Discovery of Potential Chemical Probe as Inhibitors of CXCL12 Using Ligand-Based Virtual Screening and Molecular Dynamic Simulation

6'-O-Caffeoylarbutin from Quezui Tea: A Highly Effective and Safe Tyrosinase Inhibitor

Tyrosinase is vital in fruit and vegetable browning and melanin synthesis, crucial for food preservation and pharmaceuticals. We investigated 6'-O-caffeoylarbutin's inhibition, safety, and preservation on tyrosinase. Using HPLC, we analyzed its effect on mushroom tyrosinase and confirmed reversible competitive inhibition. UV_vis and fluorescence spectroscopy revealed a stable complex formation with specific binding, causing enzyme conformational changes. Molecular docking and simulations highlighted strong binding, enabled by hydrogen bonds and hydrophobic interactions. Cellular tests showed growth reduction of A375 cells with mild HaCaT cell toxicity, indicating favorable safety. Animal experiments demonstrated slight toxicity within safe doses. Preservation trials on apple juice showcased 6'-O-caffeoylarbutin's potential in reducing browning. In essence, this study reveals intricate mechanisms and applications of 6'-O-caffeoylarbutin as an effective tyrosinase inhibitor, emphasizing its importance in food preservation and pharmaceuticals. Our research enhances understanding in this field, laying a solid foundation for future exploration.

Dronabinol as an answer to flavivirus infections: an in-silico investigation

Flavivirus infections are common in several parts of the world. Two major types of flaviviruses are dengue and zika viruses. Both these two viral infections have caused many fatalities around the world. There is an absence of a vaccine and an effective medication against these viruses. In this study, we analyzed the ability of dronabinol to act as a potential cure against these viral infections. We performed the docking of dronabinol with several viral proteins followed by molecular dynamics simulation, MM/PBSA and PCA analysis. We checked the ability of the polyphenol dronabinol to interfere with the binding of viral helicases to their cellular targets. We performed 2 D-QSAR studies, drug likeliness, ADMET and target prediction studies. From our study, we observed that dronabinol had the best docking ability against the helicase proteins of dengue and zika. Molecular dynamics simulation and MM/PBSA investigation confirmed the stability of the binding while PCA investigation showed a lowering of molecular motions in response to dronabinol docking to the helicases. Dronabinol interfered in the binding of the helicases to RNA. 2 D QSAR studies revealed a low IC50 value for dronabinol. Dronabinol showed favorable drug-likeness, ADMET properties and target prediction results. Thus we propose dronabinol be further investigated in-vitro as a cure against dengue and zika virus infections.Communicated by Ramaswamy H. Sarma.

Identification of common genes in obesity and cancer through network interaction and targeting those genes by virtual screening approach

Obesity may have an effect on cancer outcomes, resulting in global inequalities in cancer survival and death. Microarray data analysis was done to identify differentially expressed genes (DEGs) in obese and cancer patients. Total 1977 differentially expressed genes among obesity and gastric cancer, breast cancer, pancreatic cancer, and colorectal cancer were used to build a gene interaction network, which was then analyzed by using Cytoscape software. It has been identified that JUN, CXCL12, and LEP genes show a higher degree and stress, and play an important role in obesity and cancer progression. Further, CXCL12 and LEP were taken for virtual screening study with coumarin and its derivatives to develop a drug against obesity and cancer. The interactions of CXCL12 and LEP with coumarins were studied by molecular docking and it shows good interaction as well as docking score as compared to the standard one. The ADME properties were predicted to check the drug-likeness activity of coumarins and the most of the drug-likeness activities are in admire range. The Binding free energy of the docked complex was calculated by performing MM-GBSA. The molecular docking, ADME properties prediction, and MM-GBSA was performed on Maestro 12.6. The top docked score compounds were further subjected to molecular dynamic simulation to check the stability by using GROMACS. The MM-PBSA study was performed to calculate the binding energy components as well as the energy contributions of specific amino acids. The resultant compounds could be a potent anti-obesity and anti-cancer drug.Communicated by Ramaswamy H. Sarma.

Revolutionizing antiretroviral therapy for human immunodeficiency virus/AIDS: A computational approach using molecular docking, virtual screening, and 3D pharmacophore building to address therapeutic failure and propose highly effective candidates

OBJECTIVES

In the context of human immunodeficiency virus (HIV) treatment, the emergence of therapeutic failures with existing antiretroviral drugs presents a significant challenge. This study aims to employ advanced molecular modeling techniques to identify potential alternatives to current antiretroviral agents.

METHODS

The study focuses on three essential classes of antiretroviral drugs: nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs). Computational analyses were performed on a database of 3,343,652 chemical molecules to evaluate their binding affinities, pharmacokinetic properties, and interactions with viral reverse transcriptase and protease enzymes. Molecular docking, virtual screening, and 3D pharmacophore modeling were utilized to identify promising candidates.

RESULTS

Molecular docking revealed compounds with high binding energies and strong interactions at the active sites of target enzymes. Virtual screening narrowed down potential candidates with favorable pharmacological profiles. 3D pharmacophore modeling identified crucial structural features for effective binding. Overall, two molecules for class 1, 7 molecules for class 2, and 2 molecules for class 3 were selected. These compounds exhibited robust binding affinities, interactions with target enzymes, and improved pharmacokinetic properties, showing promise for more effective HIV treatments in cases of therapeutic failures.

CONCLUSION

The combination of molecular docking, virtual screening, and 3D pharmacophore modeling yielded lead compounds that hold potential for addressing HIV therapeutic failures. Further experimental investigations are essential to validate the efficacy and safety of these compounds, with the ultimate goal of advancing toward clinical applications in HIV management.

Can polyoxometalates (POMs) prevent of coronavirus 2019-nCoV cell entry? Interaction of POMs with TMPRSS2 and spike receptor domain complexed with ACE2 (ACE2-RBD): Virtual screening approaches

The unexpected appearance and global spread of COVID-19 create significant difficulties for healthcare systems and present an unusual challenge for the fast discovery of medicines to combat this fatal disease. Screening metallodrugs libraries from the medicinal inorganic chemistry society may expand the studied ‘chemical space’ and improve the probability of discovering effective anti-COVID drugs, including polyoxometalates. POMs are an oxygen-rich family of inorganic cluster systems that have previously been tested for antiviral action against different types of viruses. Human angiotensin-converting enzyme 2 (ACE2), human transmembrane protease serine 2 (TMPRSS2), and the SARS-CoV-2 spike glycoprotein are required for host cell-mediated viral entrance. Targeting these proteins demonstrates potential possibilities for preventing infections and transmissions in the initial stage. As a result, POMs with known antiviral effects were investigated for this purpose using molecular docking and dynamic simulations. This research shows that POMs can prevent SARS CoV-2 from entering cells by blocking TMPRSS2, which SARS-CoV-2 uses for spike glycoprotein priming. They may also engage with ACE2 and the spike glycoprotein and disrupt their binding by blocking the active sites. We think that a thorough investigation of POMs as possible anti-COVID-19 drugs will provide significant opportunities.