Marine-Derived Compounds for CDK5 Inhibition in Cancer: Integrating Multi-Stage Virtual Screening, MM/GBSA Analysis and Molecular Dynamics Investigations

Cyclin-dependent kinase 5 (CDK5) plays a crucial role in various biological processes, including immune response, insulin secretion regulation, apoptosis, DNA (deoxyribonucleic acid) damage response, epithelial-mesenchymal transition (EMT), cell migration and invasion, angiogenesis, and myogenesis. Overactivation of CDK5 is associated with the initiation and progression of cancer. Inhibiting CDK5 has shown potential in suppressing cancer development. Despite advancements in CDK5-targeted inhibitor research, the range of compounds available for clinical and preclinical trials remains limited. The marine environment has emerged as a prolific source of diverse natural products with noteworthy biological activities, including anti-cancer properties. In this study, we screened a library of 47,450 marine natural compounds from the comprehensive marine natural product database (CMNPD) to assess their binding affinity with CDK5. Marine compounds demonstrating superior binding affinity compared to a reference compound were identified through high-throughput virtual screening, standard precision and extra-precision Glide docking modes. Refinement of the selected molecules involved evaluating molecular mechanics-generalized born surface area (MM/GBSA) free binding energy. The three most promising compounds, (excoecariphenol B, excoecariphenol A, and zyzzyanone B), along with the reference, exhibiting favorable binding characteristics were chosen for molecular dynamics (MD) simulations for 200 nanoseconds. These compounds demonstrated interaction stability with the target during MD simulations. The marine compounds identified in this study hold potential as effective CDK5 inhibitors and warrant subsequent experimental validation.

Potential Therapeutic Target and Vaccines for SARS-CoV-2

The coronavirus has become the most interesting virus for scientists because of the recently emerging deadly SARS-CoV-2. This study aimed to understand the behavior of SARS-CoV-2 through the comparative genomic analysis with the closest one among the seven species of coronavirus that infect humans. The genomes of coronavirus species that infect humans were retrieved from NCBI, and then subjected to comparative genomic analysis using different bioinformatics tools. The study revealed that SARS-CoV-2 is the most similar to SARS-CoV among the coronavirus species. The core genes were shared by the two genomes, but there were some genes, found in one of them but not in both, such as ORF8, which is found in SARS-CoV-2. The ORF8 protein of SARS-CoV-2 could be considered as a good therapeutic target for stopping viral transmission, as it was predicted to be a transmembrane protein, which is responsible for interspecies transmission. This is supported by the molecular interaction of ORF8 with both the ORF7 protein, which contains a transmembrane domain that is essential to retaining the protein in the Golgi compartment, and the S protein, which facilitates the entry of the coronavirus into host cells. ORF1ab, ORF1a, ORF8, and S proteins of SARS-CoV-2 could be immunogenic and capable of evoking an immune response, which means that these four proteins could be considered a potential vaccine source. Overall, SARS-CoV-2 is most related to SARS-CoV. ORF8 could be considered a potential therapeutic target for stopping viral transmission, and ORF1ab, ORF1a, ORF8, and the S proteins of SARS-CoV-2 could be utilized as a potential vaccine source.

The effect of Astaxanthin on Experimentally Induced Diabetic Kidney Disease

Aim: To identify the potential renal protective effect produced by astaxanthin on streptozotocin-produced diabetic kidney disease in rats. Study Design: Male Wistar rats (n=60) were separated into six groups, control, diabetic (streptozotocin 45 mg/kg single intraperitoneal injection), diabetic + ramipril (1 mg/kg oral gavage), diabetic + astaxanthin (10mg/kg oral gavage), diabetic + astaxanthin (50 mg/kg oral gavage), and astaxanthin-alone (50 mg/kg oral gavage) group. Place and Duration of Treatment: Department of Pharmacology, College of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia. Duration of treatment was eight weeks. Methodology: Fasting blood glucose, and symptoms of diabetes were evaluated weekly. Kidneys were evaluated by measuring serum creatinine level, kidney index, and hematoxylin and eosin staining. Results: Eight-week astaxanthin treatment (50 mg/kg) in streptozotocin-produced diabetic kidney disease in rats significantly alleviated the diabetic symptoms (p = 0.05), and the decrease in body weight (P = .05) compared to nontreated diabetic rats. Nonetheless, the same dose produced a nonsignificant decline in fasting blood glucose level contrasted to diabetic rats (P = .45). Kidney index and serum creatinine of diabetic rats were significantly attenuated by both 10 and 50 mg/kg astaxanthin doses (P = .05). Additionally, renal architecture was preserved by high-dose astaxanthin treatment compared to nontreated diabetic rats. Conclusion: Astaxanthin could protect against kidney damage associated with diabetes. Nevertheless, the impact of astaxanthin on biological markers of kidney damage in diabetes and the molecular pathways implicated in diabetic kidney disease requires additional investigation.