Lead Identification for Severe Acute Respiratory Syndrome Coronavirus-2 Spike D614G Variant of COVID-19: A virtual Screening Process

COVID-19, a pandemic disease caused by single-stranded RNA virus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The structural spike (S) protein of SARS-CoV-2 plays a vital role in host cell entry, where the Angiotensin-Converting Enzyme-2 (ACE2) receptor of the human cell binds to the Receptor Binding Domain (RBD) region of the S1 domain and makes cell entry. The binding affinity of SARS-CoV-2-ACE2 is tenfold higher than the SARS-CoV-1-ACE2. Recent studies expose that the SARS-CoV-2 S D614G variant is highly infectious than D614 protein, also the D614G variant is highly stable than D614. So far, there is no effective viral-specific regimen for COVID-19. To overcome such problems, in our study, we have utilized the ZINC database to screen potent leads against the highly transmitting SARS-CoV-2 spike D614G protein, through a virtual screening procedure. We have applied three computational tools iGEMDOCK server, AutoDock version 4.2.6 and admetSAR to get active leads. The ZINC000150588351 (Elbasvir), ZINC000064540179 (Sofosbuvir analogue) and ZINC000137700912 (Sofosbuvir analogue) molecules have a greater binding affinity with the high binding energies of -8.22 kcal/mol, -8.13 kcal/mol and -7.64 kcal/mol respectively. The molecules ZINC000064540179 and ZINC000137700912 have high binding energy than their core molecule Sofosbuvir (ZINC100074252) of -4.06 kcal/mol. The ADMET prediction of these molecules reveals satisfactory human intestinal absorption and non-mutagenic property. Our results deliver valuable contributions to the design of inhibitors against COVID-19.

Effects of Ribavirin on Thickness of Testicular Capsule in Albino Rats

<p><strong>Background and Objective:</strong> Ribavirin (RBV), due to its mutagenic property, exerts cytotoxic effects on the testicular seminiferous tubules and its interstitium in various experimental animals. However, no study was done on the morphology of testicular capsule. Therefore, the present experimental study is designed to observe the transient effects of RBV in different doses on the testicular capsule thickness in albino rats.<br /><strong>Methods:</strong> A total of 72 sexually mature adult male albino rats were divided into four groups: A (control) and, B, C, D where RBV was administered intraperitoneally for 5 days in different doses (20, 100, and 200 mg/kg body weight, respectively). Group received distilled water intraperitoneally. Each group was further divided into three subgroups according to three sacrificial time points that were 20th, 40th, and 60th day from the last exposure to drug. Randomly selected rats from each group were sacrificed on every time point. Histological slides were prepared and changes were observed microscopically.<br /><strong>Results: </strong>On 20th sacrificial day, the increase in the thickness of capsules was seen in all groups with subcapsular edema in comparison to control group (p &lt; 0.001). After discontinuation of drug, histological evidence of recovery in the form of decrease in the thickness of capsule with decrease in subcapsular edema were observed in low dose groups on 40th and 60th sacrificial days as compared to high dose groups which showed late recovery on both time points (p &lt; 0.001).<br /><strong>Conclusion:</strong> The testicular capsular thickening induced by RBV is reversible after cessation of treatment.</p> <p>&nbsp;</p>

Millet Derived Flavonoids as Potential SARS-CoV-2 Main Protease Inhibitors: A Computational Approach

The on-going pandemic COVID-19 has emerged as a major health threat across the globe. At present, anti-viral drug discoveries are of great importance in combating the pandemic. Millets are known to contain numerous flavonoids with potential anti-viral properties. However, their anti-viral efficacy against SARS-CoV-2 is yet to be studied. The study uses the SARS-CoV-2 main protease (M^pro) as the potential drug target and docks with eleven millet derived flavonoids taking HIV protease inhibiting drugs nelfinavir and saquinavir as control. AutoDock Vina was used for assessing the binding affinities and strength of binding of flavonoids present in millets with the target protein M^pro. Further, the drug-likeness and pharmacokinetics properties of these flavonoids were analyzed using admetSAR. The ADMET analysis showed that isoorientin, orientin, vitexin, meletin, catechin, and myricetin possess potential mutagenic property while daidzein could have a negative effect on reproductive making these compounds as poor candidates for drug development against SARS-CoV-2. Based on the docking result and positive ADMET properties, the present study infers that apigenin may be considered as a potential inhibitor of SARS-CoV-2 M^pro and may be further investigated to test its anti-viral activities using <i>in-vitro</i> and <i>in-vivo</i> study.

Millet Derived Flavonoids as Potential SARS-CoV-2 Main Protease Inhibitors: A Computational Approach

The on-going pandemic COVID-19 has emerged as a major health threat across the globe. At present, anti-viral drug discoveries are of great importance in combating the pandemic. Millets are known to contain numerous flavonoids with potential anti-viral properties. However, their anti-viral efficacy against SARS-CoV-2 is yet to be studied. The study uses the SARS-CoV-2 main protease (M^pro) as the potential drug target and docks with eleven millet derived flavonoids taking HIV protease inhibiting drugs nelfinavir and saquinavir as control. AutoDock Vina was used for assessing the binding affinities and strength of binding of flavonoids present in millets with the target protein M^pro. Further, the drug-likeness and pharmacokinetics properties of these flavonoids were analyzed using admetSAR. The ADMET analysis showed that isoorientin, orientin, vitexin, meletin, catechin, and myricetin possess potential mutagenic property while daidzein could have a negative effect on reproductive making these compounds as poor candidates for drug development against SARS-CoV-2. Based on the docking result and positive ADMET properties, the present study infers that apigenin may be considered as a potential inhibitor of SARS-CoV-2 M^pro and may be further investigated to test its anti-viral activities using <i>in-vitro</i> and <i>in-vivo</i> study.

Millet Derived Flavonoids as Potential SARS-CoV-2 Main Protease Inhibitors: A Computational Approach

The on-going pandemic COVID-19 has emerged as a major health threat across the globe. At present, anti-viral drug discoveries are of great importance in combating the pandemic. Millets are known to contain numerous flavonoids with potential anti-viral properties. However, their anti-viral efficacy against SARS-CoV-2 is yet to be studied. The study uses the SARS-CoV-2 main protease (M^pro) as the potential drug target and docks with eleven millet derived flavonoids taking HIV protease inhibiting drugs nelfinavir and saquinavir as control. AutoDock Vina was used for assessing the binding affinities and strength of binding of flavonoids present in millets with the target protein M^pro. Further, the drug-likeness and pharmacokinetics properties of these flavonoids were analyzed using admetSAR. The ADMET analysis showed that isoorientin, orientin, vitexin, meletin, catechin, and myricetin possess potential mutagenic property while daidzein could have a negative effect on reproductive making these compounds as poor candidates for drug development against SARS-CoV-2. Based on the docking result and positive ADMET properties, the present study infers that apigenin may be considered as a potential inhibitor of SARS-CoV-2 M^pro and may be further investigated to test its anti-viral activities using <i>in-vitro</i> and <i>in-vivo</i> study.

Assessment of the mutagenicity of the technical product of N-(1-ethylpropyl)-2,6-dinitro -3,4-xylidinen

Introduction. Evaluation of genotoxicity of the pesticide technical products is one of the mandatory requirements for their toxicological and hygienic assessment. The data about mutagenic property is ambiguous for some pesticides. This may be due to the use of various active ingredients of technical products of the pesticide for testing, as they may have different profiles of relevant impurities, some of which may be potentially genotoxic. Material and methods. A technical product of N-(1-ethylpropyl)-2,6-dinitro-3,4-xylidine was tested using the bacterial reverse mutation method with Salmonella typhimurium (Ames test) and the in vivo mammalian micronucleus analysis in mouse bone marrow erythrocytes. Results. Statistically significant dose-dependent mutagenic effects of the technical product of N-(1-ethylpropyl)-2,6-dinitro-3,4-xylidine were revealed for TA97 (+S9 / -S9); TA100 (+S9 / -S9); TA102 (+S9 / -S9) and TA98 (+S9 / -S9) strains. In all cases, the fold increase of the revertant numbers mediated by the tested substance compared with the concurrent negative control was > 2 except TA98 in the presence of S9. In the micronucleus test, the technical product did not induce a statistically significant increase in the frequency of the micronucleated polychromatophilic erythrocytes in CD-1 mouse bone marrow up to 2000 mg/kg bw. Conclusion. The data suggest all technical products of pesticides entering the market should be tested for the potential genotoxicity. In such a case it is necessary to use at least two methods on different test systems for obtaining reliable results.

Assessment of the mutagenicity of the technical product of N-(1-ethylpropyl)-2,6-dinitro -3,4-xylidinen

Introduction. Evaluation of genotoxicity of the pesticide technical products is one of the mandatory requirements for their toxicological and hygienic assessment. The data about mutagenic property is ambiguous for some pesticides. This may be due to the use of various active ingredients of technical products of the pesticide for testing, as they may have different profiles of relevant impurities, some of which may be potentially genotoxic. Material and methods. A technical product of N-(1-ethylpropyl)-2,6-dinitro-3,4-xylidine was tested using the bacterial reverse mutation method with Salmonella typhimurium (Ames test) and the in vivo mammalian micronucleus analysis in mouse bone marrow erythrocytes. Results. Statistically significant dose-dependent mutagenic effects of the technical product of N-(1-ethylpropyl)-2,6-dinitro-3,4-xylidine were revealed for TA97 (+S9 / -S9); TA100 (+S9 / -S9); TA102 (+S9 / -S9) and TA98 (+S9 / -S9) strains. In all cases, the fold increase of the revertant numbers mediated by the tested substance compared with the concurrent negative control was > 2 except TA98 in the presence of S9. In the micronucleus test, the technical product did not induce a statistically significant increase in the frequency of the micronucleated polychromatophilic erythrocytes in CD-1 mouse bone marrow up to 2000 mg/kg bw. Conclusion. The data suggest all technical products of pesticides entering the market should be tested for the potential genotoxicity. In such a case it is necessary to use at least two methods on different test systems for obtaining reliable results.

Evaluation of mutagenic property of poly herbal formulation of annona squamosa, zingiber officinalis and triticum aestivum plant extracts by bacterial reverse mutation test

Cancer is the second deadliest cause among all ailments even after the development of modern research and technologies. This leads in search of alternative sources of treating cancer. Herbal formulations were considered to be the rich sources of treating agents for most of the ailments from agelong days. Bacterial Reverse Mutation method of evaluation is one among the preliminary phase incorporated to assess the mutagenic potential of herbal formulations. The selected Polyherbal Formulation (PF3) of Annona Squamosa, Zingiber Officinalis, and Triticum Aestivum in 1:1:1 ratio was evaluated for its mutagenic potential. The results with method I - Plate incorporation and method II - Preincubation indicate that, the PF3 extract at a maximum dose of 5 mg/plate did not cause a positive increase in the mean number of revertant colonies per plate with any of the tester strains either in the presence (+S9) or absence of metabolic activation (-S9). The rich flavonoids and other phytoconstituents of the formulation may be responsible for antimutative properties with the possible inactivation of mutagens or by interfering in the process of mutagenisis. The higher studies were needed to be proven further to authenticate the mutagenic potentialities.

Bypassing a 8,5′-cyclo-2′-deoxyadenosine lesion by human DNA polymerase η at atomic resolution

Oxidatively induced DNA lesions 8,5′-cyclopurine-2′-deoxynucleosides (cdPus) are prevalent and cytotoxic by impeding DNA replication and transcription. Both the 5′R- and 5′S-diastereomers of cdPu can be removed by nucleotide excision repair; however, the 5′S-cdPu is more resistant to repair than the 5′R counterpart. Here, we report the crystal structures of human polymerase (Pol) η bypassing 5′S-8,5′-cyclo-2′-deoxyadenosine (cdA) in insertion and the following two extension steps. The cdA-containing DNA structures vary in response to the protein environment. Supported by the “molecular splint” of Pol η, the structure of 5′S-cdA at 1.75-Å resolution reveals that the backbone is pinched toward the minor groove and the adenine base is tilted. In the templating position, the cdA takes up the extra space usually reserved for the thymine dimer, and dTTP is efficiently incorporated by Pol η in the presence of Mn2+. Rigid distortions of the DNA duplex by cdA, however, prevent normal base pairing and hinder immediate primer extension by Pol η. Our results provide structural insights into the strong replication blockage effect and the mutagenic property of the cdPu lesions in cells.