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.

Searching for target-specific and multi-targeting organics for Covid-19 in the Drugbank database with a double scoring approach.

The current outbreak of Covid-19 infection due to SARS-CoV-2, a virus from the coronavirus family, has become a major threat to human healthcare. The virus has already infected more than 44 M people and the number of deaths reported has reached more than 1.1 M which may be attributed to lack of medicine. The traditional drug discovery approach involves many years of rigorous research and development and demands for a huge investment which cannot be adopted for the ongoing pandemic infection. Rather we need a swift and cost-effective approach to inhibit and control the viral infection. With the help of computational screening approaches and by choosing appropriate chemical space, it is possible to identify lead drug-like compounds for Covid-19. In this study, we have used the Drugbank database to screen compounds against the most important viral targets namely 3C-like protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp) and the spike (S) protein. These targets play a major role in the replication/transcription and host cell recognition, therefore, are vital for the viral reproduction and spread of infection. As the structure based computational screening approaches are more reliable, we used the crystal structures for 3C-like main protease and spike protein. For the remaining targets, we used the structures based on homology modeling. Further, we employed two scoring methods based on binding free energies implemented in AutoDock Vina and molecular mechanics-generalized Born surface area approach. Based on these results, we propose drug cocktails active against the three viral targets namely 3CLpro, PLpro and RdRp. Interestingly, one of the identified compounds in this study i.e. Baloxavir marboxil has been under clinical trial for the treatment of Covid-19 infection. In addition, we have identified a few compounds such as Phthalocyanine, Tadalafil, Lonafarnib, Nilotinib, Dihydroergotamine, R-428 which can bind to all three targets simultaneously and can serve as multi-targeting drugs. Our study also included calculation of binding energies for various compounds currently under drug trials. Among these compounds, it is found that Remdesivir binds to targets, 3CLpro and RdRp with high binding affinity. Moreover, Baricitinib and Umifenovir were found to have superior target-specific binding while Darunavir is found to be a potential multi-targeting drug. As far as we know this is the first study where the compounds from the Drugbank database are screened against four vital targets of SARS-CoV-2 and illustrates that the computational screening using a double scoring approach can yield potential drug-like compounds against Covid-19 infection.

Phyto-Engineered Gold Nanoparticles (AuNPs) with Potential Antibacterial, Antioxidant, and Wound Healing Activities Under in vitro and in vivo Conditions.

BACKGROUND: A diabetic ulcer is one of the major causes of illness among diabetic patients that involves severe and intractable complications associated with diabetic wounds. Hence, a suitable wound-healing agent is urgently needed at this juncture. Greener nanotechnology is a very promising and emerging technology currently employed for the development of alternative medicines. Plant-mediated synthesis of metal nanoparticles has been intensively investigated and regarded as an alternative strategy for overcoming various diseases and their secondary complications like microbial infections. Hence, we are interested in developing phyto-engineered gold nanoparticles as useful therapeutic agents for the treatment of infectious diseases and wounds effectively. METHODS AND RESULTS: We have synthesized phyto-engineered gold nanoparticles from the aqueous extract of Acalypha indica and characterized using advanced bio-analytical techniques. The surface plasmon resonance feature and crystalline behavior of gold nanoparticles were revealed by ultraviolet-visible spectroscopy and X-ray diffraction, respectively. High-performance liquid chromatography analysis of the extract demonstrated the presence of different constituents, while major functional groups were interpreted by the Fourier-transform infrared spectroscopy as the various stretching vibrations appeared for important O-H (3443 cm-1), C=O (1644 cm-1) and C-O (1395 cm-1) groups. Scanning electron microscopy, high-resolution transmission electron microscopy results revealed a distribution of spherical and rod-like nanostructures with 20 nm of size. The gold nanoparticle-coated cotton fabric was evaluated for the antibacterial activity against Staphylococcus epidermidis and Escherichia coli bacterial strains which revealed remarkable inhibition at the zone of inhibition of 31 mm diameter against S. epidermidis. Further, antioxidant activity was tested for their free radical scavenging property, and the maximum antioxidant activity of the extract containing gold nanoparticles was found to be 80% at 100 µg/mL. The potent free radical scavenging property of the nanoparticles is observed at IC50 value 16.25 µg/mL. Moreover, in vivo wound-healing activity was carried out using BALB/c mice model with infected diabetic wounds and observed the stained microscopic images at different time intervals (day 2, day 7 and day 15). It was noted that in 15 days, the wound area is completely re-epithelialized due to the presence of different morphologies such as spherical, needle and triangle nanoparticles. The re-epithelialization layer is fully covered by nanoparticles on the wound area and also collagen filled in the scar tissue when compared with the control group. CONCLUSION: The pharmacological evaluation results of the study indicated an encouraging antibacterial and antioxidant activity of the greener synthesized gold nanoparticles tethered with aqueous extract of Acalypha indica. Moreover, we demonstrated enhanced in vivo wound-healing efficiency of the synthesized gold nanoparticles through the animal model. Thus, the outcome of this work revealed that the phyto-engineered gold nanoparticles could be useful for biomedical applications, especially in the development of promising antibacterial and wound-healing agents.

Structural and functional insights of STAT2-NS5 interaction for the identification of NS5 antagonist - An approach for restoring interferon signaling.

Dengue is a mosquito-borne viral infection caused by Dengue virus (DENV) and is an emerging concern in public health affecting billions of people worldwide annually with no effective drugs available till now. Immunogenic and highly conserved properties of Non-Structural Protein 5(NS5) in DENV makes it a potent marker to identify DENV infection. DENV interfere in the innate immune signaling and thereby decreases antiviral responses and favors viral replication. Viral recognition by host pathogen recognition receptors facilitates binding of interferon (IFN) to the interferon receptors that further activates both the Signal Transducer and Activator of Transcription-2 (STAT-2) a factor producing an antiviral response. The most debilitating factor of DENV infection is emaciation of human immune system by DENV- NS5. NS5 counters the antiviral response by STAT2 degradation impeding the transcriptional activation of interferon stimulated genes through interferon stimulated response elements. The present study aims to identify inhibitors for NS5 Methyl Transferase (MTase) domain and to provide an insight into the mechanism of STAT2 degradation in the host infected with DENV. Virtual screening and molecular docking studies identified five potential inhibitors ZINC84154300, ZINC08762321, ZINC08762323, ZINC12659408 and ZINC12285470 with docking scores of -10.55, -10.53, -10.78, -11.28 and -10.78 kcal/mol respectively. To further investigate the stability of the complexes, we have used Molecular Dynamics Simulations (MD). Besides, the binding free energy of top 5 docked ligands were estimated through Molecular Mechanics Generalized Born and Surface Area Solvation (MM/GBSA) methods. This study also provides an insight on the mechanism of immunological processes involved in alleviating the antiviral immune response and computational identification of potent inhibitors for viral NS5 protein.

Blocking protein kinase C signaling pathway: mechanistic insights into the anti-leishmanial activity of prospective herbal drugs from Withania somnifera.

BACKGROUND: Leishmaniasis is caused by several species of leishmania protozoan and is one of the major vector-born diseases after malaria and sleeping sickness. Toxicity of available drugs and drug resistance development by protozoa in recent years has made Leishmaniasis cure difficult and challenging. This urges the need to discover new antileishmanial-drug targets and antileishmanial-drug development. RESULTS: Tertiary structure of leishmanial protein kinase C was predicted and found stable with a RMSD of 5.8Å during MD simulations. Natural compound withaferin A inhibited the predicted protein at its active site with -28.47 kcal/mol binding free energy. Withanone was also found to inhibit LPKC with good binding affinity of -22.57 kcal/mol. Both withaferin A and withanone were found stable within the binding pocket of predicted protein when MD simulations of ligand-bound protein complexes were carried out to examine the consistency of interactions between the two. CONCLUSIONS: Leishmanial protein kinase C (LPKC) has been identified as a potential target to develop drugs against Leishmaniasis. We modelled and refined the tertiary structure of LPKC using computational methods such as homology modelling and molecular dynamics simulations. This structure of LPKC was used to reveal mode of inhibition of two previous experimentally reported natural compounds from Withania somnifera - withaferin A and withanone.