Favorable Conformation Research Articles

Favorable Symmetric Structures of Radiopharmaceutically Important Neutral Cyclen-Based Ligands

Cyclen-based ligands are prominent tools for transferring radioisotopes through the human body. A crucial criterion is the stability of their complexes, which is partly determined by the stabilization of the free ligand in solution. For the assessment of the later property, the favored conformation(s) in the solution must be known. In the present study, the conformational space of four neutral cyclen-based ligands was elucidated by a multi-step procedure: the survey of the conformational space using molecular mechanics (MM) was followed by Density Functional Theory (DFT) calculations on the low-energy conformers and evaluation of the solvent effects. The results revealed several low-energy conformers in aqueous solution. In terms of electronic energies, a significant preference of symmetric structures (C4 or C2—similar to the ligand arrangements in their metal complexes) was obtained. The thermal contributions to the Gibbs free energy (mainly the vibrational ones) tend to decrease this preference by several kJ/mol against non-symmetric structures. Nonetheless, the advantage of compact symmetric structures was confirmed in all the four studied cases.

Mitochondria-targeting artesunate-rhein conjugates: Linker-modulated cell-permeability, heme-affinity and anticancer activity

Heme, abundant in the mitochondria of cancer cells, is a key target for the anticancer activity of artemisinin (ART). Current strategies to enhance the anticancer activity of ART focus solely on its delivery to heme-enriched subcellular localizations while overlooking the decisive effects of ART-heme interactions. Here, we propose an ingenious strategy that synergizes mitochondria-targeted drug delivery and linker-mediated drug conformation modulation, thereby significantly enhancing the anticancer activity of ART. By strategically conjugating artemisinin (ART) with the mitochondria-targeting rhein (R) using different linkers, we aimed to precisely adjust the conformation of the conjugates. Comprehensive computational analysis revealed that the conjugate with the optimal linker length (C4) displayed a favorable conformation that facilitated cell permeability and exhibited the highest binding affinity to heme and Fe ions. Moreover, it exhibited superior tumor suppression capabilities both in vitro and in vivo, overcoming the uncertainty of in vivo application caused by the rapid clearance of the conventional mitochondria-targeted cation TPP+, and even inducing immunogenic cell death associated with immunotherapy. This novel strategy opens up a new avenue for the development of drug conjugate systems.

BIOM-71. EXPANDING THE SPECTRUM OFTERT PROMOTER NON-CANONICAL SEQUENCE VARIANTS IN CNS TUMORS: A CASE SERIES

Abstract Most TERT promoter (TERTp) clinically relevant sequence variants in CNS tumors are the canonical C228T and C250T mutations. Non-canonical TERTp mutations have been reported mainly in non-CNS tumors. We describe 12 CNS tumors with non-canonical TERTp variants interpreted as clinically relevant. Using clinical targeted NGS panels (2020-2024), we detected c.-100_-79dup (n=2), c.-92_-91insGGCGGCCCCGCCCCTTCCTTTC (n=1), c.-118_-117insTCCCCGGCCCAGCCCCTTCCGGG (n=1), c.-123_-76dup (n=1), c.-110_-89dup (n=2), and c.-57A>C (n=5). Most cases had chromosomal microarray (n=11) and/or methylation array data analyzed using the NCI/Bethesda v.2 classifier (n=9). All non-canonical TERTp variants occurred at a variant allele frequency suggestive of somatic clonal origin (mean, 34%; range, 18-46), and in adults (mean age, 60 years; range, 36-88). Except for the c.-57A>C variant, all non-canonical TERTp variants occurred in tumors with histological and/or molecular diagnostic features of glioblastoma, IDH-wildtype (GBM), often epigenetically aligning to this tumor type. All five tested cases matched to superfamily glioblastoma (score ≥ 0.9), with three to class GBM_RTK_I (>0.9 in 2, 0.86 in 1) and two to GBM_RTK_II (>0.9). The size and sequence of such variants suggest that these may be functionally equivalent to canonical mutations or generate favorable TERTp activation motif conformations like previously reported activating duplications. The c.-57A>C variant is a well-established oncogenic mutation observed in other cancer types but has not been reported in CNS tumors. We describe five cases with the c.-57A>C variant: one GBM matching to methylation class GBM_MES_TYP (0.99); two oligodendroglioma, IDH-mutant and 1p/19q-codeleted, one of which had methylation data matching to class O_IDH (0.99); one diffuse glioma, IDH-mutant, which was partially 1p/19q-codeleted and matched to class O_IDH (0.99); and one anaplastic meningioma, aligning to superfamily meningioma (0.99)/MNG_MAL (0.79). Our findings show that non-canonical TERTp variants typically occur in tumor types that often harbor TERTp canonical mutations, expanding the spectrum of TERTp clinically relevant variants that are molecular biomarkers in CNS tumors.

Psychometric characteristics of the decision‐making ability scale among high school students

AbstractThe process of decision‐making is a multifaceted cognitive endeavor encompassing various cognitive, emotional, psychological, and social processes. It empowers individuals to select from a range of alternatives. Its significance spans across age groups, impacting both adults and children, and the relevance of which goes beyond aiding learners in choosing their educational or professional paths; it also pertains to preparing them to navigate the diverse situations they will encounter throughout their lives. To approach this ability, we developed a scale comprising 20 items, assessing five distinct decision‐making factors. This scale was administered to a sample of 303 learners in the first and second years of the baccalaureate course (pre‐final and final years of secondary education), representing both genders, and studying in four high schools. The participants’ ages ranged between 16 and 20 years. The results of this study revealed positive psychometric properties of the scale after its apparent validity was verified. Additionally, principal component analysis, using a latent root criterion greater than one (Eigenvalue > 1), and performing Varimax rotation, resulted in five factors that represent decision‐making styles (dependent, avoidant, confident, rational, intuitive) that explain 53.67% of the total variance. Through the application of confirmatory factor analysis (CFA), the outcomes showcased favorable conformity indicators. The ratio of chi‐square value to degrees of freedom was recorded at less than 5 (x²/df = 1.531). The RMSEA index, at 0.041, remained below the accepted threshold of 0.08. The metrics (CFI, TLI, GFI, IFI) all surpassed 0.90, falling within acceptable ranges. Strong internal consistency between item scores and their respective factors was established by Pearson coefficients. The correlation coefficients between each factor's score and the total scale score were robust, ranging from 0.483 to 0.727. The Cronbach's alpha coefficient for the scale's factors ranged from 0.788 (highest) to 0.723 (lowest), with an overall scale stability coefficient of 0.748. These high coefficients collectively confirm the scale's validity, reliability, and appropriateness for implementation within the Middle East and North Africa (MENA) region.

New Synthetic Approaches for the Construction of Enantioenriched Molecules Bearing Quaternary Stereocenters

AbstractOptically active molecule architectures stand as an important class of organic compounds and occupy a key role in academic and industrial communities. Particularly, the molecules bearing quaternary carbon are of vital importance because of its favorable conformation and valuable three‐dimensional molecules, which frequently play a key role in a broad spectrum of functional materials, pharmaceutical relevant natural molecules, and agrochemicals. Over the past few decades, a large number of synthetic strategies for the enantioselective construction of compounds with chiral quaternary carbon centers have been the focus of a number of research initiatives. In this review, the state‐of‐the‐art toward the synthesis of enantioenriched molecules bearing quaternary stereocenters are summarized, which could be segmented into four categories: 1) Construction of optically active quaternary carbon centers by addition to prochiral sp2 carbon; 2) Construction of optically active all‐carbon quaternary stereocenters via substitution at non‐chiral tetra‐substituted carbon; 3) Construction of optically active all‐carbon quaternary stereocenters via kinetic resolution; 4) Construction of optically active all‐carbon quaternary stereocenters via desymmetrization reactions.

Fabrication of Thermo-Responsive Polymer-MOF@cellulase Composites with Improved Catalytic Performance for Hydrolysis of Cellulose.

Metal-organic frameworks (MOFs) are considered as an ideal enzyme support because of their porous structural superiority. However, MOFs@enzyme composites have usually compromised their hydrolysis efficiency due to the narrow space inducing unfavourable enzyme conformations. Herein, a thermo-responsive poly(N,N-dimethylacrylamide) (PD) was fixed onto the surface of UiO-66-NH2 (UiO) through a post-synthetic modification protocol. Using poly(2-vinyl-4,4 dimethylazlactone) (V) as a linker, PVD-UiO@cellulase composites were fabricated after cellulase was immobilized onto the UiO surface through covalent bonding. The composites conferred favorable cellulase conformations, boosting hydrolysis efficiency and stability, which relied on the soft PVD shell and confinement effect yielded by the curled PVD chains at high temperatures. Compared with free cellulase, the proposed composites exhibited a 33.1-fold enhancement of the Kcat values at 50 °C. The PVD-UiO@cellulase composites were applied to the hydrolysis of cellulose in the stalks and leaves of Epipremnum aureum. The results highlight the potential of smart PVD-UiO@cellulase composites in the hydrolysis of cellulose, affording a valuable platform for the preparation of unique MOFs@enzyme composites and their industrial applications.

Design and Biophysical Characterization of Second-Generation cyclic peptide LAG-3 inhibitors for cancer immunotherapy

Lymphocyte activation gene 3 (LAG-3) is an inhibitory immune checkpoint crucial for suppressing the immune response against cancer. Blocking LAG-3 interactions enables T cells to recover their cytotoxic capabilities and diminishes the immunosuppressive effects of regulatory T cells. A cyclic peptide (Cys-Val-Pro-Met-Thr-Tyr-Arg-Ala-Cys, disulfide bridge: 1–9) was recently reported as a LAG-3 inhibitor. Based on this peptide, we designed 19 derivatives by substituting tyrosine residue to maximize LAG-3 inhibition. Screening via TR-FRET assay identified 8 outperforming derivatives, with cyclic peptides 12 [Tyr6(L-3-CN-Phe)], 13 [Tyr6(L-4-NH2-Phe)], and 17 [Tyr6(L-3,5-DiF-Phe)] as top candidates. Cyclic peptide 12 exhibited the highest inhibition (IC50 = 4.45 ± 1.36 µM). MST analysis showed cyclic peptides 12 and 13 bound LAG-3 with KD values of 2.66 ± 2.06 µM and 1.81 ± 1.42 µM, respectively, surpassing the original peptide (9.94 ± 4.13 µM). Docking simulations revealed that cyclic peptide 12 exhibited significantly enhanced binding, with a docking score of −7.236 kcal/mol, outperforming the original peptide (−5.236 kcal/mol) and cyclic peptide 5 (L-4-CN-Phe) (−5.131 kcal/mol). A per-residue decomposition of the interaction energy indicated that the 3-cyano group in cyclic peptide 12 contributes to a more favorable conformation, yielding an interaction energy of −9.22 kcal/mol with Phe443 of MHC-II, compared to −6.03 kcal/mol and −5.619 kcal/mol for cyclic peptides 0 and 5, respectively. Despite promising in vitro results, cyclic peptide 12 failed to inhibit tumor growth in vivo, underscoring the importance of dual immunotherapies targeting several immune checkpoints to achieve anti-tumor efficacy.

Crystal structure and Hirshfeld surface analysis of (E)-N-(2-styrylphen-yl)benzene-sulfonamide.

The crystal structure of the title compound C20H17NO2S features hydrogen-bonding and C-H⋯π inter-actions. Hirshfeld surface analysis revealed that H⋯H, C⋯H/H⋯C and O⋯H/H⋯O inter-actions make a major contribution to the crystal packing. Docking studies were carried out to determine the binding affinity and inter-action profile of the title compound with EGFR kinase, a member of the ErbB family of receptor tyrosine kinases, which is crucial for processes such as cell proliferation and differentiation. The title compound shows a strong binding affinity with EGFR kinase, with the most favourable conformation having a binding energy of -8.27 kcal mol-1 and a predicted IC50 of 870.34 nM, indicating its potential as a promising candidate for targeted lung cancer therapy.

Multi-method analysis revealed the mechanism of substrate selectivity in NHase: A gatekeeper residue at the activity center

Recognizing the critical need to elucidate the molecular determinants of this selectivity offers a pathway to engineer enzymes with broader and more versatile catalytic capabilities. Through integrated methods including phylogenetic analysis, molecular docking, and structural analysis, we identified a pivotal amino acid residue, αTrp116, linking the substrate binding pocket and the active site of a NHase from Pseudonocardia thermophila JCM 3095 (PtNHase). This residue acts as a crucial determinant of substrate specificity within the NHase enzyme. The mutant αW116R modified the substrate specificity of PtNHase, significantly enhancing its catalytic efficiency towards aromatic substrates. The catalytic activity for aromatic compounds such as 3-Cyanopyridine was 14-fold that of the wild-type, whereas its activity for aliphatic substrates diminished to one-sixth. MD simulations revealed that replacing αTrp116 with Arg allowed aromatic nitrile substrates to achieve more favorable conformations within the active site. Based on the mutant αW116R, we further constructed a combinatorial variant Pt-4, tailored for aromatic substrates, which exhibited an enzyme activity 50 times that of the wild-type. These results highlight the critical influence of amino acid residues in the enzyme's active site on substrate specificity and offer fresh perspectives and approaches for the evolution of enzymes.

In Silico and In Vitro Investigation of Phytoconstituents from Flacourtia Jangomas as a Potential Candidate for the Treatment of Type 2 Diabetes Mellitus

AbstractFlacourtia jangomas is a plant used for centuries in Brazil, China, India, and the Malaya Peninsula to treat conditions such as diabetes, asthma, anaemia, and diarrhoea. Despite its therapeutic and economic benefits, the plant has not been popular among farmers due to its limited yield and lack of knowledge about its potential. Targeting PPARγ agonists is a promising approach for discovering and developing effective drugs to treat type 2 diabetes. Due to the activation of the PPARγ through PPARγ agonists, target genes implicated in inflammation, adipogenesis, lipid metabolism, and glucose metabolism are transcriptionally regulated. This study analysed the curated datasets of F. jangomas to identify the binding conformations of the phytoconstituents with different T2DM targets through molecular docking, molecular dynamics, and ADMET prediction approach. To determine the most favourable binding conformations of phytoconstituents that bind with the PPARγ receptors, density functional theory and principal component analysis were performed. The study reveals that the phytoconstituents of F. jangomas can act as PPARγ agonists and could be used to design and optimise the potential antidiabetic agents inspired by natural products. These findings provide a promising approach towards developing effective antidiabetic drugs.

Structural basis for CCR6 modulation by allosteric antagonists

The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the molecular basis of CCR6 activation. Here, we present two inactive CCR6 structures in ternary complexes with different allosteric antagonists, CCR6/SQA1/OXM1 and CCR6/SQA1/OXM2. The oxomorpholine analogues, OXM1 and OXM2 are highly selective CCR6 antagonists which bind to an extracellular pocket and disrupt the receptor activation network. An energetically favoured U-shaped conformation in solution that resembles the bound form is observed for the active analogues. SQA1 is a squaramide derivative with close-in analogues reported as antagonists of chemokine receptors including CCR6. SQA1 binds to an intracellular pocket which overlaps with the G protein site, stabilizing a closed pocket that is a hallmark of inactive GPCRs. Minimal communication between the two allosteric pockets is observed, in contrast to the prevalent allosteric cooperativity model of GPCRs. This work highlights the versatility of GPCR antagonism by small molecules, complementing previous knowledge of CCR6 activation, and sheds light on drug discovery targeting CCR6.

Retention of methicillin susceptibility in Staphylococcus aureus using natural adjuvant as an allosteric modifier of penicillin-binding protein 2a

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) poses a significant global public health challenge due to its resistance to conventional antibiotics, primarily mediated by the mutated penicillin-binding protein, PBP2a. This study aims to investigate the potential of phytochemicals derived from medicinal plants in the Indian subcontinent to serve as adjuvants, enhancing the efficacy of methicillin against MRSA through allosteric modification of PBP2a using molecular docking and molecular dynamics (MD) simulation. After comprehensive Absorption, Distribution, Metabolism, and Excretion (ADME) profiling, along with AMES and hepatotoxicity tests, 9 compounds were shortlisted as suitable adjuvant candidates. Among them, nimbolide, quercetin, emodin, daidzein, eriodictyol, luteolin, and apigenin exhibited strong binding affinity to the allosteric site of PBP2a, with docking scores ranging from −8.7 to −7.3 kcal/mol. These phytochemicals facilitated enhanced methicillin binding, as evidenced by improved docking scores ranging from −6.1 to −6.8 kcal/mol, compared to −5.6 kcal/mol for methicillin alone. Molecular dynamics simulations confirmed the stability and favorable conformations of phytochemical-PBP2a complexes. Quercetin and daidzein were identified as the most promising adjuvant candidates, forming stable and energetically favorable complexes with PBP2a. Experimental validation showed that quercetin, at 30 mg/mL, effectively retained methicillin's antibacterial efficacy against MRSA. This study underscores the potential of natural compounds in overcoming antibiotic resistance and suggests that phytochemical-antibiotic synergism could be a viable strategy to combat multidrug-resistant bacterial infections.

Solvent effects on the structures of the hydrated copper dication clusters

Understanding the solvation process requires an understanding of how the solvent affects the molecular cluster configurations. The current study examined the impact of solvents on the structures of the hydrated Cu2+ cation, as well as the temperature dependence, and the energetics of the hydrated Cu2+ cation clusters from sizes n=1 from n=10 (Cu2+(H2O)n=1−10). The potential energy surfaces (PESs) in the solvent phase (represented by a dielectric continuum medium) at the MP2/6-31++G(d,p) level of computation have been comprehensively investigated. We employed the integral equation formalism polarized continuum model (IEF-PCM) to describe the dielectric continuum medium. It is pointed out that changes in PESs of hydrated copper dication isomers and structural morphologies occur in the continuum medium. Thus, the relative energies are smallest at T=0 K and for the cluster populations of Cu2+(H2O)n=1−10 are modified. Thus, in the solvent phase, the competition between the conformers is more severe than in the gas phase. Furthermore, highly coordinated conformers are more favorable, and favored conformers in the gas phase are disfavored in the solvent phase. The structural investigations are validated by the analysis of Wiberg Bond Index (WBI) at 300 K. In the solvent phase, the WBIs of the most stable isomers are the smallest and the WBIs of axial bonds are lower than those of equatorial bonds. Concerning the energy analysis, the binding energies were predicted for enormous sizes (at saturation) using a fit function. Thus, the new values of the binding energies obtained are -5467.8 and ▪ in the gas and solvent phases respectively. All these observed differences are due to the effects of the implicit solvent.

Atomistic Characterization of Healthy and Damaged Hair Surfaces: A Molecular Dynamics Simulation Study of Fatty Acids on Protein Layer.

Amid the bourgeoning demand for in-silico designed, environmentally sustainable, and highly effective hair care formulations, a growing interest is evident in the exploration of realistic computational model for the hair surface. In this work, we present an atomistic model for the outermost layer of the hair surface derived through molecular dynamics simulations, which comprises 18-Methyleicosanoic acid (18-MEA) fatty acid chains covalently bound onto the keratin-associated protein 10-4 (KAP10-4) at a spacing distance of ~1 nm. Remarkably, this hair surface model facilitates the inclusion of free fatty acids (free 18-MEA) into the gaps between chemically bound 18-MEA chains, up to a maximum number that results in a packing density of 0.22 nm2 per fatty acid molecule, consistent with the optimal spacing identified through free energy analysis. Atomistic insights are provided for the organization of fatty acid chains, structural features, and interaction energies on protein-inclusive hair surface models with varying amounts of free 18-MEA (FMEA) depletion, as well as varying degrees of anionic cysteic acid from damaged bound 18-MEA (BMEA), under both dry and wet conditions. In the presence of FMEA and water, the fatty acid chains in a pristine hair surface prefers to adopt a thermodynamically favored extended chain conformation, forming a thicker protective layer (~3 nm) on the protein surface. Our simulation results reveal that, while the depletion of FMEA can induce a pronounced impact on the thickness, tilt angle, and order parameters of fatty acid chains, the removal of BMEA has a marked effect on water penetration. There is a "sweet spot" spacing between the 18-MEA whereby damaged hair surface properties can be reinstated by replenishing FMEA. Through the incorporation of the protein layer and free fatty acids, the hair surface models presented in this study enables a realistic representation of the intricate details within the hair epicuticle, facilitating a molecular scale assessment of surface properties during the formulation design process.

Computational and in-vitro Investigation of Phytochemicals from Allamanda cathartica as a Potential Candidate for the Treatment of Type 2 Diabetes mellitus

Diabetes, a chronic metabolic disease, has become a severe health problem worldwide. According to the latest data from the International Diabetes Federation (IDF), there were 537 million diabetic mellitus (DM) patients worldwide in 2021, expected to increase to 783 million by 2045. Over 90% of people with diabetes have type 2 diabetes, which is driven by socio-economic, demographic, environmental, and genetic factors. Diabetes is still a major global health issue, with prevalence rates rising all across the world. This not only imposes a significant burden on healthcare systems but also impacts the quality of life of affected individuals and their families. Therefore, there is a continuous high demand worldwide to develop novel, more effective, and easily affordable medications against diabetes. This paper illustrates the in-vitro antidiabetic activity and probable binding mechanism prediction of phytoconstituents of Allamanda cathartica against type 2 diabetes molecular targets. Through the application of bioactivity score prediction, molecular docking, and ADMET prediction approach, the potential and selective phytoconstituents with the highest binding affinity and lower toxicity were gained from the curated datasets. Further molecular dynamics simulations and DFT calculations were carried out to identify the favorable binding conformations when the top-scored phytoconstituents bind with the PPAR[Formula: see text] receptors compared to the rosiglitazone. Compound AC2 interacts with the PPAR[Formula: see text] proteins by forming seven hydrogen bonds with the amino acid residues Phe282, His449, Tyr327, His323, and Ser289. The ligand was bound to the protein during the simulation since none of the complex conformations was unstable, and no unfolding or folding occurred. Our results provided an approach to further design and optimize the natural product-inspired small druglike molecules as potential antidiabetic agents. This study highlighted that the phytoconstituents of Allamanda cathartica have antidiabetic potential through the binding of PPAR[Formula: see text], [Formula: see text]-amylase and [Formula: see text]-glucosidase proteins that can be further explored for novel antidiabetic drug development.

A theoretical approach on ADMET properties of an azo-ester based fluorophore (AEF), and it's energetics, binding stability and molecular interactions with select globular proteins

Molecular docking (Mol.Doc) approach of an azo-ester based fluorophore (AEF) with widely studied proteins like Human serum Albumin (HSA), Bovine serum Albumin (BSA), Beta lactoglobin (βLG) and Ovalbumin (OVA) were carried out. The binding affinity and strength of AEF-HSA complex is due to hydrogen-bonding (h-bonding) and hydrophobic interactions (predominantly attributed to pi-alkyl). AEF and HSA acts as h-bonding acceptor as well as donor. The energetically favored conformers of AEF-HSA complex are governed and stabilized by polar as well as non-polar amino acids. On the contrary, the pattern observed in all the conformers of AEF-BSA, AEF- βLG and AEF-OVA are energetically least favored (+ve ∆G) compared to that of HSA. The least binding affinity of AEF is towards OVA (Binding energy (BE) +581.15 Kcalmol−1 followed by βLG (+55.11) and BSA (+12.12) . Though BSA and HSA are structurally similar to each other, they vary in the binding stability with AEF. This is attributed to several unfavorable interactions that destabilize AEF-BSA complex which was not resulted in the complex existing between AEF-HSA. The energetically least stable complexes (AEF-BSA, AEF-βLG and AEF-OVA) are predominantly governed by hydrophobic interactions. However, several h-bonding interactions along with pi-sigma/pi-pi/pi-alkyl interactions result in destabilization of the above complexes. Interestingly, AEF-HSA complex stability is attributed to fewer number of hydrophobic interactions along with h-bonding interactions. The h-bonding interaction governs the stability of the complex which is the driving force. Docking studies illustrates that the binding of amino acids (AAs) in various subdomains play a significant role on the binding nature. The stability of AEF-HSA over other protein complexes in terms of BE is emphasized in the study. The energetically stable sites and sub-domains of AEF with HSA and BSA establish the site selective and site-specific nature of AEF with proteins. In silico studies provide an excellent and easier approach in establishing the molecular interactions existing between AEF with globular proteins. ADMET parameters of the guest molecule calculated exemplifies that AEF compound is less toxic and possesses high oral bioavailability. Based on the binding efficiency of AEF with albumins, the ADMET properties and drug likeliness approach of AEF provides an information on the application towards proteins in the concept of medicine and chemistry.

Chemoinformatics Study of Benzodiazepine-1, 2, 3-triazole Derivatives Targeting Butyrylcholinesterase.

This study aims to assess the potential bioactivity of newly designed benzodiazepine-1,2,3-triazole derivatives using in-silico methodologies, with a primary focus on elucidating their inhibitory interactions with the butyrylcholinesterase (BuChE) enzyme, which is implicated in Alzheimer's disease. We employed multiple linear regression (MLR) methods to conduct a quantitative structure-activity relationship (QSAR) analysis on a collection of 31 benzodiazepine-1,2,3-triazole derivatives, with the goal of investigating, assessing, and predicting their activities, as well as designing novel compounds. This approach yielded highly accurate results, with coefficients of determination (R²) of 0.77 and 0.81 for the training and test datasets, respectively. Additionally, the optimized compounds were subjected to an Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analysis, demonstrating their potential as non-hepatotoxic agents with enhanced absorption and blood-brain barrier permeability. To further validate these findings, the most favorable docking conformations were analyzed using molecular dynamics (MD) simulations with GROMACS software, predicting the stability of the formed complexes. These simulations underscored the critical role of hydrogen bonds in stabilizing the compounds at the BuChE receptor binding site. The results hold great promise for the development of innovative benzodiazepine-1,2,3-triazole derivatives as effective BuChE inhibitors, potentially leading to therapeutic interventions for Alzheimer's disease.

In-vitro and in-silico analyses of the thrombolytic potential of green kiwifruit

Cardiovascular diseases (CVDs), mainly caused by thrombosis complications, are the leading cause of mortality worldwide, making the development of alternative treatments highly desirable. In this study, the thrombolytic potential of green kiwifruit (Actinidia deliciosa cultivar Hayward) was assessed using in-vitro and in-silico approaches. The crude green kiwifruit extract demonstrated the ability to reduce blood clots significantly by 73.0 ± 1.12% (P < 0.01) within 6 h, with rapid degradation of Aα and Bβ fibrin chains followed by the γ chain in fibrinolytic assays. Molecular docking revealed six favorable conformations for the kiwifruit enzyme actinidin (ADHact) and fibrin chains, supported by spontaneous binding energies and distances. Moreover, molecular dynamics simulation confirmed the binding stability of the complexes of these conformations, as indicated by the stable binding affinity, high number of hydrogen bonds, and consistent distances between the catalytic residue Cys25 of ADHact and the peptide bond. The better overall binding affinity of ADHact to fibrin chains Aα and Bβ may contribute to their faster degradation, supporting the fibrinolytic results. In conclusion, this study demonstrated the thrombolytic potential of the green kiwifruit-derived enzyme and highlighted its potential role as a natural plant-based prophylactic and therapeutic agent for CVDs.

Neighbor effect on conformational spaces of alanine residue in azapeptides

The conformational properties of Alanine (Ala) residue have been investigated to understand protein folding and develop force fields. In this work, we examined the neighbor effect on the conformational spaces of Ala residue using model azapeptides, Ac-Ala-azaGly-NHMe (3, AaG), and Ac-azaGly-Ala-NHMe (4, aGA1). Ramachandran energy maps were generated by scanning (φ, ψ) dihedral angles of the Ala residues in models with the fixed dihedral angles (φ = ±90°, ψ = ±0° or ±180°) of azaGly residue using LCgau-BOP and LCgau-BOP + LRD functionals in the gas and water phases. The integral-equation-formalism polarizable continuum model (IEF-PCM) and a solvation model density (SMD) were employed to mimic the solvation effect. The most favorable conformation of Ala residue in azapeptide models is found as the polyproline II (βP), inverse γ-turn (γ′), β-sheet (βS), right-handed helix (αR), or left-handed helix (αL) depending on the conformation of neighbor azaGly residue in isolated form. Solvation methods exhibit that the Ala residue favors the βP, δR, and αR conformations regardless of its position in azapeptides 3 and 4 in water. Azapeptide 5, Ac-azaGly-Ala-NH2 (aGA2), was synthesized to evaluate the theoretical results. The X-ray structure showed that azaGly residue adopts the polyproline II (βP) and Ala residue adopts the right-handed helical (αR) structure in aGA2. The conformational preferences of aGA2 and the dimer structure of aGA2 based on the X-ray structure were examined to assess the performance of DFT functionals. In addition, the local minima of azapeptide 6, Ac-Phe-azaGly-NH2 (FaG), were compared with the previous experimental results. SMD/LCgau-BOP + LRD methods agreed well with the reported experimental results. The results suggest the importance of weak dispersion interactions, neighbor effect, and solvent influence in the conformational preferences of Ala residue in model azapeptides.

Repurposing of drugs against bacterial infections: A pharmacovigilance-based data mining approach.

The World Health Organization (WHO) has published a list of priority pathogens that urgently require research to develop new antibiotics. The main aim of the current study is to identify potential marketed drugs that can be repurposed against bacterial infections. A pharmacovigilance-based drug repurposing approach was used to identify potential drugs. OpenVigil 2.1 tool was used to query the FDA Adverse Event Reporting System database. The reporting odds ratio (ROR) < 1, ROR95CI upper bound <1, and no. of cases ≥30 were used for filtering and sorting of drugs. Sunburst plot was used to represent drugs in a hierarchical order using the Anatomical Therapeutic Chemical classification. Molecular docking and dynamics were performed using the Maestro and Desmond modules of Schrodinger 2023 software respectively. A total of 40 drugs with different classes were identified based on the pharmacovigilance approach which has antibacterial potential. The molecular docking results have shown energetically favored binding conformation of lisinopril against 3-deoxy-manno-octulosonate cytidylyltransferase, UDP-2,3-diacylglucosamine hydrolase, and penicillin-binding protein 3 (PBP3) of Pseudomonas aeruginosa; olmesartan, atorvastatin against lipoteichoic acids flippase LtaA and rosiglitazone and varenicline against d-alanine ligase of Staphylococcus aureus; valsartan against peptidoglycan deacetylase (SpPgdA) and atorvastatin against CDP-activated ribitol for teichoic acid precursors of Streptococcus pneumoniae. Further, molecular dynamic results have shown the stability of identified drugs in the active site of bacterial targets except lisinopril with PBP3. Lisinopril, olmesartan, atorvastatin, rosiglitazone, varenicline, and valsartan have been identified as potential drugs for repurposing against bacterial infection.