Roxadustat, a small-molecule inhibitor of hypoxia-inducible factor prolyl hydroxylase domain 2 (HIF-PHD2) has been recently overruled by the American Food and Drug Administration (FDA) in Phase 3 ...clinical trials. This study provides insights into the dynamics of Roxadustat with PHD2 and proposes two FDA-approved drugs; Pemetrexed and Valrubicin to treat chronic kidney disease (CKD). Role of chemical scaffolds such as synthetic pyrimidine-based antifolate is found critical for PHD2 inhibitory activity, which is concurrent with the experimental findings for stimulating Endogenous erythropoietin (EPO) gene expression. Furthermore, Fe+2 and Mn+2 in solution are essential for imparting structural stability to the screened carboxylic and non-carboxylic acid drugs. Comparative analysis of FDA-approved drugs namely, Roxadustat, two-hit carboxylic, and non-carboxylic-acid type compounds (Pemetrexed and Valrubicin), as well as the control ligands (KU1 and 4JR), unveil structural dynamics of Roxadustat and its failure. However, the proposed FDA compounds, Pemetrexed and Valrubicin, used to treat mesothelioma, non-small cell lung cancer, and bladder cancer should be subjected to in vitro analysis for renal anemia.
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•Roxadustat toxic trait is both experimental and computational.•Pemetrexed, an FDA-approved drug is screened as a potential PHD2 inhibitor.•Fe+2 and Mn+2 are directly involved in stabilization of metal center active site.•ASP 218 is essential for metal ions to maintain their coordination geometries.
SARS-Cov-2 Omicron variant and its highly transmissible sublineages amidst news of emerging hybrid variants strengthen the evidence of its ability to rapidly spread and evolve giving rise to ...unprecedented future waves. Owing to the presence of isolated RBD, monomeric and trimeric Cryo-EM structures of spike protein in complex with ACE2 receptor, comparative analysis of Alpha, Beta, Gamma, Delta, and Omicron assist in a rational assessment of their probability to evolve as new or hybrid variants in future. This study proposes the role of hydration forces in mediating Omicron function and dynamics based on a stronger interplay between protein and solvent with each Covid wave. Mutations of multiple hydrophobic residues into hydrophilic residues underwent concerted interactions with water leading to variations in charge distribution in Delta and Omicron during molecular dynamics simulations. Moreover, comparative analysis of interacting moieties characterized a large number of mutations lying at RBD into constrained, homologous and low-affinity groups referred to as mutational drivers inferring that the probability of future mutations relies on their function. Furthermore, the computational findings reveal a significant difference in angular distances among variants of concern due 3 amino acid insertion (EPE) in Omicron variant that not only facilitates tight domain organization but also seems requisite for characterization of mutational processes. The outcome of this work signifies the possible relation between hydration forces, their impact on conformation and binding affinities, and viral fitness that will significantly aid in understanding dynamics of drug targets for Covid-19 countermeasures. The emerging scenario is that hydration forces and hydrophobic interactions are crucial variables to probe in mutational analysis to explore conformational landscape of macromolecules and reveal the molecular origins of protein behaviors.
β-lactam antibiotics are the most widely used antimicrobial agents since the discovery of benzylpenicillin in the 1920s. Unfortunately, these life-saving antibiotics are vulnerable to inactivation by ...continuously evolving β-lactamase enzymes that are primary resistance determinants in multi-drug resistant pathogens. The current study exploits the strategy of combination therapeutics and aims at identifying novel β-lactamase inhibitors that can inactivate the β-lactamase enzyme of the pathogen while allowing the β-lactam antibiotic to act against its penicillin-binding protein target. Inhibitor discovery applied the Site-Identification by Ligand Competitive Saturation (SILCS) technology to map the functional group requirements of the β-lactamase CMY-10 and generate pharmacophore models of active site. SILCS-MC, Ligand-grid Free Energy (LGFE) analysis and Machine-learning based random-forest (RF) scoring methods were then used to screen and filter a library of 700,000 compounds. From the computational screens 74 compounds were subjected to experimental validation in which β-lactamase activity assay, in vitro susceptibility testing, and Scanning Electron Microscope (SEM) analysis were conducted to explore their antibacterial potential. Eleven compounds were identified as enhancers while 7 compounds were recognized as inhibitors of CMY-10. Of these, compound 11 showed promising activity in β-lactamase activity assay, in vitro susceptibility testing against ATCC strains (E. coli, E. cloacae, E. agglomerans, E. alvei) and MDR clinical isolates (E. cloacae, E. alvei and E. agglomerans), with synergistic assay indicating its potential as a β-lactam enhancer and β-lactamase inhibitor. Structural similarity search against the active compound 11 yielded 28 more compounds. The majority of these compounds also exhibited β-lactamase inhibition potential and antibacterial activity. The non-β-lactam-based β-lactamase inhibitors identified in the current study have the potential to be used in combination therapy with lactam-based antibiotics against MDR clinical isolates that have been found resistant against last-line antibiotics.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Globally, antibiotic-resistant and tolerated bacterial isolates of Acinetobacter species are imposing high financial cost on health care systems and as such, molecular targets with promising immune ...protection could provide substantive benefits to human healthcare. Here, we performed an in silico based proteome-wide screening for antigenic B-cell derived T-cell epitopes and their following use to design a multi-epitope peptide vaccine that can effectively engage the host immune system against Acinetobacter nosocomialis SSA3 strain. Epitopes of the fimbrial biogenesis outer membrane usher FimD protein: YQQGINNYL and YRTNYTTVG were revealed appropriate for multi-epitope peptide construct designing. This protein has no homology to the host, essential to the pathogen survival and is localized at the pathogen surface. The predicted epitopes have high affinity for the highly expressed DRB*0101 allele in humans based on the lowest IC50 value in MHCPred and have an exo-membrane topology for efficient immune system recognition. The designed multi-epitope peptide vaccine is composed of the mentioned shortlisted antigenic epitopes linked to each other through a GPGPG linker, and an EAAAK linker that joined the multi-epitope peptide to the Cholera B subunit from Vibrio cholera as an adjuvant to increase vaccine construct antigenicity. The vaccine construct was docked and simulated with a transmembrane toll-like receptor (TLR4) that revealed construct stable binding with the TLR4 through the adjuvant, allowing the epitopes exposed to the host immune system essential for generating effective innate and long-lasting adaptive immunity. The designed multi-epitope peptide vaccine may prompt the development of a vaccine to control refractory and deleterious A. nosocomialis infections.
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•A multi-epitope peptide vaccine for Acinetobacter nosocomialis.•Two epitopes of fimbrial biogenesis outer membrane usher protein were used in vaccine design.•We expect the designed recombinant vaccine to be effective for A. nosocomialis infections.
Multi-drug resistant Vibrio vulnificus is a Gram-negative bacillus responsible for diseases, such as: sepsis, septicemia, gastroenteritis, and fatal necrotizing fasciitis in humans. The treatment and ...prevention of V. vulnificus infections are challenging because of resistance to antibiotics and the non-availability of a licensed vaccine. Considering this, an in-silico based approach comprising subtractive proteomics, immunoinformatics, molecular docking, and dynamics simulation studies is applied herein to identify potential epitope vaccine candidates for the mentioned pathogen. Two potential vaccine candidates: vibC and flgL are filtered based on essentiality, outer membrane localization, virulence, antigenic, pathway mapping, and cellular protein-protein network analysis. Using immunoinformatic tools, 9-mer B-cell derived T-cell antigenic epitopes are predicted for the said shortlisted two proteins that are demonstrating excellent affinity for predominant HLA allele (DRB1*0101) in human population. Screened peptides are used further in multi-epitope peptide designing and linked to an adjuvant to enhance the immunogenic properties of the designed construct. Furthermore, the construct was docked blindly to TLR4 immune receptor, and analyzed in conformational dynamics simulation to decipher the complex affinity and understand time dependent behavior, respectively. We expect this designed in silico construct to be useful for vaccinologists to evaluate its immune protective efficacy in in vivo animal models.
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This study investigates the alterations in structural, electronic, and optical characteristics of ZnSe1−x Inx (x = 0%, 12.5%, 25%) employing the framework of density functional theory (DFT), ...utilizing generalized gradient approximation (GGA) in conjunction with the full‐potential linearized augmented plane wave (FP‐LAPW) approach. The findings reveal that pure ZnSe exhibits a direct bandgap of 1.79 eV at the Γ point, which reduces to 0 eV upon doping with Indium, indicating a transition to metallic characteristics. This change is attributed to the predominant involvement of the d‐orbital of Zn, s‐orbital of Se, and p‐orbitals of Indium in the valence band of ZnSe1−x Inx materials. Conversely, the s‐orbital of Zn predominantly contributes to the conduction band of undoped ZnSe, whereas the d‐orbitals of Indium play a significant role in the conduction band of ZnSe1−x Inx (x = 0%, 12.5%, 25%). Moreover, the study computes other optical parameters, including reflectivity, electron energy loss spectrum, extinction coefficient, refractive index, and absorption coefficient, as functions of photon energy. A notable observation is the considerable rise in the zero‐frequency dielectric constant, ε1(0), which increases from 5.0 in pure ZnSe to 40.0 and 50.0 in Indium‐doped ZnSe, highlighting a significant alteration in electronic properties. Furthermore, optical analyses demonstrate an expansion in the absorption coefficient spectrum, which extends from photon energies of 2.0 eV in pristine ZnSe to begin at 0 eV in Indium‐doped variants, indicating a broadening of the material's capacity to absorb light across a wider spectrum of photon energies. This expansion infers improved light absorption potential, which could be particularly beneficial for the fabrication of light‐emitting modules and solar energy converters. These insights underline the considerable influence that Indium incorporation exerts on the band architecture and optical responses of ZnSe, offering critical directions for the advancement of optoelectronic devices.
The depicted energy bands show that the minimum of the conduction band and the maximum of the valence band for the assessed materials converge at the Γ‐point in the first Brillouin Zone (BZ), suggesting a direct band gap of 1.79 eV for unaltered ZnSe.
Noble metals such as gold (Au), zinc (Zn), and iron (Fe) are highly significant in both fundamental and technological contexts owing to their applications in optoelectronics, optical coatings, ...transparent coatings, photodetectors, light-emitting devices, photovoltaics, nanotechnology, batteries, and thermal barrier coatings. This study presents a comprehensive investigation of the optoelectronic properties of Fe(111) and Au, Zn/Fe(111) materials using density functional theory (DFT) first-principles method with a focus on both materials' spin orientations. The optoelectronic properties were obtained employing the generalized gradient approximation (GGA) and the full-potential linearized augmented plane wave (FP-LAPW) approach, integrating the exchange-correlation function with the Hubbard potential U for improved accuracy. The arrangement of Fe(111) and Au, Zn/Fe(111) materials was found to lack an energy gap, indicating a metallic behavior in both the spin-up state and the spin-down state. The optical properties of Fe(111) and Au, Zn/Fe(111) materials, including their absorption coefficient, reflectivity, energy-loss function, refractive index, extinction coefficient, and optical conductivity, were thoroughly examined for both spin channels in the spectral region from 0.0 eV to 14 eV. The calculations revealed significant spin-dependent effects in the optical properties of the materials. Furthermore, this study explored the properties of the electronic bonding between several species in Fe(111) and Au, Zn/Fe(111) materials by examining the density distribution mapping of charge within the crystal symmetries.
Noble metals such as gold (Au), zinc (Zn), and iron (Fe) are highly significant in both fundamental and technological contexts owing to their applications in optoelectronics, light-emitting devices, photovoltaics, nanotechnology, batteries, and thermal barrier coatings.
This study aims to investigate the binding potential of chemical compounds of Senna in comparison with the experimentally tested active phytochemicals against SARS-CoV-2 protein targets to assist in ...prevention of infection by exploring multiple treatment options. The entire set of phytochemicals from both the groups were subjected to advanced computational analysis that explored functional molecular descriptors from a set of known medicinal-based active therapeutics followed by MD simulations on multiple SARS-CoV-2 target proteins. Our findings manifest the importance of hydrophobic substituents in chemical structures of potential inhibitors through cross-validation with the FDA-approved anti-3CLpro drugs. Noteworthy improvement in end-point binding free energies and pharmacokinetic profiles of the proposed compounds was perceived in comparison to the control drug, vizimpro. Moreover, the identification of common drug targets namely; AKT1, PTGS1, TNF, and DPP4 between proposed active phytochemicals and Covid19 using network pharmacological analysis further substantiate the importance of medicinal scaffolds. The structural dynamics and binding affinities of phytochemical compounds xanthoangelol_E, hesperetin, and beta-sitosterol reported as highly potential against 3CLpro in cell-based and cell-free assays are consistent with the computational analysis. Whereas, the secondary metabolites such as sennosides A, B, C, D present in higher amount in Senna exhibited weak binding affinity and instability against the spike protein, helicase nsp13, RdRp nsp12, and 3CLpro. In conclusion, the results contravene fallacious efficacy claims of Senna tea interventions circulating on electronic/social media as Covid19 cure; thus emphasizing the importance of well-examined standardized data of the natural products in hand; thereby preventing unnecessary deaths under pandemic hit situations worldwide.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In-silico pipeline is applied for identifying and designing novel inhibitors against ZIKV NS1 protein. Comparative molecular docking studies are performed to explore the binding of structurally ...diverse compounds to ZIKV NS1 by AutoDock/Vina and GOLD. The Zika virus (ZIKV) is a flavivirus, responsible for life-threatening infections and transmitted by Aedes mosquitoes in other organisms. It is associated with Guillain Barre Syndrome (GBS) and microcephaly. This epidemic increase in GBS and microcephaly convoyed the World Health Organization to affirm ZIKV a public health crisis. To combat the ZIKV infections, non-structural protein 1 (NS1), a major host-interaction molecule contributing towards replication, pathogenesis and immune evasion is targeted in the current study. For this purpose, a comprehensive study is required to develop potential novel antiviral inhibitors. Three compounds were identified through docking programs exhibiting properties which are non-toxic to human host and could inhibit the elusive ZIKV. Significant interaction with active site residues and H-bond interactions with the key residues were analyzed for these compounds using molecular dynamics simulation. Free energy calculation predicted higher affinity of Deoxycalyxin-A for ZIKV NS1. This study contributes towards fighting ZIKV infections and can help researchers in designing drug for the treatment of ZIKV.
We have explored the optoelectronic structure and related thermoelectric properties of Bi2OX2 (X = S, Se, Te) using density functional theory and spin–orbit coupling (SOC). We report herein ...calculations of the bandgap of these bismuth sulfides/oxysulfides to participate in the recent debate regarding such values. The generalized gradient approximation calculations corrected using the SOC scheme estimated bandgaps of 0.950 eV, 0.635 eV, and 0.441 eV for Bi2OS2, Bi2OSe2, and Bi2OTe2, respectively, in close agreement with experimental results and showing better accuracy compared with available theoretical calculations. This bandgap range shows the potential use of Bi2OX2 for solar cell applications. Hence, we derived their optical and thermoelectric properties. Similarly to one of the parent materials, Bi2S3, a semiconductor with special photovoltaic and thermoelectric properties, the present derivatives Bi2OX2 show promising characteristics for exploration in the near future for use in solar cells and thermoelectric devices.
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