobacterial ABC exporter that mediates rifampicin resistance, which can lead to different insights into combating rifampicin resistance.

Molecule Design for Non-Aqueous Wide-Temperature Electrolytes via the Intelligentized Screening Method

Operating a lithium-ion battery (LIB) in a wide temperature range is essential for ensuring a stable electricity supply amidst fluctuating temperatures caused by climate or terrain changes. Electrolyte plays a pivotal role in determining the temperature durability of batteries. However, specialized electrolytes designed for either low or high temperatures typically possess distinct features. Therefore, wide-temperature electrolytes (WTEs) are necessary as they encompass a combination of diverse properties, which complicates the clear instruction of WTE design. Here we represent an artificial intelligence (Al)-assisted workflow of WTE design through stepwise parameterizations and calculations. Linear mono-nitriles are identified as ideal wide-liquidus-range solvents that can "softly" solvate lithium ions by weak interactions. In addition, the explainable modules revealed the halogenoid similarity of cyanide as fluorine on the electrolyte properties (e.g. boiling point and dielectric constant). With the further introduction of an ether bond, 3-methoxypropionitrile (MPN) has been eventually determined as a main electrolyte solvent, enabling the battery operation from -60 to 120 °C. Particularly, a LiCoO2/Li cell using the proposed WTE can realize stable cycling with capacity retention reaching 72.3 % after 50 cycles under a high temperature of 100 °C.

Influence of terahertz waves on the binding of choline to choline acetyltransferase: insights from molecular dynamics simulations

Acetylcholine (Ach) is a common neurotransmitter in the central nervous system (CNS) and peripheral nervous system (PNS). It is one of the neurotransmitters in the autonomic nervous system and the main neurotransmitter in all autonomic ganglia. Experiments have confirmed that electromagnetic waves can affect the synthesis of animal neurotransmitters, but the microscopic effects of electromagnetic waves in the terahertz (THz) frequency band are still unclear. Based on density functional theory (DFT) and molecular dynamics (MD) simulation methods, this paper studies the effect of THz electromagnetic waves on the binding of choline to choline acetyltransferase (ChAT). By emitting THz waves that resonate with the characteristic vibration mode of choline near the active site, it was found that THz waves with a frequency of 45.3 THz affected the binding of choline to ChAT, especially the binding of the active site histidine His324 to choline. The main evidence is that under the action of THz waves, the binding free energy of choline to histidine His324 and ChAT at the active site was significantly reduced compared to noE, which may have a potential impact on the enzymatic synthesis of Ach. It is expected to achieve the purpose of regulating the synthesis of the neurotransmitter Ach under the action of THz waves and treat certain nervous system diseases.

A comprehensive electron wavefunction analysis toolbox for chemists, Multiwfn

Analysis of electron wavefunction is a key component of quantum chemistry investigations and is indispensable for the practical research of many chemical problems. After more than ten years of active development, the wavefunction analysis program Multiwfn has accumulated very rich functions, and its application scope has covered numerous aspects of theoretical chemical research, including charge distribution, chemical bond, electron localization and delocalization, aromaticity, intramolecular and intermolecular interactions, electronic excitation, and response property. This article systematically introduces the features and functions of the latest version of Multiwfn and provides many representative examples. Through this article, readers will be able to fully understand the characteristics and recognize the unique value of Multiwfn. The source code and precompiled executable files of Multiwfn, as well as the manual containing a detailed introduction to theoretical backgrounds and very rich tutorials, can all be downloaded for free from the Multiwfn website (http://sobereva.com/multiwfn).

Discovery of 4-(Arylethynyl)piperidine Derivatives as Potent Nonsaccharide O-GlcNAcase Inhibitors for the Treatment of Alzheimer's Disease

Inhibiting O-GlcNAcase and thereby up-regulation of the O-GlcNAc levels of tau was a potential approach for discovering AD treatments. Herein, a series of novel highly potent OGA inhibitors embracing a 4-(arylethynyl)piperidine moiety was achieved by capitalizing on the substrate recognition domain. Extensive structure-activity relationships resulted in compound 81 with significant enzymatic inhibition (IC50 = 4.93 ± 2.05 nM) and cellular potency (EC50 = 7.47 ± 3.96 nM in PC12 cells). It markedly increased the protein O-GlcNAcylation levels and reduced the phosphorylation on Ser199, Thr205, and Ser396 of tau in the OA-injured SH-SY5Y cell model, suggesting its potential role for AD treatment. In fact, an in vivo efficacy of ameliorating cognitive impairment was observed following treatment of APP/PS1 mice with compound 81 (100 mg/kg). Additionally, the appropriate plasma PK and beneficial BBB penetration properties were also observed. Compound 81 deserves to be further explored as an anti-AD agent.

Molecular Interactions of Perfluorinated and Branched Fluorine-Free Surfactants at Interfaces: Insights from a New Reliable Force Field

Per- and polyfluoroalkyl substances (PFAS) constitute a class of synthetic compounds with exceptional interfacial properties. Their widespread use in many industrial applications and consumer products, combined with their remarkable chemical and thermal stability, has led to their ubiquitous presence in environmental matrices, including surface water and groundwater. To replace PFAS with fluorine-free surfactants, it is necessary first to develop a deep molecular-level understanding of the mechanisms responsible for the exceptional properties of PFAS. For instance, it has been shown that fluorine-free surfactants with highly branched or methylated chains can achieve low surface tensions at air-water interfaces and can provide highly hydrophobic surface coatings. Although molecular simulations combined with experiments are promising for uncovering these mechanisms, the reliability of simulation results depends strongly on the accuracy of the force fields implemented. At the moment, atomistic force fields are not available to describe PFAS in a variety of environments. Ab initio methods could help fill this knowledge gap, but they are computationally demanding. As an alternative, ab initio calculations could be used to develop accurate force fields for atomistic simulations. In this work, a new algorithm is proposed, which, built from accurate ab initio calculations, yields force fields for perfluorinated sulfonic and perfluoroalkyl acids. The accuracy of the new force field was benchmarked against solvation free energy and interfacial tension data. The new force fields were then used to probe the interfacial behavior of the PFAS surfactants. The interfacial properties observed in our simulations were compared with those manifested by two branched fluorine-free surfactants. The good agreement achieved with experiments and ab initio calculations suggests that the proposed protocol could be implemented to study other perfluorinated substances and help in the design of fluorine-free surfactants for targeted applications.

Mechanism investigation of highly selective inhibitors toward phosphodiesterase 5 and 6 via the in vitro calculation and simulation

Introduction: In clinical practice, phosphodiesterase 5 (PDE5) inhibitors are commonly used to treat erectile dysfunction and pulmonary arterial hypertension. However, due to the high structural similarity between PDE5 and Phosphodiesterase 6 (PDE6), there is a risk that existing drugs will cause off-target effects on PDE6 resulting in visual disorders such as low visual acuity and color blindness. Previous research on the selectivity of PDE5 inhibitors focused on marketed drugs such as sildenafil and tadalafil. Methods: In this study, a highly selective PDE5 inhibitor, ligand3, was used as the subject, and molecular docking, molecular dynamics simulations, MM-GBSA, alanine scanning, and independent gradient model analysis were employed to investigate the biological mechanism underlying the selectivity of PDE5 inhibitors. Results and Discussion: The present work revealed that the binding mode of ligand3 to the PDE5A and PDE6C targets was distinctly different. Ligand3 exhibited stronger coulombic forces when binding to PDE5A, while showing stronger van der waals forces when binding to PDE6C. Ligand3 binds more deeply at the active site of PDE5A than at PDE6C, allowing its side chains to effectively bind to the critical TYR612, whereas in the case of the shallow binding to PDE6C, ligand3 lacks a similar effect. Mechanism investigations of highly selective inhibitors through computational simulation might provide an insight into potent treatment of drugs.

Molecular understanding of the self-assembly of an N-isopropylacrylamide delivery system for the loading and temperature-dependent release of curcumin

Global changes and drug abuse are forcing humanity to face various disease problems, and alternative therapies with safe natural substances have important research value. This paper combines various techniques in quantum chemical calculations and molecular simulations to provide molecular-level insight into the dynamics of the self-assembly of N-isopropylacrylamide (NIPAM) for loading curcumin (CUR). The results indicate that increasing the chain length of NIPAM molecules reduces their efficiency in encapsulating and locking CUR, and electrostatic interactions and van der Waals interactions are the main driving forces behind the evolution of system configurations in these processes. The isopropyl groups of NIPAM and the two phenolic ring planes of CUR are the main contact areas for the interaction between the two types of molecules. The thermosensitive effect of NIPAM can alter the distribution of isopropyl groups in NIPAM molecules around CUR. As a result, when the temperature rises from ambient temperature (300 K) to human characteristic temperature (310 K), the NIPAM-CUR interactions and radial distribution functions suggest that body temperature is more suitable for drug release. Our findings offer a vital theoretical foundation and practical guidance for researchers to develop temperature-sensitive drug delivery systems tailored for CUR, addressing its clinical application bottleneck.

Synthesis and characterization of gold(I) thiolate derivatives and bimetallic complexes for HIV inhibition

Introduction: The human immunodeficiency virus (HIV) remains a significant global health concern, with a reported high infection rate of 38.4 million cases globally; an estimated 2 million new infections and approximately 700,000 HIV/AIDS-related deaths were reported in 2021. Despite the advent of anti-retroviral therapy (ART), HIV/AIDS persists as a chronic disease. To combat this, several studies focus on developing inhibitors targeting various stages of the HIV infection cycle, including HIV-1 protease. This study aims to synthesize and characterize novel glyco diphenylphosphino metal complexes with potential HIV inhibitory properties. Method: A series of new gold(I) thiolate derivatives and three bimetallic complexes, incorporating amino phosphines and thiocarbohydrate as auxiliary ligands, were synthesized using procedures described by Jiang, et al. (2009) and Coetzee et al. (2007). Structural elucidation and purity assessment of the synthesized compounds (1-11) were conducted using micro-analysis, NMR, and infrared spectrometry. Results and Discussion: Using molecular modeling techniques, three of the metal complexes were identified as potential HIV protease inhibitors, exhibiting strong binding affinity interactions with binding pocket residues. These inhibitors demonstrated an ability to inhibit the flexibility of the flap regions of the HIV protease, similar to the known HIV protease inhibitor, darunavir. This study sheds light on the promising avenues for the development of novel therapeutic agents against HIV/AIDS.

Weakly ionized gold nanoparticles amplify immunoassays for ultrasensitive point-of-care sensors

Gold nanoparticle-based lateral flow immunoassays (AuNP LFIAs) are widely used point-of-care (POC) sensors for in vitro diagnostics. However, the sensitivity limitation of conventional AuNP LFIAs impedes the detection of trace biomarkers. Several studies have explored the size and shape factors of AuNPs and derivative nanohybrids, showing limited improvements or enhanced sensitivity at the cost of convenience and affordability. Here, we investigated surface chemistry on the sensitivity of AuNP LFIAs. By modifying surface ligands, a surface chemistry strategy involving weakly ionized AuNPs enables ultrasensitive naked-eye LFIAs (~100-fold enhanced sensitivity). We demonstrated how this surface chemistry-amplified immunoassay approach modulates nanointerfacial bindings to promote antibody adsorption and higher activity of adsorbed antibodies. This surface chemistry design eliminates complex nanosynthesis, auxiliary devices, or additional reagents while efficiently improving sensitivity with advantages: simplified fabrication process, excellent reproducibility and reliability, and ultrasensitivity toward various biomarkers. The surface chemistry using weakly ionized AuNPs represents a versatile approach for sensitizing POC sensors.

Quantum-Informed Molecular Representation Learning Enhancing ADMET Property Prediction

We examined pretraining tasks leveraging abundant labeled data to effectively enhance molecular representation learning in downstream tasks, specifically emphasizing graph transformers to improve the prediction of ADMET properties. Our investigation revealed limitations in previous pretraining tasks and identified more meaningful training targets, ranging from 2D molecular descriptors to extensive quantum chemistry simulations. These data were seamlessly integrated into supervised pretraining tasks. The implementation of our pretraining strategy and multitask learning outperforms conventional methods, achieving state-of-the-art outcomes in 7 out of 22 ADMET tasks within the Therapeutics Data Commons by utilizing a shared encoder across all tasks. Our approach underscores the effectiveness of learning molecular representations and highlights the potential for scalability when leveraging extensive data sets, marking a significant advancement in this domain.

Rational Design of Loop Dynamics for a Barrel-Shaped Enzyme by Introducing Disulfide Bonds

Loop dynamics redesign is an important strategy to manipulate protein function. Cellobiose 2-epimerase (CE) and other members of its superfamily are widely used for diverse industrial applications. The structural feature of the loops connecting barrel helices contributes greatly to the differences in their functional characteristics. Inspired by the in-silico mutation with molecular dynamics (MD) simulation analysis, we propose a strategy for identifying disulfide bond mutation candidates based on the prediction of protein flexibility and residue-residue interaction. The most beneficial mutant with the newly introduced disulfide bond would simultaneously improve both its thermostability and its reaction propensity to the targeting isomerization product. The ratio of the isomerization/epimerization catalytic rate was improved from 4:103 to 9:22. MD simulation and binding free energy calculations were applied to provide insights into molecular recognition upon mutations. The comparative analysis of enzyme/substrate binding modes indicates that the altered catalytic reaction pathway is due to less efficient binding of the native product. The key residue responsible for the observed phenotype was identified by energy decomposition and was further confirmed by the mutation experiment. The rational design of the key loop region might be a promising strategy to alter the catalytic behavior of all (α/α)6-barrel-like proteins.

Molecular Dynamics Simulation of the Interaction within the Carboxymethyl Cellulose-Modified Montmorillonite Lamellae at Aggressive CuCl2 Concentrations

To elucidate the degradation mechanism of the CMC-modified MMT composite at aggressive Cu2+ concentrations, large scale molecular dynamics simulation was conducted for CuCl2 concentrations ranging from 0 to 800 mM. Both CMC and MMT followed the Langmuir isotherm for Cu2+ adsorption, and the adsorption capacity of CMC (8.75 mmol/g) was much higher than that of MMT (0.83 mmol/g). Despite the CMC mass ratio being only 4.1%, it adsorbed up to 34.3% of the total adsorbed Cu2+. The Cu2+ attraction ability hierarchy of oxygen-containing functional groups in the CMC is as follows: carboxylic oxygens > alcoholic oxygens > carbinolic oxygens > bridging oxygens > glucose oxygens. Carboxyls were the most effective in chelating and complexing with Cu2+, and they could be intentionally added in artificially synthesized polymer-MMT composites for Cu2+ containment. Formation of the Cu2+ cation bridge between CMC and MMT at aggressive CuCl2 concentrations contributed to the transition of CMC density distribution from unimodality to bimodality and enhanced resistance of polymer elution. As the CuCl2 concentration increased, the stoichiometric ratio between the chelated Cu2+ and carboxylic oxygens increased from 1:2 to 1:1, suggesting the evolution of the Cu2+ chelation mechanism.

Supramolecular interaction between berberine hydrochloride and baicalin in aqueous solution: Reaction kinetics, spectral analysis and dynamic simulation

The current study presents a comprehensive investigation on the precipitation reaction and supramolecular interactions between berberine hydrochloride (BBR) and baicalin (BA) in an aqueous system. Utilizing a combination of multi-spectral analytical techniques and molecular dynamic simulations, we elucidated the mechanism of the complexion process. The precipitate formation was observed within a drug concentration range of 0.1-1.0 mM, and a 1:1 stoichiometry ratio of BBR to BA was established by the Job's plot method. Morphological and structural characterizations of the precipitates were conducted using DSC, FTIR and PXRD. Additionally, UV-Vis absorption and 1H NMR spectroscopy were employed to compare the spectral characteristics of the precipitates with those of individual drug solution. Molecular dynamic simulations further dissected the intermolecular interactions and self-assembly mechanisms. The precipitates formed were amorphous microparticles with an average diameter of approximately 20 μm, primarily stabilized by hydrogen bonding and π-π stacking. This study contributes foundational insights into the supramolecular interactions between BBR and BA, therefore facilitated a better understanding of the precipitation process involving flavonoid-alkaloid pairs in mixed aqueous solutions.

Restructuring Electrolyte Solvation by a Partially and Weakly Solvating Cosolvent toward High-Performance Potassium-Ion Batteries

Ether-based electrolytes are among the most important electrolytes for potassium-ion batteries (PIBs) due to their low polarization voltage and notable compatibility with potassium metal. However, their development is hindered by the strong binding between K+ and ether solvents, leading to [K+-solvent] cointercalation on graphite anodes. Herein, we propose a partially and weakly solvating electrolyte (PWSE) wherein the local solvation environment of the conventional 1,2-dimethoxyethane (DME)-based electrolyte is efficiently reconfigured by a partially and weakly solvating diethoxy methane (DEM) cosolvent. For the PWSE in particular, DEM partially participates in the solvation shell and weakens the chelation between K+ and DME, facilitating desolvation and suppressing cointercalation behavior. Notably, the solvation structure of the DME-based electrolyte is transformed into a more cation-anion-cluster-dominated structure, consequently promoting thin and stable solid-electrolyte interphase (SEI) generation. Benefiting from optimized solvation and SEI generation, the PWSE enables a graphite electrode with reversible K+ (de)intercalation (for over 1000 cycles) and K with reversible plating/stripping (the K||Cu cell with an average Coulombic efficiency of 98.72% over 400 cycles) and dendrite-free properties (the K||K cell operates over 1800 h). We demonstrate that rational PWSE design provides an approach to tailoring electrolytes toward stable PIBs.

dMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks

Generating the three-dimensional (3D) structure of small molecules is crucial in both structure- and ligand-based drug design. Structure-based drug design needs bioactive conformations of compounds for lead identification and optimization. Ligand-based drug design techniques, such as 3D shape similarity search, 3D pharmacophore model, 3D-QSAR, etc., all require high-quality small-molecule ligand conformations to obtain reliable results. Although predicting a small molecular bioactive conformer requires information from the receptor, a crystal structure of the molecule is a proper approximation to its bioactive conformer in a specific receptor because the binding pose of a small molecule in its receptor's binding pockets should be energetically close to the crystal structures. This study presents a de novo small molecular structure predictor (dMXP) with graph attention networks based on crystal data derived from the Cambridge Structural Database (CSD) combined with molecular electrostatic information calculated by density-functional theory (DFT). Two featuring strategies (topological and atomic partial change features) were employed to explore the relation between these features and the 3D crystal structure of a small molecule. These features were then assembled to construct the holistic 3D crystal structure of a molecule. Molecular graphs were encoded using a graph attention mechanism to deal with the issues of the inconsistencies of local substructures contributing to the entire molecular structure. The root-mean-square deviation (RMSDs) of approximately 80% dMXP predicted structures and the native binding poses within receptors are less than 2.0 Å.

Computational Insights into Cyclodextrin Inclusion Complexes with the Organophosphorus Flame Retardant DOPO

Cyclodextrins (CDs) were used as green char promoters in the formulation of organophosphorus flame retardants (OPFRs) for polymeric materials, and they could reduce the amount of usage of OPFRs and their release into the environment by forming [host:guest] inclusion complexes with them. Here, we report a systematic study on the inclusion complexes of natural CDs (α-, β-, and γ-CD) with a representative OPFR of DOPO using computational methods of molecular docking, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations. The binding modes and energetics of [host:guest] inclusion complexes were analyzed in details. α-CD was not able to form a complete inclusion complex with DOPO, and the center of mass distance [host:guest] distance amounted to 4-5 Å. β-CD and γ-CD allowed for a deep insertion of DOPO into their hydrophobic cavities, and DOPO was able to frequently change its orientation within the γ-CD cavity. The energy decomposition analysis based on the dispersion-corrected density functional theory (sobEDAw) indicated that electrostatic, orbital, and dispersion contributions favored [host:guest] complexation, while the exchange-repulsion term showed the opposite. This work provides an in-depth understanding of using CD inclusion complexes in OPFRs formulations.

A locally solvent-tethered polymer electrolyte for long-life lithium metal batteries

Solid polymer electrolytes exhibit enhanced Li+ conductivity when plasticized with highly dielectric solvents such as N,N-dimethylformamide (DMF). However, the application of DMF-containing electrolytes in solid-state batteries is hindered by poor cycle life caused by continuous DMF degradation at the anode surface and the resulting unstable solid-electrolyte interphase. Here we report a composite polymer electrolyte with a rationally designed Hofmann-DMF coordination complex to address this issue. DMF is engineered on Hofmann frameworks as tethered ligands to construct a locally DMF-rich interface which promotes Li+ conduction through a ligand-assisted transport mechanism. A high ionic conductivity of 6.5 × 10-4 S cm-1 is achieved at room temperature. We demonstrate that the composite electrolyte effectively reduces the free shuttling and subsequent decomposition of DMF. The locally solvent-tethered electrolyte cycles stably for over 6000 h at 0.1 mA cm-2 in Li | |Li symmetric cell. When paired with sulfurized polyacrylonitrile cathodes, the full cell exhibits a prolonged cycle life of 1000 cycles at 1 C. This work will facilitate the development of practical polymer-based electrolytes with high ionic conductivity and long cycle life.

Effect of ionic groups on the morphology and transport properties in a novel perfluorinated ionomer containing sulfonic and phosphonic acid groups: a molecular dynamics study

Combining the phosphonic acid group with the sulfonic acid group in PEMs has been shown to be an effective strategy for improving the fuel cell performance. However, the interplay of two different ionic groups and the resulting effect on the membrane properties have not been fully elucidated. Here, we used classical molecular dynamics simulation to investigate the morphologies, transport properties and effects of ionic groups in a novel perfluorinated PEM containing two ionic groups (PFSA-PFPA) in comparison to the corresponding homopolymers. Phase separations between hydrophilic and hydrophobic domains are confirmed in these PEMs and result from the evolution of water clusters formed around the ionic groups. The combination of both ionic groups brings a complicated morphological feature in PFSA-PFPA, with near-cylindrical aqueous domains of large length scales interconnected by tortuous domains of small sizes. And we found that the self-diffusion coefficients of water molecules are strongly related to morphologies, with the water transport in PFSA-PFPA lying between two analogous homopolymers. At the molecular level, we found that the sulfonic and phosphonic acid groups have distinct effects on the coordination behaviors and the dynamics of water molecules and hydronium ions. Strong electrostatic interactions lead to compact coordination structures and sluggish dynamics of hydronium ions around phosphonic acid groups, which determine the morphological evolution and transport properties in PFSA-PFPA. Our study affords insights into the relationship between molecular characteristics and transport properties bridged by phase-separated morphologies in a novel PEM containing both sulfonic acid and phosphonic acid groups, which deepens the understanding of the interplay between two ionic groups and may inspire the rational design of high-performance PEMs.

A Fully Methylated Cyclic Ether Solvent Enables Graphite Anode Cycling at Low Temperatures

Graphite anode suffers from great capacity loss and larger cell polarization under low-temperature conditions in lithium-ion batteries (LIBs), which are mainly caused by the high energy barrier for the Li+ desolvation process and sluggish Li+ transfer rate across the solid electrolyte interface (SEI). Regulating an electrolyte with an anion-dominated solvation structure could synchronously stabilize the interface and boost the reaction kinetics of the graphite anode. Herein, a highly ionic conductive electrolyte consisting of a fully methylated cyclic ether solvent of 2,2,4,4,5,5-hexamethyl-1,3-dioxolane (HMD) and fluoroethylene carbonate (FEC) cosolvent was designed. The high electron-donating effect and steric hindrance of -(CH3)2 in HMD endow the HMD-based electrolyte with high ionic conductivity but lower coordination numbers with Li+, and an anion-dominated solvation structure was formed. Such configuration can accelerate the desolvation process and induce the forming of a LiF-rich SEI film on the anode, avoiding the solvent coembedding into graphite and enhancing the ion migration rate under low temperatures. The assembled Li||graphite cell with the tame electrolyte outperformed the conventional carbonates-based cell, showing 93.8% capacity retention after 227 cycles for the DF-based cell compared to 64.7% after 150 cycles. It also exhibited a prolonged cycle life for 200 rounds with 81% capacity retention under -20 °C. Therefore, this work offers a valuable thought for solvent design and provides approaches to electrolyte design for low-temperature LIBs.

Exploring the Potential Mechanisms of Guanxinshutong Capsules in Treating Pathological Cardiac Hypertrophy based on Network Pharmacology, Computer-Aided Drug Design, and Animal Experiments

Cardiovascular diseases (CVDs) are significant causes of morbidity and mortality worldwide, and pathological cardiac hypertrophy (PCH) is an essential predictor of many heart diseases. Guanxinshutong capsule (GXST) is a Chinese patent medicine widely used in the clinical treatment of CVD, In our previous research, we identified 111 compounds of GXST. In order to reveal the potential molecular mechanisms by which GXST treats PCH, this study employed network pharmacology methods to screen for the active ingredients of GXST in treating PCH and predicted the potential targets. The results identified 26 active ingredients of GXST and 110 potential targets for PCH. Through a protein-protein interaction (PPI) network, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we confirmed AKT1, MAPK1, and MAPK3 as the core proteins in GXST treatment of PCH, thus establishing the PI3K/AKT and MAPK signaling pathways as the significant mechanisms of GXST in treating PCH. The results of molecular docking (MD) demonstrate that flavonoid naringenin and diterpenoid tanshinone iia have the highest binding affinity with the core protein. Before performing molecular dynamics simulations (MDSs), the geometric structure of naringenin and tanshinone iia was optimized using density functional theory (DFT) at the B97-3c level, and RESP2 atomic charge calculations were carried out at the B3LYP-D3(BJ)/def2-TZVP level. Further MDS results demonstrated that in the human body environment, the complex of naringenin and tanshinone iii with core proteins exhibited high stability, flexibility, and low binding free energy. Additionally, naringenin and tanshinone iia showed favorable absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics and passed the drug similarity (DS) assessment. Ultrasound cardiograms and cardiac morphometric measurements in animal experiments demonstrate that GXST can improve the PCH induced by isoproterenol (ISO). Protein immunoblotting results indicate that GXST increases the expression of P-eNOS and eNOS by activating the PI3K/AKT signaling pathway and the MAPK signaling pathway, further elucidating the mechanism of action of GXST in treating PCH. This study contributes to the elucidation of the key ingredients and molecular mechanisms of GXST in treating PCH.

Discovery of novel macrocyclic derivatives as potent and selective cyclin-dependent kinase 2 inhibitors

Cyclin-dependent kinase 2 (CDK2) is a member of CDK family of kinases (CDKs) that regulate the cell cycle. Its inopportune or over-activation leads to uncontrolled cell cycle progression and drives numerous types of cancers, especially ovarian, uterine, gastric cancer, as well as those associated with amplified CCNE1 gene. However, developing selective lead compound as CDK2 inhibitors remains challenging owing to similarities in the ATP pockets among different CDKs. Herein, we described the optimization of compound 1, a novel macrocyclic inhibitor targeting CDK2/5/7/9, aiming to discover more selective and metabolically stable lead compound as CDK2 inhibitor. Molecular dynamic (MD) simulations were performed for compound 1 and 9 to gain insights into the improved selectivity against CDK5. Further optimization efforts led to compound 22, exhibiting excellent CDK2 inhibitory activity, good selectivity over other CDKs and potent cellular effects. Based on these characterizations, we propose that compound 22 holds great promise as a potential lead candidate for drug development.

Binding of the plant-derived toxin simplexin to bovine protein kinase C: insights from molecular dynamics

Pimelea poisoning of cattle is toxicologically linked to the activation of bovine protein kinase C (PKC) by the plant-derived toxin simplexin. To understand the affinity of PKC for simplexin, we performed molecular dynamics (MD) studies of simplexin, simplexin analogues, and several other activators of PKC. Binding enthalpy calculations indicated that simplexin had the strongest affinity for PKCα-C1B among the activators studied. Key to simplexin's affinity is its ability to form more hydrogen bonds to PKC, compared to the other activators. The C-3 carbonyl group and C-20 hydroxyl group of simplexin were identified as especially important for stabilizing the PKC binding interaction. The hydrophobic alkyl chain of simplexin induces deep membrane embedding of the PKC-simplexin complex, enhancing the protein-ligand hydrogen bonding. Our findings align with previous experiments on structure-activity relationships (SAR) for simplexin analogues, and provide insights that may guide the development of interventions or treatments for Pimelea poisoning.

Analysis of the binding pattern of NIK inhibitors by computational simulation

NF-kappaB-Inducing Kinase (NIK) is a key kinase in the activation of the NF-κB non-classical signalling pathway, which has been shown to be over-activated in patients with inflammatory diseases, immune disorders and malignancies and solid tumours inducing activation of the NF-κB non-classical signalling pathway. The design of ATP-competitive small molecule inhibitors against NIK has been a hot topic in the last decade, and many efficient NIK inhibitors have been identified. In this work, I aim to unravel the mechanism of NIK inhibition by different representative NIK type I 1/2 kinase inhibitors, using ADME, molecular docking, molecular dynamics simulation, MM-PBSA analysis and 3D-QSAR analysis. This work contributes to the understanding of the efficiency of NIK inhibitor binding by revealing the basis of the efficiency of NIK inhibitors, the difference in binding modes between different inhibitors and the overall effect on NIK.Communicated by Ramaswamy H. Sarma.

Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases

The systems of noble gases are particularly instructive for molecular modeling due to the elemental nature of their interactions. They do not normally form bonds nor possess a (permanent) dipole moment, and the only forces determining their bonding/clustering stems from van der Waals forces─dispersion and Pauli repulsion, which can be modeled by empirical potential functions. Combination rules, that is, formulas to derive parameters for pair potentials of heterodimers from parameters of corresponding homodimers, have been studied at length for the Lennard-Jones 12-6 potentials but not in great detail for other, more accurate, potentials. In this work, we examine the usefulness of nine empirical potentials in their ability to reproduce quantum mechanical (QM) benchmark dissociation curves of noble gas dimers (He, Ne, Ar, Kr, and Xe homo- and heterodimers), and we systematically study the efficacy of different permutations of combination relations for each parameter of the potentials. Our QM benchmark comprises dissociation curves computed by several different coupled cluster implementations as well as symmetry-adapted perturbation theory. The two-parameter Lennard-Jones potentials were decisively outperformed by more elaborate potentials that sport a 25-30 times lower root-mean-square error (RMSE) when fitted to QM dissociation curves. Very good fits to the QM dissociation curves can be achieved with relatively inexpensive four- or even three-parameter potentials, for instance, the damped 14-7 potential (Halgren, J. Am. Chem. Soc. 1992, 114, 7827-7843), a four-parameter Buckingham potential (Werhahn et al., Chem. Phys. Lett. 2015, 619, 133-138), or the three-parameter Morse potential (Morse, Phys. Rev. 1929, 34, 57-64). Potentials for heterodimers that are generated from combination rules have an RMSE that is up to 20 times higher than potentials that are directly fitted to the QM dissociation curves. This means that the RMSE, in particular, for light atoms, is comparable in magnitude to the well-depth of the potential. Based on a systematic permutation of combination rules, we present one or more combination rules for each potential tested that yield a relatively low RMSE. Two new combination rules are introduced that perform well, one for the van der Waals radius σij as ( 1 2 ( σ i 3 + σ j 3 ) ) 1 / 3 and one for the well-depth ϵij as ( 1 2 ( ϵ i - 2 + ϵ j - 2 ) ) - 1 / 2 . The QM data and the fitted potentials were evaluated in the gas phase against experimental second virial coefficients for homo- and heterodimers, the latter of which allowed evaluation of the combination rules. The fitted models were used to perform condensed phase molecular dynamics simulations to verify the melting points, liquid densities at the melting point, and the enthalpies of vaporization produced by the models for pure substances. Subtle differences in the benchmark potentials, in particular, the well-depth, due to the level of theory used were found here to have a profound effect on the macroscopic properties of noble gases: second virial coefficients or the bulk properties in simulations. By explicitly including three-body dispersion in molecular simulations employing the best pair potential, we were able to obtain accurate melting points as well as satisfactory densities and enthalpies of vaporization.

Discovery of lupus nephritis targeted inhibitors based on De novo molecular design: comprehensive application of vinardo scoring, ADMET analysis, and molecular dynamics simulation

Lupus Nephritis (LN) is an autoimmune disease affecting the kidneys, and conventional drug studies have limitations due to its imprecise and complex pathogenesis. Therefore, the aim of this study was to design a novel Lupus Nephritis-targeted drug with good clinical due potential, high potency and selectivity by computer-assisted approach.NIK belongs to the serine/threonine protein kinase, which is gaining attention as a drug target for Lupus Nephritis. we used bioinformatics, homology modelling and sequence comparison analysis, small molecule ab initio design, ADMET analysis, molecular docking, molecular dynamics simulation, and MM/PBSA analysis to design and explore the selectivity and efficiency of a novel Lupus Nephritis-targeting drug, ClImYnib, and a classical NIK inhibitor, NIK SMI1. We used bioinformatics techniques to determine the correlation between lupus nephritis and the NF-κB signaling pathway. De novo drugs design was used to create a NIK-targeted inhibitor, ClImYnib, with lower toxicity, after which we used molecular dynamics to simulate NIK SMI1 against ClImYnib, and the simulation results showed that ClImYnib had better selectivity and efficiency. Our research delves into the molecular mechanism of protein ligands, and we have designed and validated an excellent NIK inhibitor using multiple computational simulation methods. More importantly, it provides an idea of target designing small molecules.Communicated by Ramaswamy H. Sarma.

Insights into the Structure-Function Relationship of GH70 GtfB α-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized Limosilactobacillus reuteri N1 GtfB Enzyme

α-Glucanotransferases of the CAZy family GH70 convert starch-derived donors to industrially important α-glucans. Here, we describe characteristics of a novel GtfB-type 4,6-α-glucanotransferase of high enzyme activity (60.8 U mg-1) from Limosilactobacillus reuteri N1 (LrN1 GtfB), which produces surprisingly large quantities of soluble protein in heterologous expression (173 mg pure protein per L of culture) and synthesizes the reuteran-like α-glucan with (α1 → 6) linkages in linear chains and branch points. Protein structural analysis of LrN1 GtfB revealed the potential crucial residues at subsites -2∼+2, particularly H265, Y214, and R302, in the active center as well as previously unidentified surface binding sites. Furthermore, molecular dynamic simulations have provided unprecedented insights into linkage specificity hallmarks of the enzyme. Therefore, LrN1 GtfB represents a potent enzymatic tool for starch conversion, and this study promotes our knowledge on the structure-function relationship of GH70 GtfB α-glucanotransferases, which might facilitate the production of tailored α-glucans by enzyme engineering in future.

Multiscale structure changes and mechanism of polyphenol-amylose complexes modulated by polyphenolic structures

This study was designed to investigate the effect of polyphenolic structure on the interaction strength and process between polyphenols (gallic acid (GA), epigallocatechin gallate (EGCG) and tannic acid (TA)) and amylose (AM). The results of Fourier transform infrared spectroscopy, isothermal titration calorimetry, X-ray photoelectron spectroscopy and molecular dynamic simulation (MD) suggested that the interactions between the three polyphenols and AM were noncovalent, spontaneous, low-energy and driven by enthalpy, which would be enhanced with increasing amounts of pyrogallol groups in the polyphenols. The results of turbidity, particle size and appearance of the complex solution showed that the interaction process between polyphenols and AM could be divided into three steps and would be advanced by increasing the number of pyrogallol groups in the polyphenols. At the same time, MD was intuitively employed to exhibit the interaction process between amylose and polyphenols, and it revealed that the interaction induced the aggregation of amylose and that the agglomeration degree of amylose increased with increasing number of pyrogallol groups at polyphenols. Last, the SEM and TGA results showed that TA/AM complexes had the tightest structure and the highest thermal stability (TA/AM˃EGCG/AM˃GA/AM), which could be attributed to TA having five pyrogallol groups.

Parameterization of General Organic Polymers within the Open Force Field Framework

Polymer and chemically modified biopolymer systems present unique challenges to traditional molecular simulation preparation workflows. First, typical polymer and biomolecular input formats, such as Protein Data Bank (PDB) files, lack adequate chemical information needed for the parameterization of new chemistries. Second, polymers are typically too large for accurate partial charge generation methods. In this work, we employ direct chemical perception through the Open Force Field toolkit to create a flexible polymer simulation workflow for organic polymers, encompassing everything from biopolymers to soft materials. We propose and test a new input specification for monomer information that can, along with a 3D conformational geometry, parametrize and simulate most soft-material systems within the same workflow used for smaller ligands. The monomer format encompasses a subset of the SMIRKS substructure query language to uniquely identify chemical information and repeating charges in underspecified systems through matching atomic connectivity. This workflow is combined with several different approaches for automatic partial-charge generation for larger systems. As an initial proof of concept, a variety of diverse polymeric systems were parametrized with the Open Force Field toolkit, including functionalized proteins, DNA, homopolymers, cross-linked systems, and sugars. Additionally, shape properties and radial distribution functions were computed from molecular dynamics simulations of poly(ethylene glycol), polyacrylamide, and poly(N-isopropylacrylamide) homopolymers in aqueous solution and compared to previous simulation results in order to demonstrate a start-to-finish workflow for simulation and property prediction. We expect that these tools will greatly expedite the day-to-day computational research of soft-matter simulations and create a robust atomic-scale polymer specification in conjunction with existing polymer structural notations.

Molecular dynamics investigation on synthesis of a pH- and temperature-sensitive carbon nanotube loaded with doxorubicin

The many exotic properties of carbon nanotubes (CNTs) make them a powerful attraction in the field of drug delivery systems (DDS). In this work, based on quantum chemical calculation and molecular simulation techniques, polyacrylic acid (PAA) and N-isopropyl acrylamide (NIP) are selected and acted simultaneously on the CNT to form a stable system (FCNT). As a potential DDS, FCNT captures the dispersed doxorubicin (DOX) molecules around it and maintains a stable configuration. In these processes, electrostatic and van der Waals forces act synergistically, with van der Waals forces dominating. Compared to NIP, PAA molecules exhibit stronger adhesion and encapsulation efficiency to CNT and stronger adsorption capacity to DOX. This study reveals the mechanism of action among PAA, NIP, CNT, and DOX, providing feasibility verification and prospective guidance for the experimental synthesis of PAA-NIP-CNT-type multifunctional DDS, and also broadening the idea for exploring more efficient DDS suitable for DOX.

A Fast, Convenient, Polarizable Electrostatic Model for Molecular Dynamics

We present an efficient polarizable electrostatic model, utilizing typed, atom-centered polarizabilities and the fast direct approximation, designed for efficient use in molecular dynamics (MD) simulations. The model provides two convenient approaches for assigning partial charges in the context of atomic polarizabilities. One is a generalization of RESP, called RESP-dPol, and the other, AM1-BCC-dPol, is an adaptation of the widely used AM1-BCC method. Both are designed to accurately replicate gas-phase quantum mechanical electrostatic potentials. Benchmarks of this polarizable electrostatic model against gas-phase dipole moments, molecular polarizabilities, bulk liquid densities, and static dielectric constants of organic liquids show good agreement with the reference values. Of note, the model yields markedly more accurate dielectric constants of organic liquids, relative to a matched nonpolarizable force field. MD simulations with this method, which is currently parametrized for molecules containing elements C, N, O, and H, run only about 3.6-fold slower than fixed charge force fields, while simulations with the self-consistent mutual polarization average 4.5-fold slower. Our results suggest that RESP-dPol and AM1-BCC-dPol afford improved accuracy relative to fixed charge force fields and are good starting points for developing general, affordable, and transferable polarizable force fields. The software implementing these approaches has been designed to utilize the force field fitting frameworks developed and maintained by the Open Force Field Initiative, setting the stage for further exploration of this approach to polarizable force field development.

High-throughput virtual screening to identify potential small molecule inhibitors of the Zα domain of the adenosine deaminases acting on RNA 1(ADAR1)

Changes in RNA editing are closely associated with diseases such as cancer, viral infections, and autoimmune disorders. Adenosine deaminase (ADAR1), which acts on RNA 1, plays a key role in adenosine to inosine editing and is a potential therapeutic target for these various diseases. The p150 subtype of ADAR1 is the only one that contains a Zα domain that binds to both Z-DNA and Z-RNA. The Zα domain modulates immune responses and may be suitable targets for antiviral therapy and cancer immunotherapy. In this study, we attempted to utilize molecular docking to identify potential inhibitors that bind to the ADAR1 Zα domain. The virtual docking method screened the potential activity of more than 100,000 compounds on the Zα domain of ADAR1 and filtered to obtain the highest scoring results.We identified 71 compounds promising to bind to ADAR1 and confirmed that two of them, lithospermic acid and Regaloside B, interacts with the ADAR1 Zα domain by surface plasmonic resonance technique. The molecular dynamics calculation of the complex of lithospermic acid and ADAR1 also showed that the binding effect of lithospermic acid to ADAR1 was stable.This study provides a new perspective for the search of ADAR1 inhibitors, and further studies on the anti-ADAR11 activity of these compounds have broad prospects.

Hydration Mechanism and Its Effect on the Solubility of Aripiprazole

PROPOSE

The propose is to investigate the reasons for the insolubility of Form III in water and to explore the mechanism of the hydration process of Form III.

METHODS

The conformational and cohesive energies of Form III and Form H1 were calculated using Gaussian 16 and Crystal Explorer 17. Gaussian 16 and Multiwfn 3.8 was used to calculate the molecular surface electrostatic potential of Form III and Form H1 and to calculate the energies of the stronger intermolecular interactions in the crystal structure. The behaviors of Form III in water were simulated using Gromacs 2020.6. Finally, the hydration process from Form III to Form H1 was monitored in situ using Raman spectroscopy.

RESULTS

The conformational energies of Form III and H1 are almost the same. The cohesion energy of Form H1 is much larger than that of Form III because both number of hydrogen bonds and van der Waals interactions are higher in the Form H1. During the simulation, the supercell of APZ form a supramolecular cluster. Several molecules manually dismantled from the cluster spontaneously combine to form new molecular clusters. Both increases in temperature and external energy input accelerate the hydration process.

CONCLUSIONS

More hydrogen bonds and strong van der Waals interactions in Form H1 lead to a greater stability. The overall decrease in polarity and the strong binding effect on APZ molecule clusters due to intermolecular interactions lead to the water insolubility of Form III. The hydration process from Form III to Form H1 follows a novel, dandelion sowing-like hydration mechanism.

Studying allosteric regulation of chemokines and antagonists using a nanoscale hCCR3 receptor sensor

CC chemokine receptor-3 (hCCR3), a G protein-coupled receptor (GPCR) expressed predominantly on eosinophils, is an important drug target. However, it was unclear how chemokine ligands, activators and antagonists recognize hCCR3, and quantitative measurements of hCCR3 inhibition or activation were rare. This study constructed a nanogold receptor sensor using hCCR3 as the molecular recognition element and horseradish peroxidase as the signal amplifier. We quantified the kinetic antagonism between chemokines and hCCR3 before and after adding hCCR3 antagonists. A molecular docking study was carried out to investigate how hCCR3 and its ligands work. The study results indicate chemokines interact with hCCR3 at low concentrations, and reversible hCCR3 inhibitors solely inhibit hCCR3, not CCLs. Moreover, a quantitative evaluation of hCCR3 chemokine activators and their antagonists was carried out using a directed weighted network. This offers a novel approach to quantitatively evaluate chemokine-receptor activation and antagonism together. This research could potentially offer new insights into the mechanisms of action of chemokines and drug screening.

Hydrated Eutectic Electrolyte Induced Bilayer Interphase for High-Performance Aqueous Zn-Ion Batteries with 100 °C Wide-Temperature Range

The practical implementation of aqueous zinc-ion batteries (AZIBs) encounters challenges such as dendrite growth, parasitic reactions, and severe decay in battery performance under harsh environments. Here, a novel hydrated eutectic electrolyte (HEE) composed of Zn(ClO4 )2 ·6H2 O, ethylene glycol (EG), and InCl3 solution is introduced to effectively extend the lifespan of AZIBs over a wide temperature range from -50 to 50 °C. Molecular dynamics simulations and spectroscopy analysis demonstrate that the H2 O molecules are confined within the liquid eutectic network through dual-interaction, involving coordination with Zn2+ and hydrogen bonding with EG, thus weakening the activity of free water and extending the electrochemical window. Importantly, cryo-transmission electron microscopy and spectroscopy techniques reveal that HEE in situ forms a zincophobic/zincophilic bilayer interphase by the dissociation-reduction of eutectic molecules. Specifically, the zincophilic interphase reduces the energy barrier for Zn nucleation, promoting uniform Zn deposition, while the zincophobic interphase prevents active water from contacting the Zn surface, thus inhibiting the side reactions. Furthermore, the relationships between the structural evolution of the liquid eutectic network and interfacial chemistry at electrode/electrolyte interphase are further discussed in this work. The scalability of this design strategy can bring benefits to AZIBs operating over a wide temperature range.

Green Ether Electrolytes for Sustainable High-voltage Potassium Ion Batteries

Ether-based electrolytes are promising for secondary batteries due to their good compatibility with alkali metal anodes and high ionic conductivity. However, they suffer from poor oxidative stability and high toxicity, leading to severe electrolyte decomposition at high voltage and biosafety/environmental concerns when electrolyte leakage occurs. Here, we report a green ether solvent through a rational design of carbon-chain regulation to elicit steric hindrance, such a structure significantly reducing the solvent's biotoxicity and tuning the solvation structure of electrolytes. Notably, our solvent design is versatile, and an anion-dominated solvation structure is favored, facilitating a stable interphase formation on both the anode and cathode in potassium-ion batteries. Remarkably, the green ether-based electrolyte demonstrates excellent compatibility with K metal and graphite anode and a 4.2 V high-voltage cathode (200 cycles with average Coulombic efficiency of 99.64 %). This work points to a promising path toward the molecular design of green ether-based electrolytes for practical high-voltage potassium-ion batteries and other rechargeable batteries.

Novel Natural Carrier-Free Self-Assembled Nanoparticles for Treatment of Ulcerative Colitis by Balancing Immune Microenvironment and Intestinal Barrier

Ulcerative colitis (UC) is a chronic inflammatory illness affecting the colon and rectum, with current treatment methods being unable to meet the clinical needs of ulcerative colitis patients. Although nanomedicines are recognized as promising anti-inflammatory medicines, their clinical application is limited by their high cost and unpredictable safety risks. This study reveals that two natural phytochemicals, berberine (BBR) and hesperetin (HST), self-assemble directly to form binary carrier-free multi-functional spherical nanoparticles (BBR-HST NPs) through noncovalent bonds involving electrostatic interactions, π-π stacking, and hydrogen bonding. Because of their synergistic anti-inflammatory activity, berberine-hesperetin nanoparticles (BBR-HST NPs) exhibit significantly better therapeutic effects on UC and inhibitory effects on inflammation than BBR and HST at the same dose by regulating the immune microenvironment and repairing the damaged intestinal barrier. Furthermore, BBR-HST NPs exhibit good biocompatibility and biosafety. Thus, this study proves the potential of novel natural anti-inflammatory nanoparticles as therapeutic agents for UC, which could promote the progress of drug development for UC and eventually benefit patients who suffering from it.

Addressing Challenges of Macrocyclic Conformational Sampling in Polar and Apolar Solvents: Lessons for Chameleonicity

We evaluated a workflow to reliably sample the conformational space of a set of 47 peptidic macrocycles. Starting from SMILES strings, we use accelerated molecular dynamics simulations to overcome high energy barriers, in particular, the cis-trans isomerization of peptide bonds. We find that our approach performs very well in polar solvents like water and dimethyl sulfoxide. Interestingly, the protonation state of a secondary amine in the ring only slightly influences the conformational ensembles of our test systems. For several of the macrocycles, determining the conformational distribution in chloroform turns out to be considerably more challenging. Especially, the choice of partial charges crucially influences the ensembles in chloroform. We address these challenges by modifying initial structures and the choice of partial charges. Our results suggest that special care has to be taken to understand the configurational distribution in apolar solvents, which is a key step toward a reliable prediction of membrane permeation of macrocycles and their chameleonic properties.

Strong Replaces Weak: Design of H-Bond Interactions Enables Cryogenic Aqueous Zn Metal Batteries

Despite the numerous advantages of aqueous Zn batteries, their practical application under cryogenic conditions is hindered by the freezing of the electrolyte because the abundance of hydrogen bonds (H-bonds) between H2O molecules drives the aqueous system to transform to an orderly frozen structure. Here, a design of H-bond interactions based on the guiding ideology of "strong replaces weak" is proposed. The strong H-bonds formed between introduced eutectic components and water molecules break down the weak H-bonds in the original water molecule network, which contributes to an ultralow freezing point and a high ionic conductivity of 1.7 mS cm-1 at -40 °C. Based on multiperspective theoretical simulations and tailor-made in situ cooling Raman characterizations, it has been demonstrated that substituting weak H-bonds with strong H-bonds facilitates the structural reshaping of Zn2+ solvation and remodeling of the H-bond network in the electrolyte. Endowed with this advantage, reversible and stable Zn plating/stripping behaviors could be realized at -40 °C, and the full cells display a high discharge capacity (200 mA h g-1) at -40 °C with ∼75% capacity retention after 1000 cycles. This study will expand the design philosophy of antifreezing aqueous electrolytes and provide a perspective to promote the adoption of Zn metal batteries for cryogenic environment large-scale energy storage.