Precise cuts for tailoring chromene-phenyl COX inhibitors with Ligand Designer.

Cyclooxygenases 1 and 2 (COX-1/2) are enzymes renowned for inducing inflammatory responses through the production of prostaglandins. Thus, the development of COX inhibitors has been a promising approach for identifying compounds with anti-inflammatory potential. In this study, we designed 27 new compounds (1-27) based on the structure of a previously known COX inhibitor, using the Ligand Designer tool. Our aim was to improve the affinity of the compounds with COX enzymes by inducing interactions with residue Arg120 while retaining the good π-π stacking interactions of the chromene-phenyl scaffold. Through screening based on ligand-binding free energy defined by molecular docking simulations and MM/GBSA technique, compounds 9 and 10 were identified as having the highest ability to inhibit COX proteins. The binding affinities of the two compounds with COX-1/2 were superior to those of the original NAI10 compound and the reference drug indomethacin. Our virtual screening suggests that compounds 9 and 10 have a strong ability to inhibit COX-1/2 and thus could be promising candidates for further anti-inflammatory drug studies. In essence, our study underscores the pivotal role of the N-aryl iminocoumarin scaffold in shaping the future landscape of novel anti-inflammatory drug development.

A close-up shot of protein-protein docking, from experiment to theory and reverse with the PROTAC performers.

PROTACs (Proteolysis Targeting Chimeras), heterobifunctional molecules, exhibit selectivity in degrading target proteins through E3 ubiquitin ligases. Designing effective PROTACs requires a deep understanding of the intricate binding interactions in the ternary complex (POI/PROTAC/E3 ligase), crucial for efficient target protein degradation. To address this challenge, we introduce a novel computational virtual screening method that considers essential amino acid interactions between the protein of interest and the chosen E3 ligase. This approach enhances accuracy and reliability, facilitating the strategic development of potent PROTACs. Utilizing a crystallized model of the VHL:PROTAC:SMARCA2BD ternary complex (PDB: 7Z6L), we assessed the effectiveness of our method. Our study reveals that increasing the number of essential restraints between the two proteins reduces the generated docking poses, leading to closer alignment with the experimental ternary complex. Specifically, utilizing three restraints showed the closest resemblance to the published complex, highlighting crucial interactions such as an H-bond between A:Gln 89 and B:Asn 67, along with two hydrophobic interactions: A:Gly 22 with B:Arg 69 and A:Glu 37 with B:Pro 99. This resulted in a significant decrease in the mean RMSD value from 31.8 and 31.0 Å to 24.4 Å, respectively. This underscores the importance of incorporating multiple essential restraints to enhance docking accuracy. Building on this progress, we introduce a systematic approach to design potential PROTACs between the Estrogen receptor and the E3 ligase, utilizing bridging intermediates with 4, 6, or 7 carbon atoms. By providing a more accurate and efficient means of identifying optimal PROTAC candidates, this approach has the potential to accelerate the development of targeted therapies and reduce the time and costs associated with drug discovery.Communicated by Ramaswamy H. Sarma.

Enzyme-responsive macrocyclic metal complexes for biomedical imaging.

Metal chelator-based contrast agents are used as tumor navigators for cancer diagnosis. Although approved metal chelators show excellent contrast performance in magnetic resonance imaging (MRI), large doses are required for cancer diagnoses due to rapid clearance and nonspecific accumulation throughout the body, which can compromise safety. The present study describes an enzyme-responsive metal delivery system, in which enzyme overexpressed in the tumor microenvironment selectively activates the tumor uptake of gadolinium (Gd). Gd was loaded into enzyme-responsive macrocyclam (ErMC) modified with a PEGylated enzyme-cleavable peptide resulting in Gd@ErMC. The PEGylated shell layer protected Gd@ErMC from nonspecific binding in the blood, increasing the half-life of the contrast agent. Specific cleavage of the PEGylated shell layer by the enzyme selectively liberated Gd from Gd@ErMC at the tumor site. Evaluation of the in vivo distribution of Gd@ErMC in tumor-bearing mice by MRI and positron emission tomography (PET) showed that Gd@ErMC had an extended half-life and was highly specific. Histological and serological analysis of Gd@ErMC-treated mice showed that this agent was safe. This novel enzyme-responsive contrast agent delivery system shows promise as specific theranostic agent for MR-guided radiotherapy.

A New Carvotacetone Derivative from the Aerial Part of Sphaeranthus africanus.

Sphaeranthus africanus L. is native in Vietnam. Little is known about α-glucosidase inhibition of Sphaeranthus africanus and its isolated compounds. A bioactive-guided isolation was applied to the Vietnamese Sphaeranthus africanus to find α-glucosidase inhibitory components. Eight compounds were detected and structurally elucidated. They are 3-angeloyloxy-5-[2'',3''-epoxy-2''-methylbutanoyloxy]-7-hydroxycarvotacetone, 3-angeloyloxy-5-[3''-chloro-2''-hydroxy-2''-methylbutanoyloxy]-7-hydroxycarvotacetone, 3-angeloyloxy-5-[2''R,3''R-dihydroxy-2''-methyl-butanoyloxy]-7-hydroxycarvotacetone, 3-angeloyloxy-5-[2''S,3''R-dihydroxy-2''-methylbutanoyloxy]-7-hydroxycarvotacetone, 3-angeloyloxy-5-[2''S,3''S-dihydroxy-2''-methylbutanoyloxy]-7-hydroxycarvotacetone, 5-angeloyloxy-7-hydroxy-3-tigloyloxycarvotacetone, 3-O-methylquercetin, and chrysosplenol D. Their chemical structures were elucidated by extensive 1D and 2D NMR analysis and high-resolution mass spectroscopy as well as comparisons in literature. 3-Angeloyloxy-5-[2''S,3''S-dihydroxy-2''-methylbutanoyloxy]-7-hydroxycarvotacetone is a new compound. Isolated compounds were evaluated for the α-glucosidase inhibition. Isolated compounds showed moderate activity with IC50 values ranging from 128.9-274.3 µM while others are weak. A molecular docking study was conducted, indicating that isolated compounds are potent α-glucosidase inhibitory compounds.

The anti-inflammatory activity of the compounds isolated from Dichroa febrifuga leaves.

Dichroa febrifuga Lour. is a traditional medicinal herb that has been applied in the treatment of malaria and some other infectious diseases. Studies recently have focused on the anti-inflammation of the extracts of Dichroa febrifuga Lour. although there have not many reports about which compounds play the essential role. Therefore, in this study, we isolated hydrangenoside C (1), isoarborinol (2), and methyl 1,3,4,6-tetra-O-acetyl-fructofuranoside (3) from the leaves of Dichroa febrifuga. Subsequently, the anti-inflammatory property of 1-3 was assessed using an in vivo assay of edema mouse model which was induced by carrageenan. Out of the three, 2 inhibited the edema effectively and dose-dependently, similarly to diclofenac while there was no obvious activity observed in 1 and 3. The in silico results demonstrated that 2 enables binding to 5-LOX and PLA2 via generating h-bonds. This is the first study to mention the anti-inflammation of 2 in Dichroa febrifuga Lour., and would be a contribution to further studies to elucidate the promising bioactivities of this compound.

Lobaric acid prevents the adverse effects of tetramethrin on the estrous cycle of female albino Wistar rats.

Tetramethrin (Tm) is a commonly used pesticide that has been reported to exert estrogen-antagonistic effects selectively on female rats. The present study was undertaken to assess the protective role of lobaric acid (La) on estrous cycle in Tm-treated female Wistar rats. Female rats were exposed to Tm (50 mg/kg b.w/day) only or in combination with La at low (50 mg/kg b.w/day) or high (100 mg/kg b.w/day) dose for 30 days. The results showed that Tm altered the estrous cycle of female rats by decreasing the levels of luteinizing hormone, follicular-stimulating hormone, progesterone, estrone, and estradiol while increasing testosterone level. The morphology of vaginal smears of Tm-treated female rats showed the presence of abnormal cells and/or structures at different phases of estrus cycle. Strikingly, in (Tm + La)-treated rats, all the observed adverse effects of Tm on the hormonal parameters, cell morphology, and the length of each phase of estrous cycle were significantly diminished in a dose-dependent manner. The docking results showed that La competes with Tm for Gonadotropin-Releasing Hormone (GnRH) receptor, thereby reducing the toxicity of Tm but did not cancel the response of GnRH receptor completely. In conclusion, our results designated that La could be used as a potential candidate in the management of insecticide-induced alterations of the reproductive cycle of rodents.

A computationally affordable approach for accurate prediction of the binding affinity of JAK2 inhibitors.

Janus kinase 2 (JAK2) inhibitors are potential anticancer drugs in the treatment of lymphoma, leukemia, thrombocytosis and particularly myeloproliferative diseases. However, the resemblance among JAK family members has challenged the identification of highly selective inhibitors for JAK2 to reduce undesired side effects. As a result, a robust search for promising JAK2 inhibitors using a computational approach that can effectively nominate new potential candidates to be further analyzed through laborious experimental operations has become necessary. In this study, the binding affinities of JAK2 inhibitors were rapidly and precisely estimated using the fast pulling of ligand (FPL) simulations combined with a modified linear interaction energy (LIE) method. The approach correlates with the experimental binding affinities of JAK2 inhibitors with a correlation coefficient of R = 0.82 and a root-mean-square error of 0.67 kcal•mol-1. The data reveal that the FPL/LIE method is highly approximate in anticipating the relative binding free energies of known JAK2 inhibitors with an affordable consumption of computational resources, and thus, it is very promising to be applied in in silico screening for new potential JAK2 inhibitors from a large number of molecules available.

Some Antioxidant Properties of Components from the Flower of Ochna integerrima and Their Beneficial Effects on HaCaT Keratinocytes and in Silico Analysis on Tyrosinase.

Four compounds, luteolin (1), 6-γ,γ-dimethylallylquercetin 7-O-ß-D-glucopyranoside (2), 6-γ,γ-dimethylallylkaempferol 7-O-ß-D-glucopyranoside (3), and 6-γ,γ-dimethylallyldihydrokaempferol 7-O-ß-D-glucoside (4), were isolated for the first time from AcOEt extract of the O. integerrima flower. We then evaluated the antioxidant effects of AcOEt, butanol, and MeOH extracts and their effects on H2 O2 against oxidative stress in HaCaT keratinocyte cell lines. Furthermore, 2,2-diphenyl-1-picrylhydrazyl hydrate (DPPH⋅) radical scavenging activities of 1-4 were determined and their mechanisms of action on tyrosinase were predicted by in silico studies. The results revealed that the AcOEt extract and 1-3 exhibited good DPPH⋅ radical scavenging activity. Furthermore, this extract also had a significant protective effect against H2 O2 -induced oxidative stress in HaCaT cells. In silico studies indicated that the activity of 1-3 may be due to tyrosinase inhibition with MM-GBSA free binding energies of -78.9, -70.1, and -71.1 kcal mol-1 , respectively, compared to 4 with an energy -56.9 kcal mol-1 .

Cleroda-4(18),13-dien-15,16-olide as novel xanthine oxidase inhibitors: An integrated in silico and in vitro study.

In the present study, in silico predictions and molecular docking were performed on five clerodane diterpenes (1-5) from Polyalthia longifolia seeds to evaluate their potential as xanthine oxidase (XO) inhibitors. The initial screening was conducted by target prediction using TargetNet web server application and only compounds 3 and 4 showed a potential interaction with XO. Compounds 3 and 4 were subsequently subjected to in silico analyses on XO protein structure (PDB: 1N5X) using Schrödinger Release 2020-3 followed by structural modeling & molecular simulation studies to confirm the initial prediction result and identify the binding mode of these compounds to the XO. Molecular docking results revealed that compounds 3 (-37.3 kcal/mol) and 4 (-32.0 kcal/mol) binds more stably to XO than the reference drug allopurinol (-27.0 kcal/mol). Interestingly, two residues Glu 802 and Thr 1010 were observed as the two main H-bond binding sites for both tested compounds and the allopurinol. The center scaffold of allopurinol was positioned by some π-π stacking with Phe 914 and Phe 1009, while that of compounds 3 and 4 were supported by many hydrophobic interactions mainly with Leu 648, Phe 649, Phe 1013, and Leu 1014. Additionally, the docking simulation predicted that the inhibitory effect of compounds 3 and 4 was mediated by creating H-bond with particularly Glu 802, which is a key amino acid for XO enzyme inhibition. Altogether, in vitro studies showed that compounds 3 and 4 had better inhibitory capacity against XO enzyme with IC50 values significantly (p < 0.001) lower than that of allopurinol. In short, the present study identified cleroda-4(18),13-dien-15,16-olide as novel potential XO inhibitors, which can be potentially used for the treatment of gout.

Anti-Inflammatory and Antimicrobial Activities of Compounds Isolated from Distichochlamys benenica.

Distichochlamys benenica is a native black ginger that grows in Vietnam. In point of fact, there is limitation of available information in the literature making mention of the chemical constituents and bioactive properties of this plant. This study is aimed at isolating trans-o-coumaric acid (1), trans-cinnamic acid (2), and borneol (3) from the rhizomes of D. benenica Q.B.Nguyen & Skornick and evaluate the anti-inflammatory and antimicrobial activities of 1-3 using the carrageenan paw edema model and the dilution broth method, respectively. This revealed that 1 was as effective as diclofenac in reducing the intensity of the edema development. The in silico research showed that the activity of 1 might be derived from inhibiting COX-2 by generating h-bonds at the positions of Arg 120, Tyr 355, and Arg 513 residues. The antimicrobial activities against Gram-positive strains (Staphylococcus aureus and Bacillus subtilis) were comparable, with the minimum inhibitory concentrations ranging from 1.52 to 3.37 mM. This is the first study of the bioactivity of compounds isolated from D. benenica Q.B.Nguyen & Skornick. Our results suggest that 1 may be a nature-derived compound which demonstrates the anti-inflammatory properties and inhibit the proliferation of several Gram-positive bacteria.

Antioxidant Activity of a New Xanthone Derivative from Aspidistra Letreae: In Vitro and In Silico Studies.

A new xanthone derivative, aspidxanthone A (1), and three known compounds ((2S)-1-(ß-D-galactopyranosyloxy)-3-(hexadecanoyloxy)propan-2-yl (9Z,12Z)-octadeca-9,12-dienoate (2), (25S)-spirostane-1ß,3α,5ß-triol (3), and asparenyldiol (4)) were isolated from the whole of the endemic species Aspidistra letreae in Vietnam. Their structures were elucidated by means of extensive spectroscopic analyses and comparison with published data. In this study, we report the isolation and structure elucidation of a new compound aspidxanthone A, antioxidant activities of the extract and isolates 1-4, and in silico molecular docking of aspidxanthone A. The ethyl acetate extract had good antioxidant activity with an IC50 value of 26.3 µg mL-1 . Among the isolates, aspidxanthone A exhibited DPPH reduction activity with an IC50 value of 11.2 µM, which is in the same range as that of the positive control, ascorbic acid. The mechanism of action of aspidxanthone A on the tyrosinase and xanthine oxidase proteins have been clarified by in silico studies.

N-Aryl iminochromenes inhibit cyclooxygenase enzymes via π-π stacking interactions and present a novel class of anti-inflammatory drugs.

Cyclooxygenase enzymes (COX1/2) have been widely studied and noted for their role in the biosynthesis of inflammation-induced proteins, prostaglandins and thromboxane. Multiple anti-inflammatory drugs have been developed to target these two enzymes, but most of them appeared to have notable adverse effects, especially on the cardiovascular system and lower gastrointestinal tract, suggesting an urgent need for new potent anti-inflammatory drugs. In this study, we screened twenty-two previously synthesized N-aryl iminochromenes (NAIs) for their anti-inflammatory activity by performing COX-1/2 inhibitory assays. Five compounds (1, 10, 14, 15, and 20) that gave the best in vitro anti-inflammatory results were subjected to an in vivo anti-inflammatory assay using the formalin-induced hind rat paw oedema method, followed by in silico studies using indomethacin and celecoxib as standard drugs. Among them, compound 10 stood out as the best candidate, and the percentage reduction in paw oedema at the dose of 20 mg kg-1 body weight was found to be substantially higher with compound 10 than that with indomethacin. This is mostly due to the excellent suitability of the chromene-phenyl scaffold with a highly concentrated area of aromatic residues, which produced good π-π stacking interactions. Taken together, this study strongly suggests compound 10 as a potential candidate for anti-inflammatory drug research.

Flower-like S-doped-Ni2P mesoporous nanosheet-derived self-standing electrocatalytic electrode for boosting hydrogen evolution.

Developing cost-effective, highly active, and stable electrocatalysts for boosting electrochemical hydrogen evolution reaction (HER) in alkaline media is playing a critical role in meeting the demands of the hydrogen industry in the future. Herein, an efficient HER electrocatalyst based on flowerlike S-doped Ni2P mesoporous nanosheets (NSs) supported on nickel foam (S-Ni2P NSs/NF) was developed through an effective approach. The obtained S-Ni2P NSs/NF catalyst required low overpotential of only 87.5 and 179.1 mV to reach a current density of 10 and 50 mA cm-2, respectively. Moreover, a small Tafel slope of 62.1 mV dec-1 for S-Ni2P NSs/NF demonstrated that the HER process occurred with very fast kinetics. Besides high HER activity, the synthesized S-Ni2P NSs/NF catalyst exhibited superior stability and long-term durability towards HER, which had the ability to operate for over 30 h without degradation in catalytic performance. The unique flower-like nanosheet structure with excellent mesoporous characteristics of S-Ni2P NSs/NF resulted in maximizing the electrochemical active surface area for providing a large number of electrocatalytic active sites. In addition, the S-doping effect could modulate the electronic structure of Ni species in Ni2P, leading to an acceleration of the adsorption rate of reaction intermediates on the surface of catalysts towards improving HER kinetics. The results not only demonstrate S-Ni2P NSs/NF as an active catalyst for HER, but offer an effective strategy for improving the catalytic activity of earth-abundant transition metal-based HER catalysts.

Dual COX and 5-LOX inhibition by clerodane diterpenes from seeds of Polyalthia longifolia (Sonn.) Thwaites.

Natural metabolites with their specific bioactivities are being considered as a potential source of materials for pharmacological studies. In this study, we successfully isolated and identified five known clerodane diterpenes, namely 16-oxo-cleroda-3,13(14)E-dien-15-oic acid (1), 16-hydroxy-cleroda-3,13-dien-15-oic acid (2), 16-hydroxy-cleroda-4(18),13-dien-16,15-olide (3), 3α,16α-dihydroxy-cleroda-4(18),13(14)Z-dien-15,16-olide (4), and 16α-hydroxy-cleroda-3,13(14)Z-dien-15,16-olide (5) from the methanolic extract of seeds of Polyalthia longifolia. Initially, all the isolated metabolites were investigated for COX-1, COX-2, and 5-LOX inhibitory activities using the standard inhibitory kits. Of which, compounds 3, 4, and 5 exhibited to be potent COX-1, COX-2, and 5-LOX inhibitors with the IC50 values similar or lower to those of the reference drugs. To understand the underlying mechanism, these compounds were subjected to molecular docking on COX-1, COX-2, and 5-LOX proteins. Interestingly, the in silico study results were in high accordance with in vitro studies where compounds 3, 4, and 5 hits assumed interactions and binding pattern comparable to that of reference drugs (indomethacin and diclofenac), as a co-crystallized ligand explaining their remarkable dual (COX/LOX) inhibitor actions. Taken together, our findings demonstrated that compounds 3, 4, and 5 functioned as dual inhibitors of COX/5-LOX and can contribute to the development of novel, more effective anti-inflammatory drugs with minimal side-effects.

Flower-like S-doped-Ni2P mesoporous nanosheets-derived self-standing electrocatalytic electrode for boosting hydrogen evolution.

Developing cost-effective, highly active, and stable electrocatalysts for boosting electrochemical hydrogen evolution reaction (HER) in alkaline media is playing a critical role to meet hydrogen industry in the future. Herein, an efficient HER electrocatalyst based on flowerlike S-doped Ni2P mesoporous nanosheets supported on nickel foam (S-Ni2P NSs/NF) was developed through an effective approach. The obtained S-Ni2P NSs/NF catalyst required low overpotential of only 87.5 mV and 179.1 mV to reach current density of 10 and 50 mA cm-2, respectively. Moreover, a small Tafel slope of 62.1 mV dec-1 for S-Ni2P NSs/NF demonstrated that HER process occurred with very fast kinetics. Besides high HER activity, the synthesized S-Ni2P NSs/NF catalyst exhibited superior stability and long-term durability toward HER, which had ability to operate over 30 h without degradation in catalytic performance. The unique flower-like nanosheets structure with excellent mesoporous characteristics of S-Ni2P NSs/NF resulted in maximizing electrochemical active surface area for providing a large number of electrocatalytic active sites. In addition, S doping effect could modulate electronic structure of Ni species in Ni2P, leading to accelerating rate adsorption of reaction intermediates on the surface of catalysts toward improving HER kinetics. The results not only demonstrate S-Ni2P NSs/NF as active catalyst for HER, but also offer effective strategy for improving catalytic activity of earth-abundant transition metal-based HER catalysts.

Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations.

Checkpoint kinase 1 (CHK1) is a serine/threonine-protein kinase that is involved in cell cycle regulation in eukaryotes. Inhibition of CHK1 is thus considered as a promising approach in cancer therapy. In this study, the fast pulling of ligand (FPL) process was applied to predict the relative binding affinities of CHK1 inhibitors using non-equilibrium molecular dynamics (MD) simulations. The work of external harmonic forces to pull the ligand out of the binding cavity strongly correlated with the experimental binding affinity of CHK1 inhibitors with the correlation coefficient of R = -0.88 and an overall root mean square error (RMSE) of 0.99 kcal/mol. The data indicate that the FPL method is highly accurate in predicting the relative binding free energies of CHK1 inhibitors with an affordable CPU time. A new set of molecules were designed based on the molecular modeling of interactions between the known inhibitor and CHK1 as inhibitory candidates. Molecular docking and FPL results exhibited that the binding affinities of developed ligands were similar to the known inhibitor in interaction with the catalytic site of CHK1, producing very potential CHK1 inhibitors of that the inhibitory activities should be further evaluated in vitro.

New reactions of N-tert-butylimines; formation of N-heterocycles by methyl radical elimination on flash vacuum thermolysis of N-benzylidene- and N-(2-pyridylmethylidene)-tert-butylamines.

Thermal reactions of N-benzylidene- and N-(2-pyridylmethylidene)-tert-butylamines (5 and 13) under FVT conditions have been investigated. Unexpectedly, at 800 °C, compound 5 yields 1,2-dimethylindole and 3-methylisoquinoline. In the reaction of 13 at 800 °C, 3-methylimidazo[1,5-a]pyridine was obtained as the major product. Mechanisms of these reactions have been proposed on the basis of DFT calculations. Furthermore, UV-photoelectron spectroscopy combined with FVT has been applied for direct monitoring and characterization of the thermolysis products in situ.