Mutational analysis of the spike protein of SARS-COV-2 isolates revealed atomistic features responsible for higher binding and infectivity

Introduction: The perpetual appearance of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2), and its new variants devastated the public health and social fabric around the world. Understanding the genomic patterns and connecting them to phenotypic attributes is of great interest to devise a treatment strategy to control this pandemic.Materials and Methods: In this regard, computational methods to understand the evolution, dynamics and mutational spectrum of SARS-CoV-2 and its new variants are significantly important. Thus, herein, we used computational methods to screen the genomes of SARS-CoV-2 isolated from Pakistan and connect them to the phenotypic attributes of spike protein; we used stability-function correlation methods, protein-protein docking, and molecular dynamics simulation.Results: Using the Global initiative on sharing all influenza data (GISAID) a total of 21 unique mutations were identified, among which five were reported as stabilizing while 16 were destabilizing revealed through mCSM, DynaMut 2.0, and I-Mutant servers. Protein-protein docking with Angiotensin-converting enzyme 2 (ACE2) and monoclonal antibody (4A8) revealed that mutation G446V in the receptor-binding domain; R102S and G181V in the N-terminal domain (NTD) significantly affected the binding and thus increased the infectivity. The interaction pattern also revealed significant variations in the hydrogen bonding, salt bridges and non-bonded contact networks. The structural-dynamic features of these mutations revealed the global dynamic trend and the finding energy calculation further established that the G446V mutation increases the binding affinity towards ACE2 while R102S and G181V help in evading the host immune response. The other mutations reported supplement these processes indirectly. The binding free energy results revealed that wild type-RBD has a TBE of −60.55 kcal/mol while G446V-RBD reported a TBE of −73.49 kcal/mol. On the other hand, wild type-NTD reported −67.77 kcal/mol of TBE, R102S-NTD reported −51.25 kcal/mol of TBE while G181V-NTD reported a TBE of −63.68 kcal/mol.Conclusions: In conclusion, the current findings revealed basis for higher infectivity and immune evasion associated with the aforementioned mutations and structure-based drug discovery against such variants

Mutations in ISDR may be linked to high viremia and virus resistance to IFN-alpha-2b but responsive to PEG-IFN-alpha-2a

Mutation in interferon sensitivity determining region may play role in virus resistance. Genotype 3a patient was subjected to 48 weeks combination therapy of IFN-alpha-2b plus ribavirin but he showed high levels of viremia before, during and after treatment although his ALT level became normal. His IL-8 and TNF-alpha levels werefound quite high before and after IFN-alpha-2 combination therapy. While comparing its ISDR-NS5A with end of treatment responder patient, eight mutations were observed in a 52 amino acid protein residue. Patient was advised for PEG-IFN-alpha-2a combination therapy for 24 weeks, to which he responded well after 4 week and showed sustained virologic response after 06 months of completion of therapy. His IL-8 and TNF-alpha levels also came to lower levels after treatment with PEG-IFN-alpha 2a combination therapy. In phylogenetic tree its genome (NZ1) along with another nonresponder case (NZ2) was placed close to Brazilian isolates. NZI and NZ2 showed 87 % sequence homology with each other while NZ1 had 89% sequence homology with EF208017 and 87% with EF20995. NZ2 showed 91% homology with EF208017 and 98% with EF207995 which is quite interesting. Mutations in ISDR sequence may be the reason for non response to IFN combination therapy of this HCV genotype 3 patient. ISDR of genotype 3 along with IL-8 and TNF-alpha may be screened on larger scale in Pakistani population which may help in deciding a cost effective treatment plan

A Correlation among the COVID-19 Spread, Particulate Matters, and Angiotensin-Converting Enzyme 2: A Review

Air pollution (AP) is one of the leading causes of health risks because it causes widespread morbidity and mortality every year. Its impact on the environment includes acid rain and decreased visibility, but more importantly, it also has an impact on human health. The rise of COVID-19 demonstrates the cost of failing to manage AP. COVID-19 can be spread through the air, and atmospheric particulate matters (PMs) can create a good atmosphere for the long-distance spread of the virus. Moreover, these PMs can cause lung cell inflammation, thereby increasing sensitivity and the severity of symptoms in COVID-19 patients. In this study, we emphasized the potential role of PMs in the spread of COVID-19. The relationship among COVID-19, PMs, and angiotensin-converting enzyme 2 (ACE2) (receptor involved in virus entry into lung cells and inflammation) was also summarized

First report on implementation of response surface methodology for the biodegradation of textile industrial effluents by Coniophora puteana IEBL-1

The current study was aimed to evaluate the industrial effluents biodegradation potential of an indigenous microorganism which reduced water pollution caused by these effluents. In the present study biodegradation of three textile industrial effluents was performed with locally isolated brown rot fungi named Coniophora puteana IEBL-1. Response Surface Methodology (RSM) was employed under Box Bhenken Design (BBD) for the optimization of physical and nutritional parameters for maximum biodegradation. Quality of treated effluents was checked by study of BOD, COD and analysis through HPLC. Three ligninolytic enzymes named lignin peroxidase, manganese peroxidase and laccase were also studied during the biodegradation process. The results showed that there was more than 85% biodegradation achieved for all three effluents with decrease in Biological Oxygen Demand (BOD) and Chemical Oxygen Demand (COD) below the recommended values for industrial effluent i.e. 80 mg/L for BOD and 220 mg/L for COD after optimization of nutritional parameters in the second stage. Analysis of samples through HPLC revealed the formation of less toxic diphenylamine, 3-methyldiphenylamine and N-methylaniline after treatment. The ligninolytic enzymes assays confirmed the role of lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase in biodegradation process. Lignin peroxidase with higher activity has more contribution in biodegradation of effluents under study. It can be concluded through the results that Coniophora buteana IEBL-1 is a potential fungus for the treatment of industrial effluents

Annotation of Potential Vaccine Targets and Design of a Multi-Epitope Subunit Vaccine against <i>Yersinia pestis</i> through Reverse Vaccinology and Validation through an Agent-Based Modeling Approach

Yersinia pestis is responsible for plague and major pandemics in Asia and Europe. This bacterium has shown resistance to an array of drugs commonly used for the treatment of plague. Therefore, effective therapeutics measurements, such as designing a vaccine that can effectively and safely prevent Y. pestis infection, are of high interest. To fast-track vaccine development against Yersinia pestis, herein, proteome-wide vaccine target annotation was performed, and structural vaccinology-assisted epitopes were predicted. Among the total 3909 proteins, only 5 (rstB, YPO2385, hmuR, flaA1a, and psaB) were shortlisted as essential vaccine targets. These targets were then subjected to multi-epitope vaccine design using different linkers. EAAK, AAY, and GPGPG as linkers were used to link CTL, HTL, and B-cell epitopes, and an adjuvant (beta defensin) was also added at the N-terminal of the MEVC. Physiochemical characterization, such as determination of the instability index, theoretical pI, half-life, aliphatic index, stability profiling, antigenicity, allergenicity, and hydropathy of the ensemble, showed that the vaccine is highly stable, antigenic, and non-allergenic and produces multiple interactions with immune receptors upon docking. In addition, molecular dynamics simulation confirmed the stable binding and good dynamic properties of the vaccine–TLR complex. Furthermore, in silico and immune simulation of the developed MEVC for Y. pestis showed that the vaccine triggered strong immune response after several doses at different intervals. Neutralization of the antigen was observed at the third day of injection. Conclusively, the vaccine designed here for Y. pestis produces an immune response; however, further immunological testing is needed to unveil its real efficacy

A Recurrent Nonsense Mutation in NECTIN4 Underlying Ectodermal Dysplasia-Syndactyly Syndrome with a Novel Phenotype in a Consanguineous Kashmiri Family

EDSS1, a syndrome characterized by ectodermal dysplasia-syndactyly, is inherited in an autosomal recessive manner due to mutations in the NECTIN4/PVRL4 gene. Clinical manifestations of the syndrome include defective nail plate, sparse to absent scalp and body hair, spaced teeth with enamel hypoplasia, and bilateral cutaneous syndactyly in the fingers and toes. Here, we report a consanguineous family of Kashmiri origin presenting features of EDSS1. Using whole exome sequencing, we found a recurrent nonsense mutation (NM_030916: c.181C > T, p.(Gln61 ∗)) in the NECTIN4 gene. The variant segregated perfectly with the disorder within the family. The candidate variant was absent in 50 in-house exomes pertaining to other disorders from the same population. In addition to the previously reported clinical phenotype, an upper lip cleft was found in one of the affected members as a novel phenotype that is not reported by previous studies in EDSS1 patients. Therefore, the study presented here, which was conducted on the Kashmiri population, is the first to document a NECTIN4 mutation associated with the upper lip cleft as a novel phenotype. This finding broadens the molecular and phenotypic spectrum of EDSS1