Protein-protein Docking Studies Research Articles

Role of Furin Activation Sites as Receptors for Invasion of Severe Acute Respiratory Syndrome Coronavirus-2 Into Human Cells

Objective: The severe acute type of respiratory distress caused by Coronavirus disease 2019 (COVID-19) was responsible for the global pandemic of 2019. While most of the focus of vaccine/drug molecules is on the receptor, there are certain enzymes that also need to be checked. Cell surface proteases are one of these. Activation of the virus spike protein becomes more complicated when many host proteases are involved. As many Variants of Concerns have been reported in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), this study aimed to understand the proteolytic function of Furin in each, and its involvement in virus-host interaction. Material and Methods: Spike Protein sequence alignment, furin cleavage site prediction of variants: Wuhan, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529), and protein-protein docking studies have been undertaken using appropriate bioinformatics tools. Results: It was observed that when compared to previous variations, the November 2021, outbreak of Omicron variant showed 50 amino acid substitutions in the Spike protein. Thus, in addition to the Angiotensin Converting Enzyme 2 (ACE-2) receptor, the role of virus binding sites to act as “Addition Receptors” for viral entry has been reported here. Conclusion: It was observed that substitution of basic amino acids in the Omicron variant may be responsible for the recognition of furin cleavage sites and the presence of furin cleavage site in the receptor binding domain (RBD) region will thus enhance viral transmission. If these sites are utilized in formulation of new drugs/vaccine molecules to target the furin hydrolyse sites, we may be able to add to the existing course of COVID-19 treatment.

Molecular docking analysis of α-Synuclein aggregation with Anle138b.

α-Synuclein aggregation into toxic oligomeric species is central to Parkinson's disease pathogenesis. Anle138b is a recently identified inhibitor of α-synuclein oligomerization showing promise in preclinical studies. This study employed computational approaches to elucidate Anle138b's mechanism of oligomer-specific action. The inhibitory potential of Anle138b against α-synuclein oligomers was evaluated by performing molecular docking studies using AutoDock Tools, followed by their binding pocket analysis. Further, protein-protein docking studies were performed using Hex8.0 to validate the aggregation inhibitory potential of Anle138b. Molecular docking revealed increasing binding affinity of Anle138b against higher order α-synuclein oligomers (dimer to decamer). Anle138b occupied oligomeric cavity and interacted with residues Thr54, Gly73, Val74 and Thr75 across several oligomers. Protein-protein docking showed that Anle138b interferes with α-synuclein decamer formation. These results highlight the oligomer-directed inhibitory mechanism of Anle138b, without hindering the monomeric forms and provide molecular insights to advance its therapeutic development for Parkinson's and related synucleinopathies.

Non-synonymous Single Nucleotide Polymorphisms in Human ACE2 Gene May Affect the Infectivity of SARS-CoV-2 Omicron Subvariants.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19), which first appeared in December 2019. Angiotensin I converting enzyme 2 (ACE2) receptor, present on the host cells, interacts with the receptor binding domain (RBD) of spike (S) protein of SARS-CoV-2 and facilitates the viral entry into host cells. Non-synonymous single nucleotide polymorphisms (nsSNPs) in the ACE2 gene may have an impact on the protein's stability and its function. The deleterious or harmful nsSNPs of the ACE2 gene that can change the strength as well as the pattern of interaction with the RBD of S protein were selected for this study. The ACE2:RBD interactions were analyzed by protein-protein docking study. The missense mutations A242V, R708W, G405E, D292N, Y633C, F308L, and G405E in ACE2 receptor were found to interact with RBD of Omicron subvariants with stronger binding affinity. Among the other selected nsSNPs of human ACE2 (hACE2), R768W, Y654S, F588S, R710C, R710C, A191P, and R710C were found to have lower binding affinity for RBD of Omicron subvariants. The findings of this study suggest that the nsSNPs present in the human ACE2 gene alter the structure and function of the protein and, consequently, the susceptibility to Omicron subvariants.

Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2.

The mechanisms utilized by different flaviviruses to evade antiviral functions of interferons are varied and incompletely understood. Using virological approaches, biochemical assays, and mass spectrometry analyses, we report here that the NS5 protein of tick-borne encephalitis virus (TBEV) and Louping Ill virus (LIV), two related tick-borne flaviviruses, antagonize JAK-STAT signaling through interactions with the tyrosine kinase 2 (TYK2). Co-immunoprecipitation (co-IP) experiments, yeast gap-repair assays, computational protein-protein docking and functional studies identify a stretch of 10 residues of the RNA dependent RNA polymerase domain of tick-borne flavivirus NS5, but not mosquito-borne NS5, that is critical for interactions with the TYK2 kinase domain. Additional co-IP assays performed with several TYK2 orthologs reveal that the interaction is conserved across mammalian species. In vitro kinase assays show that TBEV and LIV NS5 reduce the catalytic activity of TYK2. Our results thus illustrate a novel mechanism by which viruses suppress the interferon response.

New insights on the differential interaction of sulfiredoxin with members of the peroxiredoxin family revealed by protein-protein docking and experimental studies

Sulfiredoxin (Srx) is the enzyme that restores the peroxidase activity of peroxiredoxins (Prxs) through catalyzing the reduction of hyperoxidized Prxs back to their active forms. This process involves protein-protein interaction in an enzyme-substrate binding manner. The integrity of the Srx-Prx axis contributes to the pathogenesis of various oxidative stress related human disorders including cancer, inflammation, cardiovascular and neurological diseases. The purpose of this study is to understand the structural and molecular biology of the Srx-Prx interaction, which may be of significance for prediction of target site for the novel drug-discovery. Homology modeling and protein-protein docking approaches were applied to examine the Srx-Prx interaction using online platforms including ITASSER, Phyre2, Swissmodel, AlphaFold, MZDOCK and ZDOCK. By in-silico studies, A 26-amino acid motif at the C-terminus of Prx1 was predicted to cause a steric hindrance for the kinetics of the Srx-Prx1 interaction. These predictions were tested in-vitro using purified recombinant proteins including Srx, full-length Prxs, and C-terminus deleted Prxs. We confirmed that deletion of the C-terminus of Prxs significantly enhanced its rate of association with Srx (i.e. >1000 fold increase in the ka of the Srx-Prx1 interaction) with minimal effect on the rate of dissociation (kd). Differential interaction of Srx with individual members of the Prx family was further examined in cultured cells. Taken together, these data add novel molecular and structural insights critical for the understanding of the biology of the Srx-Prx interaction that may be of value for the development of targeted therapy for human disorders.

Virtual Screening on Molecules Targeting the Interaction Between Estrogen Receptor Beta and Murine Double Minute 2

Estrogen receptor beta (ERβ) is an isoform of estrogen receptor that plays a role in breast cancer. An E3 ubiquitin ligase, murine double minute 2 (MDM2), can bind to ERβ and degrade it. Virtual screening and protein-protein docking studies are one of the approaches that can be performed to discover FDA-approved drugs targeting the interaction of the ERβ-MDM2 complex. This study aimed to conduct virtual screening of 1615 compounds targeting the interaction between ERβ-MDM2 as an initial study to discover potential breast cancer drugs. Biovia Discovery Studio 2021, ClusPro 2.0, PyRx 8.0, and PyMOL software were utilized in this study. ERβ (PDB ID: 3OLS) and MDM2 (PDB ID: 1T4E) receptors were docked to obtain the ERβ-MDM2 protein complex. The ligands used in the virtual screening were FDA-approved drugs downloaded from the ZINC database. PIC and PLIP web tools were also utilized to analyze the amino acid residues involved in the interaction. The virtual screening results showed that ergotamine was the drug with the lowest energy score (-12.0 kcal/mol) among 1057 drugs and was able to establish the strongest interaction between ERβ-MDM2. In conclusion, based on this computational study, ergotamine strengthens the interaction between ERβ-MDM2 and thus could be used as a candidate for breast cancer drug. Thorough validation of in vitro, biochemical, and in vivo studies are needed to confirm this finding.Keywords: Estrogen receptor beta, breast cancer, protein-protein interaction, MDM2.

Virtual Evaluation of Insecticidal Potential of Fused Vip3Aa and Garlic Lectin against Fall Armyworm (Spodoptera frugiperda)

The use of transgenic crops to combat insect infestation has been proven to be an effective and environment-friendly approach. However, insecticidal proteins with a single mode of action are prone to the development of insect resistance. Researchers are now interested in combining insecticidal proteins to acquire multiple modes of action to address that problem. Here, we have performed a virtual evaluation of a fusion protein that was in silico constructed by combining the vegetative insecticidal protein (Vip3Aa) of Bacillus thurengensis and the garlic leaf lectin of Allium sativum (ASAL) with a fl exible peptide linker (GGGGS)3. Two fusion modes were conducted, one with ASAL as the N-terminus (AV) and the other where Vip3Aa is the N-terminus (VA) of the fusion construct. Molecular dynamics simulation of the fusion constructs (AV and VA) revealed their differences in conformational changes and compactness, with VA being more stable and favorable. Protein-protein docking studies against the fall armyworm aminopeptidase-N of S. frugiperda resulted in the identifi cation of interacting residues at the interface. A novel fusion protein proposed in this study would be valuable for rational design of potent insecticidal proteins with multiple modes of action.

In vitro Anti SARS-CoV-2 Activity and Docking Analysis of Pleurotus ostreatus, Lentinula edodes and Agaricus bisporus Edible Mushrooms.

BackgroundFungi are rich source of biologically active metabolites aimed for the improvement of human health through the prevention of various diseases, including infections and inflammatory disorders.AimWe aimed to in vitro examine the anti-SARS CoV-2 activity of the aqueous extract of each Pleurotus (P.) ostreatus, Lentinula (L.) edodes and Agaricus (A.) bisporus edible mushroom followed by docking analysis of certain metabolites against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-main protease (protease Mpro).MethodsAntiviral and cytotoxic effects were tested on hCoV-19/Egypt/NRC-3/2020/Vero-E6 cells and analyzed via (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide Assay (MTT) assay. Ligand-protein and protein-protein docking studies were performed to explore the interaction of different mushroom extracts at the binding site of protease Mpro. Molecular dynamics (MD) simulations were performed on the most promising ligand-target complexes to investigate their dynamic properties and confirm docking results.ResultsSubstantial antiviral activities with an IC50 of 39.19, 26.17, and 10.3.3 µg/mL and a selectivity index (SI) of 4.34, 3.44, and 1.5 for P. ostreatus, L. edodes and A. bisporus, were observed, respectively. Docking analysis revealed that, catechin from three mushroom isolates, chlorogenic acid from A. bisporus, kamperferol of P. ostreatus and quercetin from L. edodes, with a C-DOCKER interaction energy in the range of 22.8–37.61 (Kcal/mol) with protease compared to boceprevir ligand of 41.6 (Kcal/mol). Docking of superoxide dismutase, catalase from the three mushrooms, tyrosinase from A. bisporus showed ligand contact surface area with the protein as 252.74 Å2 while receptor contact surface area was 267.23 Å2.ConclusionP. ostreatus, L. edodes and A. bisporus have potential and remarkable in vitro antiviral activities against SARS-CoV-2. Quercetin from L. edodes, Kaempferol from P. ostreatus, chlorogenic acid and ascorbic acid, catechin, superoxide dismutase and catalase of the three mushrooms extracts were effectively bounded to Mpro of SARS-CoV-2 as conferred by docking analysis.

Protein-protein Docking Studies of Estrogen Receptor Alpha and TRIM56 Interaction for Breast Cancer Drug Screening

Breast cancer is the highest mortality cause in women with cancer. Protein-protein docking for target-based screening is an effective approach in breast cancer drug discovery via estrogen receptor (ER) signaling. TRIM56, an E3 ubiquitin protein ligase, can bind to and stabilize ER alpha. Thus, drug screening that can inhibit or weaken the interaction between ER alpha and TRIM56 is promising to obtain novel yet specific breast cancer drugs. In this study, we performed protein-protein docking studies for ER alpha and TRIM56 interaction and virtual screening for FDA-approved drugs from the ZINC database against ER alpha and TRIM56 complex protein model structure. We utilized Cluspro 2.0, PyRx 0.8, and Pymol 2.4.1 to conduct protein-protein docking, virtual screening, and model structure visualization. PIP and PLIP software were also applied to analyze the amino acid residue between proteins or protein-ligands. Based on the protein-protein docking, ER alpha and TRIM56 established interaction. Utilizing this complex protein as a macromolecule in the virtual screen of 1071 molecules of FDA-approved drugs, we obtain the top five lowest binding energy molecules i.e., dutasteride, dihydroergotamine, nilotinib, ergotamine, and bromocriptine. In addition, the energy binding affinity between ER alpha-dutasteride complex with TRIM56 was weakened in the presence of dutasteride. In conclusion, protein-protein docking between ER alpha-TRIM56 was able to select FDA-approved drugs that could bind to the complex, and dutasteride binding to ER alpha-TRIM56 complex weakened the interaction.Keywords: protein-protein docking, estrogen receptor alpha, TRIM56, breast cancer, ubiquitin.

Designing of a Chimeric Vaccine Using EIS (Rv2416c) Protein Against Mycobacterium tuberculosis H37Rv: an Immunoinformatics Approach.

Mycobacterium tuberculosis (Mtb) is a respiratory pathogen that causes tuberculosis (TB). There are a large number of proteins that are involved in the pathogenesis of TB. Stimulating the immune response against TB is very important to clear the pathogens from host. In the present study, an immunoinformatics conduit is used for designinganepitope based chimeric vaccine against TB. Enhanced intracellular survival (EIS) protein from Mtb is used for designing the chimeric vaccine. One B cell epitope, 8 cytotoxic T lymphocyte (CTL), and 6 helper T lymphocyte (HTL) epitopes were predicted based on the MHC allele binding, immunogenicity, antigenicity, allergenicity, toxicity and IFN epitopes. The selected epitopes were used for chimeric vaccine designing. Furthermore, 3D structure elucidation, structural refinement and validation of the designed chimeric vaccine were carried out. The 3D structure was used for protein-protein docking studies with Toll-like receptor 4 (TLR-4), followed by molecular dynamic simulation (MDS) and the interaction between the chimeric vaccine and TLR-4 complex was verified.

EhSir2c, a Sir2 homolog from the human pathogen Entamoeba histolytica interacts with a DNA repair protein, EhRAD23: Protein-protein interaction, docking and functional study

Chromosome segregation is a crucial phenomenon in the cell cycle and defects in genome segregation result in an abnormality in various cellular events. Unlike higher eukaryotes, chromosome segregation and a number of cell cycle events are unusual in the protozoan parasite Entamoeba histolytica (E. histolytica). Characterization of Sir2 proteins from E. histolytica may reveal its unique cellular events as they play role in diverse cellular processes including chromosome segregation. E. histolytica has four homologs of Sir2 proteins. EhSir2a and EhSir2b show sequence similarity towards eukaryotic Sir2 homologs, whereas EhSir2c and EhSir2d are more like prokaryotic sirtuins. Using both computational and experimental methods, EhSir2c has been characterized in this study. The three-dimensional structure of EhSir2c is predicted by homology modelling. The protein interactors of EhSir2c have been identified by yeast-two-hybrid screening against the cDNA library of E. histolytica. We have identified a novel interactor, EhRAD23 which is a homolog of UV excision repair protein RAD23. The interaction of EhSir2c and EhRAD23 was validated by pull-down assay. UV-C irradiation up-regulates the relative expression of EhSir2c, suggesting the necessity of EhSir2c in UV-induced stress in this parasite. Communicated by Ramaswamy H. Sarma

Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation.

Simple SummarySince the onset of the COVID-19 pandemic in late 2019, SARS-CoV-2 has evolved via genetic changes, resulting in numerous variants of concern (VOCs) and interest (VOIs). Using protein-protein docking and dynamics simulation, we examined the interactions of five SARS-CoV-2 variations’ receptor-binding domains with the human angiotensin-converting enzyme 2 (hACE2) receptor in host cells. A comparison of protein-protein docking and dynamics simulations showed that these point mutations significantly altered the structural behavior of the spike (S) protein, affecting RBD binding to hACE2 at the respective sites. Further research is needed to determine whether these changes affect drug–S protein binding and its potential therapeutic impact.Since the beginning of the coronavirus 19 (COVID-19) pandemic in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving through the acquisition of genomic mutations, leading to the emergence of multiple variants of concern (VOCs) and variants of interest (VOIs). Currently, four VOCs (Alpha, Beta, Delta, and Gamma) and seven VOIs (Epsilon, Zeta, Eta, Theta, Iota, Kappa, and Lambda) of SARS-CoV-2 have been identified in worldwide circulation. Here, we investigated the interactions of the receptor-binding domain (RBD) of five SARS-CoV-2 variants with the human angiotensin-converting enzyme 2 (hACE2) receptor in host cells, to determine the extent of molecular divergence and the impact of mutation, using protein-protein docking and dynamics simulation approaches. Along with the wild-type (WT) SARS-CoV-2, this study included the Brazilian (BR/lineage P.1/Gamma), Indian (IN/lineage B.1.617/Delta), South African (SA/lineage B.1.351/Beta), United Kingdom (UK/lineage B.1.1.7/Alpha), and United States (US/lineage B.1.429/Epsilon) variants. The protein-protein docking and dynamics simulation studies revealed that these point mutations considerably affected the structural behavior of the spike (S) protein compared to the WT, which also affected the binding of RBD with hACE2 at the respective sites. Additional experimental studies are required to determine whether these effects have an influence on drug–S protein binding and its potential therapeutic effect.

Improvement Thermal Stability of D-Lactate Dehydrogenase by Hydrophobin-1 and in Silico Prediction of Protein-Protein Interactions.

Hydrophobins are small surface-active proteins. They can connect to hydrophobic or hydrophilic regions and oligomerize in solution to form massive construction. In nature, these proteins are produced by filamentous fungi at different stages of growth. So far, researchers have used them in various fields of biotechnology. In this study, recombinant hydrophobin-1 (rHFB1, 7.5kDa) was used to stabilize recombinant D-lactate dehydrogenase (rD-LDH, 35kDa). rD-LDH is a sensitive enzyme deactivated and oxidized by external agents such as O2 and lights. So, its stabilization with rHFB1 can be the best index to demonstrate the positive effect of rHFB1 on preserving and improving enzyme's activity. The unique ability of rHFB1 for interacting with hydrophobic regions of rD-LDH was predicted by protein-protein docking study with ClusPro and PIC servers and confirmed by fluorescence experiments, and Colorless Native-PAGE. Measurement of thermodynamic parameters allows for authenticating the role of rHFB1 as a thermal stabilizer in the protein-protein complex (rD-LDH@rHFB1). Interaction between rHFB1 and rD-LDH improved half-life of enzyme 2.25-fold at 40°C. Investigation of the kinetic parameters proved that the presence of rHFB1 along with the rD-LDH enhancement strongly the affinity of the enzyme for pyruvate. Furthermore, an increase of Kcat/Km for complex displayed the effect of rHFB1 for improving the enzyme's catalytic efficiency.

Computational analysis of missense variants in MMP2 gene linked with Winchester syndrome and Nodulosis-Arthropathy-Osteolysis reveals structural shift in protein-protein and protein-ligand complexes

Matrix metalloproteinases - 2 (MMP2) protein stimulates multiple processes involving the nervous system, vascularization, and metastasis. Mutations in MMP2 is linked to Winchester and Nodulosis-Arthropathy-Osteolysis (NAO) syndromes. In this extensive investigation, we performed a computational analysis of 114 missense Single Nucleotide Polymorphisms (SNPs) of MMP2 protein using various in-silico algorithms. A total of 21 highly deleterious and pathogenic missense SNPs (T86K, R146H, A167T, G216E, R252P, R252L D326V, D326Y, G346S, G367S, R368L, S396R, A408P, R482C, P517L, A522E, E525K, Y543C, Y552S, K579M, M598T) were identified that probably could alter the structural and functional configuration of MMP2 gene. Moreover, conservation analysis, protein stability, TM-score and RMSD calculation, protein structure prediction and superimposition, ligand binding site prediction, protein-protein interaction, protein-ligand, and protein-protein docking studies were carried out. ConSurf analysis showed seventeen missense variants in the highly conserved regions, which were predicted as highly deleterious and pathogenic by eight in-silico platforms. Furthermore, G367S and K579M showed a greater impact on stability, structural alterations, protein-ligand and protein-protein interactions. This study will help in developing target-dependent medication for diseases and could enhance the understanding of the significance of uncharacterized missense SNPs and their interrelation with the disease. This study also contemplates the computational perception into the high-risk missense SNPs on protein structural and functional configuration.

Plausible computational insights and new atomic-level perspective of epicathechin gallate from Crataegus oxycantha extract in preventing caspase 3 activation in conditions like post-myocardial infarction

Cardiovascular disease (CVD) is the leading cause of mortality among the human species, however the non-existence of successful therapies to curtail the effect of Myocardial Infarction (MI) is a disquieting reality. Even though successful herbal formulations using Crataegus oxycantha (COC) is available, however, it is not recognized as an alternative medicine due to the lack of explanation on the molecular mechanism of COC extract on CVD conditions. In vivo studies revealed that COC extract significantly prevented caspase activation in conditions like post-MI; however, the role of a specific secondary metabolite that could be involved in this action is under quest. The present study, therefore, aims at predicting the plausible mechanism of action of key secondary metabolite in COC extract on apoptotic executioner caspase - caspase 3 during MI through in silico tools. The protein-protein interaction network, QikProp, and molecular docking studies were performed to identify the lead compound that revealed Epicatechin Gallate (ECG) of COC as an effective inhibitor against candidate MI/apoptosis mediator – caspase 3. The docked complex was further taken for molecular dynamics simulation, which was achieved through Desmond. Molecular dynamics further confirmed the stability of the binding interactions between the docked complex. The overall in silico results proved that ECG could prevent the dissociation of cleaved caspases, which is essential for their activation. Computational observations were strongly supported by experimental evidence obtained from in vivo studies in the MI-model system. From the above observations, it was concluded that computational analysis was in good agreement with the experimental analysis on ECG’s potential to prevent caspase 3 activation during MI.

Japanese encephalitis virus capsid protein interacts with non-lipidated MAP1LC3 on replication membranes and lipid droplets.

Microtubule-associated protein 1 light chain 3 (MAP1LC3) is a protein with a well-defined function in autophagy, but still incompletely understood roles in several other autophagy-independent processess. Studies have shown MAP1LC3 is a host-dependency factor for the replication of several viruses. Japanese encephalitis virus (JEV), a neurotropic flavivirus, replicates on ER-derived membranes that are marked by autophagosome-negative non-lipidated MAP1LC3 (LC3-I). Depletion of LC3 exerts a profound inhibition on virus replication and egress. Here, we further characterize the role of LC3 in JEV replication, and through immunofluorescence and immunoprecipitation show that LC3-I interacts with the virus capsid protein in infected cells. This association was observed on capsid localized to both the replication complex and lipid droplets (LDs). JEV infection decreased the number of LDs per cell indicating a link between lipid metabolism and virus replication. This capsid-LC3 interaction was independent of the autophagy adaptor protein p62/Sequestosome 1 (SQSTM1). Further, no association of capsid was seen with the Gamma-aminobutyric acid receptor-associated protein family, suggesting that this interaction was specific for LC3. High-resolution protein-protein docking studies identified a putative LC3-interacting region in capsid, 56FTAL59, and other key residues that could mediate a direct interaction between the two proteins.

Effect of α-amylase inhibitor from Withania somnifera on growth and development of Callosobruchus chinensis and in silico studies on its interactions with insect amylase

Pulse beetle (Callosobruchus chinensis) is a cosmopolitan stored grain pest of legumes responsible for significant losses in them during storage. A proteinaceous α-amylase inhibitor, isolated and purified from Withania somnifera (WSAI), affected various growth and developmental parameters of Callosobruchus chinensis. Whereas female fecundity, adult emergence and % seed damaged were found to be reduced, mean development period and feeding deterrence index increased as a function of WSAI treatment. Almost 59% relative amylase activity was observed at 50 µg/mL of WSAI and confirmed by starch activity gel assay. Longevity of survived insects of treated sets was reduced by 2 days compared to control sets. Possible homology modelled structures for WSAI and C. chinensis proteins were proposed. The In-silico protein-protein docking studies revealed the hydrogen bonding network, binding energy (−16.5 Kcal) and amino acids involved in forming interactions which will be helpful in understanding the mechanism of inhibition in future.

In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protein VP28 of white spot syndrome virus.

White spot disease caused by the white spot syndrome virus (WSSV) incurs a huge loss to the shrimp farming industry. Since no effective therapeutic measures are available, early detection and prevention of the disease are indispensable. Towards this goal, we previously identified a 12-mer phage displayed peptide (designated as pep28) with high affinity for VP28, the structural protein of the white spot syndrome virus (WSSV). The peptide pep28 was successfully used as a biorecognition probe in the lateral flow assay developed for rapid, on-site detection of WSSV. To unravel the structural determinants for the selective binding between VP28 and pep28, we used bioinformatics, structural modeling, protein-protein docking, and binding-free energy studies. We performed atomistic molecular dynamics simulations of pep28-pIII model totaling 300ns timescale. The most representative pep28-pIII structure from the simulation was used for docking with the crystal structure of VP28. Our results reveal that pep28 binds in a surface groove of the monomeric VP28 β-barrel and makes several hydrogen bonds and non-polar interactions. Ensemble-based binding-free energy studies reveal that the binding is dominated by non-polar interactions. Our studies provide molecular level insights into the binding mechanism of pep28 with VP28, which explain why the peptide is selective and can assist in modifying pep28 for its practical use, both as a biorecognition probe and a therapeutic.

Structural insights on binding mechanism of CAD complexes (CPSase, ATCase and DHOase)

Pyrimidine biosynthetic pathway enzymes constitute an important target for the development of antitumor drugs. To understand the role of binding mechanisms underlying the inborn errors of pyrimidine biosynthetic pathway, structure and function of enzymes have been analyzed. Pyrimidine biosynthetic pathway is initiated by CAD enzymes that harbor the first three enzymatic activities facilitated by Carbamoyl Phosphate Synthetase (CPSase), Aspartate Transcarbamoylase (ATCase) and Dihydroorotase (DHOase). While being an attractive therapeutic target, the lack of data driven us to study the CPSase (CarA and CarB) and its mode of binding to ATCase and DHOase which are the major limitation for its structural optimization. Understanding the binding mode of CPSase, ATCase and DHOase could help to identify the potential interface hotspot residues that favor the mechanism behind it. The mechanistic insight into the CAD complexes were achieved through Molecular modeling, Protein-Protein docking, Alanine scanning and Molecular dynamics (MD) Studies. The hotspot residues present in the CarB region of carboxy phosphate and carbamoyl phosphate synthetic domains are responsible for the assembly of CAD (CPSase-ATCase-DHOase) complexes. Overall analysis suggests that the identified hotspot residues were confirmed by alanine scanning and important for the regulation of pyrimidine biosynthesis. MD simulations analysis provided the prolonged stability of the interacting complexes. The present study reveals the novel hotspot residues such as Glu134, Glu147, Glu154, Asp266, Lys269, Glu274, Asp333, Trp459, Asp526, Asp528, Glu533, Glu544, Glu546, Glu800, Val855, Asp877, Tyr884 and Gln919 which could be targeted for structure-based inhibitor design to potentiate the CAD mediated regulation of aggressive tumors.Communicated by Ramaswamy H. Sarma

Exploring the Molecular Interactions between Neoculin and the Human Sweet Taste Receptors Through Computational Approaches

Neoculin is a sweet taste protein capable of modifying sour taste into sweet taste. Neoculin, along with other sweeteners, are received by the human sweet taste receptors T1R2 and T1R3. To date, there has been few studies regarding how neoculin interacts with the human sweet taste receptors in molecular level. In this study, computational approaches were applied to elucidate how neoculin interact with T1R2 and T1R3 at molecular level. In order to achieve this research, homology modeling for T1R2 and T1R3 was performed to predict their structure. A protein-protein docking study was conducted between neoculin and T1R2 and T1R3, which displayed a strong relationship with the previous experimental findings regarding the important residues of neoculin, and how they interact with the ATD domain of T1R3. These residues are His11, Asp91, Tyr21, Asn44, Arg48, Tyr 65, Val72, and Phe94. The best docked complexes were then subjected to molecular dynamics simulation for further analysis. The molecular dynamics simulation results showed the contributions of the important residues of neoculin in forming hydrogen bonds with the residues of the receptors. The binding energy between neoculin and each of T1R2 and T1R3 were also calculated. These results concluded that neoculin sweet taste and taste modifying abilities are only active when it binds to the amino terminal domain of T1R3.