Comprehensive approach to in silico identification and in vitro validation of anti-filarial hit molecules targeting the dimer interface of thioredoxin peroxidase 1 in Wuchereria bancrofti: a progress in anti-filariasis drug development.

Lymphatic filariasis (LF) remains a significant health challenge for populations in developing countries. LF is a parasitic disease transmitted by mosquitoes, mainly caused by the filarial nematode, Wuchereria bancrofti, prevalent in tropical and subtropical regions. Since the present drugs develop complications, including adverse side effects, lack of specificity, and development of drug resistance, the present study focused on developing the potential anti-filariasis drugs targeting crucial proteins for the nematode life cycle. We have identified the therapeutic compounds by targeting the enzyme thioredoxin peroxidase 1 (WbTPx1), which facilitates the conversion of hydrogen peroxide into water, an essential mechanism by which the nematode survives against oxidative stress in the host. This approach might resolve treatment efficacy and activity difficulties at various stages of filarial parasitic worms. We modeled the structure of WbTPx1 and employed the structure-based virtual screening approach, focusing on the dimer interface region of the protein. ADMET prediction profiles of the non-toxic, top-ranked hits with higher docking scores demonstrate higher affinity to the nematode protein than its human homolog. The molecular dynamic simulation studies show WbTPx1-hit complexes' stability and the intactness of hits in the binding site. Further, in vitro validation of identified hits using Setaria digitata, a cattle nematode, showed better IC50 and higher inhibition than the standard drug ivermectin, indicating the potential to inhibit enzyme activity and the development of drug candidates for controlling LF.

Discovery of plant-based phytochemical as effective antivirals that target the non-structural protein C of the Nipah virus through computational methods.

Nipah Virus (NiV) belongs to the Paramyxoviridae family and was first identified during an outbreak in Malaysia. Some initial symptoms include mild fever, headache and sore throat, which could escalate to respiratory illness and brain inflammation. The mortality rate of NiV infection can range from 40% to 75%, which is quite high. This is mainly due to the lack of efficient drugs and vaccines. In most instances, NiV is transmitted from animals to humans. Non-Structural Proteins (C, V and W) of the Nipah virus impede the host immune response by obstructive the JAK/STAT pathway. However, Non-Structural Proteins - C (NSP-C) plays a vital role in NiV pathogenesis, which includes IFN antagonist activity and viral RNA production. In the present study, the full-length structure of NiV-NSP-C was predicted using computational modelling, and the stability of the structure was analysed using 200 ns molecular dynamic (MD) simulation. Further, the structure-based virtual screening identified five potent phytochemicals (PubChem CID: 9896047, 5885, 117678, 14887603 and 5461026) with better binding affinity against NiV-NSP-C. DFT studies clearly showed that the phytochemicals had higher chemical reactivity, and the complex MD simulation depicted that the identified inhibitors exhibited stable binding with NiV-NSP-C. Furthermore, experimental validation of these identified phytochemicals would likely control the infection of NiV.Communicated by Ramaswamy H. Sarma.

Identification of Mulberrofuran as a potent inhibitor of hepatitis A virus 3Cpro and RdRP enzymes through structure-based virtual screening, dynamics simulation, and DFT studies.

Hepatitis is a medical condition characterized by inflammation of the liver. It is commonly caused by the hepatitis viruses A, B, C, D, and E. Hepatitis A virus (HAV) is highly contagious and can spread from infected individuals, through contaminated food, blood, or can also be water-borne. As per the statistics of World Health Organization (WHO), HAV infects about 1.4 million individuals each year globally. In this research work, we have focused on identifying natural product-based potential inhibitors for the two major enzymes of HAV namely 3C proteinase (3Cpro) and RNA-directed RNA polymerase (RdRP). The enzyme 3Cpro plays an important role in proteolytic activity that promotes viral maturation and infectivity. RNA-directed RNA polymerase facilitate viral replication and transcription. Structure-based virtual screening was carried out using NPACT database that contains a collection of 1574 curated plant-derived natural compounds that are validated by experiments. The screening procedure identified the phytochemical Mulberrofuran W, which could bind to both the targets 3Cpro and RdRP. The phytochemical Mulberrofuran W also had better binding affinity compared to the control compounds atropine and pyridinyl ester, which are previously identified inhibitors of HAV 3Cpro and RdRP, respectively. The Mulberrofuran W bound 3Cpro and RdRP complexes were subjected to 200 ns molecular dynamics simulations and were found to be stable and interacting with the active site of the enzymes throughout the course of complex MD simulations. In addition to DFT, MMGBSA studies were also performed to validate the identified potential inhibitor further. The identified phytochemical Mulberrofuran W can be considered as a new potential drug candidate and could be taken up for experimental evaluation against HAV infection.

Discovery of potent inhibitors targeting Glutathione S-transferase of Wuchereria bancrofti: a step toward the development of effective anti-filariasis drugs.

Lymphatic filariasis (LF) is one of the major health problems for the human kind in developing countries including India. LF is caused by three major nematodes namely Wuchereria bancrofti, Brugia malayi, and Brugia timori. The recent statistics of World Health Organization (WHO) showed that 51 million people were affected and 863 million people from 47 countries around worldwide remain threatened by LF. Among them, 90% of the filarial infection was caused by the nematode W. bancrofti. Approved drugs were available for the treatment of LF but many of them developed drug resistance and no longer effective in all stages of the infection. In the current research work, we explored the Glutathione S-transferase (GST) of W. bancrofti, the key enzyme responsible for detoxification that catalyzes the conjugation of reduced GSH (glutathione) to xenobiotic compounds. Initially, we analyzed the stability of the WbGST through 200 ns MD simulation and further structure-based virtual screening approach was applied by targeting the substrate binding site to identify the potential leads from small molecule collection. The in silico ADMET profiles for the top-ranked hits were predicted and the predicted non-toxic lead molecules showed the highest docking score in the range of - 12.72 kcal/mol to - 11.97 kcal/mol. The cross docking of the identified hits with human GST revealed the potential binding specificity of the hits toward WbGST. Through WbGST-lead complex simulation, the lead molecules were observed to be stable and also intactly bound within the binding site of WbGST. Based on the computational results, the five predicted non-toxic molecules were selected for the in vitro assay. The molecules showed significant percentage of inhibition against the filarial worm Setaria digitata which is the commonly used model organism to evaluate the filarial activity. In addition, the molecules also showed better IC50 than the standard drug ivermectin. The identified lead molecules will lay a significant insight for the development of new drugs with higher specificity and lesser toxicity to control and treat filarial infections.

Computational identification and experimental validation of anti-filarial lead molecules targeting metal binding/substrate channel residues of Cu/Zn SOD1 from Wuchereria bancrofti.

Lymphatic filariasis (LF) is a neglected mosquito-borne parasitic disease, widely caused by Wuchereria bancrofti (Wb) in tropical and sub-tropical countries. During a blood meal, the filarial nematodes are transmitted to humans by the infected mosquito. To counter attack the invaded nematodes, the human immune system produces reactive oxygen species. However, the anti-oxidant enzymes of nematodes counteract the host oxidative cytotoxicity. Cu/Zn Superoxide dismutase (SOD1), a member of antioxidant enzymes and are widely used by the nematodes to sustain the host oxidative stress across its lifecycle, hence targeting SOD1 to develop suitable drug molecules would help to overcome the problems related to efficacy and activity of drugs upon different stages of nematodes. In order to find the potent inhibitors, a three-dimensional structure of Cu/Zn WbSOD1 was modelled and the structural stability was analysed through simulation studies. The structure-guided virtual screening approach has been used to identify lead molecules from the ChemBridge based on the docking score, ADMET properties and protein-ligand complex stability analysis. The identified compounds were observed to interact with the copper, metal binding residues (His48, His63, His80 and His120) and catalytically important residue Arg146, which play a crucial role in the disproportionation of incoming superoxide radicals of Cu/Zn WbSOD1. Further, in vitro validation of the selected leads in the filarial worm Setaria digitata exhibited higher inhibition and better IC50 compared to the standard drug ivermectin. Thus, the identified leads could potentially inhibit enzyme activity, which could subsequently act as drug candidates to control LF.Communicated by Ramaswamy H. Sarma.

Potential inhibitors for peroxiredoxin 6 of W. bancrofti: A combined study of modelling, structure-based drug design and MD simulation.

Lymphatic filariasis (LF), a mosquito-borne parasitic disease caused by nematode Wuchereria bancrofti in tropical and sub-tropical countries. These nematodes are transferred into the human host when the infected mosquito carrying L3 larvae is released into the bloodstream during the blood ingestion process. The host immune system produces ROS (Reactive Oxygen Species) as a primary defence mechanism to remove the invading filarial worms. However, well-defined antioxidant enzymes of the nematodes scavenge the host-produced ROS to escape from oxidative stress. The enzyme peroxiredoxin 6 (Prx6) belongs to the peroxiredoxin family, catalyses hydrogen peroxide (H2O2) into water (H2O). In order to find the inhibitors that inhibit the activity of peroxiredoxin 6 of W. bancrofti. We performed the homology modelling to predict the WbPrx6 three-dimensional structure using the Schrödinger-Prime and the dynamic stability of the modelled WbPrx6 was analyzed by carrying out the molecular dynamic (MD) simulation for the time scale of 200ns. Further, the structure-based virtual screening shortlisted the hit molecules from the ChemBridge database based on the glide score. The potential lead molecules (ID: 10239274, 11112883, 79879205, 58160895, and 42133744) that have better binding and satisfied the ADMET properties were selected for further complex simulation and DFT calculations. The identified compounds interact with the N-terminal region of the thioredoxin domain, which plays a key role in reducing phospholipase A2 activity. Interestingly, upon binding the lead molecule, the fluctuation of the loop region that connects α-IV with the ß-VI plays a vital role in affecting the geometry of the active site, which in turn affects the activity WbPrx6. The outcomes of the present computational studies could help in future drug development and designing of the effective candidate to control Lymphatic filariasis.

Modelling studies reveal the importance of the C-terminal inter motif loop of NSP1 as a promising target site for drug discovery and screening of potential phytochemicals to combat SARS-CoV-2.

COVID-19 pandemic causative SARS-CoV-2 coronavirus is still rapid in progression and transmission even after a year. Understanding the viral transmission and impeding the replication process within human cells are considered as the vital point to control and overcome COVID-19 infection. Non-structural Protein 1, one among the proteins initially produced upon viral entry into human cells, instantly binds with the human ribosome and inhibit the host translation process by preventing the mRNA attachment. However, the formation of NSP1 bound Ribosome complex does not affect the viral replication process. NSP1 plays an indispensable role in modulating the host gene expression and completely steals the host cellular machinery. The full-length structure of NSP1 is essential for the activity in the host cell and importantly the loop connecting N and C-terminal domains are reported to play a role in ribosome binding. Due to the unavailability of the experimentally determined full-length structure of NSP1, we have modelled the complete structure using comparative modelling and the stability and conformational behaviour of the modelled structure was evaluated through molecular dynamics simulation. Interestingly, the present study reveals the significance of the inter motif loop to serves as a potential binding site for drug discovery experiments. Further, we have screened the phytochemicals from medicinal plant sources since they were used for several hundred years that minimizes the traditional drug development time. Among the 5638 phytochemicals screened against the functionally associated binding site of NSP1, the best five phytochemicals shown high docking score of -9.63 to -8.75 kcal/mol were further evaluated through molecular dynamics simulations to understand the binding affinity and stability of the complex. Prime MM-GBSA analysis gave the relative binding free energies for the top five compounds (dihydromyricetin, 10-demethylcephaeline, dihydroquercetin, pseudolycorine and tricetin) in the range of -45.17 kcal/mol to -37.23 kcal/mol, indicating its binding efficacy in the predicted binding site of NSP1. The density functional theory calculations were performed for the selected five phytochemicals to determine the complex stability and chemical reactivity. Thus, the identified phytochemicals could further be used as effective anti-viral agents to overcome COVID-19 and as well as several other viral infections.