In Silico Screening of Some Active Phytochemicals to Identify Promising Inhibitors Against SARS-CoV-2 Targets

BACKGROUND

There are very few small-molecule drug candidates developed against SARS-CoV-2 that have been revealed since the epidemic began in November 2019. The typical medicinal chemistry discovery approach requires more than a decade of the year of painstaking research and development and a significant financial guarantee, which is not feasible in the challenge of the current epidemic.

OBJECTIVE

This current study proposes to find and identify the most effective and promising phytomolecules against SARS-CoV-2 in six essential proteins (3CL protease, Main protease, Papain- Like protease, N-protein RNA binding domain, RNA-dependent RNA polymerase, and Spike receptor binding domain target through in silico screening of 63 phytomolecules from six different Ayurveda medicinal plants.

METHODS

The phytomolecules and SARS-CoV-2 proteins were taken from public domain databases such as PubChem and RCSB Protein Data Bank. For in silico screening, the molecular interactions, binding energy, and ADMET properties were investigated.

RESULTS

The structure-based molecular docking reveals some molecules' greater affinity towards the target than the co-crystal ligand. Our results show that tannic acid, cyanidin-3-rutinoside, zeaxanthin, and carbolactone are phytomolecules capable of inhibiting SARS-CoV-2 target proteins in the least energy conformations. Tannic acid had the least binding energy of -8.8 kcal/mol, which is better than the binding energy of its corresponding co-crystal ligand (-7.5 kcal/mol) against 3 CL protease. Also, it has shown the least binding energy of -9.9 kcal/mol with a more significant number of conventional hydrogen bond interactions against the RdRp target. Cyanidin-3-rutinoside showed binding energy values of -8.8 and -7.6 kcal/mol against Main protease and Papain-like protease, respectively. Zeaxanthin was the top candidate in the N protein RBD with a binding score of - 8.4 kcal/mol, which is slightly better when compared to a co-crystal ligand (-8.2 kcal/mol). In the spike, carbolactone was the suitable candidate with the binding energy of -7.2 kcal/mol and formed a conventional hydrogen bond and two hydrophobic interactions. The best binding affinity-scored phytomolecules were selected for the MD simulations studies.

CONCLUSION

The present in silico screening study suggested that active phytomolecules from medicinal plants could inhibit SARS-CoV-2 targets. The elite docked compounds with drug-like properties have a harmless ADMET profile, which may help to develop promising COVID-19 inhibitors.

The Spectrum of Pulmonary Histomorphology Changes in COVID-19 Cases

Introduction/Objective

Pulmonary specimens following COVID-19 virus infection demonstrate a spectrum of pulmonary histomorphology. Six patients with a history of COVID-19 infection are summarized in this review. The purpose of our study is to elucidate any possible correlations between clinical, laboratory, radiographic, and pathologic findings in COVID-19 patients. Further, we aim to characterize both non-specific and specific histomorphology and cytomorphology in COVID-19 patients.

Methods/Case Report

Six patients with known COVID-19 infection and lung biopsies/resections are identified. A chart review is performed to collect clinical histories, the results of COVID-19 PCR testing, radiographic impressions, pathologic interpretations of histology, and clinical outcomes. Information is summarized and tabulated.

Results (if a Case Study enter NA)

The most common, non-specific histological findings are focal/diffuse acute lung injury, organizing lung injury, or a combination of both patterns. Unique features of COVID-19 infection are identified in three cases, which illustrate viral cytopathic changes within hyperplastic pneumocytes. These include basophilic, vacuolated, granular cytoplasm and variably sized cytoplasmic/nuclear inclusions. Virus-loaded pneumocytes are typically identified in the organizing phase, and rarely in the acute lung injury phase. Immunohistochemical staining of anti-nuclear capsule antibody with appropriate controls shows focal positive staining in one case. SARS-CoV-2 PCR is positive in formalin-fixed paraffin-embedded (FFPE) tissue, while a serum PCR assay is negative.

Conclusion

The severity of clinical symptoms and clinical outcome are unrelated to the degree of lung involvement. Viral cytopathic changes are identified in three cases, with these specific findings associated with the organizing phase of lung injury, and either concurrent PCR positivity or positive immunohistochemical staining.

Quantifying T2-FLAIR Mismatch Using Geographically Weighted Regression and Predicting Molecular Status in Lower-Grade Gliomas

BACKGROUND AND PURPOSE

The T2-FLAIR mismatch sign is a validated imaging sign of isocitrate dehydrogenase-mutant 1p/19q noncodeleted gliomas. It is identified by radiologists through visual inspection of preoperative MR imaging scans and has been shown to identify isocitrate dehydrogenase-mutant 1p/19q noncodeleted gliomas with a high positive predictive value. We have developed an approach to quantify the T2-FLAIR mismatch signature and use it to predict the molecular status of lower-grade gliomas.

MATERIALS AND METHODS

We used multiparametric MR imaging scans and segmentation labels of 108 preoperative lower-grade glioma tumors from The Cancer Imaging Archive. Clinical information and T2-FLAIR mismatch sign labels were obtained from supplementary material of relevant publications. We adopted an objective analytic approach to estimate this sign through a geographically weighted regression and used the residuals for each case to construct a probability density function (serving as a residual signature). These functions were then analyzed using an appropriate statistical framework.

RESULTS

We observed statistically significant (P value = .05) differences between the averages of residual signatures for an isocitrate dehydrogenase-mutant 1p/19q noncodeleted class of tumors versus other categories. Our classifier predicts these cases with area under the curve of 0.98 and high specificity and sensitivity. It also predicts the T2-FLAIR mismatch sign within these cases with an under the curve of 0.93.

CONCLUSIONS

On the basis of this retrospective study, we show that geographically weighted regression-based residual signatures are highly informative of the T2-FLAIR mismatch sign and can identify isocitrate dehydrogenase-mutation and 1p/19q codeletion status with high predictive power. The utility of the proposed quantification of the T2-FLAIR mismatch sign can be potentially validated through a prospective multi-institutional study.

Hemangioendothelioma of palate: A case report with review of literature

Hemangioendothelioma commonly occurs in the superficial or deep soft tissue of the extremities, lungs, liver, bone and lymph nodes, with oral cavity being a rare location. It is usually benign but can show variable grades of malignancy. According to the histological presentation, hemangioendothelioma has been classified as epithelioid, Kaposiform, hobnail (Dabska-Retiform), epithelioid sarcoma like and composite. We present a case of ulcerated swelling of palate clinically diagnosed as pyogenic granuloma which presented a diagnostically challenging histological picture. We discuss the differential diagnoses obtained from various oral pathologists and general pathologists and substantiate the diagnosis of hemangioendothelioma based on its clinical behavior, histological features and immunohistochemical findings. In addition, we attempt to highlight the diagnostic dilemma that such cases can pose to the attending pathologists.

Correction: Development of glycolipid biosurfactant for inducing apoptosis in HeLa cells

Correction for ‘Development of glycolipid biosurfactant for inducing apoptosis in HeLa cells’ by V. Ramalingam et al., RSC Adv., 2016, 6, 64087–64096.

Development of glycolipid biosurfactant for inducing apoptosis in HeLa cells

A novel glycolipid biosurfactant produced fromStaphylococcus aureuswas used to induce apoptosis in HeLa cells.

A clinical study on the management of inguinal hernias in children on the general surgical practice

BACKGROUND

Inguinal and scrotal swellings are frequently encountered in the surgical practice, especially in children. It is also important to study the factors which are associated with inguinal hernia, especially in children, for its effective management.

OBJECTIVE

To study the factors which are associated with inguinal hernia in children.

SETTING AND DESIGN

A prospective hospital based study was undertaken in the Department of Surgery for a period of one year between 2001 to 2002. Children who were aged one day to 12 years were selected for the study. Out of 960 children who were admitted to the surgical ward, 50 children had inguinal hernia and they constituted the sample.

METHODOLOGY

The details regarding the clinical history and the examination details were collected by using a predesigned proforma. The data which was thus collected was analyzed by using the appropriate statistical tests.

RESULTS

The inguinal hernia in the study group was common in the 1-5 years age group. 90% of the study group was males; a swelling in the inguinal region was the commonest symptom. 70% of the study group was term deliveries; the swelling of the inguinal hernia was elastic in consistency in 35 cases. The swelling of the inguinal hernia was irreducible in two cases. The testis was palpable in 48 cases; a cough impulse was seen and felt in 48 cases. Tenderness of the swelling was present in 2 cases.

CONCLUSIONS

Inguinal hernia is a common congenital condition in children. Difficulties are commonly encountered by the surgeons to identify and to confirm the presence of inguinal hernia. This study will help in a better management of hernia in the paediatric age group by understanding the features of inguinal hernia.

Multiple apocrine hidrocystomas: a case report

Hidrocystomas are rare cystic lesions that form benign tumours of the sweat glands. In this report, a clinical case of multiple apocrine hidrocystomas on both the upper and lower eyelids, and on both the malar regions has been discussed. These lesions are less likely than the eccrine lesions to occur at the periorbital region.

Direct Determination of Grain Boundary Atomic Structure in SrTiO3

An atomic structure model for a 25 degrees [001] symmetric tilt grain boundary in SrTiO(3) has been determined directly from experimental data with the use of high-resolution Z-contrast imaging coupled with electron energy loss spectroscopy. The derived model of the grain boundary was refined by bond-valence sum calculations and reveals candidate sites for dopant atoms in the boundary plane. These results show how the combined techniques can be used to deduce the atomic structure of defects and interfaces without recourse to preconceived structural models or image simulations.

Evaluation of the Protective Efficacy ofAsteracantha longifoliaon Acetaminophen-Induced Liver Damage in Rats

The effect of oral administration of methanolic extract of Asteracantha longifolia (AL) seeds on acetaminophen (APAP)-induced acute liver damage in rats was investigated. The activities of marker enzymes (aspartate transaminase, alanine transaminase, alkaline phosphatase, lactate dehydrogenase, and gamma glutamyl transferase) and bilirubin level in serum and the levels of cholesterol, triglycerides, and free fatty acids in both serum and liver were found to be increased when rats were challenged with APAP. This was also associated with a significant reduction of serum and tissue phospholipids. Pretreatment with AL extract prior to the administration of APAP prevented these alterations as evidenced by liver histopathology. Results indicated that the extract could offer protection against APAP-induced liver damage, suggesting its hepatoprotective activity.

Synthesis and biological evaluation of 2,3-diarylpyrazines and quinoxalines as selective COX-2 inhibitors

Several 2,3-diaryl pyrazines and quinoxalines with 4-sulfamoyl (SO(2)NH(2))/methylsulfonyl (SO(2)Me)-phenyl pharmacophores have been synthesized and evaluated for the cyclooxygenase (COX-1/COX-2) inhibitory activity. Smaller groups such as methoxy, methyl and fluoro when substituted at/around position-4 of the adjacent phenyl ring, have great impact on the selective COX-2 inhibitory activity of the series. Many potential compounds were obtained from a brief structure-activity relationship (SAR) study. Two of these, compounds 11 and 25 exhibited excellent in vivo activity in the established animal model of inflammation. Since compound 25 possessed an amenable sulfonamide group, two of its prodrugs 48 and 49 were also synthesized. Both of them have excellent in vivo potential, and represent a new class of COX-2 inhibitor.

Butyrolactones from Aspergillus terreus

In the process development of lovastatin using Aspergillus terreus DRCC 152 in solid state fermentation, we have isolated a new butyrolactone-IV (3) along with the previously reported butyrolactone-I (1) and butyrolactone-II (2) produced under submerged conditions. The structure of compound 3 has been characterized as 3-hydroxy-5-[2-(1-hydroxy-1-methylethyl)-2(R)-2,3-dihydro-benzo[b]furan- 5 ylmethyl]-4-(4-hydroxyphenyl)-5-methoxycarbonyl-(5R)-2,5-dihydro-2 -furanone on the basis of spectroscopic studies. The absolute stereochemistry has been determined by single crystal X-ray diffraction studies. The cytotoxic and antibacterial activities of these compounds were determined.