Active Binding Sites Research Articles

Elucidating the E‐Cadherin⋯ADTC5 Interactions: A Theoretical Examination of Amino Acid Active Site Binding on the Electronic Level via Density Functional Theory

AbstractThe presence of E‐cadherin⋯E‐cadherin interactions in the intercellular space (paracellular pathway) poses a notable limitation in drug delivery across the blood‐brain barrier (BBB). ADTC5 peptide has shown promising results in improving drug delivery across the BBB by modulating E‐cadherin⋯E‐cadherin interactions. However, the study of E‐cadherin⋯ADTC5 amino acid interactions using quantum mechanics approach has not been observed clearly. Herein, we observed the interaction between E‐cadherin⋯ADTC5 amino acids using density functional theory (DFT). Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and reduced density gradient (RDG) analysis are performed to study the non‐covalent interaction in detail. The Arg55⋯Asp2 shows the strongest interaction between E‐cadherin⋯ADTC5 modulation, indicated by the highest stabilization energy (E(2)), and hydrogen bonding energy (EHB) about 22.04 and −6.90 kcal/mol, respectively. This interaction is dominated by hydrogen bonding. Such advancements could lead to significant improvements in therapeutic strategies for neurodegenerative diseases, where effective drug delivery across the BBB remains a major challenge.

Design and Synthesis of Ester Linked 1,2,3‐Triazole Quinoline Derivatives with Pancreatic β Cells Protective Activity against Oxidative Stress and Endoplasmic Reticulum Stress for Better Management of Type II Diabetes Mellitus

AbstractUnresolved endoplasmic reticulum (ER) stress and oxidative stress lead to the pathogenesis of type II diabetes mellitus (DM). Connecting links between the ER stress and oxidative stress pathways might play an important role in treatment and pathogenesis of diabetes. Here, we used network pharmacology approach to find the target proteins linking the ER stress and oxidative stress pathways. CHOP emerged as a hub protein from our results and was targeted by 16 newly designed and synthesized ester linked 1,2,3‐triazole quinoline derivatives by molecular docking. Drug likeliness prediction studies revealed all compounds as good druggable candidates. Compounds 5b (R = H, R1 = F), 5j (R = CH3, R1 = F), 5m (R = OCH3, R1 = H), and 5n (R = OCH3, R1 = F) were found to have considerable binding energies and active site amino acid interactions with CHOP. We further showed that compounds 5b, 5m, and 5n exhibited low toxicity with more than 50% cell survival and low IC50 values. These were therefore subjected to evaluate their effects on ER stress and oxidative stress. Finally, compound 5n (R = OCH3, R1 = F) was found to alleviate ER stress and is also a good antioxidant. Identification of such targets and compounds effective in improving ER stress and oxidative stress may provide new insights in the development of therapies and management of T2DM.

Structural insights into the toxicity of type II ribosome inactivating proteins (RIPs): a molecular dynamics study

Ribosome Inactivating Proteins (RIPs) act by irreversibly depurinating the 28S rRNA ricin-sarcin loop (SRL) of the eukaryotic ribosome resulting in protein synthesis inhibition. In general, they consist of two variants: Type I which is single chained (∼30 kDa), and Type II, a more toxic variant which is a Type I N-glycosidase chain covalently linked to a lectin chain. These proteins are believed to play a pivotal role in defence mechanisms. Intriguingly, non-toxic variants of such toxic proteins do exist in nature. To explore their mode of action, in the present study we have selected three toxic (Ricin, Ebulin and HmRIP) as well as two non-toxic (BGSL and SGSL) RIPs and performed molecular docking and molecular dynamic simulations with the SRL loop. This study throws light on the structural stability and plasticity of the toxic and non-toxic RIP complexes. Furthermore, analysis of the active site cavity volume and binding free energy calculations reveal that the SRL, particularly the specific adenine (A4605), is relatively unstable in the case of non-toxic RIPs which is also supported by the free binding energy calculations, and the pocket size analysis indicates the abnormal increase in active site cavity volume of non-toxic RIPs with time. This first-of-its-kind comprehensive study of toxic and non-toxic RIPs gives insights about the mode of action and the dynamic nature of their interaction with the SRL loop. These observations will be helpful in the development of toxoids against RIPs and also in designing novel therapeutic approaches against human diseases.

Nondestructively Assemble Cell Membrane-Coated Nanoparticles by Host-Guest Interactions for Efficient Capture of Bioactive Compounds.

Cell membrane-coated nanoparticles (CNPs) have emerged as an attractive nanomedical tool. The basic premise is that the surface properties of natural cells can be integrated with the physical and chemical properties of nanoparticles by coating them with cell membranes. However, the degree of preservation of membrane proteins on nanoparticles, a key indicator related to the biomedical function of these biomimetic systems, is largely affected by the coating process. Herein, we report a supramolecular cell membrane conjugation strategy mediated by host-guest interactions to assemble CNPs without compromising protein activities. β-cyclodextrin (β-CD) was rapidly and stably inserted into the cell membrane by a lipid anchor without affecting the function of membrane proteins, thus attaching host-guest sites to the membrane surface. By harnessing the excellent binding affinity between β-CD attached to the membrane surface and adamantane, a supramolecular cell membrane-magnetic nanoparticle conjugate (CDM@AMNPs) was synthesized. Thanks to the nondestructive assembly of this strategy, CDM@AMNPs were endowed with a greater number of active binding sites, exhibiting efficient adsorption performance. This supramolecular conjugation strategy mediated by nonreceptor site-based host-guest interactions proposes a scalable and cell-friendly strategy for the development of highly efficient CNPs.

Uncovering the toxic effects and adaptive mechanisms of aminated polystyrene nanoplastics on microbes in sludge anaerobic digestion system: Insight from extracellular to intracellular

The impacts of polystyrene nanoplastics (PS NPs) with amino functional groups on sludge anaerobic digestion process and the underlying microbial feedbacks remains unclear. Herein, PS NPs coated with and without amino functional groups were employed to explore their impacts on the sludge digestion performance. Experimental results showed that aminated PS NPs (PS-NH2) deteriorated the methane yield and hydrolysis rate. The Derjaguin-Landau-Verwey-Overbeek theory analysis suggested that the PS-NH2 decreased the interaction energy barrier, making it easier to contact with sludge and disrupting the structure of extracellular polymeric substances. Metagenomic analysis showed that the abundance of functional microbes (e.g., Longilinea, Leptolinea, and Methanosarcina) decreased, accompanied with lower network complexity and fewer keystone taxa. Molecular docking revealed that PS-NH2 occupy the antioxidant enzyme active binding sites through hydrogen bonding and hydrophobic interactions, impairing degradation of reactive oxygen species. The severe intracellular oxidative stress up-regulated genes associated with quorum sensing (e.g., luxI and luxR) and protein biosynthesis (e.g., algA, trpG and trpE), and further inducing compact tryptophan-like proteins as a defense against NPs. These findings provide new understanding of the toxic effects from PS-NH2 in biological systems and offer valuable insights into the regulation strategies aimed at alleviating NPs inhibition.

Interactions between nanobiochar and arsenic: Effects of biochar aging methods on arsenic binding capacity and mechanisms

Nano-biochar (nanoBC), produced from biochar aging, exhibits significant molecular heterogeneity that may affect the fate and toxicity of co-occurring pollutants. However, the interaction between nanoBC and arsenic (As) remains unclear. Herein, we simulated biochar aging through water erosion, photoaging, and thermal chemical decomposition to generate three types of nanoBC (nUBC, nPBC, and nHBC). We then investigated their distinct binding affinities and interaction mechanisms with arsenite (AsIII) and arsenate (AsV). Complementary analysis using optical spectrophotometer and high-resolution mass spectrometry revealed significant differences in properties and chemical compositions among the three nanoBCs at a size of 100 nm. Specifically, nHBC had higher yield, nPBC had higher aromaticity, and nUBC had more intricate molecular compositions and larger molecular weights. Binding experiments showed that nHBC and nUBC exhibited the highest conditional distribution coefficient (KD) for AsIII and AsV, respectively. In nHBC, a higher proportion of humic-like fluorescent component C3 enhanced its affinity for AsIII, attributed to lignin-like molecules with CHONS formulas where thiol acted as active binding sites. In contrast, the robust AsV binding capacity of nUBC stemmed from its richness in humic-like fluorescent component C1 and tryptophan-like fluorescent component C2. This is facilitated by lipid-like molecules and CHO formulas in C1 and aliphatic/peptide-like molecules and CHON formulas in C2, which provided oxygenic and nitrogen-containing groups for binding. All nanoBC had a significantly higher binding affinity for As than bulk BC. These findings provide a deeper understanding of As-nanoBC binding mechanisms at the molecular level, facilitating more accurate prediction of As fate in biochar-amended soil and associated ecosystem risks.

Clofazimine inhibits small-cell lung cancer progression by modulating the kynurenine/aryl hydrocarbon receptor axis

Small cell lung cancer (SCLC) is one of the highly metastatic malignancies that contributes to ~15 % of all lung cancers. Most SCLC patients (50–60 %) develop osteolytic bone metastases, significantly affecting their quality of life. Among several factors, environmental pollutant 2,3,7,8-Tetrachlorodibenzodioxin (TCDD) and kynurenine (Kyn), an endogenous ligand derived from tryptophan (Trp) metabolism, activate the aryl hydrocarbon receptor (AhR) and are responsible for SCLC progression and metastasis. Further, elevated AhR expression in bone cells intensifies bone resorption, making the Kyn/AhR axis a potential target for the bone metastatic propensity of SCLC. We first assessed the expression profile of AhR in human SCLC cell lines and found a significantly increased expression compared to normal lung cells. Additionally, we also evaluated the clinical significance of AhR expression in the patient samples of SCLC along with the relevance of the same in the Rb1fl/fl; Trp53fl/fl; MycLSL/LSL (RPM) mouse model using immunohistochemistry and found the higher AhR expression in the patient samples and RPM mouse tumor tissues. Using computational simulations, we found that clofazimine (CLF) binds at the activator (Kyn) binding site by forming a stable complex with AhR. The CLF binding with AhR was favored by Van der Waals and hydrophobic forces, and the proteins retained their secondary structure. Furthermore, we found that Kyn treatment potentiates the migration and clonogenic ability of SCLC cell lines by activating Erk/Akt oncogenic signaling. Blocking AhR with CLF reduces AhR expression, inhibits Kyn-mediated proliferation of SCLC cells, and induces apoptosis and cell cycle arrest in the G2/M phase; further, our examination indicates that Kyn treatment also promotes osteoblast-mediated osteoclast differentiation through RANKL. The treatment with CLF impedes RANKL expression and osteoclastogenesis, suggesting that CLF has the potential for developing SCLC therapies that have efficacies against bone metastasis.

Modeling Of the Structure of the tRolC Protein of Nicotiana tabacum and Its Functional Relation to Other Proteins

The trolC gene is a homologue of the rolC oncogene of Agrobacterium rhizogenes and most likely got into Nicotiana tabacum genome during horizontal gene transfer. This gene is quite conserved and is expressed in young organs, but its functions, like the agrobacterium rolC gene, remain unknown. The putative structure of the tRolC protein of Nicotiana tabacum, predicted using the I-TASSER service, was analyzed in the study. The presence of amino acid residues in the tRolC protein of the active center and binding site, as well as a protein-binding and ARTT loop, similar in structure to protein 6b of Agrobacterium vitis, indicates that they perform similar biological functions. Based on the data, a hypothesis was put forward about the presence of ADP-ribosyltransferase activity in the tRolC protein, which allows it to influence the growth and stress tolerance, as well as the biosynthesis of secondary metabolites by influencing the regulation of gene expression through interaction with transcription factors, RNA interference, or the manifestation of histone-like activity.

An in silico design method of a peptide bioreceptor for cortisol using molecular modelling techniques

Cortisol is established as a reliable biomarker for stress prompting intensified research in developing wearable sensors to detect it via eccrine sweat. Since cortisol is present in sweat in trace quantities, typically 8–140 ng/mL, developing such biosensors necessitates the design of bioreceptors with appropriate sensitivity and selectivity. In this work, we present a systematic biomimetic methodology and a semi-automated high-throughput screening tool which enables rapid selection of bioreceptors as compared to ab initio design of peptides via computational peptidology. Candidate proteins from databases are selected via molecular docking and ranked according to their binding affinities by conducting automated AutoDock Vina scoring simulations. These candidate proteins are then validated via full atomistic steered molecular dynamics computations including umbrella sampling to estimate the potential of mean force using GROMACS version 2022.6. These explicit molecular dynamic calculations are carried out in an eccrine sweat environment taking into consideration the protein dynamics and solvent effects. Subsequently, we present a candidate baseline peptide bioreceptor selected as a contiguous sequence of amino acids from the selected protein binding pocket favourably interacting with the target ligand (i.e., cortisol) from the active binding site of the proteins and maintaining its tertiary structure. A unique cysteine residue introduced at the N-terminus allows orientation-specific surface immobilization of the peptide onto the gold electrodes and to ensure exposure of the binding site. Comparative binding affinity simulations of this peptide with the target ligand along with commonly interfering species e.g., progesterone, testosterone and glucose are also presented to demonstrate the validity of this proposed peptide as a candidate baseline bioreceptor for future cortisol biosensor development.

AlphaFold Ensemble Competition Screens Enable Peptide Binder Design with Single-Residue Sensitivity.

Understanding the relationship between the sequence and binding energy in peptide-protein interactions is an important challenge in chemical biology. A prominent example is ubiquitin interacting motifs (UIMs), which are short peptide sequences that recognize ubiquitin and which bind individual ubiquitin proteins with a weak affinity. Though the sequence characteristics of UIMs are well understood, the relationship between the sequence and ubiquitin binding affinity has not yet been fully characterized. Herein, we study the first UIM of Vps27 as a model system. Using an experimental alanine scan, we were able to rank the relative contribution of each hydrophobic residue of this UIM to ubiquitin binding. These results were correlated with AlphaFold displacement studies, in which AlphaFold is used to predict the stronger binder by presenting a target protein with two potential peptide ligands. We demonstrate that by generating large numbers of models and using the consensus bound-state AlphaFold competition experiments can be sensitive to single-residue variations. We furthermore show that to fully recapitulate the binding trends observed for ubiquitin, it is necessary to screen AlphaFold models that incorporate a "decoy" binding site to prevent the displaced peptide from interfering with the actual binding site. Overall, it is shown that AlphaFold can be used as a powerful tool for peptide binder design and that when large ensembles of models are used, AlphaFold predictions can be sensitive to very small energetic changes arising from single-residue alterations to a binder.

The Raf/LIN-45 C-terminal distal tail segment negatively regulates signaling in Caenorhabditis elegans.

Raf protein kinases act as Ras-GTP sensing components of the ERK signal transduction pathway in animal cells, influencing cell proliferation, differentiation, and survival. In humans, somatic and germline mutations in the genes BRAF and RAF1 are associated with malignancies and developmental disorders. Recent studies shed light on the structure of activated Raf, a heterotetramer consisting of Raf and 14-3-3 dimers, and raised the possibility that a Raf C-terminal distal tail segment (DTS) regulates activation. We investigated the role of the DTS using the Caenorhabditis elegans Raf ortholog lin-45. Truncations removing the DTS strongly enhanced lin-45(S312A), a weak gain-of-function allele equivalent to RAF1 mutations found in patients with Noonan Syndrome. We genetically defined three elements of the LIN-45 DTS, which we termed the active site binding sequence (ASBS), the KTP motif, and the aromatic cluster. In the context of lin-45(S312A), mutation of each of these elements enhanced activity. We used AlphaFold to predict DTS protein interactions for LIN-45, fly Raf, and human BRAF, within the activated heterotetramer complex. We propose distinct functions for the LIN-45 DTS elements: i) the ASBS binds the kinase active site as an inhibitor, ii) phosphorylation of the KTP motif modulates DTS-kinase domain interaction, and iii) the aromatic cluster anchors the DTS in an inhibitory conformation. Human RASopathy-associated variants in BRAF affect residues of the DTS, consistent with these predictions. This work establishes that the Raf/LIN-45 DTS negatively regulates signaling in C. elegans and provides a model for its function in other Raf proteins.

A novel highly selective Fe@UiO-67-BDA/GCE sensor for efficient detecting Hg2+

A three-dimensional UiO-67-BDA with various pore structures and abundant active binding sites is constructed, and Fe@UiO-67-BDA composites with electrochemical sensing and recognition performance were further prepared by successfully loading Fe3+ ions. The different modified electrodes (Fe@UiO-67-BDA/GCE, UiO-67-BDA/GCE, Fe/GCE) and the bare electrode (GCE) were also characterized in terms of basic structure and electrochemistry, and it was found that the basic structure and electrochemical performances of Fe@UiO-67-BDA/GCE were better than those of the remaining three electrodes, with good selectivity, reproducibility and stability. And the Fe@UiO-67-BDA/GCE sensor with good electrochemical performance was constructed under the optimal working potential (Epa = 0.59 V) and experimental conditions, which was utilized to rapidly and accurately detect heavy metal ions Hg2+ by the DPV method, with a detection limit of up to 1.642 × 10−9 M. In addition, the electrochemical behavior mechanism of the Fe@UiO-67- BDA/GCE sensor was investigated. Finally, the sensor was applied to detect cosmetic heavy metal ions, and the experimental results also showed high reliability and practicality. Therefore, MOFs composite material is applied to the field of electrochemistry, because of its simple operation technology, fast detection speed and high sensitivity, so that it has a greater application prospect.

High-performance novel ZIF-67 and ZIF-67@MWNTs composite adsorbents for efficient removal of pharmaceutical contaminant from water: Exceptional capacity and excellent reusability

The removal of pharmaceutical waste products like ibuprofen (IBP) from water is very important for the environment and the health of human and aquatic organisms. In the present work, the adsorption of IBP from aqueous solution was investigated by synthesizing novel ZIF-67 and ZIF-67@MWNTs hybrid composite material by incorporating ZIF-67 particles with carboxyl functionalized multiwalled carbon nanotubes (COOH-MWNT). The synthesized ZIF-67 and ZIF-67@MWNTs adsorbents were characterized by the XPS, XRD, SEM, TEM, BET, FTIR, and TGA analysis to examine their physio-chemical properties. The synthesized novel ZIF-67 has a 1743 m2/g BET surface and 0.692 cm3/g total pore volume. The IBP adsorption process including isotherm and kinetic studies as well as the effect of different parameters i.e. pH, initial concentration, time, adsorbents, and their dosage were examined. Among all the synthesized composite materials, the ZIF-67@MWNT-50 mg material showed the highest IBP adsorption capacity of 841 ± 5 mg/g, about 467 ± 5 mg/g more than the ZIF-67 following the Langmuir and pseudo-second-order model. The enhancement in the IBP adsorption is because of the incorporation of COOH-MWNT and the presence of a large number of active binding sites which showed the van der Waal interactions, host–guest interactions, π- π interactions, and H-bonding between the adsorbate and adsorbent. For the detailed study of the IBP adsorption mechanism of ZIF-67, molecular dynamic (MD) simulations were performed. Additionally, the reusability of ZIF-67@MWNT-50 mg material via a simple regeneration method up to five cycles while maintaining about 96 % adsorption capacity of the pristine non-used ZIF-67@MWNT-50 mg material revealed its importance as an effective adsorbent for the adsorptive elimination of different pharmaceutical hazardous materials from water.

Selective electro-capacitive deionization of Yb(III) by nanospherical N-doped carbon supported nickel‑iron bimetallic oxide, nitride and phosphide

The separation of rare earth elements from the mining waste water is highly important but still facing challenge. In this study, three different porous composite electrode materials were well-designed by decorating the nickel‑iron bimetallic oxide, nitride or phosphide onto nitrogen-doped carbon nanosphere, respectively (termed as NiFeO@NC, NiFeN@NC and NiFeP@NC), and utilized in capacitive deionization device for electrosorption of Yb(III) from water under the low-voltage electric field. The characterization and electrochemical results indicated that the incorporation of N or P atom lead to the reduced specific surface area and the enhanced electrochemical properties (i.e., larger specific capacitance, lower charge transfer resistance). In addition, NiFeN@NC and NiFeP@NC exhibited the excellent electrosorption capacities of Yb(III) with 105.24 mg·g−1 and 90.31 mg·g−1, respectively, under conditions of a flow rate of 20 mL·min−1, a voltage of 1.2 V, and pH of 5.0, which was extremely higher than NiFeO@NC (i.e., 50.7 mg·g−1). Moreover, all these three materials also demonstrated the remarkable electrosorption selectivity of Yb(III) from the mixed solution, and the robust durability with over 90 % of initial capacities after ten consecutive electrosorption-desorption cycles. Furthermore, the XPS characterizations and electrosorption results revealed that the electrosorption mechanism mainly depended on the synergistic effects of intrinsic Faraday redox reaction, electric double layer capacitance and active binding sites. Therefore, this work provided a feasible strategy for the separation of rare earth elements from aqueous solution, and the prospective applications related to the recovery of rare earth elements from mining wastes or spent permanent magnets in future life.

Development of aptamer-based lateral flow devices for rapid detection of SARS-CoV-2 S protein and uncertainty assessment

The outbreak and spread of COVID-19 have highlighted the urgent need for early diagnosis of SARS-CoV-2. Nucleic acid testing as an authoritative tool, is cumbersome, time-consuming, and easy to cross-infect, while the available antibody self-testing kits are deficient in sensitivity and stability. In this study, we developed competitive aptamer-based lateral flow devices (Apt-LFDs) for the quantitative detection of SARS-CoV-2 spike (S) protein. Molecular docking simulation was used to analyze the active binding sites of the aptamer to S protein, guiding complementary DNA (cDNA) design. Then a highly efficient freezing strategy was applied for the conjugation of gold nanoparticles (AuNPs) and DNA probes. Under optimal conditions, the linear range of the constructed Apt-LFDs was 0.1–1 μg/mL, and the limit of detection (LOD) was 51.81 ng/mL. The cross-reactivity test and stability test of the Apt-LFDs showed good specificity and reliability. The Apt-LFDs had recoveries ranging from 89.45 % to 117.12 % in pharyngeal swabs. Notably, the uncertainty of the analytical result was evaluated using a “bottom-up” approach. At a 95 % confidence level, the uncertainty report of (453.37±54.86) ng/mL with k = 2 was yielded. Overall, this study provides an important reference for the convenient and reliable detection of virus proteins based on LFDs.

Antimicrobial activity of compounds identified by artificial intelligence discovery engine targeting enzymes involved in Neisseria gonorrhoeae peptidoglycan metabolism

BackgroundNeisseria gonorrhoeae (Ng) causes the sexually transmitted disease gonorrhoea. There are no vaccines and infections are treated principally with antibiotics. However, gonococci rapidly develop resistance to every antibiotic class used and there is a need for developing new antimicrobial treatments. In this study we focused on two gonococcal enzymes as potential antimicrobial targets, namely the serine protease L,D-carboxypeptidase LdcA (NgO1274/NEIS1546) and the lytic transglycosylase LtgD (NgO0626/NEIS1212). To identify compounds that could interact with these enzymes as potential antimicrobials, we used the AtomNet virtual high-throughput screening technology. We then did a computational modelling study to examine the interactions of the most bioactive compounds with their target enzymes. The identified compounds were tested against gonococci to determine minimum inhibitory and bactericidal concentrations (MIC/MBC), specificity, and compound toxicity in vitro.ResultsAtomNet identified 74 compounds that could potentially interact with Ng-LdcA and 84 compounds that could potentially interact with Ng-LtgD. Through MIC and MBC assays, we selected the three best performing compounds for both enzymes. Compound 16 was the most active against Ng-LdcA, with a MIC50 value < 1.56 µM and MBC50/90 values between 0.195 and 0.39 µM. In general, the Ng-LdcA compounds showed higher activity than the compounds directed against Ng-LtgD, of which compound 45 had MIC50 values of 1.56–3.125 µM and MBC50/90 values between 3.125 and 6.25 µM. The compounds were specific for gonococci and did not kill other bacteria. They were also non-toxic for human conjunctival epithelial cells as judged by a resazurin assay. To support our biological data, in-depth computational modelling study detailed the interactions of the compounds with their target enzymes. Protein models were generated in silico and validated, the active binding sites and amino acids involved elucidated, and the interactions of the compounds interacting with the enzymes visualised through molecular docking and Molecular Dynamics Simulations for 50 ns and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA).ConclusionsWe have identified bioactive compounds that appear to target the N. gonorrhoeae LdcA and LtgD enzymes. By using a reductionist approach involving biological and computational data, we propose that compound Ng-LdcA-16 and Ng-LtgD-45 are promising anti-gonococcal compounds for further development.

Synthesis and investigation of biological activities of some newaryl-2-((5-phenyl-1.3.4-oxadiazol-2-yl)thio)ethan-1-ones

We have synthesized a series of aryl-2-((5-phenyl-1,3,4-oxadiazol-2-yl)thio)ethan-1-one derivatives (3a-j) by nucleophilic substitution of appropriately substituted phenacyl bromides 2(a-j) with 5-phenyl-1,3,4-oxadiazole-2-thiol (1) in dichloromethane and assessed their antimycobacterial, antibacterial, and antifungal activities. Compound 3g showed significantly greater antimycobacterial, antibacterial, and antifungal efficacy than the standard drug. Subsequently, a detailed analysis of the binding mode of the most potent compounds was conducted within the active binding site, utilizing the co-crystallized structures of Mycobacterium tuberculosis (Protein Data Bank [PDB] ID 2x22) and glucosamine-6-phosphate synthase (PDB ID 2VF5).. KEYWORDS :1,3,4-Oxadiazoles derivatives, Antibacterial, Antifungal, Antimycobacterial, Molecular docking.

Druglike Molecules Binding to Large Membrane Proteins: Absolute Binding Free Energy Computation.

In this research, we employed the alchemical double-decoupling method alongside restraining potentials, coupled with the FEPMD method, to ascertain the standard binding free energy of a drug-like molecule termed BHQ and three analogous compounds engineered with progressive addition of bulky para-alkyl groups binding to SERCA (Ca2+-ATPase of skeletal muscle sarcoplasmic reticulum). Integral transmembrane proteins represent crucial drug targets in numerous therapeutic interventions, presenting computational challenges due to their considerable system sizes. Our approach integrated the generalized born potential method and the spherical solvent boundary potential method, allowing us to explicitly focus on the active binding site while treating the remainder of the system implicitly. We evaluated contributions to the standard binding free energy from distinct interaction potentials: electrostatic, repulsive, dispersive, and restraining potentials, computed separately. The resulting absolute binding free energy of BHQ (11.63 kcal/mol) closely aligns with experimental measurements (10.56 kcal/mol). Notably, an accurate estimation of the absolute binding free energy was achieved for the simplest analog, created with the addition of a single para-methyl group. However, the analog with two para-methyl groups exhibited the highest binding free energy, which disagreed with experimental results. Determining the binding free energy of the BHQ analog engineered with three para-methyl groups presented challenges in convergence and resulted in the lowest free energy among the three.

Rare germline genetic variation in PAX8 transcription factor binding sites and susceptibility to epithelial ovarian cancer.

Common genetic variation throughout the genome together with rare coding variants identified to date explain about a half of the inherited genetic component of epithelial ovarian cancer risk. It is likely that rare variation in the non-coding genome will explain some of the unexplained heritability, but identifying such variants is challenging. The primary problem is lack of statistical power to identifying individual risk variants by association as power is a function of sample size, effect size and allele frequency. Power can be increased by using burden tests which test for association of carriers of any variant in a specified genomic region. This has the effect of increasing the putative effect allele frequency. PAX8 is a transcription factor that plays a critical role in tumour progression, migration and invasion. Furthermore, regulatory elements proximal to target genes of PAX8 are enriched for common ovarian cancer risk variants. We hypothesised that rare variation in PAX8 binding sites are also associated with ovarian cancer risk, but unlikely to be associated with risk of breast, colorectal or endometrial cancer. We have used publicly available, whole-genome sequencing data from the UK 100,000 Genomes Project to evaluate the burden of rare variation in PAX8 binding sites across the genome. Data were available for 522 ovarian cancers, 2,984 breast cancers, 2,696 colorectal cancers, 836 endometrial cancers and 2253 non-cancer controls. Active binding sites were defined using data from multiple PAX8 and H3K27 ChIPseq experiments. We found no association between the burden of rare variation in PAX8 binding sites (defined in several ways) and risk of ovarian, breast or endometrial cancer. An apparent association with colorectal cancer was likely to be a technical artefact as a similar association was also detected for rare variation in random regions of the genome. Despite the null result this study provides a proof-of -principle for using burden testing to identify rare, non-coding germline genetic variation associated with disease. Larger sample sizes available from large-scale sequencing projects together with improved understanding of the function of the non-coding genome will increase the potential of similar studies in the future.

Bimodal substrate binding in the active site of the glycosidase BcX.

Bacillus circulans xylanase (BcX) from the glycoside hydrolase family 11 degrades xylan through a retaining, double-displacement mechanism. The enzyme is thought to hydrolyze glycosidic bonds in a processive manner and has a large, active site cleft, with six subsites allowing the binding of six xylose units. Such an active site architecture suggests that oligomeric xylose substrates can bind in multiple ways. In the crystal structure of the catalytically inactive variant BcX E78Q, the substrate xylotriose is observed in the active site, as well as bound to the known secondary binding site and a third site on the protein surface. Nuclear magnetic resonance (NMR) titrations with xylose oligomers of different lengths yield nonlinear chemical shift trajectories for active site nuclei resonances, indicative of multiple binding orientations for these substrates for which binding and dissociation are in fast exchange on the NMR timescale, exchanging on the micro- to millisecond timescale. Active site binding can be modeled with a 2 : 1 model with dissociation constants in the low and high millimolar range. Extensive mutagenesis of active site residues indicates that tight binding occurs in the glycon binding site and is stabilized by Trp9 and the thumb region. Mutations F125A and W71A lead to large structural rearrangements. Binding at the glycon site is sensed throughout the active site, whereas the weak binding mostly affects the aglycon site. The interactions with the two active site locations are largely independent of each other and of binding at the secondary binding site.