Computational guided identification of a citrus flavonoid as potential inhibitor of SARS-CoV-2 main protease.

Although vaccine development is being undertaken at a breakneck speed, there is currently no effective antiviral drug for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19. Therefore, the present study aims to explore the possibilities offered by naturally available and abundant flavonoid compounds, as a prospective antiviral drug to combat the virus. A library of 44 citrus flavonoids was screened against the highly conserved Main Protease (Mpro) of SARS-CoV-2 using molecular docking. The compounds which showed better CDocker energy than the co-crystal inhibitor of Mpro were further revalidated by flexible docking within the active site; followed by assessment of drug likeness and toxicity parameters. The non-toxic compounds were further subjected to molecular dynamics simulation and predicted activity (IC50) using 3D-QSAR analysis. Subsequently, hydrogen bonds and dehydration analysis of the best compound were performed to assess the binding affinity to Mpro. It was observed that out of the 44 citrus flavonoids, five compounds showed lower binding energy with Mpro than the co-crystal ligand. Moreover, these compounds also formed H-bonds with two important catalytic residues His41 and Cys145 of the active sites of Mpro. Three compounds which passed the drug likeness filter showed stable conformation during MD simulations. Among these, the lowest predicted IC50 value was observed for Taxifolin. Therefore, this study suggests that Taxifolin, could be a potential inhibitor against SARS-CoV-2 main protease and can be further analysed by in vitro and in vivo experiments for management of the ongoing pandemic.

Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation.

The Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus, SARS-CoV-2, has recently emerged as a pandemic. Here, an attempt has been made through in-silico high throughput screening to explore the antiviral compounds from traditionally used plants for antiviral treatments in India namely, Tea, Neem and Turmeric, as potential inhibitors of two widely studied viral proteases, main protease (Mpro) and papain-like protease (PLpro) of the SARS-CoV-2. Molecular docking study using BIOVIA Discovery Studio 2018 revealed, (-)-epicatechin-3-O-gallate (ECG), a tea polyphenol has a binding affinity toward both the selected receptors, with the lowest CDocker energy - 46.22 kcal mol-1 for SARS-CoV-2 Mpro and CDocker energy - 44.72 kcal mol-1 for SARS-CoV-2 PLpro, respectively. The SARS-CoV-2 Mpro complexed with (-)-epicatechin-3-O-gallate, which had shown the best binding affinity was subjected to molecular dynamics simulations to validate its binding affinity, during which, the root-mean-square-deviation values of SARS-CoV-2 Mpro-Co-crystal ligand (N3) and SARS-CoV-2 Mpro- (-)-epicatechin-3-O-gallate systems were found to be more stable than SARS-CoV-2 Mpro system. Further, (-)-epicatechin-3-O-gallate was subjected to QSAR analysis which predicted IC50 of 0.3281 nM against SARS-CoV-2 Mpro. Overall, (-)-epicatechin-3-O-gallate showed a potential binding affinity with SARS-CoV-2 Mpro and could be proposed as a potential natural compound for COVID-19 treatment.

Immunogenicity & safety of a single dose of live-attenuated Japanese encephalitis vaccine SA 14-14-2 in adults.

BACKGROUND & OBJECTIVES: Japanese encephalitis (JE) caused by mosquito-borne Flavivirus is one of the leading causes of viral encephalitis in Asia. Control strategies include vector control and human vaccination. Due to lack of immunization programmes in endemic regions, there are still high mortality and morbidity. A live-attenuated SA 14-14-2 JE vaccine (LAJEV) has been licensed and used in Asian countries, including India. We report the assessment of immunogenicity and safety of the vaccine in adults during the first mass adult vaccination campaign carried out in Assam, India. METHODS: One thousand and seventy five adults (aged ≥15 yr) who received LAJEV were monitored for adverse events following immunization for one year. The safety assessment of vaccinated population was evaluated till 28 days and at 6 and 12 months. Blood samples collected from the enrolled participants were tested by plaque reduction neutralization test (PRNT 50 ) to assess the neutralizing antibody titres (NATs) before vaccination and 28 days, six and 12 months post-vaccination (PV). RESULTS: Among the 1075 vaccinated individuals, four reported minor adverse effects from 30 min to 28 days PV. Based on the pre-vaccination NAT, the study participants were categorized as seronegative, moderately seropositive and strongly seropositive. Nearly 85.5 per cent of JE seronegative participants seroconverted by 28 days PV. The geometric mean titre (GMT) in all the three groups increased by 28 days and decreased by six and 12 months PV. Nearly 60 per cent of the moderately positive individuals exhibited four-fold rise in GMT, 28 days PV. Almost 95.5 per cent of the participants in the study population remained seroprotected at the end of 12 months PV. INTERPRETATION & CONCLUSIONS: This study on immunogenicity and safety of LAJEV in adults showed that a single dose of the live-attenuated vaccine was safe and induced protective immunity to both JE seronegative and naturally seropositive adults. Further study is required to find out long term protective efficacy of this vaccine.

Chikungunya outbreak in Garo Hills, Meghalaya: An epidemiological perspective.

BACKGROUND & OBJECTIVES: Chikungunya (CHIK) fever is a mosquito-borne disease caused by chikungunya virus (CHIKV). Chikungunya infection was first reported from India in 1963 from Kolkata. We report the serological and molecular evidence of an outbreak of chikungunya in northeast India that occurred in Tura, a hilly and forested terrain in Garo Hills district of Meghalaya. METHODS: Blood samples (3 ml) collected from hospitalized patients during the outbreak were tested for IgM antibodies against CHIKV and followed up four months later. A repeat survey was carried out in the same area after four months from where cases had been reported. Blood samples were also collected from people with history of fever and body ache in the last four months. Persons showing IgM positivity against CHIKV in the repeat survey were followed up one and a half years later. All samples were also processed by RT-PCR assay for CHIK Envelope (E) 1 gene. Immature mosquitoes were collected, link reared and identified with standard keys. Virus incrimination studies were done on Aedes aegypti and Ae. albopictus mosquitoes collected during the survey. RESULTS: Fever, headache and joint pain were the primary clinical presentations. Twenty three (35.93 %) of 64 samples reported during the outbreak were IgM positive for CHIK. Three samples showed PCR amplification. All these were IgM positive. The sequenced E1 gene revealed that the strains belonged to East Central South African (ECSA) genotype. INTERPRETATION & CONCLUSIONS: Field survey done after four months revealed that some individuals still had joint pain associated with episodes of headache and fever. It could be inferred that these persons might have contracted infection during the CHIK outbreak four months ago or during the intervening period which caused persistence of sequelae. ECSA genotype was found to be involved in the outbreak. Aedes albopictus was the predominant mosquito species collected during the outbreak.

An Update on Complications Associated with SARS-CoV-2 Infection and COVID-19 Vaccination.

Over the past two years, SARS-CoV-2 has dramatically spread worldwide and emerged as a major pandemic which has left an unprecedented mark on healthcare systems and economies worldwide. As our understanding of the virus and its epidemiology continues to grow, the acute phase clinical symptoms and long-term and vaccine-related complications are becoming more apparent. With heterogeneity in presentations, comparisons may be drawn between COVID-19-related sequelae and vaccination related adverse events. The present review article aims to address the currently available literature on the SARS-CoV-2 virus, immune responses, the pathophysiology of clinical presentations, and available vaccinations with its adverse events for the appraisal of its potential impact on the COVID-19 management system.

Integrated computational approach towards repurposing of antimalarial drug against SARS-CoV-2 main protease.

Huge vaccination drives are underway around the world for the ongoing COVID-19 pandemic. However, the search for antiviral drugs is equally crucial. As new drug discovery is a time-consuming process, repurposing of existing drugs or developing drug candidates against SARS-CoV-2 will make the process faster. Considering this, 63 approved and developing antimalarial compounds were selected to screen against main protease (Mpro) and papain-like protease (PLpro) of SARS-CoV-2 using in silico methods to find out possible new drug candidate(s). Out of 63 compounds, epoxomicin showed the best binding affinity against the Mpro with CDocker energy of - 57.511 kcal/mol without any toxic effect. This compound was further taken for molecular dynamic simulation study, where the Mpro-epoxomicin complex was found to be stable with binding free energy - 79.315 kcal/mol. The possible inhibitory potential of the selected compound was determined by 3D-QSAR analysis and found to be 0.4447 µM against SARS-CoV-2 Mpro. Finally, the structure activity relationship of the compound was analyzed and two fragments responsible for overall good binding affinity of the compound at the active site of Mpro were identified. This study suggests a safe antimalarial drug, namely epoxomicin, as a probable inhibitor of SARS-CoV-2 Mpro which needs further validation by in vitro/in vivo studies before clinical use. Supplementary Information: The online version contains supplementary material available at 10.1007/s11224-022-01916-0.

Potential anti-viral activity of approved repurposed drug against main protease of SARS-CoV-2: an in silico based approach.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) which was first reported in Wuhan province of China, has become a deadly pandemic causing alarmingly high morbidity and mortality. In the absence of new targeted drugs and vaccines against SARS-CoV-2 at present, the choices for effective treatments are limited. Therefore, considering the exigency of the situation, we focused on identifying the available approved drugs as potential inhibitor against the promising Coronavirus drug target, the Main Protease, using computer-aided methods. We created a library of U. S. Food and Drug Administration approved anti-microbial drugs and virtually screened it against the available crystal structures of Main Protease of the virus. The study revealed that Viomycin showed the highest -CDocker energy after docking at the active site of SARS-CoV-2 Main Protease. It is noteworthy that Viomycin showed higher -CDocker energy as compared to the drugs currently under clinical trial for SARS-CoV-2 treatment viz. Ritonavir and Lopinavir. Additionally, Viomycin formed higher number of H-bonds with SARS-CoV-2 Main Protease than its co-crystallised inhibitor compound N3. Molecular dynamics simulation further showed that Viomycin embedded deeply inside the binding pocket and formed robust binding with SARS-CoV-2 Main Protease. Therefore, we propose that Viomycin may act as a potential inhibitor of the Main Protease of SARS-CoV-2. Further optimisations with the drug may support the much-needed rapid response to mitigate the pandemic.Communicated by Ramaswamy H. Sarma.

A comparative study on knowledge and practice against malaria among Accredited Social Health Activists (ASHAs) of low and high endemic regions of Tripura, Northeast India.

INTRODUCTION: This study was conducted to compare and evaluate the knowledge as well as the practice of community health volunteers, Accredited social health activists (ASHAs) in low and high malaria-endemic regions of Tripura, Northeast India. MATERIALS AND METHODS: In this descriptive cross-sectional study, all ASHAs working in the randomly selected two blocks of each low and high malaria-endemic areas were included in the study. While ASHAs with less than 1-year experience were excluded from the study. The ASHAs were interviewed and information was gathered on knowledge and practice against malaria management. Chi-square test was used to identify differences in responses among the ASHAs. RESULTS: Significant differences in knowledge of mixed malarial infection (P < 0.001) and early symptoms of malaria (P = 0.005) were observed when responses of high malaria-endemic ASHAs (HMEA) were compared to low endemic ASHAs (LMEA). With respect to malaria testing skills, 83.16% HMEA affirmed that they could perform Rapid diagnostic (RD) kit tests as opposed to 57.24% LMEA, (P < 0.001). Disturbingly only two HMEA could correctly describe the duration for Pf and Pv treatment. CONCLUSION: The study identifies major lacunae in the balance of knowledge and practices of ASHAs in both study areas of Tripura. Therefore,for a successful projected malaria elimination program, community-level ASHA volunteers need to have accurate malaria knowledge and management approaches irrespective of the endemicity. This study will help to understand the operational constraints and plan educational training for ASHA volunteers in malaria-endemic regions.

Differential Expression Levels of Inflammatory Chemokines and TLRs in Patients Suffering from Mild and Severe Japanese Encephalitis.

Japanese encephalitis (JE) is a vector-borne viral disease with clinical manifestations ranging from asymptomatic to severe neurological symptoms and even leading to death. The exact pathophysiology for diverse clinical spectrum of the disease is complex and has not yet been defined. Studies have postulated that during JE infection, inflammatory cytokines and chemokines are produced after the initial recognition of viral antigens through the engagement of toll-like receptors (TLR) pathways. However, there is paucity of knowledge on the expression levels of chemokines and TLRs among mild and severely affected JE patients. Hence, to better understand disease pathogenesis, we examined the mRNA expression of chemokines, CCL2 and CCL5, and their respective receptors CCR2 and CCR5 along with TLRs viz. TLR3, TLR7, TLR8, and TLR9 in context of mild and severely Japanese encephalitis virus (JEV)-infected (n = 19) and healthy (n = 19) individuals. Our study showed significant downregulation of CCL2, CCL5, CCR2, CCR5, and TLR3 by log 0.87, 1.02, 0.82, 0.68, and 0.37-fold respectively, among mild cases compared with controls. Significant difference of gene expression among mild and severe JE cases for CCL2 (p < 0.001), CCL5 (p < 0.01), and TLR7 (p < 0.05) was observed. In conclusion, our results proposes that chemokines viz. CCL2 and CCL5 along with TLR7 may be associated with degree of pathogenesis of JE and could be putative therapeutic targets for preventing severe inflammation during viral encephalitis.

Significance of CCL2, CCL5 and CCR2 polymorphisms for adverse prognosis of Japanese encephalitis from an endemic population of India.

Japanese encephalitis (JE) is a major contributor for viral encephalitis in Asia. Vaccination programme has limited success for largely populated JE endemic countries like India and disease exposure is unavoidable. Involvement of chemokines and its co-receptors for adverse prognosis of JE have been documented both in vitro and in vivo. Identification of the genetic predisposing factor for JE infection in humans is crucial but not yet established. Therefore, we investigated the association of single nucleotide polymorphisms (SNPs) in chemokines (CCL2 and CCL5) and its co-receptors (CCR2 and CCR5) with their protein level for JE. The study enrolled 87 symptomatic JE cases (mild: severe = 24:63) and 94 asymptomatic controls. Our study demonstrated that CCL2 (rs1024611G), CCL5 (rs2280788G) and CCR2 (rs1799864A) significantly associated with JE (Odds ratio = 1.63, 2.95 and 2.62, respectively and P = 0.045, P = 0.05 and P = 0.0006, respectively). The study revealed that rs1024611G allele was associated with elevated level of CCL2. CCL5 elevation associated with JE mortality having a Cox proportional hazard of 1.004 (P = 0.033). In conclusion, SNPs of chemokine viz. CCL2 (rs1024611G) and its receptor CCR2 (rs1799864A) significantly associated with JE which may serve as possible genetic predisposing factor and CCL5 protein level may act as marker for disease survival.

Detection of West Nile virus in six mosquito species in synchrony with seroconversion among sentinel chickens in India.

BACKGROUND: West Nile virus (WNV) is a zoonotic flavivirus maintained in mosquito-bird transmission cycle. Although humans are accidental hosts, fatal outcomes following WNV infection have been reported from India. Studies have identified WNV as an important etiological agent causing acute encephalitis syndrome in Assam, Northeast India. While circulation of WNV is evident, the role of vectors and avian hosts involved in the transmission remains unclear. In this study we identified local mosquito species for evidence of WNV infection along with seroconversion among sentinel chickens. METHODS: Mosquitoes were collected and pooled species wise from June 2014 through December 2015. Virus was screened using reverse transcriptase PCR followed by sequencing and phylogenetic analysis. Sentinel chicken blood was screened for WNV antibody to assess their role in WNV transmission. RESULTS: A total of 52,882 mosquitoes belonging to 16 species were collected. WNV was detected in 18 pools of Culex vishnui, Culex tritaeniorhynchus, Culex quinquefasciatus, Culex whitmorei, Culex pseudovishnui and Mansonia uniformis. Phylogenetic analysis revealed that all mosquito derived sequences belonged to Lineage 5 and were 99-100% similar to the Assam strain of WNV isolated from human CSF sample in 2007. All sentinel chickens had seroconverted by the month of July that happens to be the peak WNV transmission month among humans as well. CONCLUSION: To the best of our knowledge, this is the first report of WNV identification from field-collected Cx. pseudovishnui and Mansonia uniformis in India. Our study demonstrates potential vectors which may play a crucial role in WNV transmission and should be considered in the vector control strategies. Additionally, our study highlights the role of sentinel chickens for WNV surveillance.

Genetic diversity and gene structure of mitochondrial region of Anopheles minimus (Diptera: Culicidae) - major malaria vector of North east India.

OBJECTIVE: To depict mitochondrial genetic variation for the first time among Anopheles minimus (An.minimus) (Diptera: Culicidae) species from two malaria endemic states of NE India. METHODS: Phylogeographic analysis was carried at 9 out of 12 sites of An.minimus confirmed malaria endemic places. RESULTS: All sequences were Adenine-Thymine rich regions. Transitions were observed in 6 sequences where 5 mutations were synonymous substitutions and in 1 case non synonymous mutation was observed. Three distinct clusters of haplotypes were generated. Haplotype diversity and low nucleotide diversity were studied. Overall negative values obtained from Tajima's D test and Fu'sFS test indicate a recent genetic population expansion. Network analysis has explained sequence diversity that was also shown by mutations in 6 sequences. CONCLUSIONS: High genetic diversity observed within the populations of An.minimus species has several possible implications for vector control in the region.