Homology Modelling of a Newly Discovered Thioredoxin Protein and Analysis of the Force Field and Electrostatic Properties

Thioredoxin is a small protein (Mr approximately 12,000) found in all living cells from archaebacteria to humans. The active site is highly conserved and has two redox-active cysteine residues in the sequence: -Trp-Cys-Gly-Pro-Cys-. Besides the function of the reduced form as a powerful protein disulfide oxidoreductase, thioredoxin is known to regulate and activate different target enzymes, i.e. ribonucleotide reductase and the mitochondrial 2-oxoacid dehydrogenase multienzyme complexes. Despite the high degree of homology between thioredoxin proteins from different species, there exists a strong variation in the capability of activating target enzymes. This is yet unexplainable, since there still exists no model of a thioredoxin/receptor complex.On the basis of the recently determined amino acid sequence of the thioredoxin Trx2 from rat mitochondria, which is known to be highly efficient in activating mitochondrial 2-oxoacid dehydrogenase multienzyme complexes, we construct the 3-D structure of this protein by homology modelling methods, using the X-ray structures of thioredoxin from E. coli and human as background information. We analyze the differences in the electrostatic properties of the different protein structures and show, that despite the observed homology between the primary sequences, the dipole moment of the protein structures shows significant variations, which might lead to deviations with respect to the binding to the target protein. Using the AMBER 4.0 program package we further investigate and compare the force field energies of the different thioredoxin structures.Electronic Supplementary Material available.     

Integrating computational and mixture-based screening of combinatorial libraries

Mixture-based synthetic combinatorial library (MB-SCL) screening is a well-established experimental approach for rapidly retrieving structure–activity relationships (SAR) and identifying hits. Virtual screening is also a powerful approach that is increasingly being used in drug discovery programs and has a growing number of successful applications. However, limited efforts have been made to integrate both techniques. To this end, we combined experimental data from a MB-SCL of bicyclic guanidines screened against the κ-opioid receptor and molecular similarity methods. The activity data and similarity analyses were integrated in a biometric analysis–similarity map. Such a map allows the molecules to be categorized as actives, activity cliffs, low similarity to the reference compounds, or missed hits. A compound with IC₅₀ = 309 nM was found in the “missed hits” region, showing that active compounds can be retrieved from a MS-SCL via computational approaches. The strategy presented in this work is general and is envisioned as a general-purpose approach that can be applied to other MB-SCLs.     

Exploring electrostatic patterns of human,murine, equine and canine TLR4/MD-2 receptors

Electrostatic interactions between phosphate anions and Toll-like receptor 4 / Myeloid differentiation factor-2 (TLR4/MD-2) protein complexes of human, murine, equine and canine species were computed. Such knowledge can provide mechanistic information about recognising LPS-like ligands, since anionic phosphate groups belong to the structural features of LPS with their diphosphorylated diglucosamine backbone. Sequence composition analyses, electrostatic interaction potentials and docked energies as well as molecular dynamics studies evaluated the phosphate interactions within the triangular LPS binding site (wedge). According to electrostatic analyses, human, horse and dog wedges possess phosphate-binding sites with indistinct positive and negative charge distributions, but the murine wedge shows a unique strong negative net charge at the site where antagonists bind in other species (Pan). Docking of a phosphate mono-anion (probe) confirmed its repulsion at this Pan site, but the Pag site of the murine wedge attracted the probe. It is occupied by phosphate groups of agonists in other species (Pag). Molecular dynamics trajectories show a variable degree of random walk across the wedges, that is, not following electrostatic preferences (neither Pag nor Pan). In summary, two opposing electrostatic patterns exist –murine versus human, equine and canine species – all of which reflect the potential dual activity mode of under-acylated ligands such as lipid IV_A.     

Synthesis,in vitro and in vivo giardicidal activity of nitrothiazole-NSAID chimeras displaying broad antiprotozoal spectrum

We designed and synthesized five new 5-nitrothiazole-NSAID chimeras as analogues of nitazoxanide, using a DCC-activated amidation. Compounds 1–5 were tested in vitro against a panel of five protozoa: 2 amitochondriates (Giardia intestinalis, Trichomonas vaginalis) and 3 kinetoplastids (Leishmania mexicana, Leishmania amazonensis and Trypanosoma cruzi). All chimeras showed broad spectrum and potent antiprotozoal activities, with IC₅₀ values ranging from the low micromolar to nanomolar order. Compounds 1–5 were even more active than metronidazole and nitazoxanide, two marketed first-line drugs against giardiasis. In particular, compound 4 (an indomethacin hybrid) was one of the most potent of the series, inhibiting G. intestinalis growth in vitro with an IC₅₀ of 0.145 μM. Compound 4 was 38-times more potent than metronidazole and 8-times more active than nitazoxanide. The in vivo giardicidal effect of 4 was evaluated in a CD-1 mouse model obtaining a median effective dose of 1.709 μg/kg (3.53 nmol/kg), a 321-fold and 1015-fold increase in effectiveness after intragastric administration over metronidazole and nitazoxanide, respectively. Compounds 1 and 3 (hybrids of ibuprofen and clofibric acid), showed potent giardicidal activities in the in vitro as well as in the in vivo assays after oral administration. Therefore, compounds 1–5 constitute promising drug candidates for further testing in experimental chemotherapy against giardiasis, trichomoniasis, leishmaniasis and even trypanosomiasis infections.     

Barriers to Social Participation among Lonely Older Adults: The Influence of Social Fears and Identity

IntroductionLoneliness among older adults is a major public health problem that may be associated with processes of social participation and identity. This study therefore sought to examine the relationship between social participation and identity in a sample of lonely older adults living independently in London, England.MethodAn inductive qualitative approach, based on semi-structured interviews and thematic analysis, was employed.ResultsParticipants commonly spoke of barriers to social participation that have been reported elsewhere, including illness/disability, loss of contact with friends/relatives, lack of a supportive community, and lack of acceptable social opportunities. However, novel findings were also derived. In particular, participants commonly minimised the difficulties they faced alone, and described attempts to avoid social opportunities. These behaviours were linked to fears about engaging in social participation opportunities, including fears of social rejection and/or exploitation, and fears of losing valued aspects of identity.DiscussionIt is concluded that social participation amongst lonely older people will not improve through the removal of previously reported barriers alone; instead, older peoples’ beliefs, fears and identities must be addressed. Suggestions for implementing these findings within community organisations are provided.     

Discrimination and Other Barriers to Accessing Health Care: Perspectives of Patients with Mild and Moderate Intellectual Disability and Their Carers

Background

People with intellectual disability have a higher prevalence of physical health problems but often experience disparities in accessing health care. In England, a number of legislative changes, policies and recommendations have been introduced to improve health care access for this population. The aim of this qualitative study was to examine the extent to which patients with intellectual disability and their carers experience discrimination or other barriers in accessing health services, and whether health care experiences have improved over the last decade years.

Method and Main Findings

Twenty nine participants (14 patient and carer dyads, and one carer) took part in semi-structured interviews. The interviews were audio-taped and transcribed and analysed using thematic analysis. Eight themes were identified. Half the participants thought that the patient had been treated unfairly or had been discriminated against by health services. There were accounts of negative staff attitudes and behaviour, and failure of services to make reasonable adjustments. Other barriers included problems with communication, and accessing services because of lack of knowledge of local services and service eligibility issues; lack of support and involvement of carers; and language problems in participants from minority ethnic groups. Most participants were able to report at least one example of good practice in health care provision. Suggestions for improving services are presented.

Conclusion

Despite some improvements to services as a result of health policies and recommendations, more progress is required to ensure that health services make reasonable adjustments to reduce both direct and indirect discrimination of people with intellectual disability.     

Structural Analysis of the Ribosome-associated Complex (RAC) Reveals an Unusual Hsp70/Hsp40 Interaction

Yeast Zuotin and Ssz are members of the conserved Hsp40 and Hsp70 chaperone families, respectively, but compared with canonical homologs, they atypically form a stable heterodimer termed ribosome-associated complex (RAC). RAC acts as co-chaperone for another Hsp70 to assist de novo protein folding. In this study, we identified the molecular basis for the unusual Hsp70/Hsp40 pairing using amide hydrogen exchange (HX) coupled with mass spectrometry and mutational analysis. Association of Ssz with Zuotin strongly decreased the conformational dynamics mainly in the C-terminal domain of Ssz, whereas Zuotin acquired strong conformational stabilization in its N-terminal segment. Deletion of the highly flexible N terminus of Zuotin abolished stable association with Ssz in vitro and caused a phenotype resembling the loss of Ssz function in vivo. Thus, the C-terminal domain of Ssz, the N-terminal extension of Zuotin, and their mutual stabilization are the major structural determinants for RAC assembly. We furthermore found dynamic changes in the J-domain of Zuotin upon complex formation that might be crucial for RAC co-chaperone function. Taken together, we present a novel mechanism for converting Zuotin and Ssz chaperones into a functionally active dimer.     

Ethnopharmacology and bioinformatic combination for leads discovery: application to phospholipase A(2) inhibitors.

A program combining ethnopharmacology and bioinformatic approaches has successfully been applied on anti-inflammatory activity. (i) An ethnobotanical study allowed the identification of several plants associated with putative anti-inflammatory properties as potential leads. (ii) On the other hand, it is well known that phospholipase A(2) is a target implicated in the pro-inflammatory process. Thus, (iii) some selected plant extracts were experimentally tested on phospholipase A(2). Finally, (iv) these experimental results combined with bioinformatic tools, such as database exploitation and molecular modeling, allowed to suggest that one compound, betulin and its oxidative form betulinic acid, might be responsible of the anti-PLA(2) activity. This suggestion was confirmed experimentally.     

Molecular Modeling Study on Dapsone and Sulfonamides Comparing Structures and Properties with Respect to Anti-Leprosy Activity

Despite the very close structural relationship between dapsone (4,4′-diaminodiphenyl sulfone, 4,4′ sulphonyldianiline, diaphenyl sulphone, DDS) and sulfanilamide (p-aminobenzene sulfonamide), being the prototype of all other sulfonamides, only dapsone shows remarkable efficient pharmacological activity against Mycobacterium leprae. Cells of certain micro-organism need para-aminobenzoic acid (PABA), the latter playing the role of natural substrate to biosynthesis of folic acid. Sufones and sulfonamides show competitive antagonism as chemical analogs of PABA. It is most surprising that, despite of sharing this molecular mechanism, only dapsone shows anti-leprosy activity in vivo. The study was accomplished using molecular mechanics (SYBYL) and semiempirical methods (MOPAC). The calculations of aromaticity, charges, protonation by MOPAC, and of lipophilicity by our empirical program LIPOP(hilicity) give evidence that dapsone is more lipophilic (log P values 0.97) than sulfanilamide (-0.67). The extremely lipophilic cell wall of Mycobacterium leprae contributes to the surprising difference in anti-leprosy activity. Sulfonamides are more or less deprotonated (45 to 99 %) at physiological pH units, whereas dapsone is totally undissociated. This results in different permeability rates into the bacterial cells in vivo. Compared to other sulfones and sulfonamides, the unique combination of high lipophilicity and low ionic dissociation favors anti-leprotic potency in dapsone. On principle, amide groups do not hinder activity, but cause acidity and subsequently dissociation.