Integrative Systems Biology Approaches to Identify Potential Biomarkers and Pathways of Cervical Cancer.

Nowadays, cervical cancer (CC) is treated as the leading cancer among women throughout the world. Despite effective vaccination and improved surgery and treatment, CC retains its fatality rate of about half of the infected population globally. The major screening biomarkers and therapeutic target identification have now become a global concern. In the present study, we have employed systems biology approaches to retrieve the potential biomarkers and pathways from transcriptomic profiling. Initially, we have identified 76 of each up-regulated and down-regulated gene from a total of 4643 differentially expressed genes. The up-regulatory genes mainly concentrate on immune-inflammatory responses, and the down-regulatory genes are on receptor binding and gamma-glutamyltransferase. The involved pathways associated with these genes were also assessed through pathway enrichment, and we mainly focused on different cancer pathways, immunoresponse, and cell cycle pathways. After the subsequent enrichment of these genes, we have identified 12 hub genes, which play a crucial role in CC and are verified by expression profile analysis. From our study, we have found that genes LILRB2 and CYBB play crucial roles in CC, as reported here for the first time. Furthermore, the survivability of the hub genes was also assessed, and among them, finally, CXCR4 has been identified as one of the most potential differentially expressed genes that might play a vital role in the survival of CC patients. Thus, CXCR4 could be used as a prognostic and/or diagnostic biomarker and a drug target for CC.

Vaccinomics approach for scheming potential epitope-based peptide vaccine by targeting l-protein of Marburg virus.

Marburg virus is one of the world's most threatening diseases, causing extreme hemorrhagic fever, with a death rate of up to 90%. The Food and Drug Administration (FDA) currently not authorized any treatments or vaccinations for the hindrance and post-exposure of the Marburg virus. In the present study, the vaccinomics methodology was adopted to design a potential novel peptide vaccine against the Marburg virus, targeting RNA-directed RNA polymerase (l). A total of 48 l-proteins from diverse variants of the Marburg virus were collected from the NCBI GenBank server and used to classify the best antigenic protein leading to predict equally T and B-cell epitopes. Initially, the top 26 epitopes were evaluated for the attraction with major histocompatibility complex (MHC) class I and II alleles. Finally, four prospective central epitopes NLSDLTFLI, FRYEFTRHF, YRLRNSTAL, and YRVRNVQTL were carefully chosen. Among these, FRYEFTRHF and YRVRNVQTL peptides showed 100% conservancy. Though YRLRNSTAL showed 95.74% conservancy, it demonstrated the highest combined score as T cell epitope (2.5461) and population coverage of 94.42% among the whole world population. The epitope was found non-allergenic, and docking interactions with human leukocyte antigens (HLAs) also verified. Finally, in vivo analysis of the recommended peptides might contribute to the advancement of an efficient and exclusively prevalent vaccine that would be an active route to impede the virus spreading. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40203-021-00080-3.

Pharmacoinformatics based elucidation and designing of potential inhibitors against Plasmodium falciparum to target importin α/ß mediated nuclear importation.

Plasmodium falciparum, the prime causative agent of malaria, is responsible for 4, 05,000 deaths per year and fatality rates are higher among the children aged below 5 years. The emerging distribution of the multi-drug resistant P. falciparum becomes a worldwide concern, so the identification of unique targets and novel inhibitors is a prime need now. In the present study, we have employed pharmacoinformatics approaches to analyze 265 lead-like compounds from PubChem databases for virtual screening. Thereafter, 15 lead-like compounds were docked within the active side pocket of importin alpha. Comparative ligand properties and absorption, distribution, metabolism, excretion, and toxicity (ADMET) profile were also assessed. Finally, a novel inhibitor was designed and assessed computationally for its efficacy. From the comparative analysis we have found that our screened compounds possess better results than the existing lead ivermectin; having the highest binding energy of -15.6 kcal/mol, whereas ivermectin has -12.4 kcal/mol. The novel lead compound possessed more fascinating output without deviating any of the rules of Lipinski. It also possessed higher bioavailability and the drug-likeness score of 0.55 and 0.71, respectively compared to ivermectin. Furthermore, the binding study was confirmed by molecular dynamics simulation over 25 ns by evaluating the stability of the complex. Finally, all the screened compounds and the novel compound showed promising ADMET properties likewise. To end, we hope that our proposed screened compounds, as well as the novel compound, might give some advances to treat malaria efficiently in vitro and in vivo.

Design of novel viral attachment inhibitors of the spike glycoprotein (S) of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) through virtual screening and dynamics.

To date, the global COVID-19 pandemic has been associated with 11.8 million cases and over 545481 deaths. In this study, we have employed virtual screening approaches and selected 415 lead-like compounds from 103 million chemical substances, based on the existing drugs, from PubChem databases as potential candidates for the S protein-mediated viral attachment inhibition. Thereafter, based on drug-likeness and Lipinski's rules, 44 lead-like compounds were docked within the active side pocket of the viral-host attachment site of the S protein. Corresponding ligand properties and absorption, distribution, metabolism, excretion, and toxicity (ADMET) profile were measured. Furthermore, four novel inhibitors were designed and assessed computationally for efficacy. Comparative analysis showed the screened compounds in this study maintain better results than the proposed mother compounds, VE607 and SSAA09E2. The four designed novel lead compounds possessed more fascinating output without deviating from any of Lipinski's rules. They also showed higher bioavailability and the drug-likeness score was 0.56 and 1.81 compared with VE607 and SSAA09E2, respectively. All the screened compounds and novel compounds showed promising ADMET properties. Among them, the compound AMTM-02 was the best candidate, with a docking score of -7.5 kcal/mol. Furthermore, the binding study was verified by molecular dynamics simulation over 100 ns by assessing the stability of the complex. The proposed screened compounds and the novel compounds may give some breakthroughs for the development of a therapeutic drug to treat SARS-CoV-2 proficiently in vitro and in vivo.

Identification of potential drug targets and inhibitor of the pathogenic bacteria Shigella flexneri 2a through the subtractive genomic approach.

Shigella flexneri 2a is one of the most pathogenic bacteria among the Shigella spp., which is responsible for dysentery and causes masses of deaths throughout the world per year. A proper identification of the potential drug targets and inhibitors is crucial for the treatment of the shigellosis due to their emerging multidrug resistance (MDR) patterns. In this study, a systematic subtractive approach was implemented for the identification of novel therapeutic targets of S. flexneri 2a (301) through genome-wide metabolic pathway analysis of the essential genes and proteins. Ligand-based virtual screening and ADMET analyses were also made for the identification of potential inhibitors as well. Initially, we found 70 essential unique proteins as novel targets. After subsequent prioritization, finally we got six unique targets as the potential therapeutic targets and their three-dimensional models were built thereafter. Aspartate-ß-semialdehyde dehydrogenase (ASD), was the most potent target among them and used for docking analysis through ligand-based virtual screening. The compound 3 (PubChem CID: 11319750) suited well as the best inhibitor of the ASD through ADMET and enzyme inhibition capacity analysis. To end, we hope that our proposed therapeutic targets and its inhibitors might give some breakthrough to treat shigellosis efficiently in in vitro.

Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA.

Shigellosis, a bacillary dysentery, is closely associated with diarrhoea in human and causes infection of 165 million people worldwide per year. Casein-degrading serine protease autotransporter of enterobacteriaceae (SPATE) subfamily protein SigA, an outer membrane protein, exerts both cytopathic and enterotoxic effects especially cytopathic to human epithelial cell type-2 (HEp-2) and is shown to be highly immunogenic. In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA of Shigella spp. At first, 44 SigA proteins from different variants of S. flexneri, S. dysenteriae, S. boydii, and S. sonnei were assessed to find the most antigenic protein. We retrieved 12 peptides based on the highest score for human leukocyte antigen (HLA) supertypes analysed by NetCTL. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. From these, FHTVTVNTL and IELAGTLTL peptides were shown to have 100% conservancy. Finally, IELAGTLTL was shown to have the highest population coverage (83.86%) among the whole world population. In vivo study of the proposed epitope might contribute to the development of functional and unique widespread vaccine, which might be an operative alleyway to thwart dysentery from the world.

Antibacterial, Anti-Diarrhoeal, Analgesic, Cytotoxic Activities, and GC-MS Profiling of Sonneratia apetala (Buch.-Ham.) Seed.

Fruits of Sonneratia apetala (Buch.-Ham.), (English: mangrove apple, Bengali: keora) both seeds and pericarps, are largely consumed as food besides their enormous medicinal application. The fruit seeds have high content of nutrients and bioactive components. The seeds powder of S. apetala was successively fractionated using n-hexane, diethyl ether, chloroform, ethyl acetate, and methanol. The fractions were used to evaluate antibacterial, anti-diarrhoeal, analgesic, and cytotoxic activities. Methanol fraction of seeds (MeS) stronly inhibited Escherichia coli strains, Salmonella Paratyphi A, Salmonella Typhi, Shigella dysenteriae, and Staphylococcus aureus except Vibrio cholerae at 500 µg/disc. All the fractions strongly inhibited castor oil induced diarrhoeal episodes and onset time in mice at 500 mg extract/kg body weight (P<0.001). At the same concentration, MeS had the strongest inhibitory activity on diarrhoeal episodes, whereas the n-hexane fraction (HS) significantly (P<0.05) prolonged diarrhoeal onset time as compared to positive control. Similarly, HS (P<0.005) inhibited acetic acid induced writhing in mice at 500 mg extract/kg, more than any other fraction. HS and diethyl ether fractions of seed strongly increased reaction time of mice in hot plate test at 500 mg extract/kg. All the fractions showed strong cytotoxic effects in brine shrimp lethality tests. Gas chromatography-mass spectrometry analysis of HS led to the identification of 23 compounds. Linoleic acid (29.9%), palmitic acid (23.2%), ascorbyl palmitate (21.2%), and stearic acid (10.5%) were the major compounds in HS. These results suggest that seeds of S. apetala could be of great use as nutraceuticals.

Physicochemical and Antioxidant Properties of Honeys from the Sundarbans Mangrove Forest of Bangladesh.

This study evaluated the physicochemical, nutritional, antioxidant, and phenolic properties of ten honey samples from the Sundarbans mangrove forest, Bangladesh. The average pH, electrical conductivity, total dissolved solid, ash, moisture, hydroxymethyl furfural, titrable acidity, and absorbance were 4.3, 0.38 mS/cm, 187.5 ppm, 0.14%, 17.88%, 4.4 mg/kg, 37.7 meq/kg, and 483 mAU, respectively. In the honeys, the average contents of Ca, Cu, Fe, K, Mg, Mn, and Na were 95.5, 0.19, 6.4, 302, 39.9, 3.4, and 597 ppm, respectively, whereas Cd, Cr, Pb, and Ni were not found. The average contents of total sugar, protein, lipid, vitamin C, polyphenols, flavonoids, and anthocyanins in the honeys were 69.3%, 0.8%, 0.29%, 107.3 mg/kg, 757.2 mg gallic acid equivalent/kg, 43.1 mg chatechin equivalent/kg, and 5.4 mg/kg, respectively. The honeys had strong 1,1-diphenyl-2-picrylhydrazyl free radical scavenging activity, reducing power and total antioxidant capacity. High-performance liquid chromatography analysis of the honey fractions revealed the quantification of six polyphenols namely, (+)-catechin, (-)-epicatechin, p-caumeric acid, syringic acid, trans-cinnamic acid, and vanillic acid at 194.98, 330.34, 74.64, 218.97, 49.55, and 118.84 mg/kg, respectively. Therefore, the honeys in the Sundarbans are of excellent quality and a prospective source of polyphenols, and antioxidants.