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Enterococcus faecalis, a gram-positive bacterium, is among the most common nosocomial pathogens due to its limited susceptibility to antibiotics and its reservoir of the genes coding for virulence factors. Bacterial enzymes such as kinases and phosphorylases play important roles in diverse functions of a bacterial cell and, thus, are potential antibacterial drug targets. In Gram-positive bacteria, HPr Kinase/Phosphorylase (HPrK/P), a bifunctional enzyme is involved in the regulation of carbon catabolite repression by phosphorylating/dephosphorylating the histidine-containing phosphocarrier protein (HPr) at Ser46 residue. Deficiencies in HPrK/P function leads to severe defects in bacterial growth. This study aimed at identifying novel inhibitors of E. faecalis HPrK/P from a commercial compound library using structure-based virtual screening. The hit molecules were purchased and their effect on enzyme activity and growth of resistant E. faecalis was evaluated in vitro. Furthermore, docking and molecular dynamics simulations were performed to study the interactions of the hit compounds with HPrK/P. Among the identified hit molecules, two compounds inhibited the phosphorylation of HPr as well as significantly reduced the growth of resistant E. faecalis in vitro. These identified potential HPrK/P inhibitors open new research avenues towards the development of novel antimicrobials against resistant Gram-positive bacteria.

Dwarf galaxies are excellent cosmological probes, because their shallow potential wells make them very sensitive to the key processes that drive galaxy evolution, including baryonic feedback, tidal interactions, and ram pressure stripping. However, some of the key parameters of dwarf galaxies, which help trace the effects of these processes, are still debated, including the relationship between their sizes and masses. We re-examine the Fornax Cluster dwarf population from the point of view of isomass-radius--stellar mass relations (IRSMRs) using the Fornax Deep Survey Dwarf galaxy Catalogue, with the centrally located (among dwarfs) $3.63 \mathcal{M}_{\odot}$~pc$^{-2}$ isodensity radius defining our fiducial relation. This relation is a powerful diagnostic tool for identifying dwarfs with unusual structure, as dwarf galaxies' remarkable monotonicity in light profile shapes, as a function of stellar mass, reduces the relation's scatter tremendously. By examining how different dwarf properties (colour, tenth-nearest-neighbour distance, etc.) correlate with distance from our fiducial relation, we find a significant population of structural outliers with comparatively lower central mass surface density and larger half-light-radii, residing in locally denser regions in the cluster, albeit with similar red colours. We propose that these faint, extended outliers likely formed through tidal disturbances, which make the dwarfs more diffuse, but with little mass loss. Comparing these outliers with ultra-diffuse galaxies (UDGs), we find that the term UDG lacks discriminatory power; UDGs in the Fornax Cluster lie both on and off of IRSMRs defined at small radii, while IRSMR outliers with masses below $\sim 10^{7.5} \mathcal{M}_{\odot}$ are excluded from the UDG classification due to their small effective radii., Comment: 16 pages (+2 appendix), 10 figures, accepted for publication in MNRAS

Proteins in the thioredoxin superfamily share a similar fold, contain a -CXXC- active site, and catalyze oxidoreductase reactions by dithiol-disulfide exchange mechanisms. Protein disulfide isomerase (PDI) has two -CGHC- active sites. For in vitro studies, oxidation/reduction of PDI during the catalytic cycle is accomplished with glutathione. Glutathione may act as electron donor/acceptor for PDI also in vivo, but at least for oxidation reactions, GSSG probably is not the major electron acceptor and PDI may not have evolved to react with glutathione with high affinity, but merely having adequate affinity for both glutathione and folding proteins/peptides. Glutaredoxins, on the other hand, have a high affinity for glutathione. They commonly have -CXFC- or -CXYC- active site, where the tyrosine residue forms part of the GSH binding groove. Mutating the active site of PDI to a more glutaredoxin-like motif increased its reactivity with glutathione. All such variants showed an increased rate in GSH-dependent reduction or GSSG-dependent oxidation of the active site, as well as a decreased rate of the native disulfide bond formation, with the magnitude of the effect increasing with glutathione concentration. This suggests that these variants lead to competition in binding between glutathione and folding protein substrates.

Proteins in the thioredoxin superfamily share a similar fold, contain a -CXXC- active site, and catalyze oxidoreductase reactions by dithiol-disulfide exchange mechanisms. Protein disulfide isomerase (PDI) has two -CGHC- active sites. For in vitro studies, oxidation/reduction of PDI during the catalytic cycle is accomplished with glutathione. Glutathione may act as electron donor/acceptor for PDI also in vivo, but at least for oxidation reactions, GSSG probably is not the major electron acceptor and PDI may not have evolved to react with glutathione with high affinity, but merely having adequate affinity for both glutathione and folding proteins/peptides. Glutaredoxins, on the other hand, have a high affinity for glutathione. They commonly have -CXFC- or -CXYC- active site, where the tyrosine residue forms part of the GSH binding groove. Mutating the active site of PDI to a more glutaredoxin-like motif increased its reactivity with glutathione. All such variants showed an increased rate in GSH-dependent reduction or GSSG-dependent oxidation of the active site, as well as a decreased rate of the native disulfide bond formation, with the magnitude of the effect increasing with glutathione concentration. This suggests that these variants lead to competition in binding between glutathione and folding protein substrates.

The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. Since the initial outbreak, the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, omicron is currently classified as a variant of concern (VOC) by the World Health Organization, as the previously circulating variants have been replaced by it. In this work, we have focused on the mutations observed in omicron sub lineages BA.1, BA.2, BA.4 and BA.5, particularly at the receptor-binding domain (RBD) of the spike protein that is responsible for the interactions with the host ACE2 receptor and binding of antibodies. Studying such mutations is particularly important for understanding the viral infectivity, spread of the disease and for tracking the escape routes of this virus from antibodies. Molecular dynamics (MD) based alchemical free energy calculations have been shown to be very accurate in predicting the free energy change, due to a mutation that could have a deleterious or a stabilizing effect on either the protein itself or its binding affinity to another protein. Here, we investigated the significance of five spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations. For comparison, we also used conventional MD simulations combined with a Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) based approach, and compared our results with the available experimental data. Overall, the alchemical free energy calculations performed far better than the MM-GBSA approach in predicting the individual impact of the mutations. When considering the experimental variation, the alchemical free energy method was able to produce a relatively accurate prediction for N501Y, the mutant that has previously been reported to increase the binding affinity to hACE2. On the other hand, the other individual mutations seem not to have a significant effect on the spike RBD binding affinity towards hACE2.

(Chymo)trypsin-like serine fold proteases belong to the serine/cysteine proteases found in eukaryotes, prokaryotes, and viruses. Their catalytic activity is carried out using a triad of amino acids, a nucleophile, a base, and an acid. For this superfamily of proteases, we propose the existence of a universal 3D structure comprising 11 amino acids near the catalytic nucleophile and base – Nucleophile-Base Catalytic Zone (NBCZone). The comparison of NBCZones among 169 eukaryotic, prokaryotic, and viral (chymo)trypsin-like proteases suggested the existence of 15 distinct groups determined by the combination of amino acids located at two “key” structure-functional positions 54T and 55T near the catalytic base His57T. Most eukaryotic and prokaryotic proteases fell into two major groups, [ST]A and TN. Usually, proteases of [ST]A group contain a disulfide bond between cysteines Cys42T and Cys58T of the NBCZone. In contrast, viral proteases were distributed among seven groups, and lack this disulfide bond. Furthermore, only the [ST]A group of eukaryotic proteases contains glycine at position 43T, which is instrumental for activation of these enzymes. In contrast, due to the side chains of residues at position 43T prokaryotic and viral proteases do not have the ability to carry out the structural transition of the eukaryotic zymogen-zyme type.

The Spitzer Survey of Stellar Structure in Galaxies (S$^{4}$G) is a detailed study of over 2300 nearby galaxies in the near-infrared (NIR), which has been critical to our understanding of the detailed structures of nearby galaxies. Because the sample galaxies were selected only using radio-derived velocities, however, the survey favored late-type disk galaxies over lenticulars and ellipticals. A follow-up Spitzer survey was conducted to rectify this bias, adding 465 early-type galaxies (ETGs) to the original sample, to be analyzed in a manner consistent with the initial survey. We present the data release of this ETG extension, up to the third data processing pipeline (P3): surface photometry. We produce curves of growth and radial surface brightness profiles (with and without inclination corrections) using reduced and masked Spitzer IRAC 3.6$\mu$m and 4.5$\mu$m images produced through Pipelines 1 and 2, respectively. From these profiles, we derive the following integrated quantities: total magnitudes, stellar masses, concentration parameters, and galaxy size metrics. We showcase NIR scaling relations for ETGs among these quantities. We examine general trends across the whole S$^{4}$G and ETG extension among our derived parameters, highlighting differences between ETGs and late-type galaxies (LTGs). ETGs are, on average, more massive and more concentrated than LTGs, and also show subtle distinctions among ETG morphological sub-types. We also derive the following scaling relations and compare with previous results in visible light: mass--size (both half-light and isophotal), mass--concentration, mass--surface brightness (central, effective, and within 1 kpc), and mass--color. We find good agreement with previous works, though some relations (e.g., mass--central surface brightness) will require more careful multi-component decompositions to be fully understood., Comment: 25 pages, 17 figures, accepted for publication in A&A

Due to the ever-increasing antimicrobial resistance there is an urgent need to continuously design and develop novel antimicrobial agents. Inspired by the broad antibacterial activities of various heterocyclic compounds such as 2-quinolone derivatives, we designed and synthesized new methyl-(2-oxo-1,2-dihydroquinolin-4-yl)-L-alaninate-1,2,3-triazole derivatives via 1,3-dipolar cycloaddition reaction of 1-propargyl-2-quinolone-L-alaninate with appropriate azide groups. The synthesized compounds were obtained in good yield ranging from 75 to 80 %. The chemical structures of these novel hybrid molecules were determined by spectroscopic methods and the antimicrobial activity of the compounds was investigated against both bacterial and fungal strains. The tested compounds showed significant antimicrobial activity and weak to moderate antifungal activity. Despite the evident similarity of the quinolone moiety of our compounds with fluoroquinolones, our compounds do not function by inhibiting DNA gyrase. Computational characterization of the compounds shows that they have attractive physicochemical and pharmacokinetic properties and could serve as templates for developing potential antimicrobial agents for clinical use.

Coagulation, complement, and innate immunity are tightly interwoven and form an alliance that can be traced back to early eukaryotic evolution. Here we employed an ecoimmunological approach using Tissue Factor Pathway Inhibitor (TFPI)-1-derived peptides from the different classes of vertebrates (i.e. fish, reptile, bird, and mammals) and tested whether they can boost killing of various human bacterial pathogens in plasma. We found signs of species-specific conservation and diversification during evolution in these peptides that significantly impact their antibacterial activity. Though all peptides tested executed bactericidal activity in mammalian plasma (with the exception of rodents), no killing was observed in plasma from birds, reptiles, and fish, pointing to a crucial role for the classical pathway of the complement system. We also observed an interference of these peptides with the human intrinsic pathway of coagulation though, unlike complement activation, this mechanism appears not to be evolutionary conserved.

Oligonucleotide-based therapy has experienced remarkable development in the past 2 decades, but its broad applications are severely hampered by delivery vectors. Widely used viral vectors and lipid nanovectors are suffering from immune clearance after repeating usage or requiring refrigerated transportation and storage, respectively. In this work, amino-modified virus-mimetic spike silica nanoparticles (NH 2 -SSNs) were fabricated using a 1-pot surfactant-free approach with controlled spike lengths, which were demonstrated with excellent delivery performance and biosafety in nearly all cell types and mice. It indicated that NH 2 -SSNs entered cells by spike-dependent cell membrane docking and dynamin-dependent endocytosis. The positively charged spikes with proper length on the surface can facilitate the efficient encapsulation of RNAs, protect the loaded RNAs from degradation, and trigger an early endosome escape during intracellular trafficking, similarly to the cellular internalization mechanism of virions. Regarding the fantastic properties of NH 2 -SSNs in nucleic acid delivery, it revealed that nanoparticles with solid spikes on the surface would be excellent vehicles for gene therapy, presenting self-evident advantages in storage, transportation, modification, and quality control in large-scale production compared to lipid nanovectors.

We investigate the origin of the extraplanar diffuse ionized gas (eDIG) and its predominant ionization mechanisms in five nearby (17-46 Mpc) low-mass ($10^9\text{-}10^{10}$ $M_{\odot}$) edge-on disk galaxies: ESO 157-49, ESO 469-15, ESO 544-27, IC 217, and IC 1553. We acquired Multi Unit Spectroscopic Explorer (MUSE) integral field spectroscopy and deep narrowband H$\alpha$ imaging of our sample galaxies. To investigate the connection between in-plane star formation and eDIG, we perform a photometric analysis of our narrowband H$\alpha$ imaging. We measure eDIG scale heights of $h_{z\text{eDIG}} = 0.59 \text{-} 1.39$ kpc and find a positive correlation between them and specific star formation rates. In all galaxies, we also find a strong correlation between extraplanar and midplane radial H$\alpha$ profiles. Using our MUSE data, we investigate the origin of eDIG via kinematics. We find ionized gas rotation velocity lags above the midplane with values between 10 and 27 km s$^{-1}$ kpc$^{-1}$. While we do find hints of an accretion origin for the ionized gas in ESO 157-49, IC 217, and IC 1553, overall the ionized gas kinematics of our galaxies do not match a steady galaxy model or any simplistic model of accretion or internal origin for the gas. We also construct standard diagnostic diagrams and emission-line maps (EW(H$\alpha$), [NII]/H$\alpha$, [SII]//H$\alpha$, [OIII]/H$\beta$) and find regions consistent with mixed OB star and hot low-mass evolved stars (HOLMES) ionization, and mixed OB-shock ionization. Our results suggest that OB stars are the primary driver of eDIG ionization, while both HOLMES and shocks may locally contribute to the ionization of eDIG to a significant degree. Despite our galaxies' similar structures and masses, we find a surprisingly composite image of ionization mechanisms and a multifarious origin for the eDIG., Comment: 21 pages, 14 figures, accepted to Astronomy & Astrophysics

Funding Information: We gratefully acknowledge the two projects – “Developmental evaluation of the Finnish sustainable development policies and transformation pathways ( PATH2030 )”, funded by the Finnish Government unit of analysis, assessment and research activities, and “Towards Eco-Welfare State: Orchestrating for Systemic Impact (ORSI)”, funded by the Strategic Research Council at the Academy of Finland (grant no. 327768 ) for their financial contributions to this study. Publisher Copyright: © 2021 The Authors No country is on its way to achieving the Sustainable Development Goals by the year 2030. The expectations for rapid transformations have not materialized, and hence a strategy combining both incremental and more radical changes is needed. Such strategies have been discussed in other fields, but they have been largely unaddressed in relation to sustainable development. This article seeks to increase understanding of how changes of various sizes interact in sustainable development policy. Here, we utilize the concept of small wins as concrete, implemented and often incremental changes that can create momentum for larger-scale changes. By analyzing key government documents and reports, interviews, questionnaires and workshop material, we study Finland's sustainable development policy. We focus on changes in the realms of the 4Is, meaning institutions, interests, information and ideas. Based on the research, Finland has been particularly successful in building multi-sectoral institutions and mainstreaming the idea of sustainable development. There is a vast information base available. In practice, however, various conflicts of interest remain unsolved. We conclude that while a sustainable development policy based solely on small wins can be too slow and incremental to meet the major sustainability challenges of our time, it would pave the way for more transformative reforms. These include, for example, the current Government Programme based on the idea of sustainable development and challenging the status quo on various fronts.

Nanoemulsions are a rapidly growing drug delivery technology capable of increasing a drug's aqueous solubility and stability. A novel oil‐in‐water nanoemulsion using a polymer, poly(decalactone) (PDL), instead of a conventional oil was recently reported. The amount of drug loading in a polymer‐based formulation is mainly governed by the drug's solubility in the polymer. Thus, herein the power of molecular dynamics simulations (MDS) for the calculation of the Hildebrand solubility parameter to predict PDL–drug miscibility is utilized. The MDS results are subsequently verified by formulating a PDL nanoemulsion with a dispersed droplet size of less than 200 nm by using a block copolymer of PDL (mPEG‐b‐PDL) as a surfactant, with seven different hydrophobic drug molecules. The MDS results are consistent with the experimental findings in terms of increment in the aqueous solubilities of the drugs in PDL nanoemulsion, where celecoxib demonstrated the highest while methotrexate exhibited the lowest solubility increment. Consequently, the reported MDS method can be utilized to predict a drug's solubility/miscibility in PDL to estimate the level of drug loading. The MDS facilitated screening of drugs could consequently emerge as an efficient approach in designing PDL nanoemulsions stabilized by mPEG‐b‐PDL or other similar systems.

Drugs that target human thymidylate synthase (hTS) are widely used in anti-cancer therapy. However, treatment with classical substrate-site-directed TS inhibitors induces its over-expression and the development of drug resistance. We thus pursued an alternative strategy that led to the discovery of TS-dimer disrupters that bind at the monomer-monomer interface and shift the dimerization equilibrium of both the recombinant and the intracellular protein toward the inactive monomers. We performed a structural, spectroscopic and kinetic investigation of the effects of these small molecules andthe best one, E7, accelerates the proteasomal degradation of hTS in cancer cells. E7 showed a superior anticancer profile to fluorouracil in a mouse model of human pancreatic and ovarian cancer. Thus, over sixty years after the discovery of the first TS prodrug inhibitor, fluorouracil, E7 breaks the link between TS inhibition and enhanced expression in response, providing a strategy to fight drug-resistant cancers.

The modification of genes in animal models has evidently and comprehensively improved our knowledge on proteins and signaling pathways in human physiology and pathology. In this review, we discuss almost 40 monogenic rare diseases that are enriched in the Finnish population and defined as the Finnish disease heritage (FDH). We will highlight how gene-modified mouse models have greatly facilitated the understanding of the pathological manifestations of these diseases and how some of the diseases still lack proper models. We urge the establishment of subsequent international consortiums to cooperatively plan and carry out future human disease modeling strategies. Detailed information on disease mechanisms brings along broader understanding of the molecular pathways they act along both parallel and transverse to the proteins affected in rare diseases, therefore also aiding understanding of common disease pathologies.

Approaches to increase the efficiency in developing drugs and diagnostics tools, including new drug delivery and diagnostic technologies, are needed for improved diagnosis and treatment of major diseases and health problems such as cancer, inflammatory diseases, chronic wounds, and antibiotic resistance. Development within several areas of research ranging from computational sciences, material sciences, bioengineering to biomedical sciences and bioimaging is needed to realize innovative drug development and diagnostic (DDD) approaches. Here, an overview of recent progresses within key areas that can provide customizable solutions to improve processes and the approaches taken within DDD is provided. Due to the broadness of the area, unfortunately all relevant aspects such as pharmacokinetics of bioactive molecules and delivery systems cannot be covered. Tailored approaches within (i) bioinformatics and computer-aided drug design, (ii) nanotechnology, (iii) novel materials and technologies for drug delivery and diagnostic systems, and (iv) disease models to predict safety and efficacy of medicines under development are focused on. Current developments and challenges ahead are discussed. The broad scope reflects the multidisciplinary nature of the field of DDD and aims to highlight the convergence of biological, pharmaceutical, and medical disciplines needed to meet the societal challenges of the 21st century.

Summary Species tropism constitutes a serious problem for developing relevant animal models of infection. Human pathogens can express virulence factors that show specific selectivity to human proteins, while their affinity for orthologs from other species can vary significantly. Suitable animal species must be used to analyse whether virulence factors are potential targets for drug development. We developed an assay that rapidly predicts applicable animal species for studying virulence factors binding plasma proteins. We used two well‐characterized Staphylococcus aureus proteins, SSL7 and Efb, to develop an ELISA‐based inhibition assay using plasma from different animal species. The interaction between SSL7 and human C5 and the binding of Efb to human fibrinogen and human C3 was studied. Affinity experiments and Western blot analyses were used to validate the assay. Human, monkey and cat plasma interfered with binding of SSL7 to human C5. Binding of Efb to human fibrinogen was blocked in human, monkey, gerbil and pig plasma, while human, monkey, gerbil, rabbit, cat and guinea pig plasma inhibited the binding of Efb to human C3. These results emphasize the importance of choosing correct animal models, and thus, our approach is a rapid and cost‐effective method that can be used to prevent unnecessary animal experiments.

The SARS-CoV-2 was confirmed to cause the global pandemic of coronavirus disease 2019 (COVID-19). The 3-chymotrypsin-like protease (3CLpro), an essential enzyme for viral replication, is a valid target to combat SARS-CoV and MERS-CoV. In this work, we present a structure-based study to identify potential covalent inhibitors containing a variety of chemical warheads. The targeted Asinex Focused Covalent (AFCL) library was screened based on different reaction types and potential covalent inhibitors were identified. In addition, we screened FDA-approved protease inhibitors to find candidates to be repurposed against SARS-CoV-2 3CLpro. A number of compounds with significant covalent docking scores were identified. These compounds were able to establish a covalent bond (C-S) with the reactive thiol group of Cys145 and to form favorable interactions with residues lining the substrate-binding site. Moreover, paritaprevir and simeprevir from FDA-approved protease inhibitors were identified as potential inhibitors of SARS-CoV-2 3CLpro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CLpro were characterized by molecular dynamics (MD) simulations. The identified compounds are potential inhibitors worthy of further development as COVID-19 drugs. Importantly, the identified FDA-approved anti-hepatitis-C virus (HCV) drugs paritaprevir and simeprevir could be ready for clinical trials to treat infected patients and help curb COVID-19. Communicated by Ramaswamy H. Sarma. ispartof: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS vol:39 issue:13 pages:4936-4948 ispartof: location:England status: published

Thick discs are nearly ubiquitous components of the discs of present-day galaxies. It has been proposed that a fraction of their stars has been accreted. Here, we aim to find whether accretion of satellites is the main thick disc formation mechanism. To do so, we observed a sample of eight nearby edge-on galaxies with the MUSE integral field unit at the VLT. Six of the galaxies have a distinct thick disc. We derived thick disc velocities and velocity dispersions for the galaxies in our sample. We devise a formalism to estimate the fractions of retrograde material in the thick discs by using kinematical maps and thin/thick dis decompositions. None of the galaxies in our sample shows strong evidence for retrograde material at large distances from the centre. Including those found in the literature, there are seventeen thick discs with studied kinematics, with only one showing unambiguous signatures of retrograde material. Literature numerical studies of dynamical friction allow us to estimate that at the current cosmic time about one in six mergers for which the stars of the accreted galaxy ended in a thick disc were retrograde. This is in tension with the observed fraction of 1/17 of galaxies with a partly retrograde thick disc. We conclude that satellite accretion is not favoured by observations to be the main thick disk formation mechanism., Comment: Accepted for publication in A&A

A new series of amino acid derivatives of quinolines was synthesized through the hydrolysis of amino acid methyl esters of quinoline carboxamides with alkali hydroxide. The compounds were purified on silica gel by column chromatography and further characterized by TLC, NMR and ESI-TOF mass spectrometry. All compounds were screened for in vitro antimicrobial activity against different bacterial strains using the microdilution method. Most of the synthesized amino acid-quinolines show more potent or equipotent inhibitory action against the tested bacteria than their correspond esters. In addition, many of them exhibit fluorescent properties and could possibly be utilized as fluorophores. Molecular docking and simulation studies of the compounds at putative bacterial target enzymes suggest that the antimicrobial potency of these synthesized analogues could be due to enzyme inhibition via their favorable binding at the fluoroquinolone binding site at the GyrA subunit of DNA gyrase and/or the ParC subunit of topoisomerase-IV.

Chemokine receptors are key regulators of cell migration in terms of immunity and inflammation. Among these, CCR5 and CXCR4 play pivotal roles in cancer metastasis and HIV-1 transmission and infection. They act as essential co-receptors for HIV and furnish a route to the cell entry. In particular, inhibition of either CCR5 or CXCR4 leads very often the virus to shift to a more virulent dual-tropic strain. Therefore, dual receptor inhibition might improve the therapeutic strategies against HIV. In this study, we aimed to discover selective CCR5, CXCR4, and dual CCR5/CXCR4 antagonists using both receptor- and ligand-based computational methods. We employed this approach to fully incorporate the interaction attributes of the binding pocket together with molecular dynamics (MD) simulations and binding free energy calculations. The best hits were evaluated for their anti-HIV-1 activity against CXCR4- and CCR5-specific NL4.3 and BaL strains. Moreover, the Ca2+ mobilization assay was used to evaluate their antagonistic activity. From the 27 tested compounds, three were identified as inhibitors: compounds 27 (CCR5), 6 (CXCR4) and 3 (dual) with IC50 values ranging from 10.64 to 64.56 μM. The binding mode analysis suggests that the active compounds form a salt bridge with the glutamates and π-stacking interactions with the aromatic side chains binding site residues of the respective co-receptor. The presented hierarchical virtual screening approach provides essential aspects in identifying potential antagonists in terms of selectivity against a specific co-receptor. The compounds having multiple heterocyclic nitrogen atoms proved to be relatively more specific towards CXCR4 inhibition as compared to CCR5. The identified compounds serve as a starting point for further development of HIV entry inhibitors through synthesis and quantitative structure-activity relationship studies., Graphical abstract Image, graphical abstract

We present the study of a magnitude limited sample (mB < 16.6 mag) of 13 late type galaxies (LTGs), observed inside the virial radius, Rvir 0.7 Mpc, of the Fornax cluster within the Fornax Deep Survey (FDS). The main objective is to use surface brightness (SB) profiles and g-i colour maps to obtain information on the internal structure of these galaxies and find signatures of the mechanisms that drive their evolution in high-density environment, which is inside the virial radius of the cluster. By modelling galaxy isophotes, we extract the azimuthally averaged surface brightness profiles in four optical bands. We also derive g-i colour profiles, and structural parameters like total magnitude and effective radius. For 10 of the galaxies in this sample, we observe a clear discontinuity in their SB profiles, derive their break radius (Br), and classify their disc-breaks into Type-II (down-bending) or Type-III (up-bending). We find that Type-II galaxies have bluer average (g-i) colour in their outer discs while Type-III galaxies are redder. Br increases with stellar mass and molecular gas mass while decreases with molecular gas-fractions. The inner and outer scale-lengths increase monotonically with absolute magnitude, as found in other works. In Fornax, galaxies with morphological type 5< T< 9 (~60 % of the sample) are located beyond the high-density, ETG-dominated regions, but no correlation found between T and the disc-break type. The main results of this work suggest that the disc-breaks of LTGs inside the virial radius of the Fornax cluster seem to have arisen through a variety of mechanisms, which is evident in their outer-disc colours and the absence of molecular gas beyond their break radius in some cases. This can result in a variety of stellar populations inside and outside the break radii., Accepted for publication in A&A. Replaced version: corrected latex typos. Full resolution pdf file is available at the following link: https://www.dropbox.com/s/7gpk6fg0whsxyye/The_Fornax_Deep_Survey_with_VST.pdf?dl=0

Human papillomavirus (HPV) induced cervical cancer is the second most common cause of death, after breast cancer, in females. Three prophylactic vaccines by Merck Sharp & Dohme (MSD) and GlaxoSmithKline (GSK) have been confirmed to prevent high-risk HPV strains but these vaccines have been shown to be effective only in girls who have not been exposed to HPV previously. The constitutively expressed HPV oncoproteins E6 and E7 are usually used as target antigens for HPV therapeutic vaccines. These early (E) proteins are involved, for example, in maintaining the malignant phenotype of the cells. In this study, we predicted antigenic peptides of HPV types 16 and 18, encoded by E6 and E7 genes, using an immunoinformatics approach. To further evaluate the immunogenic potential of the predicted peptides, we studied their ability to bind to class I major histocompatibility complex (MHC-I) molecules in a computational docking study that was supported by molecular dynamics (MD) simulations and estimation of the free energies of binding of the peptides at the MHC-I binding cleft. Some of the predicted peptides exhibited comparable binding free energies and/or pattern of binding to experimentally verified MHC-I-binding epitopes that we used as references in MD simulations. Such peptides with good predicted affinity may serve as candidate epitopes for the development of therapeutic HPV peptide vaccines. ispartof: Frontiers In Immunology vol:9 ispartof: location:Switzerland status: published

Human thymidylate synthase (hTS), a target for antiproliferative drugs, is an obligate homodimer. Single-point mutations to alanine at the monomer–monomer interface may enable the identification of specific residues that delineate sites for drugs aimed at perturbing the protein–protein interactions critical for activity. We computationally identified putative hotspot residues at the interface and designed mutants to perturb the intersubunit interaction. Dimer dissociation constants measured by a FRET-based assay range from 60 nM for wild-type hTS up to about 1 mM for single-point mutants and agree with computational predictions of the effects of these mutations. Mutations that are remote from the active site retain full or partial activity, although the substrate KM values were generally higher and the dimer was less stable. The lower dimer stability of the mutants can facilitate access to the dimer interface by small molecules and thereby aid the design of inhibitors that bind at the dimer interface.Graphical abstract

Encounters between galaxies modify their morphology, kinematics, and star formation (SF) history. The relation between these changes and external perturbations is not straightforward. The great number of parameters involved requires both the study of large samples and individual encounters where particular features, motions, and perturbations can be traced and analysed in detail. We analysed the morphology, kinematics, and dynamics of two luminous infrared spiral galaxies, NGC 5257 and NGC 5258, in which SF is mostly confined to the spiral arms, in order to understand interactions between galaxies of equivalent masses and SF processes during the encounter. Using scanning Fabry-Perot interferometry, we studied the contribution of circular and non-circular motions and the response of the ionized gas to external perturbations. We compared the kinematics with direct images of the pair and traced the SF processes and gravitational effects due to the presence of the other galaxy. The SED of each member of the pair was fitted. A mass model was fitted to the rotation curve of each galaxy. Large, non-circular motions detected in both galaxies are associated with a bar, spiral arms, and HII regions for the inner parts of the galaxies, and with the tidal interaction for the outer parts of the discs. Bifurcations in the rotation curves indicate that the galaxies have recently undergone their pericentric passage. The pattern speed of a perturbation of one of the galaxies is computed. Location of a possible corotation seems to indicate that the gravitational response of the ionized gas in the outer parts of the disc is related to the regions where ongoing SF is confined. The SED fit indicates a slightly different star formation history for each member of the pair. For both galaxies, a pseudo-isothermal halo better fits the global mass distribution., Comment: 34 pages, 13 figures, 8 tables. Accepted for publication in A&A

Sterol 14α-demethylase (cytochrome P450 family 51 (CYP51)) is an essential enzyme occurring in all biological kingdoms. In eukaryotes, it is located in the membrane of the endoplasmic reticulum. Selective inhibitors of trypanosomal CYP51s that do not affect the human CYP51 have been discovered in vitro and found to cure acute and chronic mouse Chagas disease without severe side effects in vivo. Crystal structures indicate that CYP51 may be more rigid than most CYPs, and it has been proposed that this property may facilitate antiparasitic drug design. Therefore, to investigate the dynamics of trypanosomal CYP51, we built a model of membrane-bound Trypanosoma brucei CYP51 and then performed molecular dynamics simulations of T. brucei CYP51 in membrane-bound and soluble forms. We compared the dynamics of T. brucei CYP51 with those of human CYP51, CYP2C9, and CYP2E1. In the simulations, the CYP51s display low mobility in the buried active site although overall mobility is similar in all the CYPs studied. The simulations suggest that in CYP51, pathway 2f serves as the major ligand access tunnel, and both pathways 2f (leading to membrane) and S (leading to solvent) can serve as ligand egress tunnels. Compared with the other CYPs, the residues at the entrance of the ligand access tunnels in CYP51 have higher mobility that may be necessary to facilitate the passage of its large sterol ligands. The water (W) tunnel is accessible to solvent during most of the simulations of CYP51, but its width is affected by the conformations of the heme's two propionate groups. These differ from those observed in the other CYPs studied because of differences in their hydrogen-bonding network. Our simulations give insights into the dynamics of CYP51 that complement the available experimental data and have implications for drug design against CYP51 enzymes.

The recent outbreak of Zika virus (ZIKV) infection in Brazil has developed to a global health concern due to its likely association with birth defects (primary microcephaly) and neurological complications. Consequently, there is an urgent need to develop a vaccine to prevent or a medicine to treat the infection. In this study, immunoinformatics approach was employed to predict antigenic epitopes of Zika viral proteins to aid in development of a peptide vaccine against ZIKV. Both linear and conformational B-cell epitopes as well as cytotoxic T-lymphocyte (CTL) epitopes were predicted for ZIKV Envelope (E), NS3 and NS5 proteins. We further investigated the binding interactions of altogether 15 antigenic CTL epitopes with three class I major histocompatibility complex (MHC I) proteins after docking the peptides to the binding groove of the MHC I proteins. The stability of the resulting peptide-MHC I complexes was further studied by molecular dynamics simulations. The simulation results highlight the limits of rigid-body docking methods. Some of the antigenic epitopes predicted and analyzed in this work might present a preliminary set of peptides for future vaccine development against ZIKV.

We study the frequency and dimensions of inner and outer rings in the local Universe as a function of disk parameters and the amplitude of non-axisymmetries. We use the 1320 not-highly inclined disk galaxies ($i, Accepted for publication in A&A (April 8, 2019). 16 pages, 12 figures, 2 tables, plus appendices (4 pages, 4 figures, 2 tables)

Aims. We study the morphological characteristics of boxy/peanut-shaped bulges. In particular, we are interested to determine whether most of the flux associated with bulges in galaxies with masses similar to those of the Milky Way at redshift z ~ 0 might belong to the vertically thick inner part of the bar, in a similar manner as in the Milky Way itself. At high galaxy inclinations, these structures are observed as boxy/peanut/X-shaped features, and when the view is near to face-on, they are observed as barlenses. We also study the possibility that bulges in some fraction of unbarred galaxies might form in a similar manner as the bulges in barred galaxies.Methods. We used the Spitzer Survey of Stellar Structure in Galaxies (S4 G) and the Near-IR S0 galaxy Survey (NIRS0S) to compile complete samples of galaxies with barlenses (N = 85) and X-shaped features (N = 88). A sample of unbarred galaxies (N = 41) is also selected. For all 214 galaxies unsharp mask images were created, used to recognize the X-shaped features and to measure their linear sizes. To detect possible boxy isophotes (using the B 4 -parameter), we also performed an isophotal analysis for the barlens galaxies. We use recently published N -body simulations: the models that exhibit boxy/peanut/X/barlens morphologies are viewed from isotropically chosen directions that cover the full range of galaxy inclinations in the sky. The synthetic images were analyzed in a similar manner as the observations.Results. This is the first time that the observed properties of barlenses and X-shaped features are directly compared across a wide range of galaxy inclinations. A comparison with the simulation models shows that the differences in their apparent sizes, a /r bar ≳ 0.5 for barlenses and a /r bar ≲ 0.5 for X-shapes, can be explained by projection effects. Observations at various inclinations are consistent with intrinsic abl ≈ a X ≈ 0.5r bar : here intrinsic size means the face-on semimajor axis length for bars and barlenses, and the semilength of the X-shape when the bar is viewed exactly edge-on. While X-shapes are quite common at intermediate galaxy inclinations (for i = 40°−60° their frequency is about half that of barlenses), they are seldom observed at smaller inclinations. This is consistent with our simulation models, which have a small compact classical bulge that produces a steep inner rotation slope, whereas bulgeless shallow rotation curve models predict that X-shapes should be visible even in a face-on geometry. The steep rotation curve models are also consistent with the observed trend that B 4 is positive at low inclination and with negative values for i ≳ 40°−60°; this implies boxy isophotes. In total, only about one quarter of the barlenses (with i ≤ 60°) show boxy isophotes.Conclusions. Our analyses are consistent with the idea that barlenses and X-shaped features are physically the same phenomenon. However, the observed nearly round face-on barlens morphology is expected only when at least a few percent of the disk mass is located in a central component, within a region much smaller than the size of the barlens itself. Barlenses contribute to secular evolution of galaxies, and might even act as a transition phase between barred and unbarred galaxies. We also discuss that the wide range of stellar population ages obtained for the photometric bulges in the literature are consistent with our interpretation.

We use stellar dynamical bulge/disk/halo simulations to study whether barlenses (lens-like structures embedded in the narrow bar component) are just the face-on counterparts of Boxy/Peanut/X-shapes (B/P/X) seen in edge-on bars, or if some additional physical parameter affects that morphology. A range of bulge-to-disk mass and size ratios are explored: our nominal parameters ($B/D=0.08$, $r_{\rm eff}/h_r=0.07$, disk comprising 2/3 of total force at $2.2h_r$) correspond to typical MW mass galaxies. In all models a bar with pronounced B/P/X forms in a few Gyrs, visible in edge-on view. However, the pure barlens morphology forms only in models with sufficiently steep inner rotation curves, $dV_{cir}/dr\gtrsim5V_{max}/h_r$, achieved when including a small classical bulge with $B/D\gtrsim0.02$ and $r_{\rm eff}/h_r\lesssim0.1$. For shallower slopes the central structure still resembles a barlens, but shows a clear X-signature even in low inclinations. Similar result holds for bulgeless simulations, where the central slope is modified by changing the halo concentration. The predicted sensitivity on inner rotation curve is consistent with the slopes estimated from gravitational potentials calculated from the 3.6$��$m images, for the observed barlens and X-shape galaxies in the Spitzer Survey of Stellar Structure in Galaxies (S$^4$G). For inclinations $, 11 pages, 7 figures Accepted to ApJ

This Special Issue contains thirteen articles that provide a vivid snapshot of the state-of-the-art of molecular modeling in drug design, illustrating recent advances and critically discussing important challenges [...]

We investigate barlenses in the Calar Alto Legacy Integral Field Area (CALIFA) survey galaxies, studying their morphologies, stellar populations and metallicities. Multi-component decompositions are made using the Sloan Digital Sky Survey (SDSS) images and making GALFIT models, fitting besides bulges, disks and bars, also barlenses, which are the face-on counterparts of Boxy/Peanut bulges. Similar GALFIT models as were made for the galaxies, were made also for the simulation snap-shots. For the stellar populations and metallicities in the various structure components CALIFA IFU-observations are used. We show that, when present, barlenses account for a significant portion of light of photometric bulges (i.e. the excess light on top of the disks), which highlights the importance of bars in accumulating the central galaxy mass concentrations in the cosmic timescale. Bars and barlenses are found to have similar cumulative stellar age and metallicity distributions. This is the first time that a combined morphological and stellar population analysis is used to study barlenses. We show that their stars are accumulated in a prolonged time period, concurrently with the evolution of the narrow bar., 36 pages, accepted 3.7.2018 to Astr. Astrophys

We study the colors and orientations of structures in low and intermediate inclination barred galaxies. We test the hypothesis that barlenses, roundish central components embedded in bars, could form a part of the bar in a similar manner to boxy/peanut bulges in the edge-on view. A sample of 79 barlens galaxies was selected from the S$^4$G and the NIRS0S surveys. The sizes, ellipticities, and orientations of barlenses were measured and used to define the barlens regions in the color measurements. The orientations of barlenses were studied with respect to those of the "thin bars" and the line-of-nodes of the disks. For 47 galaxies color maps were constructed using the SDSS images in five optical bands, u, g, r, i, and z. Colors of bars, barlenses, disks, and central regions of the galaxies were measured using two different approaches and color-color diagrams sensitive to metallicity, stellar surface gravity, and short lived stars were constructed. Color differences between the structure components were calculated for each individual galaxy, and presented in histogram form. We find that the colors of barlenses are very similar to those of the surrounding bars, indicating that most probably they form part of the bar. We also find that barlenses have orientations closer to the disk line-of-nodes than to the thin bars, which is consistent with the idea that they are vertically thick, in a similar manner as the boxy/peanut structures in more inclined galaxies. Typically, the colors of barlenses are similar to those of normal E/S0 galaxies. Galaxy by galaxy studies show that in spiral galaxies very dusty barlenses also exist, along with barlenses with rejuvenated stellar populations. The central regions of galaxies are found to be on average redder than bars or barlenses, although galaxies with bluer central peaks also exist., Comment: 24 pages, 10 figures, 3 appendices. Accepted for publication in A&A

Sialic acid-binding immunoglobulin-like lectin-9 (Siglec-9) on leukocyte surface is a counter-receptor for endothelial cell surface adhesin, human primary amine oxidase (hAOC3), a target protein for anti-inflammatory agents. This interaction can be used to detect inflammation and cancer in vivo, since the labeled peptides derived from the second C2 domain (C22) of Siglec-9 specifically bind to the inflammation-inducible hAOC3. As limited knowledge on the interaction between Siglec-9 and hAOC3 has hampered both hAOC3-targeted drug design and in vivo imaging applications, we have now produced and purified the extracellular region of Siglec-9 (Siglec-9-EC) consisting of the V, C21 and C22 domains, modeled its 3D structure and characterized the hAOC3-Siglec-9 interactions using biophysical methods and activity/inhibition assays. Our results assign individual, previously unknown roles for the V and C22 domains. The V domain is responsible for the unusually tight Siglec-9-hAOC3 interactions whereas the intact C22 domain of Siglec-9 is required for modulating the enzymatic activity of hAOC3, crucial for the hAOC3-mediated leukocyte trafficking. By characterizing the Siglec-9-EC mutants, we could conclude that R120 in the V domain likely interacts with the terminal sialic acids of hAOC3 attached glycans whereas residues R284 and R290 in C22 are involved in the interactions with the active site channel of hAOC3. Furthermore, the C22 domain binding enhances the enzymatic activity of hAOC3 although the sialic acid-binding capacity of the V domain of Siglec-9 is abolished by the R120S mutation. To conclude, our results prove that the V and C22 domains of Siglec-9-EC interact with hAOC3 in a multifaceted and unique way, forming both glycan-mediated and direct protein-protein interactions, respectively. The reported results on the mechanism of the Siglec-9-hAOC3 interaction are valuable for the development of hAOC3-targeted therapeutics and diagnostic tools.

1. Several G protein-coupled receptors (GPCRs), including cannabinoid CB(1) and CB(2) receptors, show constitutive activity under heterologous expression. Such a tonic response is generated in the absence of an activating ligand, and can be inhibited by inverse agonists. Neutral antagonists, however, are silent at such receptors, but can reverse both agonist and inverse agonist responses. To date, no neutral antagonist for the CB(2) receptor has been reported. 2. Here, by monitoring receptor-dependent G protein activation, we demonstrate that WIN55212-3 acts as a neutral antagonist at the human CB(2) (hCB(2)) receptor. WIN55212-3 alone, at concentrations

The recent expiration of several blockbuster pharmaceutical patents offers new opportunities for generic drug production in Africa. Moreover, 2015 marked a critical juncture; a transition from the Millennium Development Goals to Sustainable Development Goals. The implications for African economies in the area of generic drug production and global health outcomes are vast given the potential to increase access to medicines for neglected diseases and other emerging health crises. This issue-based article analyses the extent to which several coeval variables of governance and macro-economic nature can potentially create the market and institutional conditions to spur innovations for improving access to medicine via cross-sector social partnerships. Proposals for solving grand challenges in Africa’s pharmaceutical markets often fail to address the most fundamental impediments to innovation, besides being mostly donor-driven. Through document analysis, we problematize conventional formulae for healthcare governance with a measured critique of prevailing orthodoxies by offering implementable alternatives. We propose inclusive, innovative models for marshalling sustainable access to high-quality affordable medicine. We identify bottom-up and entrepreneurially viable strategic reversal of decades of systematic damages that have contributed to the underdeveloped pharmaceutical market, whilst striking a reasonable balance between what the desirable future is and what can set the stage for a durable change through game-changing market and innovative mechanisms.

Many barred spiral galaxies have an outer ring (R) or a pseudoring (R') in their outer disk. R. Buta (e.g. Buta 1995) has developed a detailed classification for different types of outer rings. Two main families of outer rings are recognized. In R1 family the major axis of the ring is perpendicular to the bar and the spiral arms wind 180° before meeting the other arm. In R2 family the major axis of the ring is parallel to the bar and the spiral arms wind 270°.The outer rings are usually considered to be related to the outer Lindblad resonance (OLR) of a rotating stellar bar. The ring shapes correspond to families of closed orbits in the vicinity of this resonance (e.g. Contopoulos & Grosbøl 1989), and also the sizes of the outer rings relative to the bar component fit to this suggestion. Furthermore, test-particle simulations which use analytical bar potentials can produce different types of outer rings near the OLR (Schwarz 1981; Byrd et al. 1994). We have obtained similar results when we modelled ringed galaxy IC 4214 by constructing the gravitational potential from near-IR observations (Buta et al. 1999; Salo et al. 1999).

Human thymidylate synthase is a homodimeric enzyme that plays a key role in DNA synthesis and is a target for several clinically important anticancer drugs that bind to its active site. We have designed peptides to specifically target its dimer interface. Here we show through X-ray diffraction, spectroscopic, kinetic, and calorimetric evidence that the peptides do indeed bind at the interface of the dimeric protein and stabilize its di-inactive form. The “LR” peptide binds at a previously unknown binding site and shows a previously undescribed mechanism for the allosteric inhibition of a homodimeric enzyme. It inhibits the intracellular enzyme in ovarian cancer cells and reduces cellular growth at low micromolar concentrations in both cisplatin-sensitive and -resistant cells without causing protein overexpression. This peptide demonstrates the potential of allosteric inhibition of hTS for overcoming platinum drug resistance in ovarian cancer.

Many enzymes and proteins are regulated by their quaternary structure and/or by their association in homo- and/or hetero-oligomer complexes. Thus, these protein-protein interactions can be good targets for blocking or modulating protein function therapeutically. The large number of oligomeric structures in the Protein Data Bank (http://www.rcsb.org/) reflects growing interest in proteins that function as multimeric complexes. In this review, we consider the particular case of homodimeric enzymes as drug targets. There is intense interest in drugs that inhibit dimerization of a functionally obligate homodimeric enzyme. Because amino acid conservation within enzyme interfaces is often low compared to conservation in active sites, it may be easier to achieve drugs that target protein interfaces selectively and specifically. Two main types of dimerization inhibitors have been developed: peptides or peptidomimetics based on sequences involved in protein-protein interactions, and small molecules that act at hot spots in protein-protein interfaces. Examples include inhibitors of HIV protease and HIV integrase. Studying the mechanisms of action and locating the binding sites of such inhibitors requires different techniques for different proteins. For some enzymes, ligand binding is only detectable in vivo or after unfolding of the complexes. Here, we review the structural features of dimeric enzymes and give examples of inhibition through interference in dimer stability. Several techniques for studying these complex phenomena will be presented.

The influence of the perturbing satellite on the planetary ring at isolated Lindblad resonances is studied with numerical computer simulations, combining the Aarseth's force polynomial method for orbit integrations with the calculation of particle-particle impacts. Observed angular momentum exchange between the satellite and the dissipative, non-selfgravitating ring agrees with the Goldreich-Tremaine formula for gravitating ring within 20%, verifying that the exerted torque is not sensitive to the details of the dominant physical processes. The theoretically predicted angular momentum luminosity reversal was also observed.

Owing to its central role in DNA synthesis, human thymi-dylate synthase (hTS) is a well-established target for che-motherapeutic agents, such as fluoropyrimidines. The useof hTS inhibitors in cancer therapy is limited by theirtoxicity and the development of cellular drug resistance.Here, with the aim of shedding light on the structuralrole of the A-helix in fluoropyrimidine resistance, we havecreated a fluoropyrimidine-resistant mutant by making asingle point mutation, Glu30Trp. We postulated thatresidue 30, which is located in the A-helix, close to butoutside the enzyme active site, could have a long-rangeeffect on inhibitor binding. The mutant shows 100 timeslower specific activity with respect to the wild-type hTSand is resistant to the classical inhibitor, FdUMP, asshown by a 6-fold higher inhibition constant. Circulardichroism experiments show that the mutant is folded.The results of molecular modeling and simulation suggestthat the Glu30Trp mutation gives rise to resistance byaltering the hydrogen-bond network between residue 30and the active site.Keywords: antitumor agents/drug resistance/humanthymidylate synthase/protein design/protein dynamicsIntroductionHuman thymidylate synthase (hTS) (EC 2.1.1.45) catalyzesthe reaction in which dUMP (2