Recent Advances in Computer-aided Antiviral Drug Design Targeting HIV-1 Integrase and Reverse Transcriptase Associated Ribonuclease H

Computational study on the mechanism of small molecules inhibiting NLRP3 with ensemble docking and molecular dynamic simulations

NLRP3 (Nucleotide-binding oligomerization domain, LRR and pyrin domain-containing protein 3) is a pivotal regulator of inflammation, with strong implications in gout, neurodegenerative diseases, and various inflammatory conditions. Consequently, the exploration of NLRP3 inhibitors is of great significance for the treatment of diseases. MCC950, NP3-146, compound (3), and YQ128 are four highly bioactive NLRP3 inhibitors that show great potential; however, their mechanism of action is currently limited to targeting the ATP binding region (NACHT site) of the NLRP3 protein. To gain deeper insights into the defining features of NLRP3 inhibitors and to develop more potent inhibitors, it is imperative to elucidate the interaction mechanism between NLRP3 and these inhibitors. In this study, we employ a comprehensive computational approach to investigate the binding mechanism between NLRP3 and representative inhibitors. Utilizing the molecular mechanics/generalized Born surface area (MM/GBSA) method, we calculate the binding free energy and pinpoint the key residues involved in the binding of the four inhibitors to NLRP3. The decomposition of binding free energy by the MM/GBSA method reveals that the residues Val71, Arg195, Ile255, Phe419, Arg422, and Met505, situated around the binding pocket, play a crucial role in conferring the high bioactivity of NLRP3 inhibitors. Furthermore, pharmacophore analysis of the four NLRP3 complexes indicates that the primary interaction between the inhibitors and NLRP3 was mainly hydrophobic interaction. Our study provides a profound understanding of the interaction mechanism between NLRP3 and its inhibitors, identifies the key residues involved, and provides theoretical guidance for the design of more efficient NLRP3 inhibitors.

Overcoming Solubility Challenges: Self-emulsifying Systems for Enhancing the Delivery of Poorly Water-Soluble Antiviral Drugs

The primary goal of drug formulation is to improve a drug's bioavailability in the body. However, poorly water-soluble drugs present challenging issues related to their solubility and bioavailability factors. Emerging technologies, such as lipid-based drug delivery systems, including micro- or nanoemulsifying drug delivery systems, have become increasingly relevant to address the above challenges. This review presents a thorough overview of self-emulsifying drug delivery systems (SEDDS). It covers the properties, principles, self-emulsification mechanism, formulation strategies, and characterization methods of SEDDS. This review also addresses the delivery of antiviral agents through SEDDS. Moreover, it summarizes the marketed formulations of SEDDS consisting of antiviral agents. This review offers a comprehensive and valuable resource for future perspectives on SEDDS and their potential applications in antiviral drug delivery.

Synthesis, virtual screening and computational approach of a quinoxaline derivative as potent anti-HIV agent targeting the reverse transcriptase enzyme

Infection by the human immunodeficiency virus still represents a continuous serious concern and a global threat to human health. Due to the appearance of multi-resistant virus strains and the serious adverse side effects of the antiretroviral therapy administered, there is an urgent need for the development of new treatment agents that are more active, less toxic, and with increased tolerability to mutations. Quinoxaline derivatives are a class of heterocyclic compounds with a wide range of organic and remedial applications. In addition, they are known to significantly inhibit HIV reverse transcriptase (RT) and HIV replication in cell cultures. For these reasons, we are investigating the synthesis and computational studies of quinoxaline derivatives with a focus on their effects on the HIV RT enzyme, and we present here the structure of one such molecule, methyl 2-[(2E)-3-oxo-1,2,3,4-tetrahydroquinoalin-2-ylidene] acetate, which was confirmed by X-ray diffraction studies. In the crystal, N-H···O and C-H···O hydrogen bonds form ribbons whose mean planes are inclined to (111) by 25.69(8)°. The ribbons are formed into stacks by C-H···π(ring) interactions and π-stacking interactions between carbonyl groups. The Hirshfeld surface map allows us to understand the nature of interactions in the contribution to crystal packing. A density functional theory (DFT) calculation was performed to optimize the geometrical parameters and then they were compared with the solid-state phase. The molecular electrostatic potential map displays reactive sites on the surface, which are responsible for intermolecular interaction in the chemical species. Computational molecular docking, in addition to molecular dynamics simulations and MMGB/PBSA binding energy techniques, was used to assess the affinity of the molecule for the HIV reverse transcriptase enzyme. The new quinoxaline derivative is more powerful in terms of binding affinity and binding conformation stability with the HIV reverse transcriptase enzyme, which suggests the molecule is a good candidate for further biological optimization.Communicated by Ramaswamy H. Sarma.

HCV genotype-specific drug discovery through structure-based virtual screening

Hepatitis C Virus (HCV) poses great threat worldwide, and is a major cause for liver cancer. HCV genome encodes polyprotein that is subsequently cleaved into independently functioning proteins, which spread viral infection in host. The Non-Structural 3 (NS3) protease is responsible for cleaving the polyprotein, and may serve as a potential drug target. Since HCV has seven genotypes, the available drugs are predominantly designed for genotype 1 (GT1), and others prevalent in Europe. Consequently, these drugs lose efficacy when they are used for different genotypes. The current perspective study aims to find potential drug candidate against genotype 3 (GT3), prevalent in South Asia. The current study employed molecular docking technique and in silico ADME prediction tool to highlight potentially active compounds against HCV NS3 GT3. The study revealed Li_PIO_114 and Li_PIH_191 as potential lead compounds, as suggested by their docking score and ADME properties. These two compounds could be further optimized to improve their drug likeliness for curing HCV GT3.