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Simultaneous inhibition of soluble epoxide hydrolase (sEH) and fatty acid amide hydrolase (FAAH) with a single small molecule represents a novel therapeutic approach in treating inflammatory pain, since both targets are involved in pain and inflammation processes. In this study using multi-target directed ligands methodology we designed and synthesized 7 quinolinyl-based dual sEH/FAAH inhibitors, using an optimized microwave-assisted Suzuki-Miyaura coupling reaction and tested their potency in human FAAH and human, rat, and mouse sEH inhibition assays. The structure-activity relationship study showed that quinolinyl moiety is well tolerated in the active sites of both enzymes, yielding several very potent dual sEH/FAAH inhibitors with the IC50 values in the low nanomolar range. The most potent dual inhibitor 4d was further evaluated in stability assay in human and rat plasma where it performed better than the standard Warfarin while in vivo study revealed that 1 mg/kg 4d can inhibit acute inflammatory pain in male rats to a similar degree as the traditional nonsteroidal anti-inflammatory drug ketoprofen (30 mg/kg) after intraperitoneal injection. ADMET prediction studies for this dual inhibitor show favorable pharmacokinetic properties which will guide the future in vivo evaluations.

Infrared (IR) microimaging is employed for selectively recording two‐dimensional plots of the individual distributions of the components n‐hexane (nC6) and 3‐methylpentane (3MP) over a single crystal of zeolite ZSM‐5 during mixture adsorption. At a pressure change from 0 to 0.02 mbar, the scenario of "overshooting" is observed, with the concentration of nC6 temporarily exceeding its equilibrium value. After the next pressure step from 0.02 to 2 mbar, 3MP is progressively driven out of the pores, in parallel with an increase in nC6 concentration. The IR microimaging results are corroborated by grand canonical Monte Carlo simulations, which help explain the peculiarities of mass transfer by providing visual representations of the distribution and packing densities of the guest molecules in the pores. [ABSTRACT FROM AUTHOR]

Mitogen‐inducible gene 6 (Mig6) is a cellular inhibitor of epidermal growth factor receptor (EGFR) that binds directly to the EGFR kinase domain and interferes with signaling. Reduced Mig6 expression is correlated with increased EGFR activity in multiple cancer models. Here, we investigated whether disease‐associated point mutations could reduce the inhibitory potency of Mig6. We show that several cancer‐associated mutations, and a mutation derived from Alzheimer's Disease patients, diminish the ability of Mig6 to bind and inhibit EGFR in vitro. In mammalian cells, the mutations decreased the Mig6‐induced suppression of basal and EGF‐stimulated autophosphorylation, MAP kinase phosphorylation, and cell migration. To probe the mechanisms by which the mutations could lead to reduced Mig6 inhibition, we constructed atomic‐level computational models of Mig6 complexed with the EGFR catalytic domain, and performed molecular dynamics simulations for wild‐type and mutant complexes. [ABSTRACT FROM AUTHOR]

Histone proteins form the building blocks of chromatin—nucleosomes. Incorporation of alternative histone variants instead of the major (canonical) histones into nucleosomes is a key mechanism enabling epigenetic regulation of genome functioning. In humans, H2A.J is a constitutively expressed histone variant whose accumulation is associated with cell senescence, inflammatory gene expression, and certain cancers. It is sequence-wise very similar to the canonical H2A histones, and its effects on the nucleosome structure and dynamics remain elusive. This study employed all-atom molecular dynamics simulations to reveal atomistic mechanisms of structural and dynamical effects conferred by the incorporation of H2A.J into nucleosomes. We showed that the H2A.J C-terminal tail and its phosphorylated form have unique dynamics and interaction patterns with the DNA, which should affect DNA unwrapping and the availability of nucleosomes for interactions with other chromatin effectors. The dynamics of the L1-loop and the hydrogen bonding patterns inside the histone octamer were shown to be sensitive to single amino acid substitutions, potentially explaining the higher thermal stability of H2A.J nucleosomes. Taken together, our study demonstrated unique dynamical features of H2A.J-containing nucleosomes, which contribute to further understanding of the molecular mechanisms employed by H2A.J in regulating genome functioning. [ABSTRACT FROM AUTHOR]

Outer mitochondrial membrane fusion, a vital cellular process, is mediated by mitofusins. However, the underlying molecular mechanism remains elusive. We have performed extensive multiscale molecular dynamics simulations to predict a model of the transmembrane (TM) domain of the yeast mitofusin Fzo1. Coarse-grained simulations of the two TM domain helices, TM1 and TM2, reveal a stable interface, which is controlled by the charge status of residue Lys716. Atomistic replica-exchange simulations further tune our model, which is confirmed by a remarkable agreement with an independent AlphaFold2 (AF2) prediction of Fzo1 in complex with its fusion partner Ugo1. Furthermore, the presence of the TM domain destabilizes the membrane, even more if Lys716 is charged, which can be an asset for initiating fusion. The functional role of Lys716 was confirmed with yeast experiments, which show that mutating Lys716 to a hydrophobic residue prevents mitochondrial fusion. [Display omitted] • Mitofusin Fzo1 is involved in outer mitochondrial membrane fusion in yeast • Multiscale molecular dynamics predict a structure of the transmembrane domain • Lys716 controls the structure of the TM domain and destabilizes the membrane • Experiments on yeast confirm the importance of Lys716 Mitofusin Fzo1 is the protein responsible for outer mitochondrial membrane fusion in yeast. Versini et al. used multiscale molecular dynamics simulations to predict the structure of its transmembrane (TM) domain. Lys716 plays a key role in the TM domain structure and membrane destabilization. Yeast experiments confirm the importance of Lys716. [ABSTRACT FROM AUTHOR]

Here, we describe (1) the AlphaFold-based structural modeling approach to identify amino acids of the photoprotein berovin that are crucial for coelenterazine binding, and (2) the production and characterization of berovin mutants with substitutions of the identified residues regarding their effects on the ability to form an active photoprotein under physiological conditions and stability to light irradiation. The combination of mutations K90M, N107S, and W103F is demonstrated to cause a shift of optimal conditions for the conversion of apo-berovin into active photoprotein towards near-neutral pH and low ionic strength, and to reduce the sensitivity of active berovin to light. According to the berovin spatial structure model, these residues are found in close proximity to the 6-(p-hydroxy)-phenyl group of the coelenterazine peroxyanion. [ABSTRACT FROM AUTHOR]

The Mycobacterium tuberculosis (Mtb) cell envelope provides a protective barrier against the immune response and antibiotics. The mycobacterial membrane protein large (MmpL) family of proteins export cell envelope lipids and siderophores; therefore, these proteins are important for the basic biology and pathogenicity of Mtb. In particular, MmpL3 is essential and a known drug target. Despite interest in MmpL3, the structural data in the field are incomplete. Utilizing homology modeling, AlphaFold, and biophysical techniques, we characterized the cytoplasmic C‐terminal domain (CTD) of MmpL3 to better understand its structure and function. Our in silico models of the MmpL11TB and MmpL3TB CTD reveal notable features including a long unstructured linker that connects the globular domain to the last transmembrane (TM) in each transporter, charged lysine and arginine residues facing the membrane, and a C‐terminal alpha helix. Our predicted overall structure enables a better understanding of these transporters. [ABSTRACT FROM AUTHOR]

Data are accumulating on the hydrolytic activity of serum albumin towards esters and organophosphates. Previously, with the help of the technology of proton nuclear magnetic resonance (1H NMR) spectroscopy, we observed the yield of acetate in the solution of bovine serum albumin and p-nitrophenyl acetate (NPA). Thus, we showed that albumin possesses true esterase activity towards NPA. Then, using the methods of molecular docking and molecular dynamics, we established site Sudlow I as the catalytic center of true esterase activity of albumin. In the present work, to expand our understanding of the molecular mechanisms of albumin pseudoesterase and true esterase activity, we investigated—in experiments in vitro and in silico—the interaction of anticoagulant warfarin (WRF, specific ligand of site Sudlow I) and benzodiazepine diazepam (DIA, specific ligand of site Sudlow II) with albumins of different species, and determined how the binding of WRF and DIA affects the hydrolysis of NPA by albumin. It was found that the characteristics of the binding modes of WRF in site Sudlow I and DIA in site Sudlow II of human (HSA), bovine (BSA), and rat (RSA) albumins have species differences, which are more pronounced for site Sudlow I compared to site Sudlow II, and less pronounced between HSA and RSA compared to BSA. WRF competitively inhibits true esterase activity of site Sudlow I towards NPA and does not affect the functioning of site Sudlow II. Diazepam can slow down true esterase activity of site Sudlow I in noncompetitive manner. It was concluded that site Sudlow I is more receptive to allosteric modulation compared to site Sudlow II. [ABSTRACT FROM AUTHOR]

Non-immunoglobulin-based scaffold proteins (SPs) represent one of the key therapeutic target-specific and high-affinity binders in modern medicine. Among their cellular targets are signaling receptors, in particular, receptor tyrosine kinases, whose dysfunction leads to the development of cancer and other serious diseases. Successful applications of SPs have been reported for HER receptor type 2 (HER2), a member of the human epidermal growth factor receptor family that regulates cell growth and differentiation. To extend the blood residence of SPs and prevent their high accumulation in the kidneys, these proteins are often fused with serum albumin. Promising results for HER2-binding activity were obtained for SP G3 from the DARPins (Designed Ankyrin Repeat Proteins) family fused with an albumin-binding domain (ABD). Interestingly, the detected HER2–G3 binding strongly depended on the position of the G3 module in the sequence of the constructs. Further improvement of these constructs for biomedical applications requires deciphering the molecular mechanism responsible for this effect. Here, we investigate the structural and dynamic aspects of ABD–G3 and G3–ABD chimeras using NMR spectroscopy and molecular modeling. Based on biophysical data, we come to the conclusion that extensive inter-domain contacts form in both constructs, although their binding interfaces and complex stability are somewhat different. Also, it is shown that the domain linker plays an important role—it limits the accessibility of the detected protein–protein binding sites, depending on the order of the domains in the chimeric molecules. These results create a solid structural basis for the rational design of new effective SP constructs targeting the signaling receptors in cells. [ABSTRACT FROM AUTHOR]

Viral infectious diseases are spread worldwide. Search for natural antiviral therapy from natural resources to overcome the serious drawbacks of synthetic chemicals is imperative. The antiviral activity against influenza virus subtype H9N2, Herpes simplex II (HSV II), Adenovirus (AdVs), and Newcastle virus (NDV) was assessed using the cytopathic effect (CPE) inhibition assay. Phytochemical investigation of Eriocephalus africanus var. africanus aerial parts led to the isolation and identification of bioactive compounds including a mixture of aromatic hydrocarbons 1 , 3 β -friedelinol 2 , eicosanol 3 , 1-hexadecanol 4 , β -sitosterol 5 , undecanol 6 , pectolinarigenin 7 , cirsilineol 8 , chrysoeriol 9 , kaempferol 10 , tricin 11 , luteolin 12 , 2,4- dihydroxyacetophenone 13 , ferulic acid 14 , β -sitosterol glucoside 15 , afzelin 16 , hesperidin 17 , kaempferitrin 18 , d-(+)–pinitol 19 and 1,5–dimethyl citrate 20. The antiviral assessment revealed promising activity for the total extract against H9N2, HSV II, NDV, and AdVs with selectivity index (SI) = 12.4, 20.8, 27.4, and 12.9, respectively. The Petroleum ether fraction (PE) had promising anti-H9N2, NDV and the adenovirus with SI = 12.1, 17.0, and 19.1, respectively. Molecular modeling study proved promising activity for β -sitosterol with H9N2 (ΔG = -7.17 Kcal/mol), kaempferitrin with HSV-II (ΔG = -7.64 Kcal/mol), 3 β -friedelinol with AdVs (ΔG = -7.63 kcal/mol), and pectolinarigenin with NDV (ΔG = -7.55 Kcal/mol.). The top 4 candidates showed promising druglikeness and drug-score with no potential toxicity except for pectolinarigenin and kaempferitrin. They showed low to high probability for intestinal absorption, no BBB permeation with zero PAINS alerts and ease for synthetic accessibility. This may establish the promising potential of such compounds for further development into clinical candidates. [Display omitted] • Chromatographic isolation and spectroscopic identification of the bioactive compounds from the aerial parts of Eriocephalus africanus var. africanus cultivated in Egypt. • In silico and in vitro antiviral activity for Eriocephalus africanus total methanol extract as well as other solvent fractions together with the previously isolated essential oil against influenza a virus subtype H9N2, Herpes simplex II, Adeno virus and Newcastle virus. • Estimation of ADME/Tox for isolated compounds. [ABSTRACT FROM AUTHOR]

Piezoelectric nanostructures have attracted significant attention owing to their capacity for converting mechanical energy into electrical energy, enabling applications in biomedical fields, actuators, and energy harvesting devices. Boron nitride nanotubes (BNNTs) exhibit unique properties that make them attractive candidates for piezoelectric applications. However, the influence of BNNT chiralities on their piezoelectric behavior has not been thoroughly explored. In this study, we investigated the piezoelectric effect of zigzag and armchair chiralities of BNNT structures, aiming to elucidate the relationship between chirality and piezoelectric response by discovering a novel protocol for simulating the electrical behavior of BNNTs at the nanoscale level. We employed a computational method to examine the piezoelectric potential of BNNT structures. First, we established an equivalent-sized three-dimensional (3D) model of zigzag and armchair BNNT structures using nanotube modeler software. The obtained models were then subjected to mesh analysis to generate finite element method simulations. The simulations were finally performed to analyze the electrical response of the BNNT structures under external mechanical forces. We observed that the electrical responses of zigzag BNNT were 1.6 times greater than armchair one. In conclusion, our study sheds light on the piezoelectric potential of zigzag and armchair chiralities of BNNT structures. Furthermore, our findings contribute to the understanding of the electrical properties of BNNTs and their potential for various medical and industrial applications. The knowledge gained from this study provides a foundation for further research and development in the field of piezoelectric nanostructures, paving the way for innovative advancements in nanotechnology. [ABSTRACT FROM AUTHOR]

A quinoxaline‐based ligand, 6,7‐dimethyl‐2,3‐di(2‐pyridyl)quinoxaline (Me2dpq), and its unique binuclear Co(II)‐Me2dpq complex were prepared and analyzed using single crystal X‐ray diffraction and several spectroscopy techniques. Hirshfeld surface analyses were also used to clarify the Me2dpq ligand and the Co(II)‐Me2dpq crystal packing. The Co(II)‐Me2dpq complex crystallized in triclinic P‐1 space group and exhibited a distorted trigonal bipyramidal geometry around the cobalt(II) ion. Each Co(II) ion coordinated to a Me2dpq ligand through two N donor centers from pyridyl and quinoxaline rings along with a terminal Cl and two bridged Cl atoms. The binding properties of the ligand and its complex with CT‐DNA were studied by several techniques, namely UV–Vis spectroscopy, fluorescence quenching, viscosity measurements, thermal denaturation, and gel electrophoresis. The CT‐DNA binding interaction tests demonstrated that both the Co(II)‐Me2dpq complex and its parent ligand bind to DNA in an intercalative way. The antioxidant studies of the novel Co(II)‐Me2dpq complex illustrated significant activity against DPPH• and OH•· radicals. The in vitro cytotoxic effect of Me2dpq ligand and its Co(II)‐complex on MCF‐7 and Hep‐G2 tumor cell lines was evaluated by using the MTT assay. The studies showed that the Co(II)‐Me2dpq complex had superior activity toward the tested cell lines. Molecular docking studies of synthesized compounds were employed to figure out the way they would associate with a biologically macromolecular target B‐DNA (PDB: 1BNA). Thus, this study is anticipated to provide novel opportunities for the successful utilization of the synthesized compounds in many medical domains. [ABSTRACT FROM AUTHOR]

The circular bioeconomy is currently a promising model for repurposing natural sources; these sources include plants due to their abundance of bioactive compounds. This study evaluated the antimicrobial properties of a Chaetomorpha linum extract. Chaetomorpha linum is an invasive macroalga from the Orbetello Lagoon (Tuscany, Italy), which grows in nutrient-rich environments and has been forming extended mats since 2005. The biomass is mechanically harvested and treated as waste, consuming considerable manpower and financial resources. As a potential way to increase the value of such waste, this study found that C. linum extract (CLE) is a source of antimicrobial compounds. The phytochemical characterization of the extract revealed the predominant presence of palmitic acid, a fatty acid with known antimicrobial activity. Based on such findings, four bacterial species of high clinical relevance (Enterococcus faecalis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli) were tested, revealing a notable antibacterial activity of the extract on Enterococcus faecalis (MIC, 32 μg/mL). Computational analyses identified a potential Enterococcus faecalis molecular target for palmitic acid, offering molecular insights on the interaction. This study presents a comprehensive in vitro and in silico approach for drug and target discovery studies by repurposing C. linum as a source of antimicrobial bioactive compounds. [ABSTRACT FROM AUTHOR]

Quantum and molecular mechanics (QM/MM) potentials are used to calculate molecular dynamics trajectories for the EYFP protein of the green fluorescent protein family. Machine learning models are constructed to establish the relationship between the geometric parameters of the chromophore in the frame of its trajectory and the properties of its electronic excitation. It is shown that it is not enough to use only bridging bonds between the phenyl and imidazolidone fragments of the chromophore as a geometric parameter, and at least two more neighboring bonds must be added to the model. The proposed models allow determination of the dipole moment variation upon excitation with an average error of 0.11 a.u. [ABSTRACT FROM AUTHOR]

In response to the global issue of water scarcity exacerbated by climate change, this study investigates the physicochemical properties of water resources within the Algerian hydrographic basin. Despite efforts to develop groundwater sources for drinking water, contamination risks from nearby agricultural and industrial activities remain significant. To address this, the study focuses on characterizing these water sources, particularly noting elevated levels of nitrates and manganese ions beyond acceptable limits. Despite the negative correlation between manganese and nitrate ions, we have modeled complexes containing both and compared them with others to assess their chemical and biological activities. This integrated approach allows us to understand complex ion interactions and propose innovative solutions for managing water resources more effectively. Through our work, we aim to contribute to the development of sustainable water management strategies, bridging the gap between theoretical modeling based on Density Functional Theory and practical applications. By combining empirical data with theoretical insights, we aspire to offer comprehensive solutions for mitigating water contamination and ensuring access to clean drinking water for communities in the Algerian hydrographic basin. [ABSTRACT FROM AUTHOR]

AbstractA novel heterocyclic compound named (Z)-5-(4-nitrobenzylidene)-3-N(3-chlorophenyl)-2-thioxothiazolidin-4-one (NCTh) was synthesized and analyzed using various techniques, including single crystal X-ray diffraction, FT-IR, UV-Vis, NMR spectroscopy, and mass spectral data methods. NCTh was observed to crystallize in the triclinic crystal system P-1 space group. To validate the experimental findings, density functional theory (DFT) calculations were performed using the B3LYP functional with the 6-311 G(d,p) basis set. The results indicated good agreement in geometrical parameters between the experimental and theoretical outcomes. The study also calculated HOMO-LUMO energies, molecular electrostatic potential (MEP), and global chemical reactivity descriptors to evaluate the compound’s reactivity. Additionally, the study conducted reduced density gradient and Hirshfeld surface analyses to reveal attractive, repulsive, and van der Waals strong and weak interactions. The calculation of thermodynamic parameters was also included. The study focused on investigating the nonlinear optical (NLO) properties of NCTh, which were characterized through key parameters such as the electric dipole moment (µ), polarizability (α), first-order hyperpolarizability (β), and second-order hyperpolarizability (γ). These properties provide insights into the material’s potential applications in optical and photonic technologies. Additionally, a molecular docking study was performed to further explore the structure-activity relationship, particularly in a biological context. The docking results revealed a strong ligand-protein interaction, with a binding energy of −10.3 kcal/mol, indicating significant affinity. Moreover, the inhibition constant (Ki) was calculated to be 0.0281 μM, suggesting a highly potent interaction, which could be relevant for drug design or biochemical applications. [ABSTRACT FROM AUTHOR]

Vitex trifolia L. is widely used as a traditional medicine owing to its secondary metabolites. This study aimed to determine the phytochemical profiling of the ethanolic extract of V. trifolia leaves (EEVL). Additionally, biological activities were investigated, supported by molecular docking studies. The total flavonoid and phenolic contents of the EEVL were 35.25 ± 0.13 mg QE/g extract and 39.55 ± 1.43 mg GAE/g extract, respectively. The EEVL exhibits anti‐inflammatory activity with a half‐maximal inhibitory concentration (IC50) value of 153.59 µg/mL. The antioxidant activity of the EEVL exhibited an IC50 value of 20.41 ± 0.08 µg/mL with the 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) radical scavenging method, a half‐maximal effective concentration value of 80.85 ± 0.39 µg/mL with the cupric‐reducing antioxidant capacity (CUPRAC) method, and a capacity of 180.58 mg QE/g extract with the ferric‐reducing antioxidant power (FRAP) method. At 16% concentration, the EEVL exhibited an antibacterial activity against some pathogenic bacteria. Molecular docking studies reported that casticin interacts with sodium diclofenac similarly toward 1PXX. However, artemitin exhibited better affinity toward 1HD2 than ascorbic acid. Thus, the EEVL has significant potential as a natural source for treating various diseases related to inflammation, oxidation, and infection. Moreover, screening of its active compounds is necessary for further exploration. [ABSTRACT FROM AUTHOR]

Two series of novel fluorinated Tubastatin A derivatives based on cyclopentane or cyclohexane substitution were first time synthesized by 5 steps at high yield. The influence of the cycloalkanes substituted N‐methylpiperidine and/or fluorinated group on the cap group of Tubastatin A for the in vitro anti‐tumor activity of seven different tumor cell lines (human hepatoma cells Bel7402 and HepG2, human nasopharyngeal carcinoma cells CNE2 and SUNE1, human breast cancer cells MDA‐MB‐231 and MCF‐7, and human pancreatic cancer cells SW1990) was investigated. Compared with Tubastatin A, these novel derivatives with fluorinated groups on the benzene ring of the cap group enhance activity, and modification of the N‐methylpiperidine to cycloalkanes of the cap group improves solubility. The most promising compound trifluoromethyl and cyclohexane substituted derivative, N‐hydroxy‐4‐((6‐(trifluoromethyl)‐1,2,3,4‐tetrahydro‐9H‐carbazol‐9‐yl)methyl) benza‐mide (6 h), had a wide range of anti‐tumor cell range, the IC50 value for human pancreatic cancer cell line SW1990 was 1.17 μM. Hence, fluorinated groups and cyclohexane result in a wide range of anti‐tumor cell range and good anti‐cancer activity. [ABSTRACT FROM AUTHOR]

AbstractThe novel, highly infectious SARS-CoV-2 virus caused millions of deaths and infections globally. At the same time, the emerged drug repurposing strategy may ultimately not yield a significant clinical benefit. Herein, we designed and synthesized a novel class of pyrazolo[3,4-d]pyrimidines (HCQ-PPs) whose structures were verified by spectral and analytical means as novel anti-SARS-CoV-2 agents. CPE-inhibition assay emerged the 6-((2-hydroxyethyl)aminomethyl) HCQ-PP-1 as the most active analog, exposing about 50% and 29% inhibition compared to remdesivir (88.75% and 70.42% inhibition) at 100 and 10 µM, respectively, indicating the pivotal role of N1, C3 and C4 functionalization. The docking results displayed a unique binding mode of HCQ-PP-1 in the SARS-CoV-2 Mpro binding pocket that could underlie its potential activity with FRED energies of −7.71 comparable to that of remdesivir (-6.71). Its drug-likeness properties met the criteria of Pfizer with an excellent ADMET profile. Therefore, this study presents a novel anti-SARS-CoV-2 lead compound that is worthy of further investigation and activity improvement. [ABSTRACT FROM AUTHOR]

Cardiovascular disease (CVD) is a leading cause of global mortality, with dyslipidemia being a significant modifiable risk factor. Dyslipidemia refers to all abnormalities in blood lipid levels. It plays a fundamental role in the development and progression of atherosclerosis. The reduction of low‐density lipoprotein (LDL) cholesterol has been shown to decrease cardiovascular risk. Cholesteryl ester transfer protein (CETP) plays a role in LDL metabolism, and its inhibition results in lower LDL levels. This study synthesizes and evaluates novel benzene sulfonamide derivatives as CETP inhibitors. Twenty compounds were synthesized and tested for their inhibitory activity using an in vitro bioassay. The results revealed that para‐methylated derivatives exhibited higher inhibitory activity compared to meta‐methylated derivatives, where compound 6n has an IC50 of 24.4 µM. Furthermore, electron withdrawing groups such as chlorine and nitro substitutions on the sulfanamido‐phenyl rings demonstrated superior inhibitory effects compared to electron donating groups. Positional isomerism of the substitutions also influenced inhibitory activity, with para substitutions being more effective. Nitro‐substituted compounds showed greater inhibition than chlorine‐substituted compounds, where compound 6t has an IC50 of 18.3 µM. Overall, this study provides valuable insights into the SAR of CETP inhibitors and identifies promising compounds for further investigation as potential therapeutics for CVD. [ABSTRACT FROM AUTHOR]

Advancements in computational techniques have revolutionized the field of drug design, offering a powerful arsenal of tools collectively known as in silico methods. This review provides an overview of the diverse computational techniques employed in the in silico assisted drug design process. From molecular docking and molecular dynamics simulations to Quantitative Structure-Activity Relationship (QSAR) models and artificial intelligence-based approaches, these methods play a pivotal role in expediting drug discovery and optimization. The utilization of molecular docking facilitates the prediction of ligand-receptor interactions, aiding in the identification of potential drug candidates. Molecular dynamics simulations contribute by unraveling the dynamic behavior of biomolecular complexes, offering insights into their stability and flexibility. QSAR models, relying on mathematical correlations between molecular descriptors and biological activities, enable the prediction of compound behaviors, guiding the optimization of lead compounds. The integration of machine learning and artificial intelligence further enhances drug design workflows. Deep learning algorithms, such as neural networks, have demonstrated remarkable capabilities in predicting complex biological activities and uncovering hidden patterns within large datasets. High-throughput screening, coupled with in silico methodologies, allows for the rapid exploration of vast chemical spaces, accelerating the identification of promising drug candidates. Despite these advancements, challenges persist, including the accurate representation of biological systems, the validation of computational predictions and the ethical implications of relying solely on in silico methods. This review critically evaluates the current state of computational techniques in silico assisted drug design, highlighting their strengths, limitations and potential future directions. The integration of computational techniques in drug design has significantly reshaped the landscape of pharmaceutical research. As these methods continue to evolve, bridging the gap between computational predictions and experimental validations, the synergy between in silico and in vitro approaches holds immense promise for the rapid and effective development of novel therapeutic agents. [ABSTRACT FROM AUTHOR]

MDA-9/Syntenin, a key scaffolding protein and a molecular hub involved in a diverse range of cell signaling responses, has proved to be a challenging target for the design and discovery of small molecule probes. In this paper, we report on the design and synthesis of small molecule ligands of this key protein. Genetic algorithm-based computational design and the five–eight step synthesis of three molecules led to ligands with affinities in the range of 1–3 µM, a 20–60-fold improvement over literature reports. The design and synthesis strategies, coupled with the structure-dependent gain or loss in affinity, afford the deduction of principles that should guide the design of advanced probes of MDA-9/Syntenin. [ABSTRACT FROM AUTHOR]

Background/Objectives: Alterations in the actin cytoskeleton correlates to tumor progression and affect critical cellular processes such as adhesion, migration and invasion. Rho-associated coiled-coil-containing protein kinases (ROCK1 and ROCK2), important regulators of the actin cytoskeleton, are frequently overexpressed in various malignancies. The aim of this study was therefore to identify the key structural features of ROCK1/ROCK2 inhibitors using computer-aided drug design (CADD) approaches. In addition, new developed ROCK inhibitors provided a significant framework for the development of multitarget therapeutics—ROCK/HDAC (histone deacetylases) multitarget inhibitors. Methods: 3D-QSAR (Quantitative structure-activity relationship study) and molecular docking study were employed in order to identify key structural features that positively correlate with ROCK inhibition. MDA-MB-231, HCC1937, Panc-1 and Mia PaCa-2 cells were used for evaluation of anticancer properties of synthesized compounds. Results: C-19 showed potent anti-cancer properties, especially enhancement of apoptosis and cell cycle modulation in pancreatic cancer cell lines. In addition, C-19 and C-22 showed potent anti-migratory and anti-invasive effects comparable to the well-known ROCK inhibitor fasudil. Conclusions: In light of the results of this study, we propose a novel multi-target approach focusing on developing dual HDAC/ROCK inhibitors based on the structure of both C-19 and C-22, exploiting the synergistic potential of these two signaling pathways to improve therapeutic efficacy in metastatic tumors. Our results emphasize the potential of multi-target ROCK inhibitors as a basis for future cancer therapies. [ABSTRACT FROM AUTHOR]

We systematically develop beneficial and practical velocity measures for accurate and efficient statistical simulations of the Langevin equation with direct applications to computational statistical mechanics and molecular dynamics sampling. Recognizing that the existing velocity measures for the most statistically accurate discrete-time Verlet-type algorithms are inconsistent with the simulated configurational coordinate, we seek to create and analyze new velocity companions that both improve existing methods as well as offer practical options for implementation in existing computer codes. The work is based on the set of GJ methods that, of all methods, for any time step within the stability criteria correctly reproduces the most basic statistical features of a Langevin system; namely correct Boltzmann distribution for harmonic potentials and correct transport in the form of drift and diffusion for linear potentials. Several new and improved velocities exhibiting correct drift are identified, and we expand on an earlier conclusion that, generally, only half-step velocities can exhibit correct, time-step independent Maxwell–Boltzmann distributions. Specific practical and efficient algorithms are given in familiar forms, and these are used to numerically validate the analytically derived expectations. One especially simple algorithm is highlighted, and the ability of one of the new on-site velocities to produce statistically correct averages for a particular damping value is specified. [ABSTRACT FROM AUTHOR]

This work combines experimental and computational modeling studies for the preparation of a composite of metformin and an organoclay, examining the advantages of a Tunisian clay used for drug delivery applications. The clay mineral studied is a montmorillonite-like smectite (Sm-Na), and the organoclay derivative (HDTMA-Sm) was used as a drug carrier for metformin hydrochloride (MET). In order to assess the MET loading into the clays, these materials were characterized by means of cation exchange capacity assessment, specific surface area measurement, and with the techniques of X-ray diffraction (XRD), differential scanning calorimetry, X-ray fluorescence spectroscopy, and Fourier-transformed infrared spectroscopy. Computational molecular modeling studies showed the surface adsorption process, identifying the clay–drug interactions through hydrogen bonds, and assessing electrostatic interactions for the hybrid MET/Sm-Na and hydrophobic interactions and cation exchange for the hybrid MET/HDTMA-Sm. The results show that the clays (Sm-Na and HDTMA-Sm) are capable of adsorbing MET, reaching a maximum load of 12.42 and 21.97 %, respectively. The adsorption isotherms were fitted by the Freundlich model, indicating heterogeneous adsorption of the studied adsorbate–adsorbent system, and they followed pseudo-second-order kinetics. The calculations of ΔGº indicate the spontaneous and reversible nature of the adsorption. The calculation of ΔH° indicates physical adsorption for the purified clay (Sm-Na) and chemical adsorption for the modified clay (HDTMA-Sm). The release of intercalated MET was studied in media simulating gastric and intestinal fluids, revealing that the purified clay (Sm-Na) and the modified organoclay (HDTMA-Sm) can be used as carriers in controlled drug delivery in future clinical applications. The molecular modeling studies confirmed the experimental phenomena, showing that the main adsorption mechanism is the cation exchange process between proton and MET cations into the interlayer space. [ABSTRACT FROM AUTHOR]

The synthetic peptide TAT-I24 (GRKKRRQRRRPPQCLAFYACFC) exerts antiviral activity against several double-stranded (ds) DNA viruses, including herpes simplex viruses, cytomegalovirus, some adenoviruses, vaccinia virus and SV40 polyomavirus. In the present study, in vitro profiling of this peptide was performed with the aim of characterizing and improving its properties for further development. As TAT-I24 contains three free cysteine residues, a potential disadvantageous feature, peptide variants with replacements or deletions of specific residues were generated and tested in various cell systems and by biochemical analyses. Some cysteine replacements had no impact on the antiviral activity, such as the deletion of cysteine 14, which also showed improved biochemical properties, while the cyclization of cysteines 14 and 20 had the most detrimental effect on antiviral activity. At concentrations below 20 µM, TAT-I24 and selected variants did not induce hemolysis in red blood cells (RBCs) nor modulated lipopolysaccharide (LPS)-induced release of cytokines, such as interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), in human peripheral blood mononuclear cells (PBMCs). These data indicate that TAT-I24 or its peptide variants are not expected to cause unwanted effects on blood cells. [ABSTRACT FROM AUTHOR]

Human serum albumin (HSA) is an endogenous inhibitor of angiotensin I-converting enzyme (ACE) and, thus, plays a key role in the renin–angiotensin–aldosterone system (RAAS). However, little is known about the mechanism of interaction between these proteins, and the structure of the HSA–ACE complex has not yet been obtained experimentally. The purpose of the presented work is to apply computer modeling methods to study the interaction of HSA with ACE in order to obtain preliminary details about the mechanism of their interaction. Ten possible HSA–ACE complexes were obtained by the procedure of macromolecular docking. Based on the number of steric and polar contacts between the proteins, three leading complexes were selected, the stabilities of which were then tested by molecular dynamics (MD) simulation. Based on the results of MD simulation, the two most probable conformations of the HSA–ACE complex were selected. The analysis of these conformations revealed that the processes of oxidation of the thiol group of Cys34 of HSA and the binding of albumin to ACE can reciprocally affect each other. Known point mutations in the albumin molecules Glu82Lys, Arg114Gly, Glu505Lys, Glu565Lys and Lys573Glu can also affect the interaction with ACE. According to the result of MD simulation, the known ACE mutations, albeit associated with various diseases, do not affect the HSA–ACE interaction. A comparative analysis was performed of the resulting HSA–ACE complexes with those obtained by AlphaFold 3 as well as with the crystal structure of the HSA and the neonatal Fc receptor (FcRn) complex. It was found that domains DI and DIII of albumin are involved in binding both ACE and FcRn. The obtained results of molecular modeling outline the direction for further study of the mechanisms of HSA–ACE interaction in vitro. Information about these mechanisms will help in the design and improvement of pharmacotherapy aimed at modulation of the physiological activity of ACE. [ABSTRACT FROM AUTHOR]

Water contamination is one of the most critical environmental issues, necessitating the development of effective wastewater treatment methods. The utilization of TiO2 photocatalysts for pollutant removal in wastewater has gained significant attention. This study aims to explore the photocatalytic properties of TiO2 modified through the introduction of different metal dopants, thus altering its electronic structure. Using the density functional theory (DFT) method, we examined the photocatalytic properties of TiO2 clusters doped with metals carrying charges of +3, +4, and +5. Our findings indicate that the incorporation of these metals led to reduced energy and increased stability for the majority of TiO2 clusters. The calculated UV-vis absorption results revealed that the wavelengths of Model B were extended further in the metal cation-doped TiO2 clusters compared to Model A. Our DFT calculations demonstrated that the photocatalytic activity of the TiO2 structure was enhanced upon doping with metals of +3, +4, and +5 valence. [ABSTRACT FROM AUTHOR]

Glycogen synthase kinase-3 (GSK-3) plays important roles in the pathogenesis of cardiovascular, metabolic, neurological disorders and cancer. Isoform-specific loss of either GSK-3α or GSK-3β often provides cytoprotective effects under such clinical conditions. However, available synthetic small molecule inhibitors are relatively non-specific, and their chronic use may lead to adverse effects. Therefore, screening for natural compound inhibitors to identify the isoform-specific inhibitors may provide improved clinical utility. Here, we screened 70 natural compounds to identify novel natural GSK-3 inhibitors employing comprehensive in silico and biochemical approaches. Molecular docking and pharmacokinetics analysis identified two natural compounds Psoralidin and Rosmarinic acid as potential GSK-3 inhibitors. Specifically, Psoralidin and Rosmarinic acid exhibited the highest binding affinities for GSK-3α and GSK-3β, respectively. Consistent with in silico findings, the kinase assay-driven IC50 revealed superior inhibitory effects of Psoralidin against GSK-3α (IC50 = 2.26 μM) vs. GSK-3β (IC50 = 4.23 μM) while Rosmarinic acid was found to be more potent against GSK-3β (IC50 = 2.24 μM) than GSK-3α (IC50 = 5.14 μM). Taken together, these studies show that the identified natural compounds may serve as GSK-3 inhibitors with Psoralidin serving as a better inhibitor for GSK-3α and Rosmarinic for GSK-3β isoform, respectively. Further characterization employing in vitro and preclinical models will be required to test the utility of these compounds as GSK-3 inhibitors for cardiometabolic and neurological disorders and cancers. Schematic diagram shows the molecular docking to simulate how natural compounds might bind to the crystal structure of GSK-3 enzymes. This was followed by additional in silico analyses, including assessments of druglikeness, potential toxicity, bioactivity scores, and pharmacokinetic properties. Through this multi-step screening process, Psoralidin and Rosmarinic acid emerged as potential inhibitors of GSK-3α and GSK-3β isoforms, respectively. Finally, based on their predicted high binding energy with both GSK-3α and GSK-3β, Psoralidin and Rosmarinic acid were selected for further testing using a kinase assay. This assay confirmed their inhibitory potential, demonstrating higher potency against GSK-3α and GSK-3β, respectively. [Display omitted] • Current GSK-3 inhibitors lack specificity and cause side effects. • This study identifies potential GSK-3 isoform-specific natural compounds. • Psoralidin is likely a better inhibitor for GSK-3α while Rosmarinic for GSK-3β. • These natural compounds may be promising future treatments. [ABSTRACT FROM AUTHOR]

Medicinal plants are enriched sources of drugs due to their chemically and functionally diverse secondary metabolites. Conventional methods of screening these bioactive metabolites require a long time, incur high costs, utilize substantial amounts of solvents, involve repeated exposure to heat (harmful for the thermo-labile compounds), and often lead to undesirable products. However, computer-aided drug discovery (CADD) has emerged as a versatile and cost-effective tool for expediting the screening of plant-based bioactive compounds. In this review, we focus on structure-based and ligand-based drug discovery approaches and their roles in rationalizing drug development. We discuss the technicalities, limitations, and successful applications of key components of structure-based (molecular docking and molecular dynamics) and ligand-based (quantitative structure–activity relationship and pharmacophore modeling) approaches in medicinal plant-derived drug discovery. Furthermore, our study highlights the significance of the pharmacokinetic and ADMET profiling of plant-based therapeutics in drug development. Besides the applications of computational drug discovery, we also briefly overview the corroborative in-silico and experimental approaches to identify potential therapeutics from medicinal plants. This study suggests that integrating advanced Machine Learning and Artificial Intelligence approaches could alleviate the challenges faced by traditional computational techniques, thus enriching the screening process. [Display omitted] • The screening of therapeutic phytochemicals remains challenging. • Computational approaches can expedite drug discovery from medicinal plants. • Structure- and ligand-based modeling are vital pillars of in-silico drug discovery. • Early-stage ADME-Tox analysis of phytocompounds aids the discovery of potent drug. • Combined in-silico and in-vitro studies can validate the drug discovery results. [ABSTRACT FROM AUTHOR]

• NMR is the gold standard for determining the solution structures of G-quadruplexes. • Higher-order G-quadruplexes (xG4s) are often not amenable to characterization by NMR. • We show how NMR can be utilized in an integrative structural biology (ISB) approach to study xG4s. • We illustrate the ISB method and provide resources and best practices for those new to the field. Guanine-rich nucleic acids can form intramolecularly folded four-stranded structures known as G-quadruplexes (G4s). Traditionally, G4 research has focused on short, highly modified DNA or RNA sequences that form well-defined homogeneous compact structures. However, the existence of longer sequences with multiple G4 repeats, from proto-oncogene promoters to telomeres, suggests the potential for more complex higher-order structures with multiple G4 units that might offer selective drug-targeting sites for therapeutic development. These larger structures present significant challenges for structural characterization by traditional high-resolution methods like multi-dimensional NMR and X-ray crystallography due to their molecular complexity. To address this current challenge, we have developed an integrated structural biology (ISB) platform, combining experimental and computational methods to determine self-consistent molecular models of higher-order G4s (xG4s). Here we outline our ISB method using two recent examples from our lab, an extended c-Myc promoter and long human telomere G4 repeats, that highlights the utility and generality of our approach to characterizing biologically relevant xG4s. [ABSTRACT FROM AUTHOR]

Millions of years of evolution have optimized many biosynthetic pathways by use of multi‐step catalysis. In addition, multi‐step metabolic pathways are commonly found in and on membrane‐bound organelles in eukaryotic biochemistry. The fundamental mechanisms that facilitate these reaction processes provide strategies to bioengineer metabolic pathways in synthetic chemistry. Using Brownian dynamics simulations, here we modeled intermediate substrate transportation of colocalized yeast–ester biosynthesis enzymes on the membrane. The substrate acetate ion traveled from the pocket of aldehyde dehydrogenase to its target enzyme acetyl‐CoA synthetase, then the substrate acetyl CoA diffused from Acs1 to the active site of the next enzyme, alcohol‐O‐acetyltransferase. Arranging two enzymes with the smallest inter‐enzyme distance of 60 Å had the fastest average substrate association time as compared with anchoring enzymes with larger inter‐enzyme distances. When the off‐target side reactions were turned on, most substrates were lost, which suggests that native localization is necessary for efficient final product synthesis. We also evaluated the effects of intermolecular interactions, local substrate concentrations, and membrane environment to bring mechanistic insights into the colocalization pathways. The computation work demonstrates that creating spatially organized multi‐enzymes on membranes can be an effective strategy to increase final product synthesis in bioengineering systems. [ABSTRACT FROM AUTHOR]

The increasing global consumption of poultry meat has led to the generation of a vast quantity of feather keratin waste daily, posing significant environmental challenges due to improper disposal methods. A growing focus is on utilizing keratinous polymeric waste, amounting to millions of tons annually. Keratins are biochemically rigid, fibrous, recalcitrant, physiologically insoluble, and resistant to most common proteolytic enzymes. Microbial biodegradation of feather keratin provides a viable solution for augmenting feather waste's nutritional value while mitigating environmental contamination. This approach offers an alternative to traditional physical and chemical treatments. This review focuses on the recent findings and work trends in the field of keratin degradation by microorganisms (bacteria, actinomycetes, and fungi) via keratinolytic and proteolytic enzymes, as well as the limitations and challenges encountered due to the low thermal stability of keratinase, and degradation in the complex environmental conditions. Therefore, recent biotechnological interventions such as designing novel keratinase with high keratinolytic activity, thermostability, and binding affinity have been elaborated here. Enhancing protein structural rigidity through critical engineering approaches, such as rational design, has shown promise in improving the thermal stability of proteins. Concurrently, metagenomic annotation offers insights into the genetic foundations of keratin breakdown, primarily predicting metabolic potential and identifying probable keratinases. This may extend the understanding of microbial keratinolytic mechanisms in a complex community, recognizing the significance of synergistic interactions, which could be further utilized in optimizing industrial keratin degradation processes. [ABSTRACT FROM AUTHOR]

Gene activity is tightly controlled by reversible chemical modifications called epigenetic marks, which are of various types and modulate gene accessibility without affecting the DNA sequence. Despite an increasing body of evidence demonstrating the role of oxidative-type modifications of histones in gene expression regulation, there remains a complete absence of structural data at the atomistic level to understand the molecular mechanisms behind their regulatory action. Owing to μs time-scale MD simulations and protein communication networks analysis, we describe the impact of histone H3 hyperoxidation (i.e., S-sulfonylation) on the nucleosome core particle dynamics. Our results reveal the atomic-scale details of the intrinsic structural networks within the canonical histone core and their perturbation by hyperoxidation of the histone H3 C110. We show that this modification involves local rearrangements of the communication networks and destabilizes the dyad, and that one modification is enough to induce a maximal structural signature. Our results suggest that cysteine hyperoxidation in the nucleosome core particle might favor its disassembly.

Krabbe disease is a sphingolipidosis characterized by the genetic deficiency of the acid hydrolase β-galactosylceramidase (GALC). Most of the studies concerning the biological role of GALC performed on Krabbe patients and Galc-deficient twitcher mice (an authentic animal model of the disease) indicate that the pathogenesis of this disorder is the consequence of the accumulation of the neurotoxic GALC substrate β-galactosylsphingosine (psychosine), ignoring the possibility that this enzyme may exert a wider biological impact. Indeed, limited information is available about the effect of GALC downregulation on the cell lipidome in adult and developing organisms. The teleost zebrafish (Danio rerio) has emerged as a useful platform to model human genetic diseases, including sphingolipidoses, and two GALC co-orthologs have been identified in zebrafish (galca and galcb). Here, we investigated the effect of the competitive and irreversible GALC inhibitor β-galactose-cyclophellitol (GCP) on the lipid profile of zebrafish embryos. Molecular modelling indicates that GCP can be sequestered in the catalytic site of the enzyme and covalently binds human GALC, and the zebrafish Galca and Galcb proteins in a similar manner. Accordingly, GCP inhibits the β-galactosylceramide hydrolase activity of zebrafish in vitro and in vivo, leading to significant alterations of the lipidome of zebrafish embryos. These results indicate that the lack of GALC activity deeply affects the lipidome during the early stages of embryonic development, and thereby provide insights into the pathogenesis of Krabbe disease.

Abstract Sulfonamide derivatives as semiconductor materials for organic optoelectronic devices, including photovoltaic (PV), have received considerable interest. In the present work, the synthesis of novel pyrogallol-sulfonamide derivatives based on a molecular hybridization approach yielded N-((4-((2,3,4-trihydroxyphenyl)diazenyl)phenyl)sulfonyl)acetamide (N-DPSA). The techniques of spectroscopy, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (1H NMR), and mass spectrum were utilized to identify the structural composition of the synthesized N-DPSA. The new N-DPSA was investigated by Hall-effect measurement to prove the positive charge carrier (hole mobility) with mobility and conductivity of 2.39 × 103 cm2/Vs and 1.76 × 10–1 1/Ω cm, respectively. Consequently, N-DPSA could be proposed as a strong candidate as a p-type semiconductor (hole transport layer (HTL)). The optical energy gap was computed at 2.03 eV, indicating the direct optical transition nature of N-DPSA. The elaborated molecular semiconductor's thermal features, molecular modelling, and electronic energy levels were also investigated. The new N-DPSA at various concentrations provided easy synthesis, cheap cost, high performance, and a straightforward design approach for a possible HTL in effective perovskite solar cells (PSCs). A PCE of 7.3% is shown for the N-DPSA-based PSC at its optimal concentration.

With the growing demand for hydrocarbon energy resources, there is a need to involve oil fields at deeper horizons in processing and increase the profitability of their development. Reduction of expenses on prospecting works is possible at revealing and substantiation of physicochemical markers of the naphthogenesis processes. One of the key markers is the transition metals content, which are both a measure of oil age and markers of potential associated processes in the migration and formation of hydrocarbons in the Earth's strata. The elemental composition of samples of oil and reservoir rocks of the Timan-Pechora field was studied. Based on the results of thermodynamic modeling, plausible processes of contact rock minerals transformation were proposed. Based on the results of molecular modeling the probable structure of vanadium and nickel host molecules in the heavy fraction of oils is proposed. The ratios of transition metal and sulfur contents were experimentally established, and assumptions about possible mechanisms of formation of deep hydrocarbon reservoirs were made. Analysis of the obtained ratios of transition metal contents in reservoir rocks and oil samples allowed to suggest possible processes of mantle fluids contact with the host rock and subsequent accumulation of hydrocarbons on sorption active rocks. According to the combined results of experimental and theoretical studies it was found that polymers of heavy fraction more selectively capture vanadium, which indicates the predominance of vanadium content in oil-bearing rocks in relation to the content of nickel. In this case, oil acts as a transport of transition metals, leaching them from the bedrock.

and its derivatives is one of the leaders in the development of highly promising biologically active compounds. The peculiarities of the chemical structure of the derivatives of this heterocycle provide a wide range of possibilities for chemical transformations that allow to obtain really effective drugs. The involvement of several substituents in chemical transformations simultaneously, which have the properties of highly reactive centers, additionally creates favorable conditions for the formation of rational ways to create a biologically active compound. Amino-, mercapto- or hydroxogroups often play the role of such groups in chemistry. The use of these groups as substituents of 1,2,4-triazole synthon provides multifaceted opportunities for directed chemical transformation. The ability of such structural fragments to form chemical interactions and bonds with biological targets has an additional positive effect in the sense of their involvement in chemical transformations on the way to the targeted production of a biologically active substance. Thus, the combination of a heterocyclic structure with a highly reactive chemical center is endowed with theoretically sound and practically significant meaning. The aim of the work is to preliminary determine the potential for creating a biologically active substance with antifungal action based on 1-alkyl derivatives of 3,5-dimethy-l-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide. Materials and methods. The toxicity of the studied compounds has been predicted using the TEST program (Toxicity Estimation Software Tool), which allowed to determine the predictive level of acute toxicity, ecotoxicity and mutagenicity. The physicochemical and pharmacokinetic parameters have been predicted, and the drug-like properties and availability of the investigated substances have been assessed using the online resource SwissADME. The determination of the most favorable spatial configuration of the ligand relative to the active site of the protein and the assessment of the strength of their interaction have been realized using the computational method of molecular docking. The ligands have been prepared using MarvinSketch 6.3.0, HyperChem 8 and AutoDock Tools-1.5.6 software. The preparation of the model enzyme has been based on the use of Discovery Studio 4.0 and AutoDock Tools-1.5.6. The practical implementation of flexible molecular docking has been carried out using the software tools of the AutoDock/Vina platform. Results. In the process of step-by-step prescreening of the formed structures of a number of 1-alkyl derivatives of 3,5-dimethyl-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide, a number of qualitative and quantitative indicators related to the physicochemical characteristics and pharmacokinetic parameters of the studied substances have been obtained. According to the results of the first stage of research, the group of substances under consideration can be predictively considered low-toxic, but with a high risk of mutagenic properties. The next stage of the work, which involved the analysis of physicochemical parameters, pharmacokinetic parameters, general drug-like properties and bioavailability, allowed us to identify 1-alkyl derivatives of 3,5-dimethyl-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide as substances with a rather positive pharmacological profile. The final stage in the form of molecular docking of the structure of the studied compounds to the active site of lanosterol 14α-demethylase allowed us to determine the nature of the chemical interaction and the type of amino acid residues that may be involved in the antifungal properties of the key ligands. The analysis of the docking results allows us to determine the privileged nature of the nonyl substituent at the first Nitrogen atom of the 1,2,4-triazole synthon in the structure of the presented series of compounds for the formation of antifungal properties. Conclusions. The general prospects for the creation of a biologically active substance with antifungal properties using 1-alkyl derivatives of 3,5-dimethyl-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide look quite realistic. Particular attention should be paid to 3,5-dimethyl-1-nonyl-4-((4-nitrobenzylidene)amino)-1,2,4-triazolium bromide as a substance with significant potential for antifungal properties, which allows us to recommend this compound for further more constructive and extended in vitro and in vivo studies.

Abstract Ubiquitin-specific peptidase 7 (USP7) is a deubiquitinating enzyme that mediates the stability and activity of numerous proteins. At basal expression levels, USP7 stabilizes p53 protein, even in the presence of excess MDM2. However, its overexpression leads to the deubiquitination of MDM2 at a rate faster than p53, leading to p53 degradation and pro-tumorigenic roles. Consequently, it is an attractive target for anticancer drug discovery via the modulation of its allosteric site from which the protein is activated. In this study, molecular modeling techniques and cheminformatics approaches were employed to unravel the potential of eighty compounds to serve as its allosteric site modulators. The compounds were initially subjected to virtual screening. Subsequently, the binding free energies of the top four compounds with the highest binding affinities were calculated, and their drug-likeness, and pharmacokinetic and toxicity profiles were evaluated. Ultimately, the complexes of the protein and hit compounds were subjected to a 100 nanoseconds (ns) molecular dynamics simulation. The results of the study revealed eight compounds from the compound library with docking scores ranging from − 7.491 to -11.43 kcal/mol, compared to P217564, which exhibited a docking score of -5.671 kcal/mol. The top four compounds with the highest affinities possessed drug-like properties, and good pharmacokinetic and toxicity profiles, and their predicted inhibitory potentials showed they will be effective at minimal concentration. Also, molecular dynamics simulation confirmed the stability of the protein-ligand complexes. Conclusively, the compounds identified in this study are worthy of further evaluation for the development of allosteric site modulators of USP7.

Iron delivery to the plasma is closely coupled to erythropoiesis, the production of red blood cells, as this process consumes most of the circulating plasma iron. In response to hemorrhage and other erythropoietic stresses, increased erythropoietin stimulates the production of the hormone erythroferrone (ERFE) by erythrocyte precursors (erythroblasts) developing in erythropoietic tissues. ERFE acts on the liver to inhibit bone morphogenetic protein (BMP) signaling and thereby decrease hepcidin production. Decreased circulating hepcidin concentrations then allow the release of iron from stores and increase iron absorption from the diet. Guided by evolutionary analysis and Alphafold2 protein complex modeling, we used targeted ERFE mutations, deletions, and synthetic ERFE segments together with cell-based bioassays and surface plasmon resonance to probe the structural features required for bioactivity and BMP binding. We define the ERFE active domain and multiple structural features that act together to entrap BMP ligands. In particular, the hydrophobic helical segment 81 to 86 and specifically the highly conserved tryptophan W82 in the N-terminal region are essential for ERFE bioactivity and Alphafold2 modeling places W82 between two tryptophans in its ligands BMP2, BMP6, and the BMP2/6 heterodimer, an interaction similar to those that bind BMPs to their cognate receptors. Finally, we identify the cationic region 96-107 and the globular TNFα-like domain 186-354 as structural determinants of ERFE multimerization that increase the avidity of ERFE for BMP ligands. Collectively, our results provide further insight into the ERFE-mediated inhibition of BMP signaling in response to erythropoietic stress.

The COVID-19 pandemic, instigated by the emergence of the novel coronavirus, SARS-CoV-2, created an incomparable global health crisis. Due to its highly virulent nature, identifying potential therapeutic agents against this lethal virus is crucial. PLpro is a key protein involved in viral polyprotein processing and immune system evasion, making it a prime target for the development of antiviral drugs to combat COVID-19. To expedite the search for potential therapeutic candidates, this review delved into computational studies. Recent investigations have harnessed computational methods to identify promising inhibitors targeting PLpro, aiming to suppress the viral activity. Molecular docking techniques were employed by researchers to explore the binding sites for antiviral drugs within the catalytic region of PLpro. The review elucidates the functional and structural properties of SARS-CoV-2 PLpro, underscoring its significance in viral pathogenicity and replication. Through comprehensive all-atom molecular dynamics (MD) simulations, the stability of drug–PLpro complexes was assessed, providing dynamic insights into their interactions. By evaluating binding energy estimates from MD simulations, stable drug–PLpro complexes with potential antiviral properties were identified. This review offers a comprehensive overview of the potential drug/lead candidates discovered thus far against PLpro using diverse in silico methodologies, encompassing drug repurposing, structure-based, and ligand-based virtual screenings. Additionally, the identified drugs are listed based on their chemical structures and meticulously examined according to various structural parameters, such as the estimated binding free energy (ΔG), types of intermolecular interactions, and structural stability of PLpro–ligand complexes, as determined from the outcomes of the MD simulations. Underscoring the pivotal role of targeting SARS-CoV-2 PLpro in the battle against COVID-19, this review establishes a robust foundation for identifying promising antiviral drug candidates by integrating molecular dynamics simulations, structural modeling, and computational insights. The continual imperative for the improvement of existing drugs and exploring novel compounds remains paramount in the global efforts to combat COVID-19. The evolution and management of COVID-19 hinge on the symbiotic relationship between computational insights and experimental validation, underscoring the interdisciplinary synergy crucial to this endeavor.

Abstract In this body of work, a chemical known as 2-cyano-N-(4-morpholino benzyl dine) acetohydrazide (CMBAH) is explored for its ability to suppress the carbidic austempered ductile iron (CADI) corrosion in 1M H2SO4. Density functional theory was used in experiments and theoretical investigations to investigate the inhibiting impact. The corrosion of CADI alloys in 1M H2SO4 produced a corrosion resistance superior to that of CADI heat treatment (H.T.). As-cast carbidic ductile iron (CDI) 4 alloy with 1.5%t Cr-Nb has a corrosion rate (C.R.) of 11.69 mm/year, which drops to 5.31 mm/year at HT-275 °C and 6.13 mm/year at HT-375 °C. When describing the adsorption of inhibitors, the Langmuir adsorption isotherm is the most effective method. The findings of the Gads show that the inhibition was induced mainly by the physisorption on the surface CADI alloys. In addition to this, it was found that the results of the experiments and the hypotheses were largely harmonious with one another. The formation of protective layers on the CADI surfaces is also visible in the images captured by the SEM. In 1M H2SO4, these Schiff base inhibitors effectively prevent corrosion caused by CADI. However, the combination of inhibitors leads to a fine microstructure with ausferrite and narrow ferrite needles, promoting corrosion resistance. The CADI needles rated an upper ausferritic microstructure with wide ferrite needles.

Guanine-rich sequences of nucleic acids, including DNA and RNA, are known to fold into non-canonical structures named G-quadruplexes (G4s). Such arrangements of these macromolecular polymers are mainly located in telomeres and in promoter regions of oncogenes and, for this reason, they represent a potential target for compounds with therapeutic applications. In fact, the ligand-mediated stabilization of G4s inhibits telomerase and the activity of transcriptional machinery and counteracts cancer cell immortalization. Flavonoids, along with other classes of small molecules, have been previously tested for their ability to stabilize G4s, but the mechanism of their interaction has not been fully elucidated. In the current work, we report a multi-technique investigation on the binding of tosylated isoflavones obtained by the B-ring modification of compounds from Maclura pomifera to a telomeric DNA sequence. Our study demonstrates that such derivatization leads to compounds showing lower binding affinity but with an increased selectivity toward G4 with respect to double-stranded DNA. The binding mode to the macromolecular target G4 was studied by combining results from electrospray mass spectrometry binding studies, nuclear magnetic resonance experiments and computational simulations. Overall, our findings show that tosylation influences the selectivity toward the macromolecular target by affecting the interaction mode with the nucleic acid.

Abstract In recent years computational methods for molecular modeling have become a prime focus of computational biology and cheminformatics. Many dedicated systems exist for modeling specific classes of molecules such as proteins or small drug-like ligands. These are often heavily tailored toward the automated generation of molecular structures based on some meta-input by the user and are not intended for expert-driven structure assembly. Dedicated manual or semi-automated assembly software tools exist for a variety of molecule classes but are limited in the scope of structures they can produce. In this work we present BuildAMol, a highly flexible and extendable, general-purpose fragment-based molecular assembly toolkit. Written in Python and featuring a well-documented, user-friendly API, BuildAMol empowers researchers with a framework for detailed manual or semi-automated construction of diverse molecular models. Unlike specialized software, BuildAMol caters to a broad range of applications. We demonstrate its versatility across various use cases, encompassing generating metal complexes or the modeling of dendrimers or integrated into a drug discovery pipeline. By providing a robust foundation for expert-driven model building, BuildAMol holds promise as a valuable tool for the continuous integration and advancement of powerful deep learning techniques. Scientific contribution BuildAMol introduces a cutting-edge framework for molecular modeling that seamlessly blends versatility with user-friendly accessibility. This innovative toolkit integrates modeling, modification, optimization, and visualization functions within a unified API, and facilitates collaboration with other cheminformatics libraries. BuildAMol, with its shallow learning curve, serves as a versatile tool for various molecular applications while also laying the groundwork for the development of specialized software tools, contributing to the progress of molecular research and innovation.

Abstract We present a methodology for the synthesis of inorganic-organic Janus-type molecules based on mono-T8 and difunctionalized double-decker silsesquioxanes (DDSQs) via hydrosilylation reactions, achieving exceptionally high yields and selectivities. The synthesized compounds were extensively characterized using various spectroscopic techniques, and their sizes and spatial arrangements were predicted through molecular modelling and density functional theory (DFT) calculations. Quantum chemical calculations were employed to examine the interactions among four molecules of the synthesized compounds. These computational results allowed us to determine the propensity for molecular aggregation, identify the functional groups involved in these interactions, and understand the changes in interatomic distances during aggregation. Understanding the aggregation behaviour of silsesquioxane molecules is crucial for tailoring their properties for specific applications, such as nanocomposites, surface coatings, drug delivery systems, and catalysts. Through a combination of experimental and computational approaches, this study provides valuable insights into the design and optimization of silsesquioxane-based Janus-type molecules for enhanced performance across various fields.

Abstract An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer–monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory–Huggins parameters and isotropic particle–particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. Scientific Contribution To our knowledge, there is currently no open computational pipeline for differential pair interaction energies at all. This work aims to contribute an (at least academically available, open) approach based on molecular force fields that provides a robust and efficient computational scheme for their automated calculation for small to medium-sized (organic) molecular dimers. The usefulness of the proposed new calculation scheme is demonstrated for the generation of mesoscopic particles with their mutual repulsive interactions.

Natural curcumin is composed of three curcuminoids, namely curcumin (CUR), deme-thoxycurcumin (DMC) and bis-demethoxycurcumin (BDMC). These compounds are utilized in various biophotonics applications, including photodynamic therapy (PDT). This work aimed to evaluate the photodynamic action (alternative to antibiotics) of synthetic curcuminoids against Staphylococcus aureus. Herein, we evaluated an optimal proportion of the three curcuminoids mixed in solution to improve photoinactivation effects. Therefore, a set of computational calculations was carried out to understand the photodynamic action (stability and mechanism) of curcuminoids. Regarding computational analysis, the curcuminoid molecules were optimized using DFT with the hybrid exchange–correlation functional M06-2X, which includes long-range correction, and the 6-311++G(d,p) basis set. DMC and BDMC were more effective as photosensitizers than curcumin at a very low concentration of 0.75 µM, inactivating more than five orders of magnitude of S. aureus. Theoretical UV-vis absorption spectra showed that at maximum absorption wavelengths, electronic transitions of the π→π* type originated from H→L excitations. The BDMC was more stable than the other two curcuminoids after photobleaching, and the fluorescence emission was also higher, which could lead to its usage as a fluorescence dye to track bacteria. In fact, the results of electronic structure calculations proved that the stability order of curcuminoids is CUR < DMC < BDMC. The mixture of synthetic curcuminoids was more effective in the inactivation of S. aureus compared to curcumin by itself; for all proposed mixtures, an equal or superior reduction was achieved.

Abstract Based on a structural family of thirty-two NR2B-selective N-Methyl-D-Aspartate receptor (NMDAR) antagonists, two phenylpiperazine derivatives labeled C37 and C39 were conceived thanks to molecular modeling techniques, as novel NMDAR inhibitors exhibiting the highest analgesic activities (of pIC50 order) against neuropathic pain, with excellent ADME-toxicity profiles, and good levels of molecular stability towards the targeted protein of NMDA receptor. Initially, the quantitative structure-activity relationships (QSARs) models were developed using multiple linear regression (MLR), partial least square regression (PLSR), multiple non-linear regression (MNLR), and artificial neural network (ANN) techniques, revealing that analgesic activity was strongly correlated with dipole moment, octanol/water partition coefficient, Oxygen mass percentage, electronegativity, and energy of the lowest unoccupied molecular orbital, whose the correlation coefficients of generated models were: 0.860, 0.758, 0.885 and 0.977, respectively. The predictive capacity of each model was evaluated by an external validation with correlation coefficients of 0.703, 0.851, 0.778, and 0.981 respectively, followed by a cross-validation technique with the leave-one-out procedure (CVLOO) with Q2 cv of 0.785, more than Y-randomization test, and applicability domain (AD), in addition to Fisher’s and Student’s statistical tests. Thereafter, ten novel molecules were designed based on MLR QSAR model, then predicted with their ADME-Toxicity profiles and subsequently examined for their similarity to the drug candidates. Finally, two of the most active compounds (C37 and C39) were chosen for molecular docking and molecular dynamics (MD) investigations during 100 ns of MD simulation time in complex with the targeted protein of NMDA receptor (5EWJ.pdb).

Abstract The available Epstein Barr virus vaccine has tirelessly harnessed the gp350 glycoprotein as its target epitope, but the result has not been preventive. Right here, we designed a global multi-epitope vaccine for EBV; with special attention to making sure all strains and preventive antigens are covered. Using a robust computational vaccine design approach, our proposed vaccine is armed with 6–16 mers linear B-cell epitopes, 4–9 mer CTL epitopes, and 8–15 mer HTL epitopes which are verified to induce interleukin 4, 10 & IFN-gamma. We employed deep computational mining coupled with expert intelligence in designing the vaccine, using human Beta defensin-3—which has been reported to induce the same TLRs as EBV—as the adjuvant. The tendency of the vaccine to cause autoimmune disorder is quenched by the assurance that the construct contains no EBNA-1 homolog. The protein vaccine construct exhibited excellent physicochemical attributes such as Aliphatic index 59.55 and GRAVY − 0.710; and a ProsaWeb Z score of − 3.04. Further computational analysis revealed the vaccine docked favorably with EBV indicted TLR 1, 2, 4 & 9 with satisfactory interaction patterns. With global coverage of 85.75% and the stable molecular dynamics result obtained for the best two interactions, we are optimistic that our nontoxic, non-allergenic multi-epitope vaccine will help to ameliorate the EBV-associated diseases—which include various malignancies, tumors, and cancers—preventively.

Within the field of Philippine folkloric medicine, the utilization of indigenous plants like Euphorbia hirta (tawa-tawa), Carica papaya (papaya), and Psidium guajava (guava) as potential dengue remedies has gained attention. Yet, limited research exists on their comprehensive effects, particularly their anti-dengue activity. This study screened 2944 phytochemicals from various Philippine plants for anti-dengue activity. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling provided 1265 compounds demonstrating pharmacokinetic profiles suitable for human use. Molecular docking targeting the dengue virus NS2b-NS3 protease’s catalytic triad (Asp 75, Ser 135, and His 51) identified ten ligands with higher docking scores than reference compounds idelalisib and nintedanib. Molecular dynamics simulations confirmed the stability of eight of these ligand–protease complexes. Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) analysis highlighted six ligands, including veramiline (−80.682 kJ/mol), cyclobranol (−70.943 kJ/mol), chlorogenin (−63.279 kJ/mol), 25beta-Hydroxyverazine (−61.951 kJ/mol), etiolin (−59.923 kJ/mol), and ecliptalbine (−56.932 kJ/mol) with favorable binding energies, high oral bioavailability, and drug-like properties. This integration of traditional medical knowledge with advanced computational drug discovery methods paves new pathways for the development of treatments for dengue.