Identification of ligand binding sites in intrinsically disordered proteins with a differential binding score

Screening ligands directly binding to an ensemble of intrinsically disordered proteins (IDP) to discover potential hits or leads for new drugs is an emerging but challenging area as IDPs lack well-defined and ordered 3D-protein structures. To explore a new IDP-based rational drug discovery strategy, a differential binding score (DIBS) is defined. The basis of DIBS is to quantitatively determine the binding preference of a ligand to an ensemble of conformations specified by IDP versus such preferences to an ensemble of random coil conformations of the same protein. Ensemble docking procedures performed on repeated sampling of conformations, and the results tested for statistical significance determine the preferential ligand binding sites of the IDP. The results of this approach closely reproduce the experimental data from recent literature on the binding of the ligand epigallocatechin gallate (EGCG) to the intrinsically disordered N-terminal domain of the tumor suppressor p53. Combining established approaches in developing a new method to screen ligands against IDPs could be valuable as a screening tool for IDP-based drug discovery.

Cytotoxicity, Antimicrobial, and In Silico Studies of Secondary Metabolites From Aspergillus sp. Isolated From Tecoma stans (L.) Juss. Ex Kunth Leaves

Endophytes are prolific producers of privileged secondary metabolites with diverse therapeutic potential, although their anticancer and antimicrobial potential still have a room for further investigation. Herein, seven known secondary metabolites namely, arugosin C (1), ergosterol (2), iso-emericellin (3), sterigmatocystin (4), dihydrosterigmatocystin (5), versicolorin B (6), and diorcinol (7) were isolated from the rice culture of Aspergillus sp. retrieved from Tecoma stans (L.) Juss. ex Kunth leaves. Their anticancer and antimicrobial activities were evaluated in MTT and agar well diffusion assays, respectively. The cytotoxicity results showed that metabolite 3 displayed the best viability inhibition on the MCF-7 breast cancer cells with IC50 = 225.21 µM, while 5 on the HepG2 hepatocellular carcinoma cells with IC50 = 161.81 µM. 5 demonstrated a 60% apoptotic mode of cell death which is virtually correlated to its high docking affinity to Hsp90 ATP binding cleft (binding score −8.4 Kcal/mol). On the other side, metabolites 4 and 5 displayed promising antimicrobial activity especially on Pseudomonas aeruginosa with MIC = 125 μg/ml. The observed effect may be likely related to their excellent in silico inhibition of the bacterial DNA-gyrase kinase domain (binding score −10.28 Kcal/mol). To the best of our knowledge, this study is the first to report the promising cytotoxic and antibacterial activities of metabolites 3, 4, and 5 which needs further investigation and renovation to therapeutic leads.

Synthesis and evaluation of vitamin-drug conjugate for its anticancer activity

Cancer is the uncontrolled growth of cells in the human body that has the ability to spread. The purpose of the study is to explore that vitamins can be used as a targeting moiety for new anticancer drugs to address issues like non-selectivity, systemic toxicity. 5-Fluorouracil acetic acid–Vitamin D3 (5FUAC-Vit.D3) conjugate has been synthesized, characterized, and evaluated for its anticancer activity. 5-FUAC-Vit.D3 conjugate was synthesized via esterification mechanism in the presence of N-Hydroxy succinimide (NHS) and 1-(3-Dimethylaminopropyl)-3-ethylcarbodiimide (EDC) by using HCL as coupling agent. Formation of 5-FUAC-Vit.D3 conjugate via esteric bond and the structure of the compounds were confirmed by spectroscopic data, i.e., IR, NMR, and mass spectra. The docking studies showed that 5-FUAC-Vit.D3 conjugate interacted at Arg-215 and Lys-47 of the human thymidylate synthase proteins, through hydrogen bonding and ionic bonds respectively with a binding score of -8.614 which is higher than only 5-FU (-3.475). So, it was proved that forming 5-FUAC-Vit.D3 conjugate shows greater binding to the target protein.

Study of Molecular Docking of Alkaloid Derivative Compounds from Stem Karamunting (Rhodomyrtus tomentosa)Against α-Glucosidase Enzymes

Karamunting plant (Rhodomyrtus tomentosa) is a traditional medicinal plant. The leaves, roots, stems, and fruits of Karamunting have been identified, and their biological activities are antioxidants, antibacterial, antidiabetic, anti-inflammatory, and anticancer that contained alkaloids, tannins, and flavonoids. The types of alkaloids found in karamunting stems are homolycorine, ismine, lycorine, maritidine and tazetine. This study aims to determine the binding score of alkaloid-derived compounds with protein α-glucosidase and determine the protein's active site bound to the ligand. The method used in this research is Protein-Ligand ANT-System (PLANTS). The results showed that the anchoring score of homolycorine was -60.83 kcal/mol, ismine -64.42 kcal/mol, lycorine -71.20 kcal/mol, maritidine -61.82 kcal/mol, and tazetine -65.02 kcal/mol. The active sites used for binding are Glu526, Gly555, and Pro556. The average score for anchoring alkaloid-derived compounds with protein α-glucosidase is 83.84%. This number indicates that karamunting stems can be used as antidiabetic.

Chloroform extract and acetyl-11-keto-beta-boswellic acid from Boswellia dalzielii stem bark induce apoptosis and cell cycle blockage in AW8507 cells

Background Globally, head and neck cancer is the sixth most common cancer. Despite the advancement in treatment, drug resistance remains a major cause for setback. In an earlier work, the authors reported that Boswellia dalzielii (Hutch) stem bark exhibited dose-dependent cytotoxicity in head and neck cancer cells, AW8507. Therefore, the cell death induction effect of Boswellia dalzielii stem bark chloroform extract in head and neck cancer cell line, AW8507, and its derived constituent on cell cycle and apoptosis proteins was further investigated. Methods The cell death induction activity of the Boswellia dalzielii stem bark chloroform fraction (CLBD) in AW8507 was determined using Annexin V-FITC/PI staining in flow cytometry. High-performance liquid chromatography-mass spectrometry was employed for compounds analysis of the CLBD, and reverse virtual screening was used to identify the mechanism of action of the compound, acetyl-11-keto-beta-boswellic acid, that was elucidated in the Boswellia dalzielii chloroform fraction. Results The data obtained showed that Boswellia dalzielii stem bark Chloroform extract increased the percentage of cells presenting for early apoptosis from 4.14 to 10.10% in AW8507 cells. High-performance liquid chromatography-mass spectrometry analysis of the chloroform fraction identified acetyl-11-keto-beta-boswellic acid. Reverse virtual screening on selected proteins showed that acetyl-11-keto-beta-boswellic acid is a multi-protein target compound. It binds preferably to phosphorylated-cyclin dependent kinase 1 (p-CDK1) (binding score = − 9.2 kcal/mol), blocking the activation of cyclin B-CDK1 needed for cell cycle progression at G2/M phase of the cell cycle. Acetyl-11-keto-beta-boswellic acid also binds more tightly with αβ tubulin (binding score = 8.9 kcal/mol) than with the standard drug, docetaxel (binding score = 8.3 kcal/mol). Conclusions The results obtained confirmed the culpability of Boswellia dalzielii-derived acetyl-11-keto-beta-boswellic acid in the obstruction of the cell cycle progression in head and neck cancer cell line, AW8507; and the induction of apoptosis earlier reported for Boswellia dalzielii (Hutch) stem bark. Additional in vitro and/or in vivo studies would be required to validate in silico observations.

Would It Be Possible to Stabilize Prefusion SARS-COV-2 Spikes with Ligands?

<p>Fusion to host cells and infection caused by Severe Acute Respiratory Syndrome coronavirus (SARS)-CoV2 was inhibited <i>in vitro</i> by PP mutations stabilizing prefusion states of their spike (S) protein native conformation, as reported by several authors. However, the possible stabilization of S by binding-ligands, rather than by mutations, have not been explored, nor it is yet known if it would be possible. In this work, the so called “spring-loaded switch-folding” (SLSF) expanding S amino acid residues 960-1010 was computationally targeted because SLSF surrounded the previously described PP mutations. The SLSF trimeric prefusion conformation consisted in 3x3 α-helices that require a transition to 3 longer α-helices before viral/host membrane fusion, similarly to what occurs in other enveloped viruses. Results of a double computational screening among hundred of thousands of natural compounds for binding to the wild-type isolated SLSF conformer predicted more leads for its trimers than for monomers. Further ranked by the number of SLSF-conformers bound, some of the predicted top-leads may deserve experimental validation. Additional screening among thousands of drugs identified Tinosorb, an star-shaped molecule, as the lowest binding-score lead to SLSF in the low nM range. However, despite its lower binding-score, 3-fold molecular symmetry and fitting the inner part of the SLSF α-helices, we were unable to experimentally show any specific inhibition of S-mediated membrane fusion using an VSV-pseudotyped infectivity assay, nor any virtual binding to S-SLSF using docking to whole native S trimers. Further exploring the star-shaped features may provide new molecular alternatives to cross-bind the α-helices of S-SLSF to hypothetically inhibit coronavirus fusion.<b></b></p>

Development of Multi-concentration Cu:Ag Bimetallic Nanoparticles as a Promising Bactericidal for Antibiotic-Resistant Bacteria as Evaluated with Molecular Docking Study

The present study is concerned with evaluating the influence of various concentrations of Ag within Cu:Ag bimetallic nanoparticles developed for use as a promising anti-bacterial agent against antibiotic-resistant bacteria. Here, Cu:Ag bimetallic nanoparticles with various concentration ratios (2.5, 5.0, 7.5, and 10 wt%) of Ag in fixed amount of Cu labeled as 1:0.025, 1:0.050, 1:0.075, and 1:0.1 were synthesized using co-precipitation method with ammonium hydroxide and deionized water as solvent, polyvinyl pyrrolidone as a capping agent, and sodium borohydride and ascorbic acid as reducing agents. These formulated products were characterized through a variety of techniques. XRD confirmed phase purity and detected the presence of distinct fcc structures belonging to Cu and Ag phases. FTIR spectroscopy confirmed the presence of vibrational modes corresponding to various functional groups and recorded characteristic peak emanating from the bimetallic. UV–visible spectroscopy revealed reduction in band gap with increasing Ag content. SEM and HR-TEM micrographs revealed spherical morphology of Ag-doped Cu bimetallic with small and large scale agglomerations. The samples exhibited varying dimensions and interlayer spacing. Bactericidal action of synthesized Cu:Ag bimetallic NPs depicted statistically significant (P < 0.05) inhibition zones recorded for various concentrations of Ag dopant against Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), and Acinetobacter baumannii (A. baumannii) ranging from (0.85–2.8 mm), (0.55–1.95 mm) and (0.65–1.85 mm), respectively. Broadly, Cu:Ag bimetallic NPs were found to be more potent against gram-positive compared with gram-negative. Molecular docking study of Ag–Cu bimetallic NPs was performed against β-lactamase which is a key enzyme of cell wall biosynthetic pathway from both S. aureus (Binding score: − 4.981 kcal/mol) and A. bauminnii (Binding score: − 4.013 kcal/mol). Similarly, binding interaction analysis against FabI belonging to fatty acid biosynthetic pathway from A. bauminnii (Binding score: − 3.385 kcal/mol) and S. aureus (Binding score: − 3.012 kcal/mol) along with FabH from E. coli (Binding score: − 4.372 kcal/mol) was undertaken. These theoretical computations indicate Cu-Ag bimetallic NPs as possible inhibitor of selected enzymes. It is suggested that exploring in vitro inhibition potential of these materials may open new avenues for antibiotic discovery.

Impact of Bi Doping into Boron Nitride Nanosheets on Electronic and Optical Properties Using Theoretical Calculations and Experiments

In the present work, boron nitride (BN) nanosheets were prepared through bulk BN liquid phase exfoliation while various wt. ratios (2.5, 5, 7.5 and 10) of bismuth (Bi) were incorporated as dopant using hydrothermal technique. Our findings exhibit that the optical investigation showed absorption spectra in near UV region. Density functional theory calculations indicate that Bi doping has led to various modifications in the electronic structures of BN nanosheet by inducing new localized gap states around the Fermi level. It was found that bandgap energy decrease with the increase of Bi dopant concentrations. Therefore, in analysis of the calculated absorption spectra, a redshift has been observed in the absorption edges, which is consistent with the experimental observation. Additionally, host and Bi-doped BN nanosheets were assessed for their catalytic and antibacterial potential. Catalytic activity of doped free and doped BN nanosheets was evaluated by assessing their performance in dye reduction/degradation process. Bactericidal activity of Bi-doped BN nanosheets resulted in enhanced efficiency measured at 0–33.8% and 43.4–60% against S. aureus and 0–38.8% and 50.5–85.8% against E. coli, respectively. Furthermore, In silico molecular docking predictions were in good agreement with in-vitro bactericidal activity. Bi-doped BN nanosheets showed good binding score against DHFR of E. coli (− 11.971 kcal/mol) and S. aureus (− 8.526 kcal/mol) while binding score for DNA gyrase from E. coli (− 6.782 kcal/mol) and S. aureus (− 7.819 kcal/mol) suggested these selected enzymes as possible target.

Doping of Mg on ZnO Nanorods Demonstrated Improved Photocatalytic Degradation and Antimicrobial Potential with Molecular Docking Analysis

Various concentrations of Mg-doped ZnO nanorods (NRs) were prepared using co-precipitation technique. The objective of this study was to improve the photocatalytic properties of ZnO. The effect of Mg doping on the structure, phase constitution, functional groups presence, optical properties, elemental composition, surface morphology and microstructure of ZnO was evaluated with XRD, FTIR, UV–Vis spectrophotometer, EDS, and HR-TEM, respectively. Optical absorption spectra obtained from the prepared samples showed evidence of blueshift upon doping. XRD results revealed hexagonal wurtzite phase of nanocomposite with a gradual decrease in crystallite size with Mg addition. PL spectroscopy showed trapping efficiency and migration of charge carriers with electron–hole recombination behavior, while HR-TEM estimated interlayer d-spacing. The presence of chemical bonding, vibration modes and functional groups at the interface of ZnO was revealed by FTIR and Raman spectra. In this study, photocatalytic, sonocatalytic and sonophotocatalytic performance of prepared NRs was systematically investigated by degrading a mixture of methylene blue and ciprofloxacin (MBCF). Experimental results suggested that improved degradation performance was shown by Mg-doped ZnO NRs. We believe that the product synthesized in this study will prove to be a beneficial and promising photocatalyst for wastewater treatment. Conclusively, Mg-doped ZnO exhibited substantial (p < 0.05) efficacy against gram-negative (G-ve) as compared to gram-positive (G+ve) bacteria. In silico molecular docking studies of Mg-doped ZnO NRs against DHFR (binding score: − 7.518 kcal/mol), DHPS (binding score: − 6.973 kcal/mol) and FabH (− 6.548 kcal/mol) of E. coli predicted inhibition of given enzymes as possible mechanism behind their bactericidal activity.

Identification of novel candidate CD8+ T cell epitopes of the SARS-CoV2 with homology to other seasonal coronaviruses

Background Individuals who have not been exposed to the SARS-CoV2 virus have been shown to have T cells that respond to the virus, possibly due to the presence of cross-reactive T cell responses to other seasonal human coronaviruses (HCoVs). Such cross-reactive T cell immunity may lead to immunopathology or protection. Results To understand the influence of such cross-reactive T cell responses, we used IEDB (Immune epitope database) and NetMHCpan (ver. 4.1) to identify candidate CD8 + T cell epitopes, restricted through HLA-A and B alleles, which are seen in a frequency of > 10% in the Sri Lankan population. Conservation analysis was carried out for these candidate epitopes with the HCoVs, OC43, HKU1, NL63 and with the current circulating different variants of SARS-CoV2. 12/18 the candidate CD8 + T cell epitopes (binding score of ≥ 0.90), which had a high degree of homology (> 75%) with the other three HCoVs were within the NSP12 and NSP13 proteins. They were predicted to be restricted through HLA-A*2402, HLA-A*201, HLA-A*206 and HLA-B alleles B*3501. 31 candidate CD8 + T cell epitopes that were specific to SARS-CoV2 virus (< 25% homology with other HCoVs) were predominantly identified within the structural proteins (spike, envelop, membrane and nucleocapsid) and the NSP1, NSP2 and NSP3. They were predominantly restricted through HLA-B*3501 (6/31), HLA-B*4001 (6/31), HLA-B*4403(7/31) and HLA-A*2402 (8/31). The candidate CD8 + T cell epitopes that were homologous or were specific, with a binding score of ≥ 0.90, were found to be highly conserved within the SARS-CoV2 variants identified so far. Conclusions It would be crucial to understand T cell responses that associate with protection and the differences in the functionality and phenotype of epitope specific T cell responses, presented through different HLA alleles common in different geographical groups in order to understand disease pathogenesis.