Phytocompounds as versatile drug-leads targeting mProtease in the SARS-CoV-2 virus: insights from a molecular dynamics study.

SARS-CoV-2 is one of the deadly outbreaks in the present era and still showing its presence around the globe. Researchers have produced various vaccines that offer protection against infection, but we have not yet found a cure for COVID-19. Currently, efforts are focused on identifying effective therapeutic approaches to treat this infectious disease. In the present work, we investigated the main protease (Mpro) protein, a crucial component in SARS-CoV-2 viral particle formation, as a drug target and proposed phytocompounds with therapeutic potential against SARS-CoV-2. Initially, several plant-based resources were exploited to screen around one thousand phytocompounds and further their physiochemical characterization and assessment of drug likeliness were performed using SwissADME. Eventually, we screened 95 compounds based on docking analysis using AutoDock Vina. Five compounds were selected having the highest affinity for Mpro for the analysis of ligand-receptor interaction using molecular dynamic (MD) simulation. Docking and MD simulation studies elucidated the promising stable interaction of selected 5 ligands with Mpro. During MD simulation of 100 ns, Abacopterin F showed the lowest binding energy (-37.13 kcal/mol) with the highest affinity towards Mpro and this compound may be proposed as a lead molecule for further investigation. This interaction may result in modulation of the Mpro activity, consequently leading to hindrance in viral particle formation. However, in-vitro and in-vivo experimental validation would be needed to process the selected phytomolecules as a therapeutic lead against SARS-CoV-2.

Copper transporter protein (MctB) as a therapeutic target to elicit antimycobacterial activity against tuberculosis.

Tuberculosis (TB) is a prehistoric infection and major etiologic agent of TB, Mycobacterium tuberculosis, which is considered to have advanced from an early progenitor species found in Eastern Africa. By the 1800s, there were approximately 800 to 1000 fatality case reports per 100,000 people in Europe and North America. This research suggests an In-silico study to identify potential inhibitory compounds for the target Mycobacterial copper transport protein (Mctb). ADME-based virtual screening, molecular docking, and molecular dynamics simulations were conducted to find promising compounds to modulate the function of the target protein. Four chemical compounds, namely Anti-MCT1, Anti-MCT2, Anti-MCT3 and Anti-MCT4 out of 1500 small molecules from the Diverse-lib of MTiOpenScreen were observed to completely satisfy Lipinski rule of five and Veber's rule. Further, significantly steady interactions with the MctB target protein were observed. Docking experiments have presented 9 compounds with less than -9.0 kcal/mol free binding energies and further MD simulation eventually gave 4 compounds having potential interactions and affinity with target protein and favorable binding energy ranging from -9.2 to -9.3 kcal/mol. We may propose these compounds as an effective candidate to reduce the growth of M. tuberculosis and may also assist present a novel therapeutic approach for Tuberculosis. In vivo and In vitro validation would be needed to proceed further in this direction.Communicated by Ramaswamy H. Sarma.

Laryngotracheal Stenosis: Our Experience in a Tertiary Care Hospital.

Laryngotracheal stenosis is a recalcitrant disease with high morbidity. Laryngotracheal stenosis can be defined as a partial or circumferential narrowing of the airway and may be congenital or acquired. Sites involved are supraglottis, glottis, or sub glottis. The goal of treating the patient with laryngotracheal stenosis is to reconstruct an adequate airway while preserving phonation and airway protection. Furthermore, there is no fixed treatment for laryngotracheal stenosis, the choice of surgical procedure is determined by the individual anatomy, involved site, length and luminal narrowing of stenotic segment and function of the larynx and trachea, together with patient factors and available facilities. To determine the most common aetiology of laryngotracheal stenosis and to study outcome of various treatment modalities and their efficacies according to the site of stenosis and time of presentation. We have prospectively studied 25 cases of laryngotracheal stenosis who presented in Department of ENT, Civil Hospital, Ahmedabad from May 2019 to December 2021. All patients with clinical suspicion of laryngotracheal stenosis underwent CECT Neck and Thorax with virtual bronchoscopy, flexible bronchoscopy and graded according to myer cotton classification and then included in study. In our study of 25 patients 19 patients had history of intubation. Out of 25 patients, 5 Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation patients had supraglottic stenosis, 14 had subglottic stenosis and 6 patients had tracheal stenosis. 20 patients were tracheostomised. Bilateral vocal cord mobility is pre requisite for any surgical intervention and for decannulation of tracheostomy tube. Laser ablation is best modality for supra glottis stenosis patients. Treatment options of subglottic and tracheal stenosis patients depends on vocal cord mobility, % of luminal narrowing and type of stenosis on flexible bronchoscopy and CT scan. Patients of subglottic or tracheal stenosis having Myer cotton grading 1 or 2 were successfully treated by Laser + Balloon dilatation while grade 3 or 4 by resection and end to end anastomosis. Endoscopic CO2 laser ablation with/without balloon dilatation gives promising results in cases of supra glottic stenosis and in soft, mucosal, short segment (< 1.5 cm), grade 1 or 2 stenosis patients with subglottic or tracheal stenosis. In patients with subglottic or tracheal stenosis having hard, cartilage framework involvement, > 1.5 cm stenotic segment, Grade 3 or 4 needed external open approach like tracheal resection and end to end anastomosis.

Repurposing FDA-approved drugs as FXR agonists: a structure based in silico pharmacological study.

Farnesoid X receptor (FXR) modulates the expression of genes involved in lipid and carbohydrate homeostasis and inflammatory processes. This nuclear receptor is likely a tumor suppressor in several cancers, but its molecular mechanism of suppression is still under study. Several studies reported that FXR agonism increases the survival of colorectal, biliary tract, and liver cancer patients. In addition, FXR expression was shown to be down-regulated in many diseases such as obesity, irritable bowel syndrome, glomerular inflammation, diabetes, proteinuria, and ulcerative colitis. Therefore, development of novel FXR agonists may have significant potential in the prevention and treatment of these diseases. In this scenario, computer-aided drug design procedures can be resourcefully applied for the rapid identification of promising drug candidates. In the present study, we applied the molecular docking method in conjunction with molecular dynamics (MD) simulations to find out potential agonists for FXR based on structural similarity with the drug that is currently used as FXR agonist, obeticholic acid. Our results showed that alvimopan and montelukast could be used as potent FXR activators and outperform the binding affinity of obeticholic acid by forming stable conformation with the protein in silico. However, further investigational studies and validations of the selected drugs are essential to figure out their suitability for preclinical and clinical trials.

Deciphering the immunogenic T-cell epitopes from spike protein of SARS-CoV-2 concerning the diverse population of India.

Scientists are rigorously looking for an efficient vaccine against the current pandemic due to the SARS-CoV-2 virus. The reverse vaccinology approach may provide us with significant therapeutic leads in this direction and further determination of T-cell/B-cell response to antigen. In the present study, we conducted a population coverage analysis referring to the diverse Indian population. From the Immune epitope database (IEDB), HLA- distribution analysis was performed to find the most promiscuous T-cell epitope out of In silico determined epitope of Spike protein from SARS-CoV-2. Epitopes were selected based on their binding affinity with the maximum number of HLA alleles belonging to the highest population coverage rate values for the chosen geographical area in India. 404 cleavage sites within the 1288 amino acids sequence of spike glycoprotein were determined by NetChop proteasomal cleavage prediction suggesting the presence of adequate sites in the protein sequence for cleaving into appropriate epitopes. For population coverage analysis, 179 selected epitopes present the projected population coverage up to 97.45% with 56.16 average hit and 15.07 pc90. 54 epitopes are found with the highest coverage among the Indian population and highly conserved within the given spike RBD domain sequence. Among all the predicted epitopes, 9-mer TRFASVYAW and RFDNPVLPF along with 12-mer LLAGTITSGWTF and VSQPFLMDLEGK epitopes are observed as the best due to their decent docking score and best binding affinity to corresponding HLA alleles during MD simulations. Outcomes from this study could be critical to design a vaccine against SARS-CoV-2 for a different set of populations within the country.Communicated by Ramaswamy H. Sarma.

Clinical Study of Surge of Mucormycosis in COVID-19 Pandemic: A Tertiary Care Center Study.

The aim of this study is to evaluate the prevalence, pathogenesis and management of mucormycosis in post covid 19 patients in our tertiary care covid dedicated hospital. A prospective cross sectional study was done in 70 patients who were admitted in the covid department of BJ Medical College, Civil hospital Ahmedabad and presented with mucormycosis during admission or after discharge over a period of 10 months from March 2020 to December 2020. Middle aged to elderly population were found to be most commonly affected with mucormycosis. It was found that majority of the affected population was uncontrolled diabeteic and had a delayed presentation to hospital due to ongoing covid pandemic crisis. Covid infection had major effect on the hormonal balance of the body as evident from the uncontrolled blood glucose levels of affected patients. In patients with mucormycosis, early detection, surgical debridement, suitable antifungal therapy, and control of risk factors like diabetes mellitus are the main parameters of successful management of this lethal infection. Early diagnosis and treatment of mucormycosis can be life saving as it is a rapidly progressing disease and have been proven fatal.

Phytochemical constituents of Inula britannica as potential inhibitors of dihydrofolate reductase: A strategic approach against shigellosis.

Shigella dysenteriae type 1 is considered as an epidemic in different developing countries, which is responsible for the most severe form of bacterial dysentery. It habitually can develop to the most severe form of dysentery with deadly complications. Development of drugs against this disease is still ongoing. Therefore, we used in silico studies to screen the Inula britannica phytocompounds that are used in traditional Chinese and Kampo Medicines and have activities against different diseases. Spinacetin, eupatin, chrysoeriol and diosmetin were successfully passed through the docking-based screening and absorption, distribution, metabolism, excretion and toxicity (ADMET) filtration. The estimated docking affinities of eupatin, diosmetin, chrysoeriol and spinacetin with Dihydrofolate reductase type 1 (DHFR-1), were -6.5, -6.5, -6.3 and -6.1 kcal/mol, respectively. Which were selected for further investigations based on their favorable ADME/Tox characteristics. Then, the 100 ns molecular dynamics (MD) simulations of apo DHFR, spinacetin-DHFR, eupatin-DHFR, chrysoeriol-DHFR and diosmetin-DHFR complexes were carried out. The RMSD fluctuations of the spinacetin, eupatin, chrysoeriol and diosmetin inside the binding site were explored. Subsequently, the effect of binding Spinacetin, eupatin, chrysoeriol and diosmetin upon the dynamic stability of protein was assessed. Additionally, Principal Component Analysis (PCA) and Hydrogen bond analysis was performed for the apo protein and the protein ligand complexes. The results revealed that chrysoeriol and eupatin has good inhibitory effects against DHFR-1 as treatment for Shigella dysenteriae type when compared to other compounds under study. Hence this study implies that eupatin and chrysoeriol are a significantly potential drug like molecule for the treatment of Shigellosis and must undergo validation through in vivo and in vitro experiments.Communicated by Ramaswamy H. Sarma.

Immunoinformatic based analytics on T-cell epitope from spike protein of SARS-CoV-2 concerning Indian population.

The whole world is drastically affected by the current pandemic due to severe virus, SARS-CoV-2 and scientists are rigorously looking for the efficient vaccine against it that become an emergent issue. Reverse vaccinology approach may provide us with significant therapeutic leads in this direction and further determination of T-cell / B-cell response to antigen. In the present study, we conducted population coverage analysis referring to the diverse Indian population. By using tools from Immune epitope database (IEDB), HLA- distribution analysis was performed to find the most promiscuous T-cell epitope out of In silico determined epitope of Spike protein from SARS-CoV-2. Selection of these epitopes have been conducted based on their binding affinity with the maximum number of HLA alleles belong to the highest population coverage rate values for the chosen geographical area in India. 404 cleavage sites within the 1288 amino acids sequence of spike glycoprotein were determined by NetChop proteasomal cleavage prediction suggesting that this protein has adequate sites in the protein sequence for cleaving into appropriate epitopes. For population coverage analysis, 221 selected epitopes are considered that shows the projected population coverage as 83.08% with 19.29 average hit (average number of epitope hits/HLA combinations recognized by the population) and 5.91 pc90 (minimum number of epitope hits/HLA combinations recognized by 90% of the population). 54 epitopes are found with the highest coverage among the Indian population and highly conserved within the given spike RBD domain sequence. Docking analysis of each epitope with their respective allele suggests that the epitope NSFTRGVYY represents highest binding affinity with docking score -7.6 kcal/mol with its allele HLA-C*07:01 among all the epitopes. Since the Covid-19 cases are still in progress and seem to remain like this until we find an effective vaccine, moreover in countries like India, vast diversity in the population may present a hindrance to particular vaccine efficiency. Outcomes from this study could be critical to design vaccine against SARS-CoV-2 for a different set of the population within the country.

Smokeless tobacco use, birth weight, and gestational age: population based, prospective cohort study of 1217 women in Mumbai, India.

OBJECTIVE: To study the effect of using smokeless tobacco during pregnancy on babies' birth weight and gestational age at birth. DESIGN: Population based, prospective cohort study using a house to house approach. SETTING: Eight primary health post areas in the city of Mumbai (Bombay), India. PARTICIPANTS: 1217 women who were three to seven months pregnant and planning to deliver in the study area. 1167 women (96%) were followed up. MAIN OUTCOME MEASURES: Birth weight and gestational age in singleton births. RESULTS: Smokeless tobacco use was associated with an average reduction of 105 g in birth weight (95% confidence interval 30 g to 181 g) and a reduction in gestational age of 6.2 (3.0 to 9.4) days. The odds ratio for low birth weight was 1.6 (1.1 to 2.4), adjusted by logistic regression for maternal age, education, socioeconomic status, weight, anaemia, antenatal care, and gestational age. The adjusted odds ratio for preterm delivery (< 37 weeks) was 1.4 (1.0 to 2.1); for delivery before 32 weeks it was 4.9 (2.1 to 11.8) and before 28 weeks it was 8.0 (2.6 to 27.2). CONCLUSIONS: Consumption of smokeless tobacco during pregnancy decreases gestational age at birth and birth weight independent of gestational age. It should receive specific attention as a part of routine prenatal care.

High caesarean rates in Madras (India): a population-based cross sectional study.

OBJECTIVE: To estimate the population caesarean section rate in urban India. DESIGN: Population-based cross sectional study. SETTING: Madras City (Chennai), India. Seven hundred and eighty resident women who delivered in Madras between June 1997 and May 1999. METHODS: Cluster sampling was done using streets as cluster units. Thirty clusters were selected from 1255 clusters by the probability proportion to size method and 26 women were selected randomly from each cluster. MAIN OUTCOME MEASURES: Total and primary caesarean rates. RESULTS: Total population caesarean section rate was 32.6% (95% CI 27-38) and primary caesarean section rate was 25% (95% CI 20-30). Total caesarean section rates in the public, charitable and private sectors were 20%, 38% and 47%, respectively. Private sector deliveries had an odds ratio of 2.4 (95% CI 1.5, 3.8) of a primary caesarean section delivery in comparison with the public sector after adjustment for parity, age at delivery of mother and educational status. CONCLUSIONS: Forty-seven percent of births by caesarean section in the private sector is alarming and could implicate private sector care as the main contributing factor behind the high population caesarean section rates. Policymakers should urgently institute systems for accountability and ethical practice and regularly monitor all medical interventions, before large scale exploitation of the rural markets begins.

Human papillomavirus type 16 E6 and E7 gene variations in Indian cervical cancer.

OBJECTIVES: Human papillomavirus type 16 is a causative factor for development of cervical cancer. The E6 and E7 genes of HPV 16 are critical to the process of immortalization and transformation of host cells. Recent reports suggest that variants of these two genes may contribute to the risk of malignant progression of cancer in the uterine cervix. However, no data exist on sequence variations of HPV 16 E6 and E7 genes that may exist in India. Therefore, we examined intratype variations in the E6 and E7 viral genes in DNA isolated from HPV 16-positive cervical scrapes and biopsies. METHODS: The open reading frames of the E6 and E7 genes were amplified by PCR and then directly sequenced by the fluorescent dye dideoxy termination method.Results. In addition to the prototype E6 gene sequence, five sets of mutations of the E6 gene were identified. The European prototype (350T) was detected in 9.1% of the study group while the European variant (350G) was seen in 28% of patients. The remaining variants (a combination of the 350G mutation with 335T, 145T, or 419G) were significantly associated with cases compared to controls. The 350G + 145T variant was found at much higher incidence in cases in younger women, suggesting that this variant may be associated with aggressive tumor behavior. Interestingly the 350G + 419G combination was found only in controls. There was no significant association between the four genotypes of E7 and any stage of tumor progression or age. CONCLUSIONS: The results indicate that specific mutations in the E6 gene are found in young Indian women with high-grade squamous intraepithelial lesions and invasive cancer, suggesting that these mutations represent more oncogenically active HPV 16. Whether this increased oncogenecity is due to differences in p53 inactivation, ineffective keratinocyte differentiation, and/or altered response to the immune system by these oncogenic E6 mutants remains to be clarified.

Polymorphism at codon 72 of p53, human papillomavirus, and cervical cancer in South India.

PURPOSE: It has been suggested that host genetic factors play a role in human papillomavirus (HPV)-associated tumorigenesis, although the issue continues to be a focus of much debate. Previous studies have reported that a common polymorphism of the wild type p53 gene at codon 72 of exon 4 (Arg/Arg) is associated with a sevenfold increased risk of HPV-associated cancer compared to Arg/Pro and Pro/Pro polymorphisms. In vitro studies also suggested that the Arg/Arg polymorphism was much more susceptible to HPV 16 E6-mediated degradation as compared to other allelic forms. Subsequent studies published since this initial report indicated geographical differences with respect to the role of Arg/Arg polymorphism in increasing the risk of HPV-associated cervical cancer. METHODS: In this study we analyzed leukocyte DNA from a total of 421 subjects for the Arg/Arg, Arg/Pro or Pro/Pro p53 polymorphisms at various stages of the cervical tumor progression spectrum, using allele-specific PCR. All subjects were from the Thiruvananthapuram District of South India. HPV genotyping was done for all subjects using either DNA extracted from cervical biopsies or exfoliated cervical cells. All subjects were grouped on the basis of both of cyto-pathology and HPV status. RESULTS: The distribution of p53 genotypes was not significantly different in all study groups (HPV positive vs HPV negative and cases vs controls comparisons). Homozygosity for Arg/Arg was not associated with increased risk for cervical cancer. CONCLUSION: We find no evidence for any association between homozygosity for p53 arginine with either cervical dysplasia, cervical carcinoma or HPV infection in the population from South India.

Cellular manifestations of human papillomavirus infection in laryngeal tissues.

BACKGROUND AND OBJECTIVES: Although epidemiologic studies have suggested human papillomavirus (HPV) to be an etiological agent in laryngeal carcinogenesis, little is known on the cellular manifestations of HPV infection in these tumors. In this study, we investigated the frequency of HPV infection in various neoplastic and non-neoplastic laryngeal tissue and its association with expression of the proliferating cell nuclear antigen (PCNA) and the tumor suppressor protein p53. METHODS: Tissues were analyzed by polymerase chain reaction (PCR) for the presence of HPV and by immunocytochemistry for the expression of p53 and PCNA. RESULTS: None of the six normal laryngeal tissues showed the presence of HPV. Thirteen out of the 16 papillomas were positive for HPV, while 15 out of the 44 invasive cancers were HPV positive. PCNA expression increased as the lesion progressed through increasing histological abnormality (r = 0.64400, P = 0.00000). The correlation between the type of laryngeal neoplasm and p53 accumulation was significant (r = 0.54839, P = 0.00000). Significant correlation was also evident between presence of HPV and p53 accumulation (r = 0.34259, P = 0.00424) and PCNA expression (r = 0.036024, P = 0.00266) indicating that HPV positive tumors showed significant p53 accumulation and increased proliferation. There was also correlation between p53 and PCNA expression (r = 0.67475, P = 0.00000) indicating that in all tumors with p53 accumulation, there was a corresponding increase in PCNA expression. CONCLUSIONS: The results suggests that changes in p53 and PCNA expression may be associated with HPV infection, and could play a role in laryngeal carcinogenesis.