Ligand coupling mechanism of the human serotonin transporter differentiates substrates from inhibitors

The presynaptic serotonin transporter (SERT) clears extracellular serotonin following vesicular release to ensure temporal and spatial regulation of serotonergic signalling and neurotransmitter homeostasis. Prescription drugs used to treat neurobehavioral disorders, including depression, anxiety, and obsessive-compulsive disorder, trap SERT by blocking the transport cycle. In contrast, illicit drugs of abuse like amphetamines reverse SERT directionality, causing serotonin efflux. Both processes result in increased extracellular serotonin levels. By combining molecular dynamics simulations with biochemical experiments and using a homologous series of serotonin analogues, we uncovered the coupling mechanism between the substrate and the transporter, which triggers the uptake of serotonin. Free energy analysis showed that only scaffold-bound substrates could initiate SERT occlusion through attractive long-range electrostatic interactions acting on the bundle domain. The associated spatial requirements define substrate and inhibitor properties, enabling additional possibilities for rational drug design approaches.

Peroxidasin Inhibition by Phloroglucinol and Other Peroxidase Inhibitors

Human peroxidasin (PXDN) is a ubiquitous peroxidase enzyme expressed in most tissues in the body. PXDN represents an interesting therapeutic target for inhibition, as it plays a role in numerous pathologies, including cardiovascular disease, cancer and fibrosis. Like other peroxidases, PXDN generates hypohalous acids and free radical species, thereby facilitating oxidative modifications of numerous biomolecules. We have studied the inhibition of PXDN halogenation and peroxidase activity by phloroglucinol and 14 other peroxidase inhibitors. Although a number of compounds on their own potently inhibited PXDN halogenation activity, only five were effective in the presence of a peroxidase substrate with IC50 values in the low μM range. Using sequential stopped-flow spectrophotometry, we examined the mechanisms of inhibition for several compounds. Phloroglucinol was the most potent inhibitor with a nanomolar IC50 for purified PXDN and IC50 values of 0.95 μM and 1.6 μM for the inhibition of hypobromous acid (HOBr)-mediated collagen IV cross-linking in a decellularized extracellular matrix and a cell culture model. Other compounds were less effective in these models. Most interestingly, phloroglucinol was identified to irreversibly inhibit PXDN, either by mechanism-based inhibition or tight binding. Our work has highlighted phloroglucinol as a promising lead compound for the design of highly specific PXDN inhibitors and the assays used in this study provide a suitable approach for high-throughput screening of PXDN inhibitors.

Exploring the bi-directional relationship and shared genes between depression and stroke via NHANES and bioinformatic analysis

Background: Stroke and depression are the two most common causes of disability worldwide. Growing evidence suggests a bi-directional relationship between stroke and depression, whereas the molecular mechanisms underlying stroke and depression are not well understood. The objectives of this study were to identify hub genes and biological pathways related to the pathogenesis of ischemic stroke (IS) and major depressive disorder (MDD) and to evaluate the infiltration of immune cells in both disorders. Methods: Participants from the United States National Health and Nutritional Examination Survey (NHANES) 2005-2018 were included to evaluate the association between stroke and MDD. Two differentially expressed genes (DEGs) sets extracted from GSE98793 and GSE16561 datasets were intersected to generate common DEGs, which were further screened out in cytoHubba to identify hub genes. GO, KEGG, Metascape, GeneMANIA, NetworkAnalyst, and DGIdb were used for functional enrichment, pathway analysis, regulatory network analysis, and candidate drugs analysis. ssGSEA algorithm was used to analyze the immune infiltration. Results: Among the 29706 participants from NHANES 2005-2018, stroke was significantly associated with MDD (OR = 2.79,95% CI:2.26-3.43, p < 0.0001). A total of 41 common upregulated genes and eight common downregulated genes were finally identified between IS and MDD. Enrichment analysis revealed that the shared genes were mainly involved in immune response and immune-related pathways. A protein-protein interaction (PPI) was constructed, from which ten (CD163, AEG1, IRAK3, S100A12, HP, PGLYRP1, CEACAM8, MPO, LCN2, and DEFA4) were screened. In addition, gene-miRNAs, transcription factor-gene interactions, and protein-drug interactions coregulatory networks with hub genes were also identified. Finally, we observed that the innate immunity was activated while acquired immunity was suppressed in both disorders. Conclusion: We successfully identified the ten hub shared genes linking the IS and MDD and constructed the regulatory networks for them that could serve as novel targeted therapy for the comorbidities.

Native glycosylation and binding of the antidepressant paroxetine in a low-resolution crystal structure of human myeloperoxidase

Human myeloperoxidase (MPO) utilizes hydrogen peroxide to oxidize organic compounds and as such plays an essential role in cell-component synthesis, in metabolic and elimination pathways, and in the front-line defence against pathogens. Moreover, MPO is increasingly being reported to play a role in inflammation. The enzymatic activity of MPO has also been shown to depend on its glycosylation. Mammalian MPO crystal structures deposited in the Protein Data Bank (PDB) present only a partial identification of their glycosylation. Here, a newly obtained crystal structure of MPO containing four disulfide-linked dimers and showing an elaborate collection of glycans is reported. These are compared with the glycans identified in proteomics studies and from 18 human MPO structures available in the PDB. The crystal structure also contains bound paroxetine, a blocker of serotonin reuptake that has previously been identified as an irreversible inhibitor of MPO, in the presence of thiocyanate, a physiological substrate of MPO.

Combination of electroconvulsive stimulation with ketamine or escitalopram protects the brain against inflammation and oxidative stress induced by maternal deprivation and is critical for associated behaviors in male and female rats

This study aimed at evaluating the treatment effects with ketamine, electroconvulsive stimulation (ECS), escitalopram, alone or in combination in adult rats of both sexes, subjected to the animal model of maternal deprivation (MD). All groups were subjected to the forced swimming test (FST), splash and open field tests. The prefrontal cortex (PFC), hippocampus and serum were collected to analyze oxidative stress and inflammatory parameters. MD induced depressive-like behavior in the FST test in males and reduced grooming time in male and female rats. The treatments alone or combined reversed depressive and anhedonic behavior in females. In males, all treatments increased grooming time, except for ECS + escitalopram + ketamine. MD increased lipid peroxidation and protein carbonylation, nitrite/nitrate concentration and myeloperoxidase activity in the PFC and hippocampus of males and females. However, the treatment's response was sex dependent. Catalase activity decreased in the PFC of males and the PFC and hippocampus of females, and most treatments were not able to reverse it. MD increased the inflammation biomarkers levels in the PFC and hippocampus of males and females, and most treatments were able to reverse this increase. In all groups, a reduction in the interleukin-10 levels in the PFC and hippocampus of female and male rats was observed. Our study shows different responses between the sexes in the patterns evaluated and reinforces the use of the gender variable as a biological factor in MDD related to early stress and in the response of the therapeutic strategies used.

Role of Neutrophils in the Pathogenesis of Nonalcoholic Steatohepatitis

Nonalcoholic fatty liver disease (NAFLD) includes a spectrum of liver disorders, from fatty liver to nonalcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular carcinoma. Compared with fatty liver, NASH is characterized by increased liver injury and inflammation, in which liver-infiltrating immune cells, with neutrophil infiltration as a hallmark of NASH, play a critical role in promoting the progression of fatty liver to NASH. Neutrophils are the first responders to injury and infection in various tissues, establishing the first line of defense through multiple mechanisms such as phagocytosis, cytokine secretion, reactive oxygen species production, and neutrophil extracellular trap formation; however, their roles in the pathogenesis of NASH remain obscure. The current review summarizes the roles of neutrophils that facilitate the progression of fatty liver to NASH and their involvement in inflammation resolution during NASH pathogenesis. The notion that neutrophils are potential therapeutic targets for the treatment of NASH is also discussed.

Inhibition of Myeloperoxidase

Myeloperoxidase participates in innate immune defense mechanism through formation of microbicidal reactive oxidants and diffusible radical species. A unique activity is its ability to use chloride as a cosubstrate with hydrogen peroxide to generate chlorinating oxidants such as hypochlorous acid, a potent antimicrobial agent. However, chronic MPO activation can lead to indiscriminate protein modification causing tissue damage, and has been associated with chronic inflammatory diseases, atherosclerosis, and acute cardiovascular events. This has attracted considerable interest in the development of therapeutically useful MPO inhibitors. Today, based on the profound knowledge of structure and function of MPO and its biochemical and biophysical differences with the other homologous human peroxidases, various rational and high-throughput screening attempts were performed in developing specific irreversible and reversible inhibitors. The most prominent candidates as well as MPO inhibitors already studied in clinical trials are introduced and discussed.

Integration of an Inhibitor-like Rule and Structure-based Virtual Screening for the Discovery of Novel Myeloperoxidase Inhibitors

Myeloperoxidase (MPO) is an attractive therapeutic target against inflammation. Herein, we developed an inhibitor-like rule, based on known MPO inhibitors, and generated a target database containing 6546 molecules with privileged inhibitory properties. Using a structure-based approach validated by decoys, robust statistical metrics, redocking, and cross-docking, we selected 10 putative MPO inhibitors with high chemical diversity. At 20 μM, six of these 10 compounds (i.e., 60% success rate) inhibited more than 20% of the chlorinating activity of the enzyme. Additionally, we found that compound ZINC9089086 forms hydrogen bonds with Arg233 and with the hemic carboxylate. It makes a π-stacking interaction with the heme group and displays a high affinity for the enzyme active site. When incubated with purified MPO, ZINC9089086 inhibited the chlorinating activity of the enzyme with an IC₅₀ of 2.2 ± 0.1 μM in a reversible manner. Subsequent experiments revealed that ZINC9089086 inhibited hypochlorous acid production in dHL-60 cells and human neutrophils. Furthermore, the theoretical ADME/Tox profile indicated that this compound exhibits low toxicity risks and adequate pharmacokinetic parameters, thus making ZINC9089086 a very promising candidate for preclinical anti-inflammatory studies. Overall, our study shows that integrating an inhibitor-like rule with a validated structure-based methodology is an excellent approach for improving the success rate and molecular diversity of novel MPO inhibitors with good pharmacokinetics and toxicological profiles. By combining these tools, it was possible to increase the assurance rate, which ultimately diminishes the costs and time needed for the acquisition, synthesis, and evaluation of new compounds.

Molecular Mechanisms of Drug Action: X-ray Crystallography at the Basis of Structure-based and Ligand-based Drug Design

Biological systems are recognized for their complexity and diversity and yet we sometimes manage to cure disease via the administration of small chemical drug molecules. At first, active ingredients were found accidentally and at that time there did not seem a need to understand the molecular mechanism of drug functioning. However, the urge to develop new drugs, the discovery of multipurpose characteristics of some drugs, and the necessity to remove unwanted secondary drug effects, incited the pharmaceutical sector to rationalize drug design. This did not deliver success in the years directly following its conception, but it drove the evolution of biochemical and biophysical techniques to enable the characterization of molecular mechanisms of drug action. Functional and structural data generated by biochemists and structural biologists became a valuable input for computational biologists, chemists and bioinformaticians who could extrapolate in silico, based on variations in the structural aspects of the drug molecules and their target. This opened up new avenues with much improved predictive power because of a clearer perception of the role and impact of structural elements in the intrinsic affinity and specificity of the drug for its target. In this chapter, we review how crystal structures can initiate structure-based drug design in general.

Novel serotonin transporter regulators: Natural aristolane- and nardosinane- types of sesquiterpenoids from Nardostachys chinensis Batal

Serotonin transporter (SERT) is a classic target of drug discovery for neuropsychiatric and digestive disorders, and against those disorders, plants of Nardostachys genus have been valued for centuries in the systems of Traditional Chinese Medicine, Ayurvedic and Unani. Herein, chemical investigation on the roots and rhizomes of Nardostachys chinensis Batal. led to the isolation of forty sesquiterpenoids including six new aristolane-type sesquiterpenoids and six new nardosinane-type sesquiterprenoids. Their structures were elucidated by extensive spectroscopic methods, combined with analyses of circular dichroism and single-crystal X-ray diffraction data. To explore natural product scaffolds with SERT regulating activity, a high-content assay for measurement of SERT function in vitro was conducted to evaluate the SERT regulating properties of these isolates. In conclusion, eleven compounds could be potential natural product scaffolds for developing drug candidates targeting SERT. Among which, kanshone C of aristolane-type sesquiterpenoid inhibited SERT most strongly, while desoxo-nachinol A of nardosinane-type sesquiterpenoid instead enhanced SERT potently.

From Dynamic Combinatorial Chemistry to in Vivo Evaluation of Reversible and Irreversible Myeloperoxidase Inhibitors

The implementation of dynamic combinatorial libraries allowed the determination of highly active reversible and irreversible inhibitors of myeloperoxidase (MPO) at the nanomolar level. Docking experiments highlighted the interaction between the most active ligands and MPO, and further kinetic studies defined the mode of inhibition of these compounds. Finally, in vivo evaluation showed that one dose of irreversible inhibitors is able to suppress the activity of MPO after inducing inflammation.

Characterization of chemical features of potent myeloperoxidase inhibitors

BACKGROUND

Despite its important role in the immune system, myeloperoxidase (MPO) is implicated in a wide range of inflammatory syndromes due to its oxidative product HOCl. The oxidative damages caused by MPO make it a new target for developing promising anti-inflammatory agents. In this paper, we tried to understand the mechanism of MPO inhibition in order to facilitate the drug design, to develop more accurate virtual tests and to understand the structure-activity relationship.

RESULTS

Based on docking experiments, kinetic studies and in vitro tests, it is determined that a potent MPO inhibitor must possess an oxidizable group in addition to a high affinity with the active site. At last, a new hit was found in this work namely 4-(3-hydroxy-phenoxy)-butylamine (5) that has IC50 of 86 nM.

CONCLUSION

Hydroxy-phenoxy alkylamine derivatives were found to be promising MPO inhibitors and they may represent an important starting point in the development of more potent MPO inhibitors.

Posttranslational protein modifications by reactive nitrogen and chlorine species and strategies for their prevention and elimination

Proteins are subject to various posttranslational modifications, some of them being undesired from the point of view of metabolic efficiency. Prevention of such modifications is expected to provide new means of therapy of diseases and decelerate the process of aging. In this review, modifications of proteins by reactive nitrogen species and reactive halogen species, is briefly presented and means of prevention of these modifications and their sequelae are discussed, including the denitrase activity and inhibitors of myeloperoxidase.