Insilico drug repurposing using FDA approved drugs against Membrane protein of SARS-CoV-2.

The novel coronavirus (SARS-CoV-2) outbreak has started taking away the millions of lives worldwide. Identification of known and approved drugs against novel coronavirus disease (COVID-19) seems to be an urgent need for the repurposing of the existing drugs. So, here we examined a safe strategy of using approved drugs of SuperDRUG2 database against modeled membrane protein (M-protein) of SARS-CoV-2 which is essential for virus assembly by using molecular docking-based virtual screening. A total of 3639 drugs from SuperDRUG2 database and additionally 14 potential drugs reported against COVID-19 proteins were selected. Molecular docking analyses revealed that nine drugs can bind the active site of M-protein with desirable molecular interactions. We therefore applied molecular dynamics simulations and binding free energy calculation using MM-PBSA to analyze the stability of the compounds. The complexes of M-protein with the selected drugs were simulated for 50 ns and ranked according to their binding free energies. The binding mode of the drugs with M-protein was analyzed and it was observed that Colchicine, Remdesivir, Bafilomycin A1 from COVID-19 suggested drugs and Temozolomide from SuperDRUG2 database displayed desirable molecular interactions and higher binding affinity towards M-protein. Interestingly, Colchicine was found as the top most binder among tested drugs against M-protein. We therefore additionally identified four Colchicine derivatives which can bind efficiently with M-protein and have better pharmacokinetic properties. We recommend that these drugs can be tested further through in vitro studies against SARS-CoV-2 M-protein.

Screening of phytochemical compounds of Tinospora cordifolia for their inhibitory activity on SARS-CoV-2: an in silico study.

In the present study, we explored phytochemical constituents of Tinospora cordifolia in terms of its binding affinity targeting the active site pocket of the main protease (3CL pro) of SARS-CoV-2 using molecular docking study and assessed the stability of top docking complex of tinosponone and 3CL pro using molecular dynamics simulations with GROMACS 2020.2 version. Out of 11 curated screened compounds, we found the significant docking score for tinosponone, xanosporic acid, cardiofolioside B, tembetarine and berberine in Tinospora cordifolia. Based on the findings of the docking study, it was confirmed that tinosponone is the potent inhibitor of main protease of SARS-CoV-2 with the best binding affinity of -7.7 kcal/mol. Further, ADME along with toxicity analysis was studied to predict the pharmacokinetics and drug-likeness properties of five top hits compounds. The molecular dynamics simulation analysis confirmed the stability of tinosponone and 3CL pro complex with a random mean square deviation (RMSD) value of 0.1 nm. The computer-aided drug design approach proved that the compound tinosponone from T. cordifolia is a potent inhibitor of 3CL main protease of SARS-CoV-2. Further, the in vitro and in vivo-based testing will be required to confirm its inhibitory effect on SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Design of multi-epitope vaccine candidate against SARS-CoV-2: a in-silico study.

The best therapeutic strategy to find an effective vaccine against SARS-CoV-2 is to explore the target structural protein. In the present study, a novel multi-epitope vaccine is designed using in silico tools that potentially trigger both CD4 and CD8 T-cell immune responses against the novel Coronavirus. The vaccine candidate was designed using B and T-cell epitopes that can act as an immunogen and elicits immune response in the host system. NCBI was used for the retrieval of surface spike glycoprotein, of novel corona virus (SARS-CoV-2) strains. VaxiJen server screens the most important immunogen of all the proteins and IEDB server gives the prediction and analysis of B and T cell epitopes. Final vaccine construct was designed in silico composed of 425 amino acids including the 50S ribosomal protein adjuvant and the construct was computationally validated in terms of antigenicity, allergenicity and stability on considering all critical parameters into consideration. The results subjected to the modeling and docking studies of vaccine were validated. Molecular docking study revealed the protein-protein binding interactions between the vaccine construct and TLR-3 immune receptor. The MD simulations confirmed stability of the binding pose. The immune simulation results showed significant response for immune cells. The findings of the study confirmed that the final vaccine construct of chimeric peptide could able to enhance the immune response against nCoV-19.

Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: A computational study.

The aim of this study was to develop an appropriate anti-viral drug against the SARS-CoV-2 virus. An immediately qualifying strategy would be to use existing powerful drugs from various virus treatments. The strategy in virtual screening of antiviral databases for possible therapeutic effect would be to identify promising drug molecules, as there is currently no vaccine or treatment approved against COVID-19. Targeting the main protease (pdb id: 6LU7) is gaining importance in anti-CoV drug design. In this conceptual context, an attempt has been made to suggest an in silico computational relationship between US-FDA approved drugs, plant-derived natural drugs, and Coronavirus main protease (6LU7) protein. The evaluation of results was made based on Glide (Schrödinger) dock score. Out of 62 screened compounds, the best docking scores with the targets were found for compounds: lopinavir, amodiaquine, and theaflavin digallate (TFDG). Molecular dynamic (MD) simulation study was also performed for 20 ns to confirm the stability behaviour of the main protease and inhibitor complexes. The MD simulation study validated the stability of three compounds in the protein binding pocket as potent binders.

Bioactive molecules of probiotic bacteria and their mechanism of action: a review.

The bacteria residing in the gut environment do play a pivotal role in metabolic activities of the host. The metabolites produced by these bacteria affect the physiology and health of the host. The gut bacteria are exposed to environmental conditions where multiple factors such as lifestyle, stress, antibiotics, host genetics and infections have an influence on them. In case of pathogenesis of a disease, the gut bacterial composition is altered which leads to a diseased state. This stage is due to colonization of bacterial pathogens in the gut environment. The pathological condition can be alleviated by administering probiotic strains into the gut environment. The probiotic strains produce therapeutic molecules such as amino acids, vitamins, bacteriocins, enzymes, immunomodulatory compounds and short-chain fatty acids. This review discusses recent evidences of the impact of bioactive molecules produced by probiotic bacteria and their mechanism of action in the gut environment to maintain homeostasis and health of the host without any effect on beneficial bacteria sharing the same niche. In addition, the manufacturing challenges of probiotic products for various applications are discussed here.

Emulsifying activity of a biosurfactant produced by a marine bacterium.

Biosurfactants produced by biofilm-forming bacteria have great applications in biotechnology, pharmaceutical, food engineering, bioremediation, and biohydrometallurgy industries. This study aimed to find out the bacteria that produce novel exopolymers (EPSs) which can find potential role in oil biodegradation. A screening procedure was performed to detect EPS-producing bacteria. The EPS producing isolate was identified as Acinetobacter species by 16S rDNA analysis. The polymer produced by the isolate has shown significant emulsification and surfactant activities, and the activities were compared to some of the commercial emulsifiers. The EPS has been partially characterized by FTIR analysis and has been proved to be a glycolipoprotein. This is one of the very few reports on Acinetobacter species producing EPS with surfactant properties.

Topical anesthetic abuse ring keratitis: report of four cases.

PURPOSE: We present the clinicopathologic correlations of two case and two other clinical cases of topical anesthetic abuse keratopathy that were originally diagnosed as Acanthamoeba keratitis because of ring keratitis presentation and characteristic history. METHODS: Four patients who were referred to us with suspected Acanthamoeba keratitis are included. Each was initially treated for amoebic keratitis, by using established protocols, and only later was the true origin (topical anesthetic abuse) uncovered. The clinical and surgical histories, pathologic analysis of the corneal specimens, and follow-up of < or = 4 years are included. RESULTS: Our four cases show another cause for ring infiltration of the cornea. Two cases resulted in corneal transplantation and multiple other medical or surgical treatments in an attempt to restore vision but had poor outcomes of finger-counting vision. Two other cases responded to intensive medical treatments with return of useful vision. Evaluation of the surgical specimens revealed a previously unpublished finding of near total cell death within the corneal stroma. CONCLUSION: Topical anesthetic abuse resulting in sight-threatening keratitis may be seen as a masquerade syndrome in many cases. Because of the often poor outcome, we must be aware of this entity, prevent abuse, and be vigilant in our prohibition of topical anesthetic for any therapeutic use.

Antibodies against striated muscle, connective tissue and nuclear antigens in patients with thyroid-associated ophthalmopathy: should Graves' disease be considered a collagen disorder?

The identity and subcellular localization of the principal extraocular muscle (EOM) antigens and prevalences of the corresponding serum autoantibodies in thyroid-associated ophthalmopathy (TAO) need to be clarified. We have used porcine eye muscle tissue, which expresses all autoantigens identified in human tissue, as substrate in an indirect immunofluorescence assay. Several different patterns of antibody binding to EOM tissue antigens were observed with sera from patients with TAO namely, membrane, cytoplasmic, interstitial (endomysial) and nuclear. Overall, sera from 75% of patients with TAO contained one or more antibodies reactive with EOM, compared to 32% of patients with Graves' hyperthyroidism, 38% with Hashimoto's thyroiditis, and 16% of normals. All sera which reacted with EOM membrane or cytoplasmic antigens also reacted with the same antigen(s) in other skeletal muscle, but not in the other tissues tested. Sera from 31% of patients with TAO, but only 7% of those with Hashimoto's thyroiditis, and no patient with Graves' hyperthyroidism without evident ophthalmopathy, contained antinuclear antibodies (ANA). The most common nuclear fluorescence pattern was the finely speckled type typically associated with anti-Sm or anti-RNP antibodies. Significant positive correlations in patients with TAO were found between (i) EOM dysfunction and ANA (ii) eye disease of < 1 yr duration and EOM membrane-reactive antibodies and (iii) eye disease of < 1 yr duration and interstitial (endomysial) tissue-reactive antibodies. Although patients with Graves' disease do not usually exhibit other signs or immunologic features of a generalized collagen disorder, the finding of high prevalences of ANA and anti-striated muscle antibodies and, less often, anti-connective tissue antibodies in patients with ophthalmopathy, is consistent with it being a collagen-like disorder of the striated muscle, connective tissue and the thyroid. The reason why the inflammatory process is mainly limited to these tissues is unclear although cross reaction of ANA with tissue specific proteins or increased expression of muscle and connective tissue antigens in the orbit and skin, are possibilities.

The role of postoperative irradiation in the management of sphenoid wing meningiomas. A preliminary report.

PURPOSE: To determine whether postoperative radiation therapy decreases recurrence rates in subtotally excised and recurrent sphenoid wing meningiomas. METHODS: Patients with primary subtotally excised and recurrent sphenoid wing meningiomas who underwent surgery between 1981 and 1994 (n = 105) were prospectively followed for recurrence. Postoperative radiation was not recommended in patients who had complete excision; therefore, their recurrence rates were not evaluated in this study. Patients with malignant meningiomas also were excluded from analysis. Recurrence was defined as evidence of tumor growth on neuroimaging with or without clinical symptoms. RESULTS: Follow-up information was available for 86 patients; 69 had primary subtotally excised tumors and 17 had recurrent tumors. Follow-up information was unavailable in the remaining 19 patients. Tumor location and histopathology, type of surgery performed, and patient sex and age were similar in the irradiated and nonirradiated subgroups. Postoperative irradiation was delivered to 31 patients with primary tumors and 11 with recurrent tumors; none of these 42 patients had recurrence during a mean observation period of 4.2 and 3.5 years, respectively. The nonirradiated group consisted of 38 patients with primary tumors and 6 with recurrent tumors; 16 of 18 patients who had primary meningiomas had a recurrence and 5 of 6 who had recurrent tumors had another relapse (mean interval between resection and recurrence, 4.4 years and 14 months, respectively). CONCLUSIONS: Postoperative radiation appeared to delay recurrence in subtotally excised and recurrent sphenoid wing meningiomas during the time frame of this study.

Serum antibodies reactive with eye muscle antigens and the TSH receptor in a euthyroid subject who developed ophthalmopathy and Graves' hyperthyroidism.

Serum antibodies reactive with eye muscle autoantigens, in particular a 64-kDa protein that is also expressed in the thyroid, and the TSH receptor, are associated with the ophthalmopathy that occurs in about 50% of patients with Graves' hyperthyroidism. We have had the opportunity to study a euthyroid, apparently normal, 35-year-old woman with a family history of thyroid autoimmunity and "colitis" but no clinical or biochemical evidence for thyroid disease or ophthalmopathy, who developed Graves' hyperthyroidism and ophthalmopathy together 18 months later. Serum taken when the patient was first seen was positive for antibodies reactive with (i) 9 different eye muscle proteins ranging in size from 15 to 130 kDa, notably those of 64, 55, and 50 kDa, by immunoblotting with eye muscle membranes, (ii) eye muscle and Müller's muscle cell membrane antigens in antibody-dependent cell-mediated cytotoxicity (ADCC), (iii) an eye muscle cytoplasmic antigen in indirect immunofluorescence, and (iv) the TSH receptor as measured in a radioreceptor binding inhibition assay. When she developed Graves' disease, serum concentration of antibodies to the 55-kDa protein had decreased from +2 to +/-, those reactive with other eye muscle antigens had not changed significantly, and TSH receptor antibodies had increased 3-fold. This case report suggests that antibodies reactive with eye muscle antigens and the TSH receptor are markers of the ophthalmopathy and able to predict its development in predisposed subjects. The significance of these findings needs to be confirmed in a prospective study of first-degree relatives of patients with thyroid-associated ophthalmopathy and patients with Graves' hyperthyroidism without eye signs.

Antibody-dependent cell-mediated cytotoxicity against orbital target cells in thyroid-associated ophthalmopathy and related disorders; close relationship between serum cytotoxic antibodies and parameters of eye muscle dysfunction.

We have carried out tests for antibody-dependent cell-mediated cytotoxicity (ADCC) against extra ocular muscle (EOM), Müller's muscle, orbital fibroblasts and skeletal muscle in patients with thyroid-associated ophthalmopathy (TAO) and related eye disorders. Cytotoxicity was measured as lactate dehydrogenase (LDH) release and results expressed as % cytotoxicity. Tests were positive, with EOM cells, in 65% of patients with TAO, 75% with ocular myopathy, a variant of TAO in which periorbital inflammation is minimal, 50% with euthyroid Graves' disease defined as ophthalmopathy associated with subclinical thyroiditis and in 50% of patients with stable lid lag and retraction but no other signs of progressive ophthalmopathy, but in only 13% of patients with Graves' hyperthyroidism without ophthalmopathy, 10% with Hashimoto's thyroiditis and 14% of patients with other thyroid disorders. Tests were positive, with Müller's muscle cells, in 40% of patients with TAO, 25% with ocular myopathy, 40% with euthyroid Graves' disease, 44% with lid lag, 19% with Graves'hyperthyroidism, 50% with Hashimoto's thyroiditis and in 37.5% of patients with other thyroid disorders. When skeletal muscle cells were used as target, tests were positive in 13% of patients with TAO, 31% with lid lag, 25% with Graves' hyperthyroidism and in 29% of patients with Hashimoto's thyroiditis, but in no patient with euthyroid Graves' disease or other thyroid disorders. Tests were negative in all patients and normals tested when EOM-derived fibroblasts were used as targets in ADCC. A significant positive correlation between % cytotoxicity against EOM cells and the severity of the eye muscle dysfunction expressed as an eye muscle index, was observed in patients with TAO. There was a significant negative correlation between the duration of eye disease and % cytotoxicity against EOM cells, suggesting higher titers of cytotoxic antibodies in the early stages of TAO. There was no correlation between % cytotoxicity and serum level of anti-TSH receptor antibodies, measured in a radioreceptor assay. These findings suggest that autoimmunity against Müller's muscle may play a role in the pathogenesis of persistent lid lag and retraction. The nature of the EOM and Müller's muscle autoantigens recognized by cytotoxic antibodies in the serum of patients with TAO and related eye disorders is unknown.

Intraocular irrigating solutions. A randomized clinical trial of balanced salt solution plus and dextrose bicarbonate lactated Ringer's solution.

BACKGROUND: Two intraocular irrigating solutions which differ principally by the presence of oxidized glutathione were compared in this randomized, masked, prospective study to discern differences in preservation of endothelial cell size. METHODS: Sixty-four patients undergoing extracapsular cataract extractions were randomized between two irrigating solution groups, Balanced Salt Solution (BSS) Plus (n = 30) and dextrose bicarbonate lactated Ringer's solution (n = 34). Preoperative and postoperative endothelial specular photomicrographs were analyzed for cell size and hexagonality, and the two groups were compared using repeated measures analysis of variance. RESULTS: Fifty-eight subjects (91%) completed the 2-month study. Change in cell size for the BSS Plus group (n = 28) (mean +/- standard error, 29.4 +/- 12.3 microns2) was not significantly different from the dextrose bicarbonate lactated Ringer's solution group (n = 30) (27.5 +/- 12.9 microns2) (P = 0.92). Groups did not differ significantly in percent hexagonality (P = 0.57) or in the variability of cell size (P = 0.61). CONCLUSION: The presence of glutathione in BSS Plus and other minor electrolyte differences between the solutions is not more advantageous with regard to endothelial cell size than dextrose bicarbonate lactated Ringer's solution for standard extracapsular cataract surgery. Cost per 500-microliters bottle of BSS plus is $62 compared with $9.80 for dextrose bicarbonate lactated Ringer's solution.

The stress of child sexual abuse examinations.

The objective of this paper was to determine if the medical evaluation of sexual abuse victims is stressful by heart rate variability monitoring. The design of the study was a case series of children referred for sexual abuse examination to determine child stress response monitored by heart rate variability during baseline, disclosure, and anogenital examination with photographs. The setting was a referral center for the investigation of child sexual abuse in two sites (Reno and Las Vegas, Nevada, USA). Patients included a consecutive sample of 30 children; 15 in Reno ranging in age from 3-10 years with a mean age of 7.1 (1 male and 14 females); 15 in Las Vegas ranging in age from 6-10 years with a mean age of 7.8 (3 males and 12 females). Measurements and results were: each subject's heart rate was obtained during the first 3 minutes of the baseline, disclosure, and the anogenital examination with photographs, using a telemetric Vantage Performance Heart Watch consisting of a 5.5 x 1.25 inch transmitter attached to a chest strap and a microcomputer wristwatch attached to the subject's non-dominant wrist. Heart rates were taken every 5 or 15 seconds throughout the entire examination. A follow-up home visit was made 6 weeks after the examination to determine the replicability of clinic baseline measures and child behavioral sequelae. Physiologic measurements did not show statistically significant stress responses when children were prepared according to the clinic protocol in Reno and Las Vegas. There was a trend toward more responsivity among some of the older subjects during the anogenital examination with photographs, and when clinic procedures inadvertently overlapped several procedures at the same time (anogenital examination, photographs and disclosure). The conclusion of the study was that child sexual abuse investigations may be accomplished without undue psychophysiological stress when recommended precautions are taken.