Bioactive Phytoconstituents as Potent Inhibitors of Tyrosine-Protein Kinase Yes (YES1): Implications in Anticancer Therapeutics

Tyrosine-protein kinase Yes (YES1) belongs to the Tyrosine-protein kinase family and is involved in several biological activities, including cell survival, cell–cell adhesion, cell differentiation, and cytoskeleton remodeling. It is highly expressed in esophageal, lung, and bladder cancers, and thus considered as an attractive drug target for cancer therapy. In this study, we performed a virtual screening of phytoconstituents from the IMPPAT database to identify potential inhibitors of YES1. Initially, the molecules were retrieved on their physicochemical properties following the Lipinski rule of five. Then binding affinities calculation, PAINS filter, ADMET, and PASS analyses followed by an interaction analysis to select safe and clinically better hits. Finally, two compounds, Glabrene and Lupinisoflavone C (LIC), with appreciable affinities and a specific interaction towards the AlphaFold predicted structure of YES1, were identified. Their time-evolution analyses were carried out using an all-atom molecular dynamics (MD) simulation, principal component analysis, and free energy landscapes. Altogether, we propose that Glabrene and LIC can be further explored in clinical settings to develop anticancer therapeutics targeting YES1 kinase.     

Phytochemical Characterization,Antioxidant and Anti-Inflammatory Effects of Cleome arabica L. Fruits Extract against Formalin Induced Chronic Inflammation in Female Wistar Rat: Biochemical,Histological, and In Silico Studies

In recent decades, the use of herbs and plants has been of great interest, as they have been the sources of natural products, commonly named as bioactive compounds. In specific, the natural compounds from the Capparaceae family which has been proved to have antioxidant, anti-inflammatory, antimicrobial and anti-carcinogenic activities, by several studies. Cleome arabica L. (CA) specie is the most used medicinal plants in Tunisia and elsewhere in North African countries for treatment of various diseases including diabetes, rheumatism, inflammation, cancer, and digestive disorders. The current work was undertaken to estimate the total phenolic, flavonoid and condensed tannin contents, to identify and quantify the polyphenolic compounds, and to evaluate the antioxidant and the anti-inflammatory proprieties of CA fruits extract against formalin induced chronic inflammation in Female Wistar rats. In fact, the antioxidant activity was tested by Diphenyl-1-Picrylhydrazyl free radical scavenging (DPPH), Ferric reducing antioxidant power (FRAP) and Nitric Oxide radical (NO·). Anti-inflammatory effect of fruits extract was examined using formalin (2%) induced paw edema in rats. Molecular docking tools were used to investigate the interaction of some compounds from CA fruits extract with the cyclooxygenase-2 (COX-2) target protein. Our results showed that, the total phenolic, flavonoid and tannins contents, which were assessed by the Folin-Ciocalteu, Quercetin, and Catechin methods, respectively, were 230.22 mg gallic acid equivalent/g dry weight (mg GAE/g DW), 55.08 mg quercetin equivalent/g dry weight (QE/g DW) and 15.17 mg catechin equivalents/g dry weight (CatE/g DW), respectively. HPLC analysis revealed the presence of five polyphenolic compounds whose catechin was found to be the most abundant compounds. The antioxidant activity of extract was quantified by DPPH, FRAP and NO· tests and IC₅₀ reached the values of 3.346 mg/mL, 2.306 and 0.023 mg/mL, respectively. Cleome fruits ameliorated the histological integrity of the skin and alleviated the disruptions in hematological parameters (WBC, LYM, RBC, and HGB), inflammatory cytokines (IL-1β, IL-6, TNF-α), C-reactive protein, and some oxidative stress markers (TBARS (−49%) and AOPP (−42%) levels, SOD (+33%) and GPx (+75%) activities, and GSH (+49%) content) induced by formalin injection. Moreover, the in-silico investigation had shown that CA fruits extract compounds have a stronger interaction with COX-2 active site, more than the reference drug “indomethacin” (two H-bonds). Our research gives pharmacological backing to the healthcare utilization of Cleome plant in the treatment of inflammatory diseases and oxidative harm.     

In Silico Mining of Terpenes from Red-Sea Invertebrates for SARS-CoV-2 Main Protease (Mpro) Inhibitors

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19 pandemic, which generated more than 1.82 million deaths in 2020 alone, in addition to 83.8 million infections. Currently, there is no antiviral medication to treat COVID-19. In the search for drug leads, marine-derived metabolites are reported here as prospective SARS-CoV-2 inhibitors. Two hundred and twenty-seven terpene natural products isolated from the biodiverse Red-Sea ecosystem were screened for inhibitor activity against the SARS-CoV-2 main protease (M^pro) using molecular docking and molecular dynamics (MD) simulations combined with molecular mechanics/generalized Born surface area binding energy calculations. On the basis of in silico analyses, six terpenes demonstrated high potency as M^pro inhibitors with ΔG_binding ≤ −40.0 kcal/mol. The stability and binding affinity of the most potent metabolite, erylosides B, were compared to the human immunodeficiency virus protease inhibitor, lopinavir. Erylosides B showed greater binding affinity towards SARS-CoV-2 M^pro than lopinavir over 100 ns with ΔG_binding values of −51.9 vs. −33.6 kcal/mol, respectively. Protein–protein interactions indicate that erylosides B biochemical signaling shares gene components that mediate severe acute respiratory syndrome diseases, including the cytokine- and immune-signaling components BCL2L1, IL2, and PRKC. Pathway enrichment analysis and Boolean network modeling were performed towards a deep dissection and mining of the erylosides B target–function interactions. The current study identifies erylosides B as a promising anti-COVID-19 drug lead that warrants further in vitro and in vivo testing.     

Comparative Study on Curcumin Loaded in Golden Pompano (Trachinotus blochii) Head Phospholipid and Soybean Lecithin Liposomes: Preparation,Characteristics and Anti-Inflammatory Properties

In this study, we compared the characteristics and in vitro anti-inflammatory effects of two curcumin liposomes, prepared with golden pompano head phospholipids (GPL) and soybean lecithin (SPC). GPL liposomes (GPL-lipo) and SPC liposomes (SPC-lipo) loaded with curcumin (CUR) were prepared by thin film extrusion, and the differences in particle size, ζ-potential, morphology, and storage stability were investigated. The results show that GPL-lipo and SPC-lipo were monolayer liposomes with a relatively small particle size and excellent encapsulation rates. However, GPL-lipo displayed a larger negative ζ-potential and better storage stability compared to SPC-lipo. Subsequently, the effects of phospholipids in regulating the inflammatory response of macrophages were evaluated in vitro, based on the synergistic effect with CUR. The results showed that both GPL and SPC exerted excellent synergistic effect with CUR in inhibiting the lipopolysaccharide (LPS)-induced secretion of nitric oxide (NO), reactive oxygen species (ROS), and pro-inflammatory genes (tumor necrosis factor (TNF)-α, interleukin 1β (IL-β), and interleukin 6 (IL-6)) in RAW264.7 cells. Interestingly, GPL-lipo displayed superior inhibitory effects, compared to SPC-lipo. The findings provide a new innovative bioactive carrier for development of stable CUR liposomes with good functional properties.     

5-(Indol-2-yl)pyrazolo[3,4-b]pyridines as a New Family of TASK-3 Channel Blockers: A Pharmacophore-Based Regioselective Synthesis

TASK channels belong to the two-pore-domain potassium (K_2P) channels subfamily. These channels modulate cellular excitability, input resistance, and response to synaptic stimulation. TASK-channel inhibition led to membrane depolarization. TASK-3 is expressed in different cancer cell types and neurons. Thus, the discovery of novel TASK-3 inhibitors makes these bioactive compounds very appealing to explore new cancer and neurological therapies. TASK-3 channel blockers are very limited to date, and only a few heterofused compounds have been reported in the literature. In this article, we combined a pharmacophore hypothesis with molecular docking to address for the first time the rational design, synthesis, and evaluation of 5-(indol-2-yl)pyrazolo[3,4-b]pyridines as a novel family of human TASK-3 channel blockers. Representative compounds of the synthesized library were assessed against TASK-3 using Fluorometric imaging plate reader—Membrane Potential assay (FMP). Inhibitory properties were validated using two-electrode voltage-clamp (TEVC) methods. We identified one active hit compound (MM-3b) with our systematic pipeline, exhibiting an IC₅₀ ≈ 30 μM. Molecular docking models suggest that compound MM-3b binds to TASK-3 at the bottom of the selectivity filter in the central cavity, similar to other described TASK-3 blockers such as A1899 and PK-THPP. Our in silico and experimental studies provide a new tool to predict and design novel TASK-3 channel blockers.     

神经氨酸酶与3-(3-戊氧基)安息香酸作用机制的理论研究

运用柔性分子对接和分子动力学方法, 深入研究了4-(氮乙酰氨基)-5-胍基-3-(3-戊氧基)安息香酸(BA)与各类型神经氨酸酶(N1, N2, N9亚型和B型)间的作用机制. 结果显示, BA与各类型神经氨酸酶结合模式存在差异, 但作用机制比较相似: 与它们的活性腔均匹配良好, 并形成稳定的复合体系, 最大结合能分别等于－1233.62, －1385.72, －663.11, －1058.87 kJ•mol^－1. 这表明BA对各类型神经氨酸酶均有良好的抑制效果. 进一步分析发现, BA与各类型神经氨酸酶活性腔内保守关键氨基酸残基发生较强的静电和氢键作用, 而与易突变氨基酸残基作用较弱, 表明了活性腔内易突变氨基酸残基发生突变也不会对抑制效果造成明显影响. 因此, BA是一种极具应用前景的新型抗流感病毒药物. 结合以前的研究结果, 我们提出了以BA为底物的抗流感病毒药物的修饰方向.     

Inhibitory Effect of DMSO on Halohydrin Dehalogenase: Experimental and Computational Insights into the Influence of an Organic Co-solvent on the Structural and Catalytic Properties of a Biocatalyst

Although the application of organic solvents in biocatalysis is well explored, in-depth understanding of the interactions of solvent with proteins, in particular oligomeric ones, is still scant. Understanding these interactions is essential in tailoring enzymes for industrially relevant catalysis in nonaqueous media. In our study, the homotetrameric enzyme halohydrin dehalogenase (HHDH) from Agrobacterium radiobacter AD1 (HheC) was investigated, as a model system, in DMSO/water solvent mixtures. DMSO, the most commonly used co-solvent for biocatalytic transformations, was found to act as a mixed-type inhibitor with a prevalent competitive contribution. Even 5 % (v/v) DMSO inhibits the activity of HheC by half. Molecular dynamics (MD) simulations showed that DMSO keeps close to Ser-Tyr catalytic residues forming alternate H-bonds with them. Stability measurements paired with differential scanning calorimetry, dynamic light scattering methods and MD studies revealed that HheC maintains its structural integrity with as much as 30 % (v/v) DMSO.     

金属磷酸铝分子筛CdAPO-5的合成、结构及催化性能(Ⅰ)

用水热晶化法，以TEAOH（四乙基氢氧化铵）为模板剂会成出了CdAPO-5分子筛晶体。对样品进行XRD、IR、电子探针等分析，确认其具有AIPO4－5型分子筛结构，属六方晶系，并证实金属Cd进入分子筛的结构骨架，同时对其吸附性能、热稳定性及催化活性进行研究，结果表明CdAPO-5分子筛作为催化剂不仅热稳定性好，机械强度高，且对乙炔水合制乙醛、乙醇脱水制乙醚等反应具有良好的催化性能。     

分子动力学与第一原理研究二氧化铈(CeO2)n (n=1～5)纳米粒子的结构性质

二氧化铈纳米粒子(CeO2)n(n=1～5)材料为固态氧化燃料电池中的催化剂,因此了解其不同尺寸结构的性质是非常重要的.在本论文中使用分子动力学(molecular dynamics)模拟结合火焰算法(FIRE algorithm)计算得到二氧化铈的最小能量结构.再应用密度泛函理论方法(density functional theory)对这些结构进一步计算,得到更精确的最低能量结构.     

Temperature effects on spreading of water nano‐droplet on poly(methyl methacrylate): A molecular dynamics simulation study

In this article, the effect of temperature on the spreading behavior of a water nano‐droplet on poly(methyl methacrylate) substrate is investigated. The contact angle analysis illustrates that the spreading process occurs in a stage‐like manner and the increase in temperature causes a regime change from partial to total wetting. The interaction energy distributions show that there exist sites on the surface which could trap water molecules and provide a better path for other molecules to overcome the asperities. Estimations of the coefficients of self‐diffusivity suggest that temperature has a major effect in the reorientation stage, which results in the formation of the interfacial layer. In the second stage of spreading, temperature affects the process by providing sufficient energy for water molecules to overcome the interactions with the substrate. Therefore, this stage is controlled by the movement of water molecules on the surface and is highly influenced by their interaction with the surface asperities, strong interaction sites, and the carbonyl groups. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1532–1541     

Deep Learning and Structure-Based Virtual Screening for Drug Discovery against NEK7: A Novel Target for the Treatment of Cancer

NIMA-related kinase7 (NEK7) plays a multifunctional role in cell division and NLRP3 inflammasone activation. A typical expression or any mutation in the genetic makeup of NEK7 leads to the development of cancer malignancies and fatal inflammatory disease, i.e., breast cancer, non-small cell lung cancer, gout, rheumatoid arthritis, and liver cirrhosis. Therefore, NEK7 is a promising target for drug development against various cancer malignancies. The combination of drug repurposing and structure-based virtual screening of large libraries of compounds has dramatically improved the development of anticancer drugs. The current study focused on the virtual screening of 1200 benzene sulphonamide derivatives retrieved from the PubChem database by selecting and docking validation of the crystal structure of NEK7 protein (PDB ID: 2WQN). The compounds library was subjected to virtual screening using Auto Dock Vina. The binding energies of screened compounds were compared to standard Dabrafenib. In particular, compound 762 exhibited excellent binding energy of −42.67 kJ/mol, better than Dabrafenib (−33.89 kJ/mol). Selected drug candidates showed a reactive profile that was comparable to standard Dabrafenib. To characterize the stability of protein–ligand complexes, molecular dynamic simulations were performed, providing insight into the molecular interactions. The NEK7–Dabrafenib complex showed stability throughout the simulated trajectory. In addition, binding affinities, pIC50, and ADMET profiles of drug candidates were predicted using deep learning models. Deep learning models predicted the binding affinity of compound 762 best among all derivatives, which supports the findings of virtual screening. These findings suggest that top hits can serve as potential inhibitors of NEK7. Moreover, it is recommended to explore the inhibitory potential of identified hits compounds through in-vitro and in-vivo approaches.     

Structural and Dynamic Properties of Monoclonal Antibodies Immobilized on CNTs: A Computational Study

Due to the widespread application of carbon nanotube (CNT)‐based materials in nanomedicine, it is nowadays of paramount importance to unravel at the atomistic level of detail the structural properties of such bioconjugates in order to rationalize and predict the effect exerted by the graphitic framework on the bio‐active counterpart. In this paper, we report for the first time all‐atom explicit solvent molecular dynamics (MD) simulations investigating the structural and dynamic properties of a noncovalent bioconjugate in which the monoclonal Cetuximab antibody (Ctx) is adsorbed on a CNT surface. Upon selection of the three most representative adsorption modes as obtained by docking studies, force‐field MD and DFT simulations unambiguously showed that hydrophobic interactions mainly govern the adsorption of the protein on the graphitic surface. Two main adsorption poses have been predicted: a pose‐fab (p‐fab) and pose‐fc (p‐fc) (fab = fragment antigen binding region; fc = fragment crystallizable region), the former being favored with small‐diameter tubes (≤40 Å). In all the predicted poses, the secondary structure of Ctx is largely unaffected by the presence of the graphitic surface and, consistently with previous literature studies, our simulations reveal that positively charged amino acidic residues, such as Lys and Arg, predominantly contribute to the stabilization of the CNT?Ctx complex acting like surfactants. The predicted structural models are consistent with the experimental data, for which the immobilization of the antibody on CNTs does not disrupt the structural and recognition properties of the Ctx, consequently supporting the reliability of the used bioconjugation strategy for engineering stable and responsive hybrid nanomaterials for therapeutic applications. Moreover, a remarkable structural similarity of Ctx with antibodies of different isotypes suggests that in principle the CNT framework can interact in the same manner with all antibodies currently used in clinical applications.     

To Affinity and Beyond: A Personal Reflection on the Design and Discovery of Drugs

Faced with new and as yet unmet medical need, the stark underperformance of the pharmaceutical discovery process is well described if not perfectly understood. Driven primarily by profit rather than societal need, the search for new pharmaceutical products—small molecule drugs, biologicals, and vaccines—is neither properly funded nor sufficiently systematic. Many innovative approaches remain significantly underused and severely underappreciated, while dominant methodologies are replete with problems and limitations. Design is a component of drug discovery that is much discussed but seldom realised. In and of itself, technical innovation alone is unlikely to fulfil all the possibilities of drug discovery if the necessary underlying infrastructure remains unaltered. A fundamental revision in attitudes, with greater reliance on design powered by computational approaches, as well as a move away from the commercial imperative, is thus essential to capitalise fully on the potential of pharmaceutical intervention in healthcare.     

A Bis-Chelating / Ligand for the Synthesis of Heterobimetallic Platinum(II)/Rhenium(I) Complexes: Tools for the Optimization of a New Class of Platinum(II) Anticancer Agents

The two independent and coordination sites of a newly synthesized bis[2-(hydroxyphenyl)-1,2,4-triazole] platform have been exploited to prepare four monometallic neutral ()Pt^II complexes carrying DMSO, pyridine, triphenylphosphine, or N-heterocyclic carbene as the fourth ligand. Then, the second coordination site was used to introduce an IR-active rhenium tricarbonyl entity, affording the four corresponding heterobimetallic neutral Pt^II/Re^I complexes, as well as a cationic Pt^II/Re^I derivative. X-ray crystallographic studies showed that distortion of the organic platform occurred to accommodate the coordination geometry of both metal centers. No ligand exchange or transchelation occurred upon incubation of the Pt^II complexes in aqueous environment or in the presence of Fe^III, respectively. The antiproliferative activity of the ligand and complexes was first screened on the triple-negative breast cancer cell line MDA-MB-231. Then, the IC₅₀ values of the most active candidates were determined on a wider panel of human cancer cells (MDA-MB-231, MCF-7, and A2780), as well as on a nontumorigenic cell line (MCF-10A). Low micromolar activities were reached for the complexes carrying a DMSO ligand, making them the first examples of highly active, but hydrolytically stable, Pt^II complexes. Finally, the characteristic mid-IR signature of the {Re(CO)₃} fragment in the Pt/Re heterobimetallic complexes was used to quantify their uptake in breast cancer cells.     

Structure and Processing Properties of Nine Yam (Dioscorea opposita Thunb) Starches from South China: A Comparison Study

In order to explore the processing and application potential of Chinese yam starch, nine kinds of Chinese yam starch (GY11, GY5, GY2, GXPY, LCY, SFY, MPY, SYPY, ASY) from South China were collected and characterized. The chemical composition, rheological properties, thermal properties, and in vitro starch digestion were compared, and the correlation between the structure and processing properties of these yam starches was analyzed using Pearson correlation. The results show that GY2 had the highest amylose content of 28.70%. All the yam starches were similarly elliptical, and all the yam starch gels showed pseudoplastic behavior. Yam starches showed similar pasting temperatures and resistant starch content, but SYPY showed the largest particle size (28.4 μm), SFY showed the highest setback (2712.33 cp), and LCY showed the highest peak viscosity (6145.67 cp) and breakdown (2672.33 cp). In addition, these yam starches also showed different crystal types (A-type, B-type, C-type), relative crystallinity (26.54–31.48%), the ratios of 1045/1022 cm⁻¹ (0.836–1.213), pasting properties, and rheological properties, so the yam starches have different application potentials. The rheological and pasting properties were related to the structural properties of starch, such as DI, Mw, and particle size, and were also closely related to the thermodynamic properties. The appropriate processing methods and purposes of the processed products of these yam starches can be selected according to their characteristics.