Blocking the interaction between S100A9 protein and RAGE V domain using S100A12 protein

Virtual Probing on the Influence of Ca2+ and Zn2+ Bound S100A8 and S100A9 Proteins Towards their Interaction Against Pattern Recognition Receptors Aggravating Rheumatoid Arthritis

Danger-associated molecular patterns (DAMPs) are released on the onset of tissue injury or death, which tend to trigger innate immunity and regulate various immune pathways. Among the various DAMP molecules, S100A8 and S100A9 belonging to Ca2+ binding proteins with EF-hands and Zn2+ ion binding sites have been implicated in aggravating the pathogenesis of rheumatoid arthritis (RA), upon interaction with pattern recognition receptors (PRR) such as TLR4, RAGE and CD36 receptors. Thus, the present study aims to assess the effect of Ca2+ or Zn2+ ions on the interaction of S100A8 and S100A9 proteins towards the PRRs. Protein-protein interaction analysis showed that the TLR4-S100A8Ca2+Zn2+, TLR4-S100A8 Zn2+, RAGE-S100A8/A8Zn2+, RAGE-S100A8/A8Ca2+, CD36-S100A8Ca2+, and CD36-S100A9/A9Ca2+ showed higher affinity against each other. The 100 ns molecular dynamics simulation showed that the TLR4-S100A8Ca2+, RAGE-S100A8/A8Ca2+ and CD36-S100A8Ca2+ complexes showed minimal fluctuations in their trajectory indicating that Ca2+ bound complexes were more stable than the other complexes. Furthermore, SPR analysis showed that S100A9 exhibited higher binding affinity towards PRRs in the presence of Ca2+ and Zn2+ ions. Considering the fact that physiological levels of both Ca2+ and Zn2+ ions play a critical role in the binding of S100A8 and S100A9 proteins against the PRRs, it can be emphasized that the S100A9 and RAGE receptors could be the critical players in the RA pathogenesis due to its impeccable binding towards the PRRs in the presence of both Ca2+ and Zn2+ ions. Nonetheless, further in vivo, and in vitro studies are imperative to validate these findings and identify potential targets for RA treatment.

Binding of Pro-Inflammatory Proteins S100A8 or S100A9 to Amyloid-β Peptide Suppresses Its Fibrillation

Human serum albumin (HSA) is a natural depot of amyloid-β peptide (Aβ), a key player in Alzheimer's disease (AD). HSA and pro-inflammatory Ca2+-binding proteins S100A8 and S100A9 are involved in Aβ metabolism and its deposition in the brain, serving as probable triggers and therapeutic targets in AD, but their interplay with regard to Aβ binding/fibrillation is unclear. To this end, here we explore the in vitro binding of Ca2+-bound S100A8 or S100A9 to monomeric Aβ and the influence of the S100 proteins on Aβ fibrillation. The equilibrium dissociation constants of the complexes of dimeric S100A8/S100A9 with Aβ40/42 estimated by biolayer interferometry are 1-5 µM. S100A8 and S100A9 interfere with HSA binding to Aβ. Thioflavin T assay and electron microscopy data show that micromolar S100A8/S100A9 inhibit Aβ40 fibrillation, and the inhibitory effect of S100A8 exceeds that for HSA. The competition for Aβ between HSA and S100A8/S100A9 may contribute to the Aβ-HSA imbalance in the pro-inflammatory conditions in AD.

In silico pentapeptide design for the inhibition between S100 calcium-binding A9 (S100A9) proteins

CONTEXT

S100 calcium-binding protein A9 (S100A9) is easily assembled into amyloid aggregates in solution. These amyloid aggregates cause retinal toxicity and act as an attachment core for Aβ fibrillar plaques that contribute to Alzheimer's disease progression. The overexpression of S100A9 is also noticed in various malignancies. Therefore, the S100A9 amyloid formation inhibition is of significant interest. In comparison with small-molecule drugs, short peptides demonstrate higher specificity, potency, and biosafety. Hence, it could be beneficial to identify potential peptides to inhibit or disrupt S100A9 amyloid aggregation. Typical peptide design and identification via experimental means requires extensive preparation procedures and is limited to random selection of peptides. Virtual screening therefore offers an unbiased, higher throughput, and economically efficient approach in peptide drug development. Here, we reported in silico pentapeptide design against S100A9 and studied the interaction of pentapeptide with S100A9 that leads to the binding of the peptide with S100A9.

METHOD

Docking simulation resulted in three top binding free energy tripeptides (WWF, WPW, and YWF) with comparable affinity towards a known S100A9 inhibitor (polyphenol oleuropein aglycone; OleA). Subsequently, pentapeptides that consist of the three core tripeptides were selected from a pre-constructed pentapeptide library for further evaluation with docking simulation. Based on best docked binding free energy, two pentapeptides (WWPWH and WPWYW) were selected and subjected to 500 ns molecular dynamics (MD) simulation to study the important features that lead to the binding with S100A9. MMGBSA binding free energy calculation estimated - 30.38, - 24.58, and - 30.31 kcal/mol for WWPWH, WPWYW, and OleA, respectively. The main driving force for pentapeptide-S100A9 recognition was contributed by the electrostatic interaction. The results demonstrate that at in silico level, this workflow is able to design potential pentapeptides that are comparable with OleA and might be the lead molecule for future use to disaggregate S100A9 fibrils.

S100A8 and S100A9 in Cancer

S100A8 and S100A9 are Ca²⁺ binding proteins that belong to the S100 family. Primarily expressed in neutrophils and monocytes, S100A8 and S100A9 play critical roles in modulating various inflammatory responses and inflammation-associated diseases. Forming a common heterodimer structure S100A8/A9, S100A8 and S100A9 are widely reported to participate in multiple signaling pathways in tumor cells. Meanwhile, S100A8/A9, S100A8, and S100A9, mainly as promoters, contribute to tumor development, growth and metastasis by interfering with tumor metabolism and the microenvironment. In recent years, the potential of S100A8/A9, S100A9, and S100A8 as tumor diagnostic or prognostic biomarkers has also been demonstrated. In addition, an increasing number of potential therapies targeting S100A8/A9 and related signaling pathways have emerged. In this review, we will first expound on the characteristics of S100A8/A9, S100A9, and S100A8 in-depth, focus on their interactions with tumor cells and microenvironments, and then discuss their clinical applications as biomarkers and therapeutic targets. We also highlight current limitations and look into the future of S100A8/A9 targeted anti-cancer therapy.

Pathophysiology of RAGE in inflammatory diseases

The receptor for advanced glycation end products (RAGE) is a non-specific multi-ligand pattern recognition receptor capable of binding to a range of structurally diverse ligands, expressed on a variety of cell types, and performing different functions. The ligand-RAGE axis can trigger a range of signaling events that are associated with diabetes and its complications, neurological disorders, cancer, inflammation and other diseases. Since RAGE is involved in the pathophysiological processes of many diseases, targeting RAGE may be an effective strategy to block RAGE signaling.

Interactions between S100A9 and Alpha-Synuclein: Insight from NMR Spectroscopy

S100A9 is a pro-inflammatory protein that co-aggregates with other proteins in amyloid fibril plaques. S100A9 can influence the aggregation kinetics and amyloid fibril structure of alpha-synuclein (α-syn), which is involved in Parkinson's disease. Currently, there are limited data regarding their cross-interaction and how it influences the aggregation process. In this work, we analyzed this interaction using solution 19F and 2D ¹⁵N-¹H HSQC NMR spectroscopy and studied the aggregation properties of these two proteins. Here, we show that α-syn interacts with S100A9 at specific regions, which are also essential in the first step of aggregation. We also demonstrate that the 4-fluorophenylalanine label in alpha-synuclein is a sensitive probe to study interaction and aggregation using 19F NMR spectroscopy.

Key Genes Associated With Non-Alcoholic Fatty Liver Disease and Polycystic Ovary Syndrome

Background: Polycystic ovary syndrome (PCOS) is the most common metabolic and endocrinopathies disorder in women of reproductive age and non-alcoholic fatty liver (NAFLD) is one of the most common liver diseases worldwide. Previous research has indicated potential associations between PCOS and NAFLD, but the underlying pathophysiology is still not clear. The present study aims to identify the differentially expressed genes (DEGs) between PCOS and NAFLD through the bioinformatics method, and explore the associated molecular mechanisms. Methods: The microarray datasets GSE34526 and GSE63067 were downloaded from Gene Expression Omnibus (GEO) database and analyzed to obtain the DEGs between PCOS and NAFLD with the GEO2R online tool. Next, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for the DEGs were performed. Then, the protein-protein interaction (PPI) network was constructed and the hub genes were identified using the STRING database and Cytoscape software. Finally, NetworkAnalyst was used to construct the network between the targeted microRNAs (miRNAs) and the hub genes. Results: A total of 52 genes were identified as DEGs in the above two datasets. GO and KEGG enrichment analysis indicated that DEGs are mostly enriched in immunity and inflammation related pathways. In addition, nine hub genes, including TREM1, S100A9, FPR1, NCF2, FCER1G, CCR1, S100A12, MMP9, and IL1RN were selected from the PPI network by using the cytoHubba and MCODE plug-in. Then, four miRNAs, including miR-20a-5p, miR-129-2-3p, miR-124-3p, and miR-101-3p, were predicted as possibly the key miRNAs through the miRNA-gene network construction. Conclusion: In summary, we firstly constructed a miRNA-gene regulatory network depicting interactions between the predicted miRNA and the hub genes in NAFLD and PCOS, which provides novel insights into the identification of potential biomarkers and valuable therapeutic leads for PCOS and NAFLD.

Discerning the promising binding sites of S100/calgranulins and their therapeutic potential in atherosclerosis

INTRODUCTION

Atherosclerosis is a chronic inflammatory disease in which the members of S100 family proteins (calgranulins) bind with their receptors, particularly receptor for advanced glycation end products (RAGE) and toll-like receptor-4 (TLR-4) and play a key role in the pathogenesis and progression of disease. Thus, these proteins could be considered as potential biomarkers and therapeutic targets in the treatment of atherosclerotic inflammation.

AREAS COVERED

This review summarizes the pathology of S100A8, S100A9, and S100A12 in the development of atherosclerosis and reveals key structural features of these proteins which are potentially critical in their pathological effects. This article focuses on the translational significance of antagonizing these proteins by using small molecules in patent literature, clinical and preclinical studies and also discusses future approaches that could be employed to block these proteins in the treatment of atherosclerosis.

EXPERT OPINION

Based on the critical role of S100/calgranulins in the regulation of atherosclerosis, these proteins are potential targets to develop better therapeutic options in the treatment of inflammatory diseases. However, further research is still needed to clarify their exact molecular mechanism by analyzing their detailed structural features that can expedite future research to develop novel therapeutics against these proteins to treat atherosclerotic inflammation.

Development of anti-thrombotic vaccine against human S100A9 in rhesus monkey

In post-stroke patients, a decreased adherence to antiplatelet drugs is a major challenge in the prevention of recurrent stroke. Previously, we reported an antiplatelet vaccine against S100A9 in mice, but the use of Freund’s adjuvant and the difference in amino acid sequences in epitopes between mice and humans were problematic for clinical use. Here, we redesigned the S100A9 vaccine for the common sequence in both humans and monkeys and examined its effects in cynomolgus monkeys with Alum adjuvant. First, we assessed several candidate epitopes and selected 102 to 112 amino acids as the suitable epitope, which could produce antibodies. When this peptide vaccine was intradermally injected into 4 cynomolgus monkeys with Alum, the antibody against human S100A9 was successfully produced. Anti-thrombotic effects were shown in two monkeys in a mixture of vaccinated serum and fresh whole blood from another cynomolgus monkey. Additionally, the anti-thrombotic effects were partially inhibited by the epitope peptide, indicating the feasibility of neutralizing anti-thrombotic effects of produced antibodies. Prolongation of bleeding time was not observed in vaccinated monkeys. Although further studies on increasing the effect of vaccine and safety are necessary, this vaccine will be a promising approach to improve adherence to antiplatelet drugs in clinical settings.

Differential expression and role of S100 proteins in chronic rhinosinusitis

PURPOSE OF REVIEW

Immune system modulators have been under investigation to help elucidate the underlying pathophysiologies of chronic rhinosinusitis (CRS). Psoriasin (S100A7) and calgranulins (S100A8, S100A9, and S100A12) are S100 proteins that have been studied for their immune-mediating responses to pathogens within the context of CRS. This review highlights the expression patterns and proposed roles of S100 proteins in CRS with (CRSwNP) and without (CRSsNP) nasal polyps.

RECENT FINDINGS

Elevated levels of S100A7 and S100A12 were measured in the sinonasal tissues of patients with CRSsNP compared with CRSwNP and controls. S100A12 expression in CRSsNP was significantly correlated to disease severity. Contrastingly, increased S100A8, S100A9, and S100A8/A9 levels were demonstrated in the nasal polyp tissues of patients with CRSwNP compared with those in inferior turbinate and uncinate tissues of patients with CRSsNP and controls.

SUMMARY

The reported differential expression patterns and activities of psoriasin and calgranulins suggest that S100 proteins exert unique and concerted roles in mediating immunity in different subtypes of CRS. These studies will enable further investigations focused on understanding the immune-modulating mechanisms of S100 proteins in different inflammatory signaling pathways and disease phenotypes of CRS toward the pursuit of identifying new biomarkers and targets for improved outcomes.

S100P Interacts with p53 while Pentamidine Inhibits This Interaction

S100P, a small calcium-binding protein, associates with the p53 protein with micromolar affinity. It has been hypothesized that the oncogenic function of S100P may involve binding-induced inactivation of p53. We used 1H-15N HSQC experiments and molecular modeling to study the molecular interactions between S100P and p53 in the presence and absence of pentamidine. Our experimental analysis indicates that the S100P-53 complex formation is successfully disrupted by pentamidine, since S100P shares the same binding site for p53 and pentamidine. In addition, we showed that pentamidine treatment of ZR-75-1 breast cancer cells resulted in reduced proliferation and increased p53 and p21 protein levels, indicating that pentamidine is an effective antagonist that interferes with the S100P-p53 interaction, leading to re-activation of the p53-21 pathway and inhibition of cancer cell proliferation. Collectively, our findings suggest that blocking the association between S100P and p53 by pentamidine will prevent cancer progression and, therefore, provide a new avenue for cancer therapy by targeting the S100P-p53 interaction.

Blocking the interface region amongst S100A6 and RAGE V domain via S100B protein

The Ca²⁺-mediated S100 family protein S100A6 has a crucial task in various intracellular and extracellular activities thereby demonstrating a possible involvement in the advancement and development of malignant tumors. S100A6 has been found to associate with receptor for advanced glycation end products, RAGE, through its extracellular extension. This extension is famously identified as a prominent receptor for many S100 family associates. Additionally, S100A6 binds to S100B protein and forms a heterodimer. Thus, we consider the S100B protein to be a prospective drug molecule to obstruct the interacting regions amongst S100A6 and RAGE V domain. We applied the NMR spectroscopy method to locate the binding area amid the S100A6m (mutant S100A6, cysteine at 3rd position of S100A6 is replaced with serine, C3S) and S100B proteins. The ¹H-¹⁵N HSQC NMR titrations revealed the probable requisite dynamics of S100A6m and S100B interfaces. Utilizing data from the NMR titrations as input parameters, we ran the HADDOCK program and created a S100A6m-S100B heterodimer complex. The obtained complex was then superimposed with the reported complex of S100A6m-RAGE V domain. This superimposition displayed the possibility of S100B to be a potential antagonist that can block the interface area of the S100A6m and the RAGE V domain. Moreover, an in vitro cancer model using SW480 cells in water-soluble tetrazolium-1 assay (WST-1) showed a noticeable change in the cell proliferation as an effect of these proteins. Our study indicates the possibility to develop a S100B-like competitor that could play a key role in the treatment of S100- and RAGE-mediated human diseases.

Pentamidine inhibit S100A4 - p53 interaction and decreases cell proliferation activity

Metastasis-associated S100A4 protein is a small calcium-binding protein typically overexpressed in several tumor forms, and it is widely accepted that S100A4 plays a significant role in the metastasis of cancer. Tumor suppressor p53 is one of the S100A4's main targets. Previous reports show that through p53, S100A4 regulates collagen expression and cell proliferation. When S100A4 interacts with p53, the S100A4 destabilizes wild type p53. In the current study, based on ¹H-¹⁵N HSQC NMR experiments and HADDOCK results, S100A4 interacts with the intrinsically unstructured transactivation domain (TAD) of the protein p53 and the pentamidine molecules in the presence of calcium ions. Our results suggest that the p53 TAD and pentamidine molecules share similar binding sites on the S100A4 protein. This observation indicates that a competitive binding mechanism can interfere with the binding of S100A4-p53 and increase the level of p53. Also, we compare different aspects of p53 activity in the WST-1 test using MCF 7 cells. We found that the presence of a pentamidine molecule results in higher p53 activity, which is also reflected in less cell proliferation. Collectively, our results indicate that disrupting the S100A4-p53 interaction would prevent cancer progression, and thus S100A4-p53 inhibitors provide a new avenue for cancer therapy.

S100A12 in Digestive Diseases and Health: A Scoping Review

Calgranulin proteins are an important class of molecules involved in innate immunity. These members of the S100 class of the EF-hand family of calcium-binding proteins have numerous cellular and antimicrobial functions. One protein in particular, S100A12 (also called EN-RAGE or calgranulin C), is highly abundant in neutrophils during acute inflammation and has been implicated in immune regulation. Structure-function analyses reveal that S100A12 has the capacity to bind calcium, zinc, and copper, processes that contribute to nutritional immunity against invading microbial pathogens. S100A12 is a ligand for the receptor for advanced glycation end products (RAGE), toll-like receptor 4 (TLR4), and CD36, which promote cellular and immunological pathways to alter inflammation. We conducted a scoping review of the existing literature to define what is known about the association of S100A12 with digestive disease and health. Results suggest that S100A12 is implicated in gastroenteritis, necrotizing enterocolitis, gastritis, gastric cancer, Crohn's disease, irritable bowel syndrome, inflammatory bowel disease, and digestive tract cancers. Together, these results reveal S100A12 is an important molecule broadly associated with the pathogenesis of digestive diseases.

Development of Predictive Models for Identifying Potential S100A9 Inhibitors Based on Machine Learning Methods

S100A9 is a potential therapeutic target for various disease including prostate cancer, colorectal cancer, and Alzheimer's disease. However, the sparsity of atomic level data, such as protein-protein interaction of S100A9 with RAGE, TLR4/MD2, or CD147 (EMMPRIN) hinders the rational drug design of S100A9 inhibitors. Herein we first report predictive models of S100A9 inhibitory effect by applying machine learning classifiers on 2D-molecular descriptors. The models were optimized through feature selectors as well as classifiers to produce the top eight random forest models with robust predictability and high cost-effectiveness. Notably, optimal feature sets were obtained after the reduction of 2,798 features into dozens of features with the chopping of fingerprint bits. Moreover, the high efficiency of compact feature sets allowed us to further screen a large-scale dataset (over 6,000,000 compounds) within a week. Through a consensus vote of the top models, 46 hits (hit rate = 0.000713%) were identified as potential S100A9 inhibitors. We expect that our models will facilitate the drug discovery process by providing high predictive power as well as cost-reduction ability and give insights into designing novel drugs targeting S100A9.

Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain

In this report, using NMR and molecular modeling, we have studied the structure of lysozyme-S100A6 complex and the influence of tranilast [N-(3, 4-dimethoxycinnamoyl) anthranilic acid], an antiallergic drug which binds to lysozyme, on lysozyme-S100A6 and S100A6-RAGE complex formation and, finally, on cell proliferation. We have found that tranilast may block the S100A6-lysozyme interaction and enhance binding of S100A6 to RAGE. Using WST1 assay, we have found that lysozyme, most probably by blocking the interaction between S100A6 and RAGE, inhibits cell proliferation while tranilast may reverse this effect by binding to lysozyme. In conclusion, studies presented in this work, describing the protein-protein/-drug interactions, are of great importance for designing new therapies to treat diseases associated with cell proliferation such as cancers.