WaterMap guided structure-based virtual screening for acetylcholinesterase inhibitors

Identification of 5-nitroindazole as a multitargeted inhibitor for CDK and transferase kinase in lung cancer: a multisampling algorithm-based structural study

Lung cancer is the second most common cancer, which is the leading cause of cancer death worldwide. The FDA has approved almost 100 drugs against lung cancer, but it is still not curable as most drugs target a single protein and block a single pathway. In this study, we screened the Drug Bank library against three major proteins- ribosomal protein S6 kinase alpha-6 (6G77), cyclic-dependent protein kinase 2 (1AQ1), and insulin-like growth factor 1 (1K3A) of lung cancer and identified the compound 5-nitroindazole (DB04534) as a multitargeted inhibitor that potentially can treat lung cancer. For the screening, we deployed multisampling algorithms such as HTVS, SP and XP, followed by the MM\GBSA calculation, and the study was extended to molecular fingerprinting analysis, pharmacokinetics prediction, and Molecular Dynamics simulation to understand the complex's stability. The docking scores against the proteins 6G77, 1AQ1, and 1K3A were - 6.884 kcal/mol, - 7.515 kcal/mol, and - 6.754 kcal/mol, respectively. Also, the compound has shown all the values satisfying the ADMET criteria, and the fingerprint analysis has shown wide similarities and the water WaterMap analysis that helped justify the compound's suitability. The molecular dynamics of each complex have shown a cumulative deviation of less than 2 Å, which is considered best for the biomolecules, especially for the protein-ligand complexes. The best feature of the identified drug candidate is that it targets multiple proteins that control cell division and growth hormone mediates simultaneously, reducing the burden of the pharmaceutical industry by reducing the resistance chance.

The application of WaterMap-guided structure-based virtual screening in novel drug discovery

INTRODUCTION

Nowadays, it is widely accepted that water molecules play a key role in binding a ligand to a molecular target. Neglecting water molecules in the process of molecular recognition was the result of several failures of the structure-based drug discovery campaigns. The application of WaterMap, in particular WaterMap-guided molecular docking, enables the reasonably accurate and quick description of the location and energetics of water molecules at the ligand-protein interface.

AREAS COVERED

In this review, the authors shortly discuss the importance of water in drug design and discovery and provide a brief overview of the computational approaches used to predict the solvent-related effects for the purposes of presenting WaterMap in the context of other available techniques and tools. A concise description of WaterMap concept is followed by the presentation of WaterMap-assisted virtual screening literature published between 2013 and 2023.

EXPERT OPINION

In recent years, WaterMap software has been extensively used to support structure-based drug design, in particular structure-based virtual screening. Indeed, it is a useful tool to rescore docking results considering water molecules in the binding pocket. Although WaterMap allows for the consideration of the dynamic behavior of water molecules in the binding site, for best accuracy, its application in conjunction with other techniques such as molecular mechanics-generalized Born surface area of FEP (Free Energy Perturbation) is recommended.

Zirconium-Based Metal-Organic Frameworks as Acriflavine Cargos in the Battle against Coronaviruses─A Theoretical and Experimental Approach

In this study, we present a complementary approach for obtaining an effective drug, based on acriflavine (ACF) and zirconium-based metal-organic frameworks (MOFs), against SARS-CoV-2. The experimental results showed that acriflavine inhibits the interaction between viral receptor-binding domain (RBD) of spike protein and angiotensin converting enzyme-2 (ACE2) host receptor driving viral cell entry. The prepared ACF@MOF composites exhibited low (MOF-808 and UiO-66) and high (UiO-67 and NU-1000) ACF loadings. The drug release profiles from prepared composites showed different release kinetics depending on the local pore environment. The long-term ACF release with the effective antiviral ACF concentration was observed for all studied ACF@MOF composites. The density functional theory (DFT) calculations allowed us to determine that π-π stacking together with electrostatic interaction plays an important role in acriflavine adsorption and release from ACF@MOF composites. The molecular docking results have shown that acriflavine interacts with several possible binding sites within the RBD and binding site at the RBD/ACE2 interface. The cytotoxicity and ecotoxicity results have confirmed that the prepared ACF@MOF composites may be considered potentially safe for living organisms. The complementary experimental and theoretical results presented in this study have confirmed that the ACF@MOF composites may be considered a potential candidate for the COVID-19 treatment, which makes them good candidates for clinical trials.