Structural insights into pharmacophore-assisted in silico identification of protein-protein interaction inhibitors for inhibition of human toll-like receptor 4 - myeloid differentiation factor-2 (hTLR4-MD-2) complex

Helicobacter pylori antigens as immunomodulators of immune system

Helicobacter pylori (H. pylori) is one of the most prevalent human pathogens and the leading cause of chronic infection in almost half of the population in the world (~59%). The bacterium is a major leading cause of chronic gastritis, gastric and duodenal ulcers, and two type of malignancies, gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. Despite the immune responses mounted by the host, the bacteria are not cleared from the body resulting in a chronic infection accompanied by a chronic inflammation. Herein, a review of the literature discussing H. pylori antigens modulating the immune responses is presented. The mechanisms that are involved in the modulation of innate immune response, include modulation of recognition by pattern recognition receptors (PRRs) such as modulation of recognition by toll like receptors (TLR)4 and TLR5, modulation of phagocytic function, and modulation of phagocytic killing mediated by reactive oxygen species (ROS) and nitric oxide (NO). On the other hands, H. pylori modulates acquired immune response by the induction of tolerogenic dendritic cells (DCs), modulation of apoptosis, induction of regulatory T cells, modulation of T helper (Th)1 response, and modulation of Th17 response.

Inhibition of the TLR4/NF-κB pathway promotes the polarization of LPS-induced BV2 microglia toward the M2 phenotype

This study aimed to investigate whether the inhibition of the TLR4/NF-κB pathway can promote lipopolysaccharide (LPS)-induced microglial polarization from the M1 to M2 phenotype, and thus exert neuroprotection. LPS-induced microglia were used as a model for inflammation in vitro. TLR4-specific inhibitor resatorvid (TAK-242) and NF-κB inhibitor pyrrolidine dithiocarbamate (PDTC) were used to verify the effect of the TLR4/NF-κB pathway on microglia activation and polarization. Cell proliferation was measured by cell counting, and nitric oxide (NO) and reactive oxygen species (ROS) release was measured using the Griess reagent and ROS kit, respectively. Immunofluorescence and RT-qPCR analyses were used to detect the expression of microglial activation markers, phenotypic markers, related pathway molecules, and inflammatory factors. TLR4 specific inhibitor TAK-242 and NF-κB inhibitor PDTC alleviated LPS-induced microglia over-activation by inhibiting the TLR4/NF-κB pathway, and reduced LPS-stimulated cell proliferation and the release of NO, ROS, TNF-a, and IL-6 and IL-1β. Meanwhile, TAK-242 and PDTC promoted LPS-induced polarization of microglia from M1 to M2 phenotype, decreased the expression of microglial activation marker Iba1 and M1 phenotypic markers (TNF-a and CD86), and increased the expression of M2 phenotypic markers (Arg-1 and CD206). The mechanism may be related to inhibiting the TLR4/NF-κB pathway. The inhibition of the TLR4/NF-κB pathway can promote LPS-induced polarization of BV2 microglia from M1 phenotype to M2 phenotype.

Mechanisms of NLRP3 inflammasome activation and the development of peptide inhibitors

The Nucleotide-binding domain leucine-rich repeat and pyrin domain containing receptor 3 (NLRP3), a member of the nucleotide-binding oligomerization domain (NOD) like receptors (NLRs) family, plays an important role in the innate immune response against pathogen invasions. NLRP3 inflammasome consisting of NLRP3 protein, the adapter protein apoptosis-associated speck-like protein containing a caspase recruitment domain (CARD) (ASC), and the effector protein pro-caspase-1, is central to this process. Upon activation, NLRP3 inflammasome initiates the release of inflammatory cytokines and triggers a form of cell death known as pyroptosis. Dysregulation or inappropriate activation of NLRP3 has been implicated in various human diseases, including type 2 diabetes, colitis, depression, and gout. Consequently, understanding the mechanism underlying NLRP3 inflammasome activation is critical for the development of therapeutic drugs. In the pursuit of potential therapeutic agents, peptides present several advantages over small molecules. They offer higher selectivity, increased potency, reduced toxicity, and fewer off-target effects. The advancements in molecular biology have expanded the opportunities for applying peptides in medicine, unlocking their vast medical potential. This review begins by providing a comprehensive summary of recent research progress regarding the mechanisms governing NLRP3 inflammasome activation. Subsequently, we offer an overview of current peptide inhibitors capable of modulating the NLRP3 inflammasome activation pathway.

Rational approaches to discover SARS-CoV-2/ACE2 interaction inhibitors: Pharmacophore-based virtual screening, molecular docking, molecular dynamics and binding free energy studies

The lack of effective treatment remains a bottleneck in combating the current coronavirus family pandemic, particularly coronavirus 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The infection of host cells by SARS-CoV-2 is mediated by the binding of its receptor-binding domain (RBD) on the spike (S) glycoprotein to the host angiotensin-converting enzyme (ACE2) receptor. As all developed and available vaccines against COVID-19 do not provide long-term immunity, the creation of an effective drug for the treatment of COVID-19 is necessary and cannot be ignored. Therefore, the aim of this study is to present a computational screening method to identify potential inhibitor candidates with a high probability of blocking the binding of RBD to the ACE2 receptor. Pharmacophore mapping, molecular docking, molecular dynamics (MD) simulations, and binding free-energy analyses were performed to identify potential inhibitor candidates against ACE2/SARS-CoV-2. In conclusion, we propose the compound PubChem-84280085 as a potential inhibitor of protein-protein interactions to disrupt the binding of the SARS-CoV-2-RBD to the ACE2 receptor.

Identification and Molecular Mechanism of Novel Immunomodulatory Peptides from Gelatin Hydrolysates: Molecular Docking, Dynamic Simulation, and Cell Experiments

The purpose of this study was to identify donkey-hide gelatin-derived immunomodulatory peptides targeting Toll-like receptor 4-myeloid differentiation 2 (TLR4-MD2) and elucidate their binding modes using physicochemical property prediction, molecular docking, molecular dynamics simulations, and in vitro cell experiments. After hydrolyzing gelatin, 519 peptides were identified by liquid chromatography-tandem mass spectrometry. Peptides VQLSGEEK and GFSGLDGAKG bound to TLR4-MD2 with high binding affinity. In TLR4-MD2, Arg90, Ser118, Phe126, Tyr131, and Arg264 were key residues involved in the binding of these peptides. The RMSD and R_g values demonstrated that VQLSGEEK-TLR4-MD2 and GFSGLDGAKG-TLR4-MD2 complexes had stable and compact conformations. VQLSGEEK and GFSGLDGAKG were found to increase the cell viability and phagocytic activity of RAW264.7 macrophages; significantly promote the production of cytokines TNF-α, IL-1β, and IL-6 in cells; and inhibit the overproduction of nitric oxide (NO) and cytokines in lipopolysaccharide (LPS)-induced RAW264.7 cells. Our results provided preliminary evidence that VQLSGEEK and GFSGLDGAKG could function as two-way immunomodulatory peptides with immunostimulatory and anti-inflammatory activities.

Toll-like receptors in cardiac hypertrophy

Toll-like receptors (TLRs) are a family of pattern recognition receptors (PRRs) that can identify pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs). TLRs play an important role in the innate immune response, leading to acute and chronic inflammation. Cardiac hypertrophy, an important cardiac remodeling phenotype during cardiovascular disease, contributes to the development of heart failure. In previous decades, many studies have reported that TLR-mediated inflammation was involved in the induction of myocardium hypertrophic remodeling, suggesting that targeting TLR signaling might be an effective strategy against pathological cardiac hypertrophy. Thus, it is necessary to study the mechanisms underlying TLR functions in cardiac hypertrophy. In this review, we summarized key findings of TLR signaling in cardiac hypertrophy.

Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review

Lipopolysaccharide (LPS) is the primary component of the outer leaflet of Gram-negative bacterial outer membranes. LPS elicits an overwhelming immune response during infection, which can lead to life-threatening sepsis or septic shock for which no suitable treatment is available so far. As a result of the worldwide expanding multidrug-resistant bacteria, the occurrence and frequency of sepsis are expected to increase; thus, there is an urge to develop novel strategies for treating bacterial infections. In this regard, gaining an in-depth understanding about the ability of LPS to both stimulate the host immune system and interact with several molecules is crucial for fighting against LPS-caused infections and allowing for the rational design of novel antisepsis drugs, vaccines and LPS sequestration and detection methods. Molecular dynamics (MD) simulations, which are understood as being a computational microscope, have proven to be of significant value to understand LPS-related phenomena, driving and optimizing experimental research studies. In this work, a comprehensive review on the methods that can be combined with MD simulations, recently applied in LPS research, is provided. We focus especially on both enhanced sampling methods, which enable the exploration of more complex systems and access to larger time scales, and free energy calculation approaches. Thereby, apart from outlining several strategies for surmounting LPS-caused infections, this work reports the current state-of-the-art of the methods applied with MD simulations for moving a step forward in the development of such strategies.

TLR4-Targeting Therapeutics: Structural Basis and Computer-Aided Drug Discovery Approaches

The integration of computational techniques into drug development has led to a substantial increase in the knowledge of structural, chemical, and biological data. These techniques are useful for handling the big data generated by empirical and clinical studies. Over the last few years, computer-aided drug discovery methods such as virtual screening, pharmacophore modeling, quantitative structure-activity relationship analysis, and molecular docking have been employed by pharmaceutical companies and academic researchers for the development of pharmacologically active drugs. Toll-like receptors (TLRs) play a vital role in various inflammatory, autoimmune, and neurodegenerative disorders such as sepsis, rheumatoid arthritis, inflammatory bowel disease, Alzheimer's disease, multiple sclerosis, cancer, and systemic lupus erythematosus. TLRs, particularly TLR4, have been identified as potential drug targets for the treatment of these diseases, and several relevant compounds are under preclinical and clinical evaluation. This review covers the reported computational studies and techniques that have provided insights into TLR4-targeting therapeutics. Furthermore, this article provides an overview of the computational methods that can benefit a broad audience in this field and help with the development of novel drugs for TLR-related disorders.

Computational Approaches for Elucidating Protein-Protein Interactions in Cation Channel Signaling

BACKGROUND

The lipid bilayer of the plasma membrane is impermeable to ions, yet changes in the flux of ions across the cell membrane are critical regulatory events in cells. Because of their regulatory roles in a range of physiological processes, such as electrical signaling in muscles and neurons, to name a few, these proteins are one of the most important drug targets.

OBJECTIVE

This review mainly focused on the computational approaches for elucidating proteinprotein interactions in cation channel signaling.

DISCUSSION

Due to continuously advanced facilities and technologies in computer sciences, the physical contacts of macromolecules of channel structures have been virtually visualized. Indeed, techniques like protein-protein docking, homology modeling, and molecular dynamics simulation are valuable tools for predicting the protein complex and refining channels with unreleased structures. Undoubtedly, these approaches will greatly expand the cation channel signaling research, thereby speeding up structure-based drug design and discovery.

CONCLUSION

We introduced a series of valuable computational tools for elucidating protein-protein interactions in cation channel signaling, including molecular graphics, protein-protein docking, homology modeling, and molecular dynamics simulation.