Higher Binding Energy Research Articles

Computational study of phytochemical derived bioactive compounds of Vernonia amygdalina as a potential inhibitor of Topoisomerase IV in pneumonia

Several of the bacteria responsible for pneumonia had become resistant to available antibiotics. According to the WHO, the resistance of Klebsiella pneumonia to Ciprofloxacin is 79.4%, making infections such as pneumonia and several diseases more difficult, if not impossible to treat. The prevalence of antimicrobial resistance is a global problem and among the 10 top global health threats facing humanity. With the projection of 10 million deaths per year by 2050 due to bacterial infections associated with antibiotic resistance according to WHO, there is an urgent need to identify an alternative approach to curb the incessant antimicrobial resistance and a complementary approach is to employ the use of naturally occurring compounds with potent antibacterial activities. We employed structural bioinformatics and theoretical chemistry techniques via molecular docking, and pharmacokinetic study, to identify novel S. pneumoniae topoisomerase IV inhibitors. The stringent molecular docking identified Arg140, Arg81, Glu55, Pro84, Met83, and Asn51, as principal amino acid residues for topoisomerase IV ligand interactions. Ten of the bioactive compounds found in Vernonia amygdalina showed a higher binding energy when compared to the reference compound (Ciprofloxacin). The overall analysis of MD results and binding free energy calculations reveal that Luteolin and 7-O-methylwogonin displayed stable trajectories with acceptable RMSD values and sufficient high negative energies throughout the MD simulation run of 100ns. These identified bioactive compounds in this study can be taken further for in vitro and In vivo studies to examine their efficacy against Pneumonia.

Synthesis and characterizations of zinc oxide nanorods by cost effective aqueous hydrothermal technique for solid state lighting applications

Zinc oxide (ZnO) is recognized as the most promising and often utilized semiconducting material due to its exceptional physical, chemical, optical, and relatively low-cost production features, as well as its ecologically beneficial nature. ZnO is a prominent candidate owing to its wide band gap (3.37 eV at room temperature) as well as its high exciton binding energy (60 meV) for the next generation of ultraviolet and blue optoelectronic devices. This would be achieved through the development of hybrid heterostructured LED devices with low manufacturing costs by blending gallium nitride (GaN) with zinc oxide (ZnO), which serves as the most efficient opto-electronic device. Due to its high electron mobility, high transparency in the visible wavelength spectrum, and low work function, ZnO is also a highly investigated transparent conducting oxide thin film for several applications. Besides, their incredible optical capabilities, ZnO-based optical devices, such as light-emitting diodes (LEDs) and laser diodes (LDs), have drawn a great deal of interest. This reported research work demonstrates the growth of high-density, high-aspect-ratio ZnO nanorod (NR) arrays on p-type gallium nitride substrates employing low-cost facial aqueous hydrothermal syntheses with optimised growing conditions. Additionally, a top-down chemical etching technique is adapted for fabricating zinc oxide nanotubes. High-quality ZnO nanorods with high intensity that were a few microns long were found across the GaN substrate with FESEM analysis. The chemical composition of the grown nanorods is confirmed with EDAX analysis. The wurtzite crystalline structure and c-axis orientation of the grown ZnO NR-arrays were identified in X-ray diffraction studies. A Schimadzu UV–Vis–NIR spectrophotometer was used to record the optical curve, and the energy gap was determined to be 3.24 eV by plotting the Tauc curve. The good optical quality of the harvested nanorods is ensured by the narrow near-band-edge (NBE) emission at 384 nm and defect emission peaks detected through photoluminescence analyses. Grown specimens are also subjected to Raman spectrum analyses, and the obtained results are presented.

Turmeric-Black Cumin Essential Oils and Their Capacity to Attenuate Free Radicals, Protein Denaturation, and Cancer Proliferation.

Turmeric rhizomes (Curcuma longa) and black cumin seeds (Nigella sativa) are polyherbal ingredients used for the management of cancer and other chronic inflammatory diseases in Nigerian ethnomedicine. Previous studies have shown the antioxidant, anti-inflammatory, and anticancer activities of the individual plant extracts. However, the two spices have not been biologically potentiated in their combined form. Therefore, this study obtained essential oils (EOs) from the combined spices and evaluated their inhibitory effects on free radicals, protein denaturation, and cancer proliferation. The EOs were extracted by hydro-distillation (HD) and characterized by gas chromatography-mass spectrometry (GC-MS). In vitro antioxidant assessment was conducted based on DPPH, hydrogen peroxide (H2O2), nitric oxide (NO), and ferric ion (Fe3+) radical scavenging assays. The cytotoxicity of the oil against non-tumorigenic (HEK293) and cancerous (HepG2 and HeLa) cell lines was determined following the MTT cell viability assay. An in silico molecular docking analysis of the oil constituents was also performed. Six batches of EOs I-VI were afforded, comprising twenty-two major constituents, with aromatic Ar-turmerone being the most prominent compound. There was a marked improvement in the bioactivity of the oils upon repeated HD and as a combination. The batch VI oil exhibited the best activity, with a cytotoxicity (CC50) of 10.16 ± 1.69 µg/100 µL against the HepG2 cell line, which was comparable to 5-fluorouracil (standard, CC50 = 8.59 ± 1.33 µg/100 µL). In silico molecular docking suggested δ-curcumene, Ar-curcumene, Ar-turmerol, and Ar-turmerone among the promising compounds based on their high binding energy scores with NOX2, NF-κB, and mdm2 proteins. In conclusion, the oils from the turmeric-black cumin combined possess a considerable inhibition ability against free radicals, protein denaturation, and cancer proliferation. This study's findings further underscore the effectiveness of turmeric-black cumin as a polyherbal medicinal ingredient.

Investigation on Anti‐plasmodial Agents Against wild‐type PfDHFR Through In Silico Computational Tools

AbstractMalaria is the most severe and common parasitic infection, with P. falciparum responsible for the majority of cases and deaths each year. As anti‐malarial drug resistance continues to increase, novel compounds with anti‐ P. falciparum activity must be identified. In search of a new molecule to cure the resistant malarial parasite, a total of 1,70,269 ligands from the Asinex BioDesign library 2021.2 were virtually screened using AutoDock Vina against wild‐type P. falciparum dihydrofolate reductase‐thymidylate synthase (PfDHFR‐TS). The computational molecular modeling investigations indicated the discovery of seventeen new compounds (2‐18) with higher binding energy compared to the PfDHFR‐TS inhibitor, pyrimethamine (1). Furthermore, the study employing drug‐likeness criteria and their ADMET profile suggested that these hits were the most promising drug candidates due to higher absorption and druggability. Furthermore, GROMACS 2023.4 was used to perform the molecular dynamics simulations on the foremost compound (2) having sufficient stability, leading to a key step towards the search of novel PfDHFR‐TS inhibitors against malaria.

Performance evaluation of SILAR deposited Rb-Doped ZnO thin films for photodetector applications

ZnO-based photodetectors (PDs) compose a remarkable optoelectronic device field due to their high optical transmittance, electrical conductivity, wide band gap, and high binding energy. This study examined the visible light photodetector performance of the pristine and Rubidium (Rb)-doped ZnO thin films. The influence of Rb doping amount (2, 4, and 6 wt% in solution) on the electrical, optical, and structural properties of the ZnO-based thin films produced by the Successive Ion Layer Adsorption and Reaction (SILAR) technique was analyzed. Structural analyses showed that all peaks correspond to hexagonal wurtzite structure with no other peak from Rb-based phases, suggesting the high quality of the crystalline pristine and Rb-doped ZnO thin films. The morphology of the thin films shows homogenous layers formed of nanoparticles where particle size was first decreased and then increased with the increasing Rb doping according to Scanning Electron Microscope (SEM) morphology analysis. Besides that, Raman spectroscopy analyses indicate that the phonon lifetimes of the ZnO-based thin films slightly increased due to the improvement of the crystal quality with the increasing amount of Rb in the SILAR solution. Photosensor measurements of the nanostructured pristine and Rb-doped ZnO thin films were measured at different light power intensities under the visible light environment. Photosensor properties were examined depending on the doping amount and light power density. In light of the literature review, our study is the first to produce Rb-doped ZnO thin films via the SILAR method, which has a promising potential for photosensor applications.Graphical

Influence of Edges and Interlayer Electron-phonon Coupling in WS2/h-BN Heterostructure.

The semiconducting layered transition metal dichalcogenides (e.g., WS2) are excellent candidates for the realization of optoelectronic and nanophotonic applications on account of their band gap tunability, high binding energy and oscillator strength of the excitons, strong light-matter interaction, appreciable charge carrier mobility, and valleytronic properties. However, the photoluminescence (PL) emissions are reported to show a nonuniform spatial distribution, with the edges emitting features like defect-bound excitons and biexcitons at low temperatures in addition to the typical excitons and trions. The appearance of these additional PL features has been shown in the literature to have a strong dependence on the presence of S-vacancies and excess charge carriers. We demonstrate an enhancement of the defect-bound excitons and biexcitons by creating a heterostructure of WS2 with h-BN where the coupling between the charge carriers in WS2 with the polar phonons in h-BN governs the enhancement. Furthermore, we have performed a comprehensive resonant Raman study with varying polarization and magnetic field which not only confirms the presence of electron-phonon coupling in WS2/h-BN heterostructure, it further demonstrates a thermally induced differential resonance behavior with the excitonic level and the defect-induced midgap states (due to S-vacancies at the edge of WS2) exhibited by a dome-shaped behavior of the Raman intensities with temperature for the normal and defect-induced phonon modes. The defect-bound Raman modes exhibit maximum resonance at ∼240 K while normal Raman modes show at ∼280 K owing to a thermal variation of the electronic states.

In-silico screening of bioactive compounds of Moringa oleifera as potential inhibitors targeting HIF-1α/VEGF/GLUT-1 pathway against Breast Cancer.

Breast cancer is among the most heterogeneous and aggressive diseases and a foremost cause of death in women globally. Hypoxic activation of HIF-1α in breast cancers triggers the transcription of a battery of genes encoding proteins that facilitate tumor growth and metastasis and is correlated with a poor prognosis. Based on the reported cytotoxic and anti-cancer properties of Moringa oleifera (Mo), this study explores the inhibitory effect of bioactive compounds from M.oleifera and breast cancer target proteins HIF-1α, VEGF, and GLUT-1 in silico. The X-ray crystallographic structures of HIF-1α, VEGF, and GLUT1 were sourced from the Protein Data Bank(PDB) and docked with 70 3D PubChem structures of bioactive compounds of M.oleifera using AutoDock Vina, and binding modes were analyzed using Discovery Studio. Five compounds with the highest binding energies were selected and further drug-likeness, oral bioavailability, ADME, and toxicity profiles were analyzed using SwissADME, ADMETSaR, and ADMETlab 3.0 web server. Out of the screened 70 bioactive compounds, the top five compounds with the best binding energies were identified namely Apigenin, Ellagic Acid, Isorhamnetin, Luteolin, and Myricetin with each receptor. Molecular docking results indicated that the ligands interact strongly with the target HIF-1α, VEGF, and GLUT-1 receptors through hydrogen bonds and hydrophobic interactions. These compounds showed favorable drug-like and pharmacokinetic properties, possessed no substantial toxicity, and were fairly bioavailable. Results suggested that the compounds possess strong potential in developing putative lead compounds targeting HIF-1α that are safe natural plant-based drugs against breast cancer.

Stabilizing Zinc Anode through Ion Selection Sieving for Aqueous Zn-Ion Batteries.

Uncontrollable dendrite growth and corrosion induced by reactive water molecules and sulfate ions (SO42-) seriously hindered the practical application of aqueous zinc ion batteries (AZIBs). Here we construct artificial solid electrolyte interfaces (SEIs) realized by sodium and calcium bentonite with a layered structure anchored to anodes (NB@Zn and CB@Zn). This artificial SEI layer functioning as a protective coating to isolate activated water molecules, provides high-speed transport channels for Zn2+, and serves as an ionic sieve to repel negatively charged anions while attracting positively charged cations. The theoretical results show that the bentonite electrodes exhibit a higher binding energy for Zn2+. This demonstrates that the bentonite protective layer enhances the Zn-ion deposition kinetics. Consequently, the NB@Zn//MnO2 and CB@Zn//MnO2 full-battery capacities are 96.7 and 70.4 mAh g-1 at 2.0 A g-1 after 1000 cycles, respectively. This study aims to stabilize Zn anodes and improve the electrochemical performance of AZIBs by ion-selection sieving.

Revealing the key antioxidant compounds and potential action mechanisms of Chinese Cabernet Sauvignon red wines by integrating UHPLC-QTOF-MS-based untargeted metabolomics, network pharmacology and molecular docking approaches

In recent years, red wine drinking has become more popular in China owing to its antioxidant effects. However, the key antioxidant compounds and their action mechanisms of Chinese red wines are still unclear. Herein, the antioxidant activities and chemical compositions of 45 Chinese Cabernet Sauvignon red wine samples were determined using chemical antioxidant assays and an UHPLC-QTOF-MS-based untargeted metabolomics method. The key antioxidant compounds in red wines and potential action mechanisms were revealed by integrating network pharmacology and molecular docking approaches. Results showed that there are 8 key antioxidant compounds in the red wine samples. These compounds are involved in several metabolic pathways in the body, particularly PI3K/AKT. What's more, they bind to the core antioxidant targets through hydrogen bonding and hydrophobic interaction. Among them, myricetin, laricitrin, 2,3,8-tri-O-methylellagic acid and AKT1 have the highest binding energies. This study could provide the theoretical basis for further investigation of physiological activities and functions of Chinese red wines.

Ligand‐Pinning Induced Size Modulation of CsPbI3 Perovskite Quantum Dots for Red Light‐Emitting Diodes

AbstractPerovskite quantum dots (PQDs) show high potential for new‐generation light‐emitting diodes (LEDs) due to their outstanding optoelectronic properties. Even though the red PQD‐LEDs can be realized through mixing halide in the PQDs to tune their spectroscopies, the PQDs may suffer from phase separation under a high electric field, predominantly affecting LED applications. Herein, a ligand‐pinning‐assisted approach is reported to tune the spectroscopies of CsPbI3 PQDs, in which vinyl phosphonic acid (VPA) is applied as function ligands to regulate the nucleation and growth of PQDs during the synthesis. Systematically experimental studies and theoretical calculations are conducted to comprehensively understand the functions of the VPA ligands during the PQD synthesis, which reveals that the VPA ligands with high binding energy with Pb2+ cations could firmly anchor on the surface matrix of PQDs without desorption, regulating the growth of PQDs and thus resulting in tunable spectroscopies being realized. Meanwhile, VPA could also renovate the defective surface matrix of PQDs, substantially diminishing trap‐induced nonradiative recombination. Consequently, red PQD‐LEDs deliver a high external quantum efficiency of 22.83%, which is significantly improved compared with the control devices. This work provides a new avenue to tune the spectroscopies of PQDs toward high‐performing LEDs.

Organic-Inorganic Rubrene/WS2 Heterostructure for Broadband Detection and Polarization Imaging.

Organic single crystals exhibit improved carrier mobility, longer exciton diffusion length, anisotropic charge transport, and unique linear dichroism, while its high exciton binding energy seriously limits the free-carrier generation and photoelectric conversion efficiency. Layered van der Waals heterostructures, which integrate organic crystals with high mobility two-dimensional (2D) inorganic semiconductors, are promising for promoting exciton dissociation and boosting sensitivity by utilizing the interfacial potential and photogating effect. In this work, organic single-crystal rubrene is integrated with a few-layer WS2 to design the high-performance photodetector. The device exhibits an excellent responsivity of 1000 A W-1, and a fast speed of 180 μs, which is far superior to the individual WS2 device. Equally importantly, this device provides excellent polarization detection performance by virtue of the anisotropic properties of rubrene, and the dichroic ratios are 1.56, 1.5, and 1.7 for 375, 405, and 658 nm irradiation, respectively. Finally, several high-resolution single-pixel broadband polarization imaging was demonstrated. Our work shows that organic-inorganic heterostructure is an essential candidate for improving optoelectronics performance and has potential for polarization imaging.

Quantized Microcavity Polariton Lasing Based on InGaN Localized Excitons.

Exciton-polaritons, which are bosonic quasiparticles with an extremely low mass, play a key role in understanding macroscopic quantum effects related to Bose-Einstein condensation (BEC) in solid-state systems. The study of trapped polaritons in a potential well provides an ideal platform for manipulating polariton condensates, enabling polariton lasing with specific formation in k-space. Here, we realize quantized microcavity polariton lasing in simple harmonic oscillator (SHO) states based on spatial localized excitons in InGaN/GaN quantum wells (QWs). Benefiting from the high exciton binding energy (90 meV) and large oscillator strength of the localized exciton, room-temperature (RT) polaritons with large Rabi splitting (61 meV) are obtained in a strongly coupled microcavity. The manipulation of polariton condensates is performed through a parabolic potential well created by optical pump control. Under the confinement situation, trapped polaritons are controlled to be distributed in the selected quantized energy sublevels of the SHO state. The maximum energy spacing of 11.3 meV is observed in the SHO sublevels, indicating the robust polariton trapping of the parabolic potential well. Coherent quantized polariton lasing is achieved in the ground state of the SHO state and the coherence property of the lasing is analyzed through the measurements of spatial interference patterns and g(2)(τ). Our results offer a feasible route to explore the manipulation of macroscopic quantum coherent states and to fabricate novel polariton devices towards room-temperature operations.

Synthesis and study of the impact of calcination duration on the properties of Al4(ZnO)96 nanoparticles

Aluminium doped zinc oxide (Al4(ZnO)96) nanoparticles were synthesized using new sogel method at 40 °C, with zinc acetate dihydrate (Zn(CH3COO)2·2 H2O) and aluminium nitrate nonahydrate (Al(NO3)3·9 H2O) as precursors. The samples underwent analysis using various structural and optical techniques to investigate the effect of calcination duration on the properties. Prolonged calcination durations led to a significant reduction of oxygen at the grain boundaries, influencing particle size and crystallization. According to TEM-histogram analysis, the most probable size for 28.5 % of nanoparticles fell within the range of 15–20 nm, which aligns closely with the estimated particle size determined by XRD analysis. The material displayed a significant direct bandgap of approximately 3.283 eV, which increased with the duration of calcination. The band gap was affected by changes in phase, strain, and particle size, attributed to the presence of defect states and a substantial concentration of localized states. Additionally, the material exhibited excellent chemical stability and a significantly high binding energy. Moreover, the optical bandgap widened as the width of the Urbach tails in the localized states decreased with an increase in the duration of calcination.

Molecular docking aided machine learning for the identification of potential VEGFR inhibitors against renal cell carcinoma.

Renal cell carcinoma is a highly vascular tumor associated with vascular endothelial growth factor (VEGF) expression. The Vascular Endothelial Growth Factor -2 (VEGF-2) and its receptor was identified as a potential anti-cancer target, and it plays a crucial role in physiology as well as pathology. Inhibition of angiogenesis via blocking the signaling pathway is considered an attractive target. In the present study, 150 FDA-approved drugs have been screened using the concept of drug repurposing against VEGFR-2 by employing the molecular docking, molecular dynamics, grouping data with Machine Learning algorithms, and density functional theory (DFT) approaches. The identified compounds such as Pazopanib, Atogepant, Drosperinone, Revefenacin and Zanubrutinib shown the binding energy - 7.0 to - 9.5kcal/mol against VEGF receptor in the molecular docking studies and have been observed as stable in the molecular dynamic simulations performed for the period of 500ns. The MM/GBSA analysis shows that the value ranging from -44.816 to -82.582kcal/mol. Harnessing the machine learning approaches revealed that clustering with K = 10 exhibits the relevance through high binding energy and satisfactory logP values, setting them apart from compounds in distinct clusters. Therefore, the identified compounds are found to be potential to inhibit the VEGFR-2 and the present study will be a benchmark to validate the compounds experimentally.

Adsorption in Pyrene-Based Metal-Organic Frameworks: The Role of Pore Structure and Topology.

Pore topology and chemistry play crucial roles in the adsorption characteristics of metal-organic frameworks (MOFs). To deepen our understanding of the interactions between MOFs and CO2 during this process, we systematically investigate the adsorption properties of a group of pyrene-based MOFs. These MOFs feature Zn(II) as the metal ion and employ a pyrene-based ligand, specifically 1,3,6,8-tetrakis(p-benzoic acid)pyrene (TBAPy). Including different additional ligands leads to frameworks with distinctive structural and chemical features. By comparing these structures, we could isolate the role that pore size, the presence of open-metal sites (OMS), metal-oxygen bridges, and framework charges play in the CO2 adsorption of these MOFs. Frameworks with constricted pore structures display a phenomenon known as the confinement effect, fostering stronger MOF-CO2 interactions and higher uptakes at low pressures. In contrast, entropic effects dominate at elevated pressures, and the MOF's pore volume becomes the driving factor. Through analysis of the CO2 uptakes of the benchmark materials ─some with narrower pores and others with larger pore volumes─it becomes evident that structures with narrower pores and high binding energies excel at low pressures. In contrast, those with larger volumes perform better at elevated pressures. Moreover, this research highlights that open-metal sites and inherent charges within the frameworks of ionic MOFs stand out as CO2-philic characteristics.

Metal-decorated M-graphene for high hydrogen storage capability and reversible hydrogen release

With the increasing demand for green energy, the design of effective hydrogen storage materials is becoming particularly important. In this work, the hydrogen storage performances of the metal atoms (Li, Ca, and Sc) decorated two–dimensional (2D) M-graphenes were investigated with density functional theory (DFT) calculations. The metal atoms can be substantially anchored on the M-graphene surface in single–atom formation revealed by the high binding energy, which is ascribed to the remarkable charge transfers between metal atom and M-graphene. Each metal atom can capture six H2 molecules at most in single–atom decorated M-graphene. The H2 adsorption energies are in the range from −0.139 to −0.375 eV, following an order of Sc@M-graphene > Ca@M-graphene > Li@M-graphene. The affinity ability of metal–decorated M-graphene for hydrogen can be enhanced by adding an external electric field. The multi–metal atoms decorated M-graphenes, Li4C16(H2)8, Ca4C16(H2)12, and Sc4C16(H2)12 complexes show high gravimetric densities (6.06 ∼ 6.78 wt%) and a favorable binding energy window (−0.167 to −0.418 eV), meeting the department of energy (DOE)’s criteria. The thermodynamic properties were in detail studied by considering temperature and pressure effects. AIMD simulations at different temperatures indicate that the efficient release of hydrogen can occur at room temperature. Our results show that the M-graphenes with Li, Ca, and Sc decorated have high hydrogen storage capacity and reversible hydrogen release performance. This work may be useful for designing novel 2D carbon–based materials for hydrogen storage.

Cucurbitacins mitigate vascular neointimal hyperplasia by suppressing cyclin A2 expression and inhibiting VSMC proliferation.

Restenosis frequently occurs after percutaneous angioplasty in patients with vascular occlusion and seriously threatens their health. Substantial evidence has revealed that preventing vascular smooth muscle cell proliferation using a drug-eluting stent is an effective approach to improve restenosis. Cucurbitacins have been demonstrated to exert an anti-proliferation effect in various tumors and a hypotensive effect. This study aims to investigate the role of cucurbitacins extracted from Cucumis melo L. (CuECs) and cucurbitacin B (CuB) on restenosis. C57BL/6 mice were subjected to left carotid artery ligation and subcutaneously injected with CuECs or CuB for 4 weeks. Hematoxylin-Eosin, immunofluorescence and immunohistochemistry staining were used to evaluate the effect of CuECs and CuB on neointimal hyperplasia. Western blot, real-time PCR, flow cytometry analysis, EdU staining and cellular immunofluorescence assay were employed to measure the effects of CuECs and CuB on cell proliferation and the cell cycle invitro. The potential interactions of CuECs with cyclin A2 were performed by molecular docking. The results demonstrated that both CuECs and CuB exhibited significant inhibitory effects on neointimal hyperplasia and proliferation of vascular smooth muscle cells. Furthermore, CuECs and CuB mediated cell cycle arrest at the S phase. Autodocking analysis demonstrated that CuB, CuD, CuE and CuI had high binding energy for cyclin A2. Our study also showed that CuECs and CuB dramatically inhibited FBS-induced cyclin A2 expression. Moreover, the expression of cyclin A2 in CuEC- and CuB-treated neointima was downregulated. CuECs, especially CuB, exert an anti-proliferation effect in VSMCs and may be potential drugs to prevent restenosis.

Identification of potential PIM-2 inhibitors via ligand-based generative models, molecular docking and molecular dynamics simulations.

Proviral Integrations of Moloney-2 (PIM-2) kinase is a promising target for various cancers and other diseases, and its inhibitors hold potential for treating related diseases. However, there is currently no clinically available PIM-2 inhibitor. In this study, we constructed a generative model for de novo PIM-2 inhibitor design based on artificial intelligence, performed molecular docking and molecular dynamics (MD) simulations to develop an efficient PIM-2 inhibitor generative model and discover potential PIM-2 inhibitors. First, we designed a generative model based on a Bi-directional Long Short-Term Memory (BiLSTM) framework combined with a transfer learning strategy and generated a new PIM-2 small molecule library using existing active drug databases. The generated compound library was then virtually screened by molecular docking and scaffold similarity comparison, identifying 10 initial hit compounds with better performance. Next, using the inhibitor in the crystal structure as a positive control, we performed two rounds of MD simulations, with lengths of 100ns and 500ns, respectively, to study the dynamic stability of the protein-ligand systems of the 10 compounds with PIM-2. Analyzed the interactions with key hinge region residues, binding free energies, and changes in the ATP pocket size. The generative model demonstrates good molecular generation capability and can generate efficient novel molecules with similar physicochemical properties as active PIM-2 drugs. Among the 10 initially selected hit compounds, 5 compounds C3 (-29.69kcal/mol), C4 (-33.31kcal/mol), C5 (-28.59kcal/mol), C8 (-34.68kcal/mol), and C9 (-25.88kcal/mol) have higher binding energies with PIM-2 than the positive drug 3YR (-26.18kcal/mol). The MD simulation results are consistent with the docking analysis, these compounds have lower and more stable RMSD values for the complex systems with the reported positive drug 3YR and PIM-2 complex system. They can form long-term stable interactions with active site and the hinge region of PIM-2, which suggests these compounds are likely to have potent inhibitory effects on PIM-2. This study provides an efficient generative model for PIM-2 inhibitor research and discovers 5 potential novel PIM-2 inhibitors.

Step-by-step design of new phenyl-1,2,3-triazole derivatives with improved anti-corrosive properties: A combined DFT and MD simulation study

In this study, 35 new inhibitors were designed theoretically through the step-by-step strategy based on a new organic non-planar inhibitor 1-benzyl-4-phenyl-1H-1,2,3-triazole (BPT). The first step is to replace one parent phenyl group by six other groups (–Cl, –Br, –OH, –NH2, –OCH3, –thiazole) with heteroatoms, trying to add the adsorption sites and reduce the energy gap. The second step is to use two bridge groups (–S–, –NH–) to displace the original bridge group (–CH2), or to delete the bridge group directly, tending to further add the adsorption sites, reduce the energy gap and change BPT to planar molecules. The final step is to use the combination of oxa and carbonylation substitution strategy on the six compounds with lowest energy gap obtained from the previous two step modifications, in order to further add the adsorption sites, reduce the energy gap and change BPT to planar molecules. Based on the quantum chemical calculations, it is found that main key parameters to anti-corrosive properties like the softness, electron affinity and energy gap were improved greatly compared to BPT. Three new planar molecules (E5, E6 and E6) which have high chemical reactivity, high binding energy with metals, and low energy gap were found successfully, which may be attractive potential inhibitors used as the corrosion inhibition to Fe-related alloy. The corrosion inhibition mechanism of E5 to E7 is different to that of BPT, in which the whole structure will make contributions to the interaction with metals to increase the binding energy and the corrosion inhibition efficiency. This work may provide a unique view for the design and development of new advanced inhibitor.

Phytochemical analysis of Robinia pseudoacacia flowers and leaf: quantitative analysis of natural compounds and molecular docking application

Phenolic compounds are widely found and well-known secondary metabolites in plants. Identification, and quantification of phenolic compounds, and determination of their biological activities reveal the unknown secrets of plants. Robinia pseudoacacia (RP) is known as the white-flowered false acacia and is distributed in Northern Anatolia in Turkey. Spectrophotometric and chromatographic techniques are used to identify the presence and amount of phenolics. In this study, RP flowers and leaves were extracted with methanol and analyzed by LC-MS/MS to determine their phytochemical content. Salicylic acid and syringic acid were found as major products in leaves and flowers. RP extracts have been reported to have antibacterial activity and BChE inhibitory properties. Therefore, the BChE and DD peptidase enzyme inhibitory properties of the main components salicylic acid and syringic acid were investigated by molecule docking (MolDock). According to MolDock results, syringic acid interacted with BChE and DD peptidase and was calculated as a MolDock score of -79.38, and -71.25, with binding energies -5.90, and -5.40 kcal/mol respectively. Salicylic acid interacted with BChE and DD peptidase and was calculated as a MolDock score of -63.54, and -66.18, with binding energies of -6.10, and -5.70 kcal/mol respectively. As a result, salicylic acid had higher binding energy in its interactions with BChE and DD peptidase enzymes. In theory, salicylic acid can be used as a good BChE and DD peptidase inhibitor.