Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling.

HIV-1 Vpr is a multifunctional accessory protein consisting of 96 amino acids that play a critical role in viral pathogenesis. Among its diverse range of activities, Vpr can create a cation-selective ion channel within the plasma membrane. However, the oligomeric state of this channel has not yet been elucidated. In this study, we investigated the conformational dynamics of Vpr helices to model the ion channel topology. First, we employed a series of multiscale simulations to investigate the specific structure of monomeric Vpr in a membrane model. During the lipid bilayer self-assembly coarse grain simulation, the C-terminal helix (residues 56-77) effectively formed the transmembrane region, while the N-terminal helix exhibited an amphipathic nature by associating horizontally with a single leaflet. All-atom molecular dynamics (MD) simulations of full-length Vpr inside a phospholipid bilayer show that the C-terminal helix remains very stable inside the bilayer core in a vertical orientation. Subsequently, using the predicted C-terminal helix orientation and conformation, various oligomeric states (ranging from tetramer to heptamer) possibly forming the Vpr ion channel were built and further evaluated. Among these models, the pentameric form exhibited consistent stability in MD simulations and displayed a compatible conformation for a water-assisted ion transport mechanism. This study provides structural insights into the ion channel activity of the Vpr protein and the foundation for developing therapeutics against HIV-1 Vpr-related conditions.

Peptide based vaccine designing against endemic causing mammarenavirus using reverse vaccinology approach.

The rodent-borne Arenavirus in humans has led to the emergence of regional endemic situations and has deeply emerged into pandemic-causing viruses. Arenavirus have a bisegmented ambisense RNA that produces four proteins: glycoprotein, nucleocapsid, RdRp and Z protein. The peptide-based vaccine targets the glycoprotein of the virus encountered by the immune system. Screening of B-Cell and T-Cell epitopes was done based on their immunological properties like antigenicity, allergenicity, toxicity and anti-inflammatory properties were performed. Selected epitopes were then clustered and epitopes were stitched using linker sequences. The immunological and physico-chemical properties of the vaccine construct was checked and modelled structure was validated by a 2-step MD simulation. The thermostability of the vaccine was checked followed by the immune simulation to test the immunogenicity of the vaccine upon introduction into the body over the course of the next 100 days and codon optimization was performed. Finally a 443 amino acid long peptide vaccine was designed which could provide protection against several members of the mammarenavirus family in a variety of population worldwide as denoted by the epitope conservancy and population coverage analysis. This study of designing a peptide vaccine targeting the glycoprotein of mammarenavirues may help develop novel therapeutics in near future.

In silico designing of an epitope-based peptide vaccine cocktail against Nipah virus: an Indian population-based epidemiological study.

Nipah virus, a zoonotic virus from the family Paramyxoviridae has led to significant loss of lives till date with the most recent outbreak in India reported in Kerala. The virus has a considerably high mortality rate along with lack of characteristic symptoms which results in the delay of the virus detection. No specific vaccine is available for the virus although monoclonal antibody treatment has been seen to be effective along with favipiravir. The high mortality and complications caused by the virus underscores the necessity to develop alternative modes of vaccination. One such method has been designed in this study using peptide cocktail consisting of the immunologically important epitopes for use as vaccine. The human leucocytic antigens that are used for the study were analyzed for their presence in various ethnic Indian populations. This study may serve as a new avenue for development of more efficient peptide cocktail vaccines in recent future based on the population genetics and ethnicity.

Exploring the chemical space for potential inhibitors against cell surface binding protein of Mpox virus using molecular fingerprint based screening approach.

Mpox virus is the latest member of the Poxviridae family of which small pox virus is a member. Monekypox virus has led to thousands of infections across the globe. Poxvirus gains entry into the cell making use of glycosaminoglycans like chondroitin sulphate and heparan sulphate. The interaction of the Mpox virus protein E8L also called cell surface binding protein is crucial for host cell attachment, membrane fusion and viral entry into the host cell leading to establishment of infection thus making this protein a very attractive therapeutic target. In this study we have tried to utilize the chondroitin sulphate binding groove present in the protein and identify molecules which are structurally similar to chondroitin sulphate. These molecules can thus occupy the same pocket but with a better binding affinity than chondroitin sulphate in order to outcompete the latter molecule from binding to the E8L protein and thus prevent it from performing its function. This study may pave the way for development of highly efficient therapeutics against the Mpox virus and further curb its infective potential.Communicated by Ramaswamy H. Sarma.

Repurposing of drug molecules from FDA database against Hepatitis C virus E2 protein using ensemble docking approach.

Hepatitis C virus, a member of the Flaviviridae family and genus Hepacivirus, is an enveloped, positively single stranded RNA virus. Its surface consists of a heterodimer of E1 and E2 proteins which play a crucial role in receptor binding and membrane fusion. In this study we have used in silico virtual screening by utilizing ensemble docking on the approved drugs. These drugs can bind with high efficiency to the 36 prominent conformations of the CD81 binding site clustered from a total of 3 µs MD simulation data on the E2 protein. We started with 9213 compounds from the FDA list of drugs and progressively came down to 5 compounds which have been seen to bind with very high efficiency to not only all the conformations but also the two predicted druggable pockets that encompass the CD81 binding site. MM/PBSA binding energy calculations also point to the highly stable interaction of the compounds to the E2 protein. This study may in future broaden the arsenal of therapeutics for use against HCV infection and lead to more effective care against the virus.

Computer-aided de novo design and optimization of novel potential inhibitors of HIV-1 Nef protein.

Nef is a small accessory protein pivotal in the HIV-1 viral replication cycle. It is a multifunctional protein and its interactions with kinases in host cells have been well characterized through many in vitro and structural studies. Nef forms a homodimer to activate the kinases and subsequently the phosphorylation pathways. The disruption of its homodimerization represents a valuable approach in the search for novel classes of antiretroviral. However, this research avenue is still underdeveloped as just a few Nef inhibitors have been reported so far, with very limited structural information about their mechanism of action. To address this issue, we have employed an in silico structure-based drug design strategy that combines de novo ligand design with molecular docking and extensive molecular dynamics simulations. Since the Nef pocket involved in homodimerization has high lipophilicity, the initial de novo-designed structures displayed poor drug-likeness and solubility. Taking information from the hydration sites within the homodimerization pocket, structural modifications in the initial lead compound have been introduced to improve the solubility and drug-likeness, without affecting the binding profile. We propose lead compounds that can be the starting point for further optimizations to deliver long-awaited, rationally designed Nef inhibitors.

In silico investigation of binding propensity of hematoxylin derivative and damnacanthal for their potential inhibitory effect on HIV-1 Vpr from different subtypes.

HIV-1, the causative agent of AIDS leads to many deaths worldwide though few options are available as therapeutics. To deal with the continuous mutation in the virus genome, requirement of new drugs is always there. Subtype variation plays a crucial role in case of HIV-1 therapeutics development. In this study, we want to investigate some pre examined molecules that can be effective for HIV-1 VPR. Inhibition of several protein-protein interactions with the small molecules will lead to identify some molecules as therapeutics other than the conventional drugs. We retrieved the sequences of different subtypes from the database and representative sequences were identified. Representative structures were modelled and validated using MD simulations. Forty molecules, showing anti Vpr activity in vitro were identified from literature survey and those were docked with each subtype representative structures. Two molecules a stable Hematoxylin Derivative (SHD) and Damnacanthal (D3), these were shown to be bind more effectively for all the subtypes. The stability of the protein and those two small molecule complexes were identified again with MD simulation followed by the binding energy calculation. Thus, these molecules can be thought as any option other than the conventional drug targeting HIV-1 Vpr.Communicated by Ramaswamy H. Sarma.

Designing of nanobodies against Dengue virus Capsid: a computational affinity maturation approach.

Dengue virus, an arbovirus, is one of the most prevalent diseases in the tropical environment and leads to huge number of casualties every year. No therapeutics are available till date against the viral disease and the only medications provide symptomatic relief. In this study, we have focused on utilizing conventional nanobodies and repurposing them for Dengue. Computationally affinity matured, best binding nanobodies tagged with constant antibody regions, could be proposed as therapeutics. These could also be applied for drug delivery purposes due to their high specificity against the viral Capsid. Another application of these nanobodies has been thought to utilize them for diagnostic purposes, to use the nanobodies for viral detection from patient samples at the earliest stage using ELISA. This study may open a new avenue for immunologic study in foreseeable future with the usage of the same molecules for multiple purposes. HighlightsNatural nanobodies against viruses were modified for use against Dengue virus Capsid conserved regions.Computational affinity maturation was performed making use of change in binding affinities upon mutating various residues in the complementary determining regions.Docking studies performed to inspect the docking groove, interface analysis and energy calculations.MM/GBSA calculations done to calculate binding free energy of the complex to determine stability of the complex.Communicated by Ramaswamy H. Sarma.

In silico study on miRNA regulation and NSs protein interactome characterization of the SFTS virus.

Severe fever with thrombocytopenia syndrome causing virus i.e. SFTS virus has increased in the last few years. The underlying cause and mechanism of disease progression and development of symptoms is not well known. Many viruses including Hepatitis B, Hepatitis C, HIV-1, Herpes virus, Dengue virus and many others have been seen to regulate their functions at the miRNA level. This study aimed to find out those cellular miRNAs, which can be mimicked or antagonized by the viral genome and analyze the effect of these miRNAs on various gene functions. Investigations in this study suggest a correlation between miRNA regulation with the disease symptoms and progression. By exhaustive literature survey we have tried to identify the interacting partners of the Non Structural S (NSs) protein and characterized the protein-protein interactions. The binding interface that can serve as target for therapeutic studies involving the interfacial residues was analyzed. This study would serve as an avenue to design therapeutics making use of not only protein-protein interactions but also miRNA based regulation as well.

Prediction of infectivity of SARS-CoV-2 virus based on Spike-hACE-2 interaction.

The COVID-19 pandemic caused by SARS-CoV-2 results almost 3 M death worldwide and till continuing in spite of having several vaccine against the virus. One of the main reasons is the mutations occur in the virus to cope with the environment. Detail study of genomics and proteomics level of each components may help to combat the situation. Spike (S) protein that covers the surface of the virus helps in entry by encountering the host receptor Human Angiotensin-Converting Enzyme-2 (hACE-2) with other different roles. In this study, we accomplish our work with the mutations in receptor binding domain (RBD) of Spike (S) protein considering different aspects like the hACE-2 variants in human populations to get an idea about the varying infectivity of different strains for different population. Several other parameters affecting the viral infectivity and in different diseased condition were also studied which may guide to a better insight in developing future therapeutics.

In Silico Study of Mutational Stability of SARS-CoV-2 Proteins.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), an enveloped RNA virus transmits by droplet infection thus affects the respiratory system. Different genomes have been reported globally for SARS-CoV-2 with moderate level of mutation which makes it harder to combat the virus. Mutational profiling and the relevant evolutionary aspect of coronavirus proteins namely spike glycoprotein, membrane protein, envelope protein, nucleoprotein, ORF1ab, ORF3a, ORF6, ORF7a, ORF7b and ORF8 were studied by in silico experiments. Clustering of the protein sequences and calculation of residue relative abundance were done to get an idea about the protein conservancy as well as finding out some representative sequences for phylogenetic and ancestral reconstruction. By mutational profiling and mutation analysis, the effect of mutations on the protein stability and their functional implication were studied. This study indicates the mutational effect on the proteins and their relevance in evolution, which directs us towards a better understanding of these variations and diversification of SARS-CoV-2 for useful future therapeutic study and thus aid in designing therapeutic agents keeping the highly variable regions in mind.

Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model.

COVID-19 caused by SARS-CoV-2 have become a global pandemic with serious rate of fatalities. SARS-CoV and MERS-CoV have also caused serious outbreak previously but the intensity was much lower than the ongoing SARS-CoV-2. The main infectivity factor of all the three viruses is the spike glycoprotein. In this study we have examined the intrinsic dynamics of the prefusion, lying state of trimeric S protein of these viruses through Normal Mode Analysis using Anisotropic Network Model. The dynamic modes of the S proteins of the aforementioned viruses were compared by root mean square inner product (RMSIP), spectral overlap and cosine correlation matrix. S proteins show homogenous correlated or anticorrelated motions among their domains but direction of Cα atom among the spike proteins show less similarity. SARS-CoV-2 spike shows high vertically upward motion of the receptor binding motif implying its propensity for binding with the receptor even in the lying state. MERS-CoV spike shows unique dynamical motion compared to the other two S protein indicated by low RMSIP, spectral overlap and cosine correlation value. This study will guide in developing common potential inhibitor molecules against closed state of spike protein of these viruses to prevent conformational switching from lying to standing state.

In silico designing of peptide based vaccine for Hepatitis viruses using reverse vaccinology approach.

Five different Hepatitis virus from different viral species cause viral-hepatitis, which is a life threatening disease leading to a high number of loss of lives every year. The mode of infection and transmission is different for each species and mostly spreads by direct contact and body fluids (for HBV and HCV). No such vaccine is available that can cure all types of Hepatitis with cross-protection. Thus our study involves a peptide based vaccine design with the help of Immunoinformatics approach. We focused only on the secretory and extracellular proteins of each types and identified their epitopes. Epitopes were examined for antigenicity, allergenicity, toxicity, anti-inflammatory property and IFN-γ induction. The short-listed peptides were stitched using linkers and TLR4 adjuvant. This final vaccine was proven to have good physico-chemical and structural properties. Simulation study to determine structural stability of the vaccine showed good result. Docking structure of vaccine with TLR4 has high affinity binding. Immune-simulation reveals favourable induction of immune response with high level of interleukins production important for immunity. Periplasmic expression in E.coli K12 strain was quite satisfactory. This study of designing recombinant chimeric vaccine using reverse vaccinology method provides some idea about the vaccine production against Hepatitis virus.