Antigenic Peptide Prediction From E6 and E7 Oncoproteins of HPV Types 16 and 18 for Therapeutic Vaccine Design Using Immunoinformatics and MD Simulation Analysis

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

Stilbenoid compounds inhibit NF-κB-mediated inflammatory responses in the Drosophila intestine

IntroductionStilbenoid compounds have been described to have anti-inflammatory properties in animal models in vivo, and have been shown to inhibit Ca2+-influx through the transient receptor potential ankyrin 1 (TrpA1).MethodsTo study how stilbenoid compounds affect inflammatory signaling in vivo, we have utilized the fruit fly, Drosophila melanogaster, as a model system. To induce intestinal inflammation in the fly, we have fed flies with the intestinal irritant dextran sodium sulphate (DSS).ResultsWe found that DSS induces severe changes in the bacteriome of the Drosophila intestine, and that this dysbiosis causes activation of the NF-κB transcription factor Relish. We have taken advantage of the DSS-model to study the anti-inflammatory properties of the stilbenoid compounds pinosylvin (PS) and pinosylvin monomethyl ether (PSMME). With the help of in vivo approaches, we have identified PS and PSMME to be transient receptor ankyrin 1 (TrpA1)-dependent antagonists of NF-κB-mediated intestinal immune responses in Drosophila. We have also computationally predicted the putative antagonist binding sites of these compounds at Drosophila TrpA1.DiscussionTaken together, we show that the stilbenoids PS and PSMME have anti-inflammatory properties in vivo in the intestine and can be used to alleviate chemically induced intestinal inflammation in Drosophila

Interactions between polymeric nanoparticles and different buffers as investigated by zeta potential measurements and molecular dynamics simulations

Zeta potential is an essential surface parameter in the characterization of nanoparticles, determined at the interface of loosely bound ions (diffuse layer) at the nanoparticle surface and free ions in solution. The ionic concentration and pH of the solution are known to, by definition, influence the composition of the diffuse layer and zeta potential accordingly. Thus, to fix the solution's pH for valid zeta potential measurements, buffers are frequently used. However, an issue that remains largely neglected is that buffers could also additionally alter the electrokinetic properties of nanoparticles through specific molecular interactions. Therefore, a thorough molecular understanding of buffer-nanoparticle interactions is needed to correctly implement zeta potential results. Thus, in order to study nanoparticle-buffer interactions, we first adopted a simple experimental approach of measuring zeta potential of common polymeric nanoparticle systems at different buffer concentrations, pH, and nanoparticle-buffer fraction ratios. We observed that zwitterionic/cationic buffer molecules impart significant interference to the electrokinetic properties of structurally diverse polymer nanoparticles, by causing zeta potential suppression or even inversion during the experiments. In parallel, advancement in computation resources nowadays allow studying intermolecular interactions of nanoparticles and other complex molecules by molecular dynamics (MD) simulations. Thus, by performing MD simulations for six different polymeric nanomaterials with commonly used buffer molecules, we found that noncovalent interactions play a significant role in altering the observed zeta potential values, which may contribute to erroneous results and false particle characterizations if not taken properly into account in zeta potential measurements.</p

In Situ Coupled Electrochemical-Goniometry as a Tool to Reveal Conformational Changes of Charged Peptides

The opportunity to manipulate cell functions by regulating bioactive surfaces is a potentially promising approach for organic bioelectronics. Here, the tuning of the orientation of charged peptides by means of an electrical input observed via optical tensiometry is reported. A stimuli-responsive self-assembled monolayer (SAM) with specially designed charged peptides is used as a model system to switch between two separate hydrophilic states. The underwater contact angle (UCA) technique is used to measure changes in the wetting property of a dichloromethane droplet under electrical stimuli. The observed changes in the UCA of the bio-interface can be understood in terms of a change in the surface energy between the ON and OFF states. Molecular dynamics simulations in an electric field have been performed to verify the hypothesis of the orientational change of the charged peptides upon electrical stimulation. In addition, X-ray photoelectron spectroscopy (XPS) is performed to clarify the stability of the functionalized electrodes. Finally, the possibility of using such a novel switching system as a tool to characterize bioactive surfaces is discussed

Governing pharmaceutical innovations in Africa: Inclusive models for accelerating access to quality medicines

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

High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2

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

Molecular Modeling in Drug Design

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 [...

A rapid method for selecting suitable animal species for studying pathogen interactions with plasma protein ligands in vivo

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