Bioinformatics and System Biology Approach to Reveal the Interaction Network and the Therapeutic Implications for Non-Small Cell Lung Cancer Patients With COVID-19

Subtractive genomics and drug repurposing strategies for targeting Streptococcus pneumoniae: insights from molecular docking and dynamics simulations

Introduction

Streptococcus pneumoniae is a Gram-positive bacterium responsible for severe infections such as meningitis and pneumonia. The increasing prevalence of antibiotic resistance necessitates the identification of new therapeutic targets. This study aimed to discover potential drug targets against S. pneumoniae using an in silico subtractive genomics approach.

Methods

The S. pneumoniae genome was compared to the human genome to identify non-homologous sequences using CD-HIT and BLASTp. Essential genes were identified using the Database of Essential Genes (DEG), with consideration for human gut microflora. Protein-protein interaction analyses were conducted to identify key hub genes, and gene ontology (GO) studies were performed to explore associated pathways. Due to the lack of crystal structure data, a potential target was modeled in silico and subjected to structure-based virtual screening.

Results

Approximately 2,000 of the 2,027 proteins from the S. pneumoniae genome were identified as non-homologous to humans. The DEG identified 48 essential genes, which was reduced to 21 after considering human gut microflora. Key hub genes included gpi, fba, rpoD, and trpS, associated with 20 pathways. Virtual screening of 2,509 FDA-approved compounds identified Bromfenac as a leading candidate, exhibiting a binding energy of -26.335 ± 29.105 kJ/mol.

Discussion

Bromfenac, particularly when conjugated with AuAgCu2O nanoparticles, has demonstrated antibacterial and anti-inflammatory properties against Staphylococcus aureus. This suggests that Bromfenac could be repurposed as a potential therapeutic agent against S. pneumoniae, pending further experimental validation. The approach highlights the potential for drug repurposing by targeting proteins essential in pathogens but absent in the host.

COVID‐19 and cancer: Dichotomy of the menacing dilemma

The coronavirus disease 2019 (COVID‐19) pandemic brought about unprecedented challenges to global healthcare systems. Among the most vulnerable populations are cancer patients, who face dilemmas due to their compromised immune systems and the intricate interplay with the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus. This comprehensive review delves into the multifaceted relationship between COVID‐19 and cancer. Through an analysis of existing literature and clinical data, this review unravels the structural intricacies of the virus and examines its profound implications for cancer patients, thereby bridging the knowledge gap between virology and oncology. The review commences with an introduction regarding the COVID‐19 pandemic and cancer. It then transitions into a detailed examination of the SARS‐CoV‐2 virus and its variants such as Alpha (PANGO lineage B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529 lineage). Subsequently, an insightful analysis of the impact of COVID‐19 on major cancer types (viz., Lung, Colon, Brain, and gastrointestinal cancer) is elaborated. Finally, the therapeutic avenues, oncological care, and management are discussed. The nexus between COVID‐19 and cancer adds a layer of complexity to patient care, emphasizing the importance of tailored approaches for those grappling with both conditions. Amid the landscape defined by the evolving viral strains, this review navigates through the multifaceted implications of COVID‐19 on cancer patients and underscores the significance of integrating virology and oncology.

Computational Biology Helps Understand How Polyploid Giant Cancer Cells Drive Tumor Success

Precision and organization govern the cell cycle, ensuring normal proliferation. However, some cells may undergo abnormal cell divisions (neosis) or variations of mitotic cycles (endopolyploidy). Consequently, the formation of polyploid giant cancer cells (PGCCs), critical for tumor survival, resistance, and immortalization, can occur. Newly formed cells end up accessing numerous multicellular and unicellular programs that enable metastasis, drug resistance, tumor recurrence, and self-renewal or diverse clone formation. An integrative literature review was carried out, searching articles in several sites, including: PUBMED, NCBI-PMC, and Google Academic, published in English, indexed in referenced databases and without a publication time filter, but prioritizing articles from the last 3 years, to answer the following questions: (i) "What is the current knowledge about polyploidy in tumors?"; (ii) "What are the applications of computational studies for the understanding of cancer polyploidy?"; and (iii) "How do PGCCs contribute to tumorigenesis?"

Ginsenoside Rg3, a promising agent for NSCLC patients in the pandemic: a large-scale data mining and systemic biological analysis

Introduction

Non-small cell lung cancer (NSCLC) patients are particularly vulnerable to the Coronavirus Disease-2019 (COVID-19). Currently, no anti-NSCLC/COVID-19 treatment options are available. As ginsenoside Rg3 is beneficial to NSCLC patients and has been identified as an entry inhibitor of the virus, this study aims to explore underlying pharmacological mechanisms of ginsenoside Rg3 for the treatment of NSCLC patients with COVID-19.

Methods

Based on a large-scale data mining and systemic biological analysis, this study investigated target genes, biological processes, pharmacological mechanisms, and underlying immune implications of ginsenoside Rg3 for NSCLC patients with COVID-19.

Results

An important gene set containing 26 target genes was built. Target genes with significant prognostic value were identified, including baculoviral IAP repeat containing 5 (BIRC5), carbonic anhydrase 9 (CA9), endothelin receptor type B (EDNRB), glucagon receptor (GCGR), interleukin 2 (IL2), peptidyl arginine deiminase 4 (PADI4), and solute carrier organic anion transporter family member 1B1 (SLCO1B1). The expression of target genes was significantly correlated with the infiltration level of macrophages, eosinophils, natural killer cells, and T lymphocytes. Ginsenoside Rg3 may benefit NSCLC patients with COVID-19 by regulating signaling pathways primarily involved in anti-inflammation, immunomodulation, cell cycle, cell fate, carcinogenesis, and hemodynamics.

Conclusions

This study provided a comprehensive strategy for drug discovery in NSCLC and COVID-19 based on systemic biology approaches. Ginsenoside Rg3 may be a prospective drug for NSCLC patients with COVID-19. Future studies are needed to determine the value of ginsenoside Rg3 for NSCLC patients with COVID-19.