RNA-dependent Polymerase Research Articles

Discovering new potential inhibitors to SARS-CoV-2 RNA dependent RNA polymerase (RdRp) using high throughput virtual screening and molecular dynamics simulations

RNA dependent RNA polymerase (RdRp), is an essential in the RNA replication within the life cycle of the severely acute respiratory coronavirus-2 (SARS-CoV-2), causing the deadly respiratory induced sickness COVID-19. Remdesivir is a prodrug that has seen some success in inhibiting this enzyme, however there is still the pressing need for effective alternatives. In this study, we present the discovery of four non-nucleoside small molecules that bind favorably to SARS-CoV-2 RdRp over the active form of the popular drug remdesivir (RTP) and adenosine triphosphate (ATP) by utilizing high-throughput virtual screening (HTVS) against the vast ZINC compound database coupled with extensive molecular dynamics (MD) simulations. After post-trajectory analysis, we found that the simulations of complexes containing both ATP and RTP remained stable for the duration of their trajectories. Additionally, it was revealed that the phosphate tail of RTP was stabilized by both the positive amino acid pocket and magnesium ions near the entry channel of RdRp which includes residues K551, R553, R555 and K621. It was also found that residues D623, D760, and N691 further stabilized the ribose portion of RTP with U10 on the template RNA strand forming hydrogen pairs with the adenosine motif. Using these models of RdRp, we employed them to screen the ZINC database of ~ 17 million molecules. Using docking and drug properties scoring, we narrowed down our selection to fourteen candidates. These were subjected to 200 ns simulations each underwent free energy calculations. We identified four hit compounds from the ZINC database that have similar binding poses to RTP while possessing lower overall binding free energies, with ZINC097971592 having a binding free energy two times lower than RTP.

The exploration of phytocompounds theoretically combats SARS-CoV-2 pandemic against virus entry, viral replication and immune evasion

BackgroundThe novel coronavirus disease-2019 (COVID-19) that emerged in China, is an extremely contagious and pathogenic viral infection caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) that has sparked a global pandemic. The few and limited availability of approved therapeutic agents or vaccines is of great concern. Urgently, Remdesivir, Nirmatrelvir, Molnupiravir, and some phytochemicals including polyphenol, flavonoid, alkaloid, and triterpenoid are applied to develop as repurposing drugs against the SARS-CoV-2 invasion. MethodsThis study was conducted to perform molecular docking and absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis of the potential phytocompounds and repurposing drugs against three targets of SARS-CoV-2 proteins (RNA dependent RNA polymerase, RdRp, Endoribonclease, S-protein of ACE2-RBD). ResultsThe docking data illustrated Arachidonic acid, Rutin, Quercetin, and Curcumin were highly bound with coronavirus polyprotein replicase and Ebolavirus envelope protein. Furthermore, anti- Ebolavirus molecule Remedesivir, anti-HIV molecule Chloroquine, and Darunavir were repurposed with coronavirus polyprotein replicase as well as Ebolavirus envelope protein. The strongest binding interaction of each targets are Rutin with RdRp, Endoribonclease with Amentoflavone, and ACE2-RBD with Epigallocatechin gallate. ConclusionsTaken altogether, these results shed a light on that phytocompounds have a therapeutic potential for the treatment of anti-SARS-CoV-2 may base on multi-target effects or cocktail formulation for blocking viral infection through invasion/activation, transcription/reproduction, and posttranslational cleavage to battle COVID-19 pandemic.

Novel CYP11A1-Derived Vitamin D and Lumisterol Biometabolites for the Management of COVID-19.

Vitamin D deficiency is associated with a higher risk of SARS-CoV-2 infection and poor outcomes of the COVID-19 disease. However, a satisfactory mechanism explaining the vitamin D protective effects is missing. Based on the anti-inflammatory and anti-oxidative properties of classical and novel (CYP11A1-derived) vitamin D and lumisterol hydroxymetabolites, we have proposed that they would attenuate the self-amplifying damage in lungs and other organs through mechanisms initiated by interactions with corresponding nuclear receptors. These include the VDR mediated inhibition of NFκβ, inverse agonism on RORγ and the inhibition of ROS through activation of NRF2-dependent pathways. In addition, the non-receptor mediated actions of vitamin D and related lumisterol hydroxymetabolites would include interactions with the active sites of SARS-CoV-2 transcription machinery enzymes (Mpro;main protease and RdRp;RNA dependent RNA polymerase). Furthermore, these metabolites could interfere with the binding of SARS-CoV-2 RBD with ACE2 by interacting with ACE2 and TMPRSS2. These interactions can cause the conformational and dynamical motion changes in TMPRSS2, which would affect TMPRSS2 to prime SARS-CoV-2 spike proteins. Therefore, novel, CYP11A1-derived, active forms of vitamin D and lumisterol can restrain COVID-19 through both nuclear receptor-dependent and independent mechanisms, which identify them as excellent candidates for antiviral drug research and for the educated use of their precursors as nutrients or supplements in the prevention and attenuation of the COVID-19 disease.

Identification of 6ω-cyclohexyl-2-(phenylamino carbonylmethylthio)pyrimidin-4(3H)-ones targeting the ZIKV NS5 RNA dependent RNA polymerase.

Zika virus (ZIKV), a mosquito-borne flavivirus, is a global health concern because of its association with severe neurological disorders such as neonatal microcephaly and adult Guillain-Barre syndrome. Although many efforts have been made to combat ZIKV infection, there is currently no approved vaccines or antiviral drugs available and there is an urgent need to develop effective anti-ZIKV agents. In this study, 26 acetylarylamine-S-DACOs derivatives were prepared, and eight of them were found to have inhibitory activity against Zika virus. Among these substances, 2-[(4-cyclohexyl-5-ethyl-6-oxo-1,6-dihydropyrimidin-2-yl)thio]-N-(3,5-difluorophenyl)acetamide (4w) with the best anti-ZIKV activity was selected for in-depth study of antiviral activity and mechanism of action. Here, we discovered 4w targeted on the ZIKV NS5 RNA -dependent RNA polymerase (RdRp), which exhibited good in vitro antiviral activity without cell species specificity, both at the protein level and at the RNA level can significantly inhibit ZIKV replication. Preliminary molecular docking studies showed that 4w preferentially binds to the palm region of NS5A RdRp through hydrogen bonding with residues such as LYS468, PHE466, GLU465, and GLY467. ZIKV NS5 RdRp enzyme activity experiment showed that 4w could directly inhibit ZIKV RdRp activity with EC50 = 11.38 ± 0.51 μM. In antiviral activity studies, 4w was found to inhibit ZIKV RNA replication with EC50 = 6.87 ± 1.21 μM. ZIKV-induced plaque formation was inhibited with EC50 = 7.65 ± 0.31 μM. In conclusion, our study disclosed that acetylarylamine-S-DACOs is a new active scaffolds against ZIKV, among which compound 4w was proved to be a potent novel anti-ZIKV compound target ZIKV RdRp protein. These promising results provide a future prospective for the development of ZIKV RdRp inhibitors.

COVID-19 THERAPY: COMPARISON EFFECTIVITY BETWEEN REMDESIVIR AND FAVIPIRAVIR

ntroduction: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) is the virus that causes Coronavirus Disease 2019 (COVID-19), a disease of global concern(1). Remdesivir and favipiravir are antiviral drugs that are considered COVID19 therapy, as described in Indonesia's 3rd COVID-19 Management Guidelines. They have a similar mechanism, specifically by inhibiting RNA dependent RNA polymerase of the virus (3). Several studies have reported that patients who were treated with these antivirals had a shorter hospital stays (4–6). However, the comparison of efficacy between remdesivir and favipiravir is still unknown. Methods: An observational analytic study was done using a retrospective cohort design. Eighty-eight medical records of COVID-19 patients between January 2021 to August 2021 are collected by consecutive sampling techniques, and this research was carried out at Gotong Royong Hospital Surabaya. Results: Based on the statistical analysis test, there was no clinical improvement difference found, neither patients received remdesivir nor favipiravir based on their clinical manifestations, such as ventilation support and chest X-ray, measured by WHO ordinal scale (p=0,486 ; p>0,05 on the first week and p=0,942 ; p>0,05 on the second week). Conclusions: Improved clinical manifestations were seen in the second week of therapy, either in patients who received remdesivir or favipiravir, but there was no significant effectivity difference between those drugs.

Novel α-aminophosphonate derivates synthesis, theoretical calculation, Molecular docking, and in silico prediction of potential inhibition of SARS-CoV-2

Using the Density Functional Theory approach and in silico docking, the current study analyzes the inhibitory role of a novel α-aminophosphonate derivative against SARS-CoV-2 major protease (Mpro) and RNA dependent RNA polymerase (RdRp) of SARS-CoV-2. FT-IR, UV–Vis, and NMR (1H, 13C, 31P) approaches were used to produce and confirm the novel α-aminophosphonate derivative. The quantum chemical parameters were detremined, and the reactivity of the synthesized molecule was discussed using DFT at the B3LYP/6-31G(d,p) level. In addition, the inhibitory function of the investigated derivative for SARS-CoV-2 major protease (Mpro) and RNA dependent RNA polymerase (RdRp) was estimated using in silico docking. These discoveries could pave the way for novel SARS-CoV-2 therapies to develop and be tested.

The first Chinese oral anti-COVID-19 drug Azvudine launched

The first Chinese oral anti-COVID-19 drug Azvudine launched

Studies on Distribution of Sugarcane Yellow Leaf Virus in Commercially Grown Sugarcane Varieties in Andhra Pradesh

Background: Among the diseases of sugarcane, Sugarcane yellow leaf disease (YLD) is one of the most prevalent diseases of sugarcane posing serious threat to the sugarcane cultivation worldwide. The current study aims at studying the distribution of SCYLV in the major sugarcane-growing of Andhra Pradesh and determining sequence identities, sequence variations and phylogenetic relationships between the SCYLV isolates reported earlier from India and worldwide. Methods: ORF1 and ORF2 regions of the viral genome coding for RNA dependent RNA Polymerase (RdRP) was amplified from twelve of the samples using the gene specific primers viz., SCYLV-F3 and SCYLV-R3. The ORF1 and ORF2 regions were studied for sequence similarity at nucleotide and aminoacid level and phylogentic relationships were established with the other SCYLV isolates. Result: The multiple sequence analysis of the isolates under the study with 22 similar sequences of SYLCV isolates reported from India and worldwide revealed 90.6-100% identities with IND, REU, BRA, CHN, HAW, CUB, COL and PER genotypes reported worldwide. The Indian isolates showed close phylogenetic relationship with the CUB and COL isolates. Hence it was confirmed from the study that SCYLV isolates collected from major sugarcane growing regions of Andhra Pradesh closely related to SCYLV-CUB and SCYLV-COL genotypes.

Unveiling the multitargeted potential of N-(4-Aminobutanoyl)-S-(4-methoxybenzyl)-L-cysteinylglycine (NSL-CG) against SARS CoV-2: a virtual screening and molecular dynamics simulation study

The coronaviridae family has caused the most destruction among all the viral families in modern sciences. It is one of the recently discovered and added members of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which has caused the global pandemic and significant destruction worldwide. However, scientists worldwide have developed vaccines, which are being given to humans. The mutated strain of the virus has caused various uncertainties about whether the discovered drug and vaccines affect it. Even after the World Health Organization's approval for the vaccines, their effectiveness and protection ratio are still a major concern. At the community level, to this date, there is no medicine available to cure the patients. In this study, we have screened the vast library from Drug Bank and identified N-(4-Aminobutanoyl)-S-(4-methoxybenzyl)-L-cysteinylglycine (NSL-CG) that can work against two major targets of SARS CoV-2, replication-transcription and RNA dependent polymerase. Further, we have performed the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and molecular dynamics simulation of the compound with both proteins individually, giving us enough evidence that the said drugs can work against the two targets together. Inhibiting the action of any of both proteins may lead to retaining the virus, and having a dual-targeted drug can be an extra precise measure for this process. The NSL-CG is an experimental drug belonging to the peptidomimetics class included in the small group of drugs with a docking score of −9.079 kcal/mol with replication-transcription −7.885 kcal/mol with RNA-dependent polymerase. Hence, through the complete flowed study, the NSL-CG can be further experimentally validated in in-vitro and in-vivo conditions before human utilisation. Communicated by Ramaswamy H. Sarma

Exploration of Luteolin as Potential Anti-COVID-19 Agent: Molecular Docking, Molecular Dynamic Simulation, ADMET and DFT Analysis

Background: Coronavirus disease-2019 (COVID-19) has recently emerged as a pandemic respiratory disease with mild to severe pneumonia symptoms. No clinical antiviral agent is available so far. However, several repurposing drugs and vaccines are being given to individuals or in clinical trials against SARS-CoV-2 Objective: The aim of this study is to uncover the potential effects of Luteolin (Lut) as an inhibitor of SARS-CoV2 encoded proteins via utilizing computational tools. Method: Molecular modelling to unfold the anti-SARS-CoV2 potential of Lut along with reference drugs namely remdesivir and nafamostat was performed by the use of molecular docking, molecular dynamic (MD) simulation, absorption, distribution, metabolism, excretion, toxicity (ADMET) and density functional theory (DFT) methods against the five different SARS-CoV-2 encoded key proteins and one human receptor protein. The chemical reactivity of Luteolin is done through prediction of HOMO-LUMO gap energy and other chemical descriptors analysis. Results: In the present study, Lut binds effectively in the binding pockets of spike glycoprotein (6VSB), ADP phosphatase of NSP3 (6W02), and RNA dependent RNA polymerase (7AAP) protein receptors with significant values of docking scores -7.00, -7.25, and -6.46 respectively as compared to reference drugs remdesivir and nafamostat. Conclusion:: Thus, Lut can act as a therapeutic agent and is orally safe for human consumption as predicted by molecular modelling against SARS-CoV-2 in the treatment of COVID-19.

PPP2R5D promotes hepatitis C virus infection by binding to viral NS5B and enhancing viral RNA replication

BackgroundHepatitis C virus (HCV) infection increased the risk of hepatocellular carcinoma. Identification of host factors required for HCV infection will help to unveil the HCV pathogenesis. Adaptive mutations that enable the replication of HCV infectious clones could provide hints that the mutation-carrying viral protein may specifically interact with some cellular factors essential for the HCV life cycle. Previously, we identified D559G mutation in HCV NS5B (RNA dependent RNA polymerase) important for replication of different genotype clones. Here, we searched for the factors that potentially interacted with NS5B and investigated its roles in HCV infection.MethodsWild-type-NS5B and D559G-NS5B of HCV genotype 2a clone, J6cc, were ectopically expressed in hepatoma Huh7.5 cells, and NS5B-binding proteins were pulled down and identified by mass spectrometry. The necessity and mode of action of the selected cellular protein for HCV infection were explored by experiments including gene knockout or knockdown, complementation, co-immunoprecipitation (Co-IP), colocalization, virus infection and replication, and enzymatic activity, etc.ResultsMass spectrometry identified a number of cellular proteins, of which protein phosphatase 2 regulatory subunit B’delta (PPP2R5D, the PP2A regulatory B subunit) was one of D559G-NS5B-pulled down proteins and selected for further investigation. Co-IP confirmed that PPP2R5D specifically interacted with HCV NS5B but not HCV Core and NS3 proteins, and D559G slightly enhanced the interaction. NS5B also colocalized with PPP2R5D in the endoplasmic reticulum. Knockdown and knockout of PPP2R5D decreased and abrogated HCV infection in Huh7.5 cells, respectively, while transient and stable expression of PPP2R5D in PPP2R5D-knockout cells restored HCV infection to a level close to that in wild-type Huh7.5 cells. Replicon assay revealed that PPP2R5D promoted HCV replication, but the phosphatase activity and catalytic subunit of PP2A were not affected by NS5B.ConclusionsPPP2R5D interactes with HCV NS5B and is required for HCV infection in cultured hepatoma cells through facilitating HCV replication.

Revealing Anti-viral Potential of Siddha Formulation Manjal noi Kudineer against Hepatitis C Viral - RNA Dependent RNA Polymerase Using in-silico Docking Technique

Revealing Anti-viral Potential of Siddha Formulation Manjal noi Kudineer against Hepatitis C Viral - RNA Dependent RNA Polymerase Using in-silico Docking Technique

Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland.

RNA viromes of nine commonly encountered Ochlerotatus mosquito species collected around Finland in 2015 and 2017 were studied using next-generation sequencing. Mosquito homogenates were sequenced from 91 pools comprising 16–60 morphologically identified adult females of Oc. cantans, Oc. caspius, Oc. communis, Oc. diantaeus, Oc. excrucians, Oc. hexodontus, Oc. intrudens, Oc. pullatus and Oc. punctor/punctodes. In total 514 viral Reverse dependent RNA polymerase (RdRp) sequences of 159 virus species were recovered, belonging to 25 families or equivalent rank, as follows: Aliusviridae, Aspiviridae, Botybirnavirus, Chrysoviridae, Chuviridae, Endornaviridae, Flaviviridae, Iflaviridae, Negevirus, Partitiviridae, Permutotetraviridae, Phasmaviridae, Phenuiviridae, Picornaviridae, Qinviridae, Quenyavirus, Rhabdoviridae, Sedoreoviridae, Solemoviridae, Spinareoviridae, Togaviridae, Totiviridae, Virgaviridae, Xinmoviridae and Yueviridae. Of these, 147 are tentatively novel viruses. One sequence of Sindbis virus, which causes Pogosta disease in humans, was detected from Oc. communis from Pohjois-Karjala. This study greatly increases the number of mosquito-associated viruses known from Finland and presents the northern-most mosquito-associated viruses in Europe to date.

Evidence for yeast artificial synthesis in SARS-CoV-2 and SARS-CoV-1 genomic sequences

Background: Knowledge about the origin of SARS-CoV-2 is necessary for both a biological and epidemiological understanding of the COVID-19 pandemic. Evidence suggests that a proximal evolutionary ancestor of SARS-CoV-2 belongs to the bat coronavirus family. However, as further evidence for a direct zoonosis remains limited, alternative modes of SARS-CoV-2 biogenesis should also be considered. Results: Here we show that the genomes of SARS-CoV-2 and SARS-CoV-1 significantly diverge from other SARS-like coronaviruses through short chromosomal sequences from the yeast S. cerevisiae at focal positions that are known to be critical for host cell invasion, virus replication, and host immune response. For SARS-CoV-1, we identify two sites: one at the start of the RNA dependent RNA polymerase gene, and the other at the start of the spike protein’s receptor binding domain; for SARS-CoV-2, one at the start of the viral replicase domain, and the other toward the end of the spike gene past its domain junction. At this junction, we detect a highly specific stretch of yeast origin covering the critical furin cleavage site insert PRRA, which has not been seen in other lineage b betacoronaviruses. As yeast is not a natural host for this virus family, we propose an artificial synthesis model for viral constructs in yeast cells based on co-transformation of virus DNA plasmids carrying yeast selectable genetic markers followed by intra-chromosomal homologous recombination through gene conversion. Highly differential yeast sequence patterns congruent with chromosomes harboring specific auxotrophic markers further support yeast artificial synthesis. Conclusions: These results provide evidence that the genomes of SARS-CoV-1 and SARS-CoV-2 contain sequence information that points to their artificial synthesis in genetically modified yeast cells. Our data specifically allow the identification of the yeast S. cerevisiae as a potential recombination donor for the critical furin cleavage site in SARS-CoV-2.

PH-responsive glycine functionalized magnetic iron oxide nanoparticles for SARS-CoV-2 RNA extraction from clinical sample.

The recent outbreak of the novel corona virus disease 2019 (COVID-19) has been made a serious global impact due to its high infectivity and severe symptoms. The Severe Acute Respiratory Syndrome (SARS-CoV-2) RNA extraction is considered as one of the most important steps in COVID-19 detection. Several commercially available kits and techniques are currently being used for specific extraction of SARS-CoV-2 RNA. However, such methods are time consuming and expensive due to the requirement of trained labors, and several chemical reagents. To overcome the mentioned limitations, magnetic RNA adsorption methodology of glycine functionalized iron oxide nanoparticles (GNPs) was established. It showed an efficient potential in SARS-CoV-2 RNA extraction due to pH responsive nature of GNPs. The highly magnetic pH responsive GNPs were synthesized by one-pot co-precipitation method. Random morphology and average 20 nm size of GNPs were denoted by Transmission Electron Microscopy (TEM). X-ray diffractometer (XRD) showed the crystalline magnetite nature. Fourier transform infrared spectroscopy (FT-IR) and UV–visible spectrometry confirmed the presence of glycine on the surface of magnetic nanoparticles. Furthermore, the magnetic nature and thermal properties of GNPs were examined by vibrating sample magnetometer (VSM) and thermo-gravimetric analysis (TGA), respectively. In this study, glycine performed the role of RNA adsorbent. The adsorption of RNA onto the surface of GNPs was achieved in acidic medium (pH 6). In contrary, the elution of RNA from the surface of GNPs was achieved in basic medium (pH 8). The purity of obtained RNA was analyzed by UV–visible spectrometry. Further, the obtained RNA was examined for the presence of SARS-CoV-2 specific Envelope (E), RNA dependent RNA polymerase (RDRP) and Nucleocapsid (N) genes using an RT-PCR analysis. It showed the sudden rise in amount of these genes after 25 cycles of RT-PCR and hence indicated the efficient RNA extraction by GNPs. Agarose gel electrophoresis was used for validation of the quantity and quality of RNA extracted from SARS-CoV-2 patient’s sample. The reusability studies of GNPs were performed by monitoring the repeated use of GNPs for SARS-CoV-2 RNA extraction. This method possesses potential role in the field of disease diagnosis. The extraction results of RNA from SARS-CoV-2 patient’s sample indicated that the GNPs have an outstanding property over the current existing extraction protocols. It leads to the new advancements in extraction and detection of RNA.Graphical Graphical abstract of the pH responsive SARS-CoV-2 RNA extraction by using glycine functionalized magnetic iron oxide nanoparticles (GNPs) which were prepared by modified cost effective one pot chemical synthesis method. Prepared GNPs were characterized by XRD, FT-IR and UV-Visible spectrometry, Scanning electron microscopy (SEM) and Transmission electron microscopy (TEM). Glycine present on the surface of nanoparticles (NPs) played an important role in pH responsive RNA extraction procedure. When nanoparticles added in acidic (pH < 7) medium, glycine gained positive surface charge hence overall surface charge of NPs became positive. Thereby SARS-CoV-2 RNA adsorption/binding occurred on the surface of GNP. Later, the RNA-GNP complex was separated by an external magnet. Separated complex was added in basic (pH > 7) medium to elute RNA from GNP. This phenomenon occurred due to surface negative charge of glycine that caused charge repulsion with RNA. Eluted RNA was examined qualitatively and quantitatively by RT-PCR, nanodrop technique and agarose gel electrophoresis. Results were compared with kit based extracted RNA. Supplementary InformationThe online version contains supplementary material available at 10.1007/s10853-022-07464-6.

Repurposing antiviral phytochemicals from the leaf extracts of Spondias mombin (Linn) towards the identification of potential SARSCOV-2 inhibitors

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a pneumonia-like disease with a pattern of acute respiratory symptoms, currently remains a significant public health concern causing tremendous human suffering. Although several approved vaccines exist, vaccine hesitancy, limited vaccine availability, high rate of viral mutation, and the absence of approved drugs account for the persistence of SARS-CoV-2 infections. The investigation of possibly repurposing of phytochemical compounds as therapeutic alternatives has gained momentum due to their reported affordability and minimal toxicity. This study investigated anti-viral phytochemical compounds from ethanolic leaf extracts of Spondias mombin L as potential inhibitor candidates against SARS-CoV-2. We identified Geraniin and 2-O-Caffeoyl-(+)-allohydroxycitric acid as potential SARS-CoV-2 inhibitor candidates targeting the SARS-CoV-2 RNA-dependent polymerase receptor-binding domain (RBD) of SARS-CoV-2 viral S-protein and the 3C-like main protease (3CLpro). Geraniin exhibited binding free energy (ΔGbind) of − 25.87 kcal/mol and − 21.74 kcal/mol towards SARS-CoV-2 RNA-dependent polymerase and receptor-binding domain (RBD) of SARS-CoV-2 viral S-protein respectively, whereas 2-O-Caffeoyl-(+)-allohydroxycitric acid exhibited a ΔGbind of − 32 kcal/mol towards 3CLpro. Molecular Dynamics simulations indicated a possible interference to the functioning of SARS-CoV-2 targets by the two identified inhibitors. However, further in vitro and in vivo evaluation of these potential SARS-CoV-2 therapeutic inhibitor candidates is needed.

Resveratrol and Its Natural Analogues Inhibit RNA Dependant RNA Polymerase (RdRp) of Rhizopus oryzae in Mucormycosis through Computational Investigations

Mucormycosis (or black fungus infection) is a life-threatening, but rare fungal infection with predominant occurrence in immunosuppressed patients following the SARS-CoV-2 infection. Rhizopus oryzae (R. O.) causes about 70% of all cases of mucormycosis. RNA dependent RNA polymerase (RdRp) is a key fungal protein implicated in the genome replication and multiplication of R. oryzae. In view of biological significance of resveratrol (RES), rich in grape skin extract, on various microbial infections and inflammatory diseases including gum infections and periodontitis, our present study was aimed at in silico investigation of RES and its two natural analogues, piceatannol (3,5,3',4'-tetrahydroxy-trans-stilbene, PIC), and 3,5,4'-trimethoxy-trans-stilbene (TMS) for their development as successful antifungal agents targeting the R. O. specific RdRp to combat the deadly mucormycosis. Due to the unavailability of the three-dimensional structure of R. O. RdRp in the Protein Database Bank (PDB), the protein structure of RdRp was modeled using the target sequence of RT/Duplex (Set-Met) (PDB ID: 6AR3, 3.41 Å) by homology modeling. Using the modeled structure of R. O. RdRp, docking and molecular dynamics (MD) simulation studies were carried out in Schrödinger suite version 2021-2 software. The findings of docking, MD simulations and MM-PBSA binding energies conclude that the RES, PIC and TMS possess predictable and stable binding affinity/interactions to the R. O. RdRp. These bioactive compounds could potentially inhibit the activity of R. O. RdRp. Further, density function theory (DFT) analysis (B3LYP, 6-311 G* basis set) was performed, and results of DFT analysis indicate that the compound PIC could be a more potential inhibitor for R. O. RdRp over RES. In in silico drug-likeness and ADMET prediction studies, all of the compounds exhibited acceptable drug-likeness, the Lipinski’s rule of five and pharmacokinetic parameters. Finally, it can be concluded that RES and its two natural analogues, PIC and TMS are the potential inhibitors of R. O. RdRp based on docking, MD and DFT studies.

Withaniasomnifera phytochemicals possess SARS-CoV-2 RdRp and human TMPRSS2 protein binding potential.

Coronavirus disease-19 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has infected approximately 26 million people and caused more than 6 million deaths globally. Spike (S)-protein on the outer surface of the virus uses human trans-membrane serine protease-2 (TMPRSS2) to gain entry into the cell. Recent reports indicate that human dipeptidyl peptidase-4 inhibitors (DPP4 or CD26) could also be utilized to check the S-protein mediated viral entry into COVID-19 patients. RNA dependent RNA polymerase (RdRp) is another key virulence protein of SARS-CoV-2 life cycle. The study aimed to identify the potential anti-SARS-CoV-2 inhibitors present in Withania somnifera (Solanaceae) using computer aided drug discovery approach. Molecular docking results showed that flavone glycoside, sugar alcohol, and flavonoid present in W. somnifera showed − 11.69, − 11.61, − 10.1, − 7.71 kcal/mole binding potential against S-protein, CD26, RdRp, and TMPRSS2 proteins. The major standard inhibitors of the targeted proteins (Sitagliptin, VE607, Camostat mesylate, and Remdesivir) showed the − 7.181, − 6.6, − 5.146, and − 7.56 kcal/mole binding potential. Furthermore, the lead phytochemicals and standard inhibitors bound and non-bound RdRp and TMPRSS2 proteins were subjected to molecular dynamics (MD) simulation to study the complex stability and change in protein conformation. The result showed energetically favorable and stable complex formation in terms of RMSD, RMSF, SASA, Rg, and hydrogen bond formation. Drug likeness and physiochemical properties of the test compounds exhibited satisfactory results. Taken together, the present study suggests the presence of potential anti-SARS-CoV-2 phytochemicals in W. somnifera that requires further validation in in vitro and in vivo studies.Graphical Supplementary informationThe online version contains supplementary material available at 10.1007/s42535-022-00404-4.

Genome-wide identification, in silico characterization and expression analysis of the RNA helicase gene family in chickpea (C. arietinum L.)

The RNA helicases are an important class of enzymes which are known to influence almost every aspect of RNA metabolism. The majority of RNA helicases belong to the SF2 (superfamily 2) superfamily, members of which are further categorized into three separate subfamilies i.e., the DEAD, DEAH and DExD/H-box subfamilies. In chickpea, these RNA helicases have not been characterized until now. A genome-wide analysis across the chickpea genome led to the identification of a total of 150 RNA helicase genes which included 50 DEAD, 33 DEAH and 67 DExD/H-box genes. These were distributed across all the eight chromosomes, with highest number on chromosome 4 (26) and least on chromosome 8 (8). Gene duplication analysis resulted in identification of 15 paralogous gene pairs with Ka/Ks values < 1, indicating towards the genes being under purifying selection during the course of evolution. The promoter regions of the RNA helicase genes were enriched in cis-acting elements like the light and ABA-responsive elements. The drought responsiveness of the genes was analysed by studying the expression profiles of few of these genes, in two different genotypes, the cultivated variety ICC 8261 (kabuli, C. arietinum) and the wild accession ILWC 292 (C. reticulatum), through qRT-PCR. These genotypes were selected based on their drought responsiveness in a field experiment, where it was observed that the percentage (%) reduction in relative water content (RWC) and membrane stability index (MSI) for the drought stressed plants after withholding water for 24 days, over the control or well-watered plants, was least for both the genotypes. The genes CaDEAD50 and CaDExD/H66 were identified as drought-responsive RNA helicase genes in chickpea. The protein encoded by the CaDExD/H66 gene shares a high degree of homology with one of the CLSY (CLASSY) proteins of A. thaliana. We hypothesize that this gene could possibly be involved in regulation of DNA methylation levels in chickpea by regulating siRNA production, in conjunction with other proteins like the Argonaute, RNA dependent RNA polymerases and Dicer-like proteins.

THE EVOLUTION OF ANTIVIRAL AGENT MOLNUPIRAVIR FOR TREATMENT AND PROPHYLAXIS OF COVID-19 IN PANDEMIC- REVIEW ARTICLE

COVID-19 is currently well known among the general population. The current pandemic treatment requires patient compliant, safe, tolerable, and orally effective. RNA dependent RNA polymerase (RdRp) is an important enzyme involved in RNA synthesis by the formation of phosphodiester bonds within the virus. Effective oral antiviral agents are urgently needed to treat, block transmission and prevent progression to severe illness in COVID-19. Molnupiravir is a orally active RdRp inhibitor. The Developmental steps of molnupiravir includes prophylactic efcacy in a ferret model and its therapeutic efcacy against COVID-19 patients has been proven.