Molecular docking studies with rabies virus glycoprotein to design viral therapeutics

Pangenomic and immunoinformatics based analysis of Nipah virus revealed CD4+ and CD8+ T-Cell epitopes as potential vaccine candidates

Introduction: Nipah (NiV) is the zoonotic deadly bat-borne virus that causes neurological and respiratory infections which ultimately lead to death. There are 706 infected cases reported up till now especially in Asia, out of which 409 patients died. There is no vaccine and effective treatment available for NiV infections and we have to timely design such strategies as world could not bear another pandemic situation. Methods: In this study, we screened viral proteins of NiV strains based on pangenomics analysis, antigenicity, molecular weight, and sub-cellular localization. The immunoproteomics based approach was used to predict T-cell epitopes of MHC class-I and II as potential vaccine candidates. These epitopes are capable to activate CD4+, CD8+, and T-cell dependent B-lymphocytes. Results: The two surface proteins including fusion glycoprotein (F) and attachment glycoprotein (G) are antigenic with molecular weights of 60 kDa and 67 kDa respectively. Three epitopes of F protein (VNYNSEGIA, PNFILVRNT, and IKMIPNVSN) were ranked and selected based on the binding affinity with MHC class-I, and 3 epitopes (VILNKRYYS, ILVRNTLIS, and VKLQETAEK) with MHC-II molecules. Similarly, for G protein, 3 epitopes each for MHC-I (GKYDKVMPY, ILKPKLISY, and KNKIWCISL) and MHC-II (LRNIEKGKY, FLIDRINWI, and FLLKNKIWC) with substantial binding energies were predicted. Based on the physicochemical properties, all these epitopes are non-toxic, hydrophilic, and stable. Conclusion: Our vaccinomics and system-level investigation could help to trigger the host immune system to prevent NiV infection.

Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management

Molecular docking is a computational technique that predicts the binding affinity of ligands to receptor proteins. Although it has potential uses in nutraceutical research, it has developed into a formidable tool for drug development. Bioactive substances called nutraceuticals are present in food sources and can be used in the management of diseases. Finding their molecular targets can help in the creation of disease-specific new therapies. The purpose of this review was to explore molecular docking's application to the study of dietary supplements and disease management. First, an overview of the fundamentals of molecular docking and the various software tools available for docking was presented. The limitations and difficulties of using molecular docking in nutraceutical research are also covered, including the reliability of scoring functions and the requirement for experimental validation. Additionally, there was a focus on the identification of molecular targets for nutraceuticals in numerous disease models, including those for sickle cell disease, cancer, cardiovascular, gut, reproductive, and neurodegenerative disorders. We further highlighted biochemistry pathways and models from recent studies that have revealed molecular mechanisms to pinpoint new nutraceuticals' effects on disease pathogenesis. It is convincingly true that molecular docking is a useful tool for identifying the molecular targets of nutraceuticals in the management of diseases. It may offer information about how nutraceuticals work and support the creation of new therapeutics. Therefore, molecular docking has a bright future in nutraceutical research and has a lot of potentials to lead to the creation of brand-new medicines for the treatment of disease.

In-silico drug design for the novel Karachi-NF001 strain of brain-eating amoeba: Naegleria fowleri

Naegleria fowleri (N. fowleri) is a free-living thermophilic amoeba of fresh water and soil. The amoeba primarily feeds on bacteria but can be transmitted to humans upon contact with freshwater sources. Furthermore, this brain-eating amoeba enters the human body through the nose and travels to the brain to cause primary amebic meningoencephalitis (PAM). N. fowleri has been reported globally since its discovery in 1961. Recently a new strain of N. fowleri named Karachi-NF001 was found in a patient who had traveled from Riyadh, Saudi Arabia to Karachi in 2019. There were 15 unique genes identified in the genome of the Karachi-NF001 strain compared to all the previously reported strains of N. fowleri worldwide. Six of these genes encode well-known proteins. In this study, we performed in-silico analysis on 5 of these 6 proteins, namely, Rab family small GTPase, NADH dehydrogenase subunit 11, two Glutamine-rich protein 2 proteins (locus tags: 12086 and 12110), and Tigger transposable element-derived protein 1. We conducted homology modeling of these 5 proteins followed by their active site identification. These proteins were subjected to molecular docking against 105 anti-bacterial ligand compounds as potential drugs. Subsequently, the 10 best-docked compounds were determined for each protein and ranked according to the number of interactions and their binding energies. The highest binding energy was recorded for the two Glutamine-rich protein 2 proteins with different locus tags, and results have shown that the protein-inhibitor complex was stable throughout the simulation run. Moreover, future in-vitro studies could validate the findings of our in-silico analysis and identify potential therapeutic drugs against N. fowleri infections.

Identification of new small molecule monoamine oxidase-B inhibitors through pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation studies

The discovery of a safe and efficacious drug is a complex, time-consuming, and expensive process. Computational methodologies driven by cheminformatics tools play a central role in the high-throughput lead discovery and optimization process especially when the structure of the biological target is known. Monoamine oxidases are the membrane-bound FAD-containing enzymes and the isoform monoamine oxidase-B (MAO-B) is an attractive target for treating diseases like Alzheimer's disease, Parkinson's disease, glioma, etc. In the current study, we have used a pharmacophore-based virtual screening technique for the identification of new small molecule MAO-B inhibitors. Safinamide was used for building a pharmacophore model and the developed model was used to probe the ZINC database for potential hits. The obtained hits were filtered against drug-likeness and PAINS. Out of the hit's library, two compounds ZINC02181408, ZINC08853942 (most active), and ZINC53327382 (least active) were further subjected to molecular docking and dynamics simulation studies to assess their virtual binding affinities and stability of the resultant protein-ligand complex. The docking studies revealed that active ligands were well accommodated within the active site of MAO-B and interacted with both substrate and entrance cavity residues. MD simulation studies unveiled additional hydrogen bond interactions with the substrate cavity residues, Tyr398 and Tyr435 that are crucial for the catalytic role of MAO-B. Moreover, the predicted ADMET parameters suggest that the compounds ZINC08853942 and ZINC02181408 are suitable for CNS penetration. Thus, the attempted computational campaign yielded two potential MAO-B inhibitors that merit further experimental investigation.Communicated by Ramaswamy H. Sarma.

The Molecular Docking of Flavonoids Isolated from Daucus carota as a Dual Inhibitor of MDM2 and MDMX

BACKGROUND

Cancer is characterized by overexpression of p53 associated proteins, which down-regulate P53 signaling pathway. In cancer therapy, p53 activity can be restored by inhibiting the interaction of MDMX (2N0W) and MDM2 (4JGR) proteins with P53 protein.

OBJECTIVE

In the current, study in silico approaches were adapted to use a natural product as a source of cancer therapy.

METHODS

In the current study in silico approaches were adapted to use a natural product as a source of cancer therapy. For in silico studies, Chemdraw and Molecular Operating Environment were used for structure drawing and molecular docking, respectively. Flavonoids isolated from D. carota were docked with cancerous proteins.

RESULT

Based on the docking score analysis, we found that compound 7 was the potent inhibitor of both cancerous proteins and can be used as a potent molecule for inhibition of 2N0W and 4JGR interaction with p53.

CONCLUSION

Thus the compound 7 can be used for the revival of p53 signaling pathway function however, intensive in vitro and in vivo experiments are required to prove the in silico analysis.

Polyethylene glycol-coated zinc oxide nanoparticle: an efficient nanoweapon to fight against herpes simplex virus type 1

AIM

We aimed to determine the possible inhibitory effects of zinc oxide nanoparticles (ZnO-NPs) and polyethylene glycol (PEG)-coated ZnO-NPs (ZnO-PEG-NPs) on herpes simplex virus type 1 (HSV-1).

MATERIALS & METHODS

PEGylated ZnO-NPs were synthesized by the mechanical method. Antiviral activity was assessed by 50% tissue culture infectious dose (TCID₅₀) and real-time PCR assays. To confirm the antiviral activity of ZnO-NPs on expression of HSV-1 antigens, indirect immunofluorescence assay was also conducted.

RESULTS

200 μg/ml ZnO-PEG-NPs could result in 2.5 log₁₀ TCID₅₀ reduction in virus titer, with inhibition rate of approximately 92% in copy number of HSV-1 genomic DNA.

CONCLUSION

ZnO-PEG-NPs could be proposed as a new agent for efficient HSV-1 inhibition. Our results indicated that PEGylation is effective in reducing cytotoxicity and increasing antiviral activity of nanoparticles.

A Systematic Study on Structure and Function of ATPase of Wuchereria bancrofti

BACKGROUND

Analyzing the structures and functions of different proteins of Wuchereria bancrofti is very important because till date no effective drug or vaccine has been discovered to treat lymphatic filariasis (LF). ATPase is one of the most important proteins of Wuchereria bancrofti. Adenosine triphosphate (ATP) converts into adenosine diphosphate (ADP) and a free phosphate ion by the action of these ATPase enzymes. Energy releases from these dephosphorylation reactions drive the other chemical reactions in the cell.

MATERIALS AND METHODS

In this study we worked on the protein ATPase of Wuchereria bancrofti which has been annotated from National Center for Biotechnology Information (NCBI). Various computational tools and databases have been used to determine the various characteristics of that enzyme such as physiochemical properties, secondary structure, three-dimensional (3D) structure, conserved domain, epitope, and their molecular evolutionary relationship.

RESULT

Subcellular localization of ATPase was identified and we have found that 55.5% are localized in the cytoplasm. Secondary and 3D structure of this protein was also predicted. Both structure and function analysis of ATPase of Wuchereria bancrofti showed unique nonhomologous epitope sites and nonhomologous antigenicity sites. Moreover, it resulted in 15 ligand drug-binding sites in its tertiary structure.

CONCLUSION

Structure prediction of these proteins and detection of binding sites and antigenicity sites from this study would indicate a potential target aiding docking studies for therapeutic designing against filariasis.