In Silico Designed Axl Receptor Blocking Drug Candidates Against Zika Virus Infection

The release of host-derived antibodies bound to the variant surface glycoprotein (VSG) of Trypanosoma brucei cannot be explained by pH-dependent conformational changes of the VSG dimer

Background

Trypanosoma brucei is a protozoan parasite that evades the mammalian host's adaptive immune response by antigenic variation of the highly immunogenic variant surface glycoprotein (VSG). VSGs form a dense surface coat that is constantly recycled through the endosomal system. Bound antibodies are separated in the endosome from the VSG and destroyed in the lysosome. For VSGs it has been hypothesized that pH-dependent structural changes of the VSG could occur in the more acidic environment of the endosome and hence, facilitate the separation of the antibody from the VSG.

Methods

We used size exclusion chromatography, where molecules are separated according to their hydrodynamic radius to see if the VSG is present as a homodimer at both pH values. To gain information about the structural integrity of the protein we used circular dichroism spectroscopy by exposing the VSG in solution to a mixture of right- and left-circularly polarized light and analysing the absorbed UV spectra. Evaluation of protein stability and molecular dynamics simulations at different pH values was performed using different computational methods.

Results

We show, for an A2-type VSG, that the dimer size is only slightly larger at pH 5.2 than at pH 7.4. Moreover, the dimer was marginally more stable at lower pH due to the higher affinity (ΔG = 353.37 kcal/mol) between the monomers. Due to the larger size, the predicted epitopes were more exposed to the solvent at low pH. Moderate conformational changes (ΔRMSD = 0.35 nm) in VSG were detected between the dimers at pH 5.2 and pH 7.4 in molecular dynamics simulations, and no significant differences in the protein secondary structure were observed by circular dichroism spectroscopy.

Conclusions

Thus, the dissociation of anti-VSG-antibodies in endosomes cannot be explained by changes in pH.

Current Update on Rotavirus in-Silico Multiepitope Vaccine Design

Rotavirus gastroenteritis is one of the leading causes of pediatric morbidity and mortality worldwide in infants and under-five populations. The World Health Organization (WHO) recommended global incorporation of the rotavirus vaccine in national immunization programs to alleviate the burden of the disease. Implementation of the rotavirus vaccination in certain regions of the world brought about a significant and consistent reduction of rotavirus-associated hospitalizations. However, the efficacy of licensed vaccines remains suboptimal in low-income countries where the incidences of rotavirus gastroenteritis continue to happen unabated. The problem of low efficacy of currently licensed oral rotavirus vaccines in low-income countries necessitates continuous exploration, design, and development of new rotavirus vaccines. Traditional vaccine development is a complex, expensive, labor-intensive, and time-consuming process. Reverse vaccinology essentially utilizes the genome and proteome information on pathogens and has opened new avenues for in-silico multiepitope vaccine design for a plethora of pathogens, promising time reduction in the complete vaccine development pipeline by complementing the traditional vaccinology approach. A substantial number of reviews on licensed rotavirus vaccines and those under evaluation are already available in the literature. However, a collective account of rotavirus in-silico vaccines is lacking in the literature, and such an account may further fuel the interest of researchers to use reverse vaccinology to expedite the vaccine development process. Therefore, the main focus of this review is to summarize the research endeavors undertaken for the design and development of rotavirus vaccines by the reverse vaccinology approach utilizing the tools of immunoinformatics.

Topological bio-scaling analysis as a universal measure of protein folding

Scaling relationships for polymeric molecules establish power law dependencies between the number of molecular segments and linear dimensions, such as the radius of gyration. They also establish spatial topological properties of the chains, such as their dimensionality. In the spatial domain, power exponents α = 1 (linear stretched molecule), α = 0.5 (the ideal chain) and α = 0.333 (compact globule) are significant. During folding, the molecule undergoes the transition from the one-dimensional linear to the three-dimensional globular state within a very short time. However, intermediate states with fractional dimensions can be stabilized by modifying the solubility (e.g. by changing the solution temperature). Topological properties, such as dimension, correlate with the interaction energy, and thus by tuning the solubility one can control molecular interaction. We investigate these correlations using the example of a well-studied short model of Trp-cage protein. The radius of gyration is used to estimate the fractal dimension of the chain at different stages of folding. It is expected that the same principle is applicable to much larger molecules and that topological (dimensional) characteristics can provide insights into molecular folding and interactions.

Homology Modelling, Docking-based Virtual Screening, ADME Properties, and Molecular Dynamics Simulation for Identification of Probable Type II Inhibitors of AXL Kinase

Background:

AXL kinase is an important member of the TAM family for kinases which is involved in most cancers. Considering its role in different cancers due to its pro-tumorigenic effects and its involvement in the resistance, it has gained importance recently. Majority of research carried out is on Type I inhibitors and limited studies have been carried out for Type II inhibitors. Taking this into consideration, we have attempted to build Homology models to identify the Type II inhibitors for the AXL kinase.

Methods:

Homology Models for DFG-out C-helix-in/out state were developed using SWISS Model, PRIMO, and Prime. These models were validated by different methods and further evaluated for stability by molecular dynamics simulation using Desmond software. Selected models PED1-EB and PEDI1-EB were used for the docking-based virtual screening of four compound libraries using Glide software. The hits identified were subjected to interaction analysis and shortlisted compounds were subjected to Prime MM-GBSA studies for energy calculation. These compounds were also docked in the DFG-in state to check for binding and elimination of any compounds that may not be Type II inhibitors. The Prime energies were calculated for these complexes as well and some compounds were eliminated. ADMET studies were carried out using Qikprop. Some selected compounds were subjected to molecular dynamics simulation using Desmond for evaluating the stability of the complexes.

Results:

Out of 78 models inclusive of both DFG-out C-helix-in and DFG-out C-helix-out, 5 models were identified after different types of evaluation as well as validation studies. 1 model representing each type (PED1-EB and PEDI1-EB) was selected for the screening studies. The screening studies resulted in the identification of 29 compounds from the screen on PED1-EB and 10 compounds from the screen on PEDI1-EB. Hydrogen bonding interactions with Pro621, Met623, and Asp690 were observed for these compounds primarily. In some compounds, hydrogen bonding with Leu542, Glu544, Lys567, and Asn677 as well as pi-pi stacking interactions with either Phe622 or Phe691 were also seen. 4 compounds identified from PED1-EB screen were subjected to molecular dynamics simulation and their interactions were found to be consistent during the simulation. 2 compounds identified from PEDI1-EB screen were also subjected to the simulation studies, however, their interactions with Asp690 were not observed for a significant time and in both cases differed from the docked pose.

Conclusion:

Multiple models of DFG-out conformations of AXL kinase were built, validated and used for virtual screening. Different compounds were identified in the virtual screening, which may possibly act as Type II inhibitors for AXL kinase. Some more experimental studies can be done to validate these findings in future. This study will play a guiding role in the further development of the newer Type II inhibitors of the AXL kinase for the probable treatment of cancer.

Ugonin J Acts as a SARS-CoV-2 3C-like Protease Inhibitor and Exhibits Anti-inflammatory Properties

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes severe “flu-like” symptoms that can progress to acute respiratory distress syndrome (ARDS), pneumonia, renal failure, and death. From the therapeutic perspective, 3-chymotrypsin-like protein (3CLpro) is a plausible target for direct-acting antiviral agents because of its indispensable role in viral replication. The flavonoid ugonin J (UJ) has been reported to have antioxidative and anti-inflammatory activities. However, the potential of UJ as an antiviral agent remains unexplored. In this study, we investigated the therapeutic activity of UJ against SARS-CoV-2 infection. Importantly, UJ has a distinct inhibitory activity against SARS-CoV-2 3CLpro, compared to luteolin, kaempferol, and isokaempferide. Specifically, UJ blocks the active site of SARS-CoV-2 3CLpro by forming hydrogen bonding and van der Waals interactions with H163, M165 and E166, G143 and C145, Q189, and P168 in subsites S1, S1′, S2, and S4, respectively. In addition, UJ forms strong, stable interactions with core pharmacophore anchors of SARS-CoV-2 3CLpro in a computational model. UJ shows consistent anti-inflammatory activity in inflamed human alveolar basal epithelial A549 cells. Furthermore, UJ has a 50% cytotoxic concentration (CC₅₀) and a 50% effective concentration (EC₅₀₎ values of about 783 and 2.38 µM, respectively, with a selectivity index (SI) value of 329, in SARS-CoV-2-infected Vero E6 cells. Taken together, UJ is a direct-acting antiviral that obstructs the activity of a fundamental protease of SARS-CoV-2, offering the therapeutic potential for SARS-CoV-2 infection.

AXL, an Important Host Factor for DENV and ZIKV Replication

Flaviviruses, as critically important pathogens, are still major public health problems all over the world. For instance, the evolution of ZIKV led to large-scale outbreaks in the Yap island in 2007. DENV was considered by the World Health Organization (WHO) as one of the 10 threats to global health in 2019. Enveloped viruses hijack a variety of host factors to complete its replication cycle. Phosphatidylserine (PS) receptor, AXL, is considered to be a candidate receptor for flavivirus invasion. In this review, we discuss the molecular structure of ZIKV and DENV, and how they interact with AXL to successfully invade host cells. A more comprehensive understanding of the molecular mechanisms of flavivirus-AXL interaction will provide crucial insights into the virus infection process and the development of anti-flavivirus therapeutics.

Novel Approach for Characterizing Propofol Binding Affinities to Serum Albumins from Different Species

The interaction between the main carrier (serum albumin, SA) of endogenous and exogenous compounds in the bloodstream of different species (human, bovine, canine, rat, rabbit, and sheep) and a general anesthetic agent (propofol, PR) was investigated using an experimental technique (high-performance liquid chromatography) and computational methods (molecular docking, molecular dynamics, sequence, and phylogenetic analyses). The obtained results revealed the differences in the PR binding affinity to various homologous forms of this protein with reliable statistics (R ² = 0.9 and p-value < 0.005), correlating with the evolutionary relationships among SAs from different species. Additionally, the protein conformational changes (root-mean-square deviation ≈ 1.0 Å) and amino acid conservation of binding sites in protein domains were detected, contributing to the SA-PR binding modes. Overall, the outcomes from this study might provide a novel methodology to assess protein-ligand interactions and to gain some interesting insights into drug pharmacokinetics and pharmacodynamics to explain its variations among different species.

The innate immune response in Zika virus infection

Zika virus (ZIKV; Flaviviridae, Flavivirus) was discovered in 1947 in Uganda, Africa, from the serum of a sentinel Rhesus monkey (Macaca mulatta). It is an enveloped, positive-sense, single-stranded RNA virus, which encodes a single polyprotein that is cleaved into 10 individual proteins. In 2015, the Zika-epidemic in Brazil was marked mainly by the exponential growth of microcephaly cases and other congenital defects. With regard to host-pathogen relationships, understanding the role of the immune response in the pathogenesis ZIKV infection is challenging. The innate immune response is the first-line immunological defence, in which pathogen-associated molecular patterns are recognized by pattern-recognition receptors that trigger macrophages, dendritic cells, natural killer cells and endothelial cells to produce several mediators, which modulate viral replication and immune evasion. In this review, we have summarized current knowledge on the innate immune response against ZIKV.

Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus

Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment of the public health risk of newly emerging strains of the pathogens by comparing them with existing strains/pathogens using fast computational sequence comparison methods; (c) implementation of vaccine design methods in order to produce a set of probable peptide vaccine candidates for quick synthesis/production and testing in the laboratory; and (d) designing of novel therapeutic molecules and their laboratory testing as well as validation of new drugs or repurposing of drugs for use against ZIKV. For each of these stages, we provide an extensive review of the technical challenges and current state-of-the-art. Further, we outline the future areas of research and discuss how they can work together to proactively combat ZIKV or future emerging pathogens.

Targeting of host cell receptor tyrosine kinases by intracellular pathogens

Intracellular pathogens use complex and tightly regulated processes to enter host cells. Upon initial interactions with signaling proteins at the surface of target cells, intracellular microbes activate and co-opt specific host signaling pathways that mediate cell surface-cytosol communications to facilitate pathogen internalization. Here, we discuss the roles of host receptor tyrosine kinases (RTKs) in the establishment of productive infections by major intracellular pathogens. We evaluate the gaps in the current understanding of this process and propose a comprehensive approach for assessing the role of host cell signaling in the biology of intracellular microorganisms and viruses. We also discuss RTK-targeting strategies for the treatment of various infections.

Pathophysiology and Mechanisms of Zika Virus Infection in the Nervous System

In 2015, public awareness of Zika virus (ZIKV) rose in response to alarming statistics of infants with microcephaly being born to women who were infected with the virus during pregnancy, triggering global concern over these potentially devastating consequences. Although we have discovered a great deal about the genome and pathogenesis of this reemergent flavivirus since this recent outbreak, we still have much more to learn, including the nature of the virus-host interactions and mechanisms that determine its tropism and pathogenicity in the nervous system, which are in turn shaped by the continual evolution of the virus. Inevitably, we will find out more about the potential long-term effects of ZIKV exposure on the nervous system from ongoing longitudinal studies. Integrating clinical and epidemiological data with a wider range of animal and human cell culture models will be critical to understanding the pathogenetic mechanisms and developing more specific antiviral compounds and vaccines.