The Chemistry of Neurodegeneration: Kinetic Data and Their Implications

Exploring ligands that target von Willebrand factor selectively under oxidizing conditions through docking and molecular dynamics simulations

The blood protein von Willebrand factor (VWF) is a large multimeric protein that, when activated, binds to blood platelets, tethering them to the site of vascular injury and initiating blood coagulation. This process is critical for the normal hemostatic response, but especially under inflammatory conditions, it is thought to be a major player in pathological thrombus formation. For this reason, VWF has been the target for the development of anti-thrombotic therapeutics. However, it is challenging to prevent pathological thrombus formation while still allowing normal physiological blood coagulation, as currently available anti-thrombotic therapeutics are known to cause unwanted bleeding, in particular intracranial hemorrhage. This work explores the possibility of inhibiting VWF selectively under the inflammatory conditions present during pathological thrombus formation. In particular, the A2 domain of VWF is known to inhibit the neighboring A1 domain from binding to the platelet surface receptor GpIbα, and this auto-inhibitory mechanism has been shown to be removed by oxidizing agents released during inflammation. Hence, finding drug molecules that bind at the interface between A1 and A2 only under oxidizing conditions could restore such an auto-inhibitory mechanism. Here, by using a combination of computational docking, molecular dynamics simulations, and free energy perturbation calculations, a ligand from the ZINC15 database was identified that binds at the A1A2 interface, with the interaction being stronger under oxidizing conditions. The results provide a framework for the discovery of drug molecules that bind to a protein selectively in the presence of inflammatory conditions.

The Scope of the Applicability of Non-relativistic DFT Calculations of NMR Chemical Shifts in Pyridine-Metal Complexes for Applied Applications

Heavy metals are toxic, but it is impossible to stop using them. Considering the variety of molecular systems in which they can be present, the multicomponent nature and disorder of the structure of such systems, one of the most effective methods for studying them is NMR spectroscopy. This determines the need to calculate NMR chemical shifts for expected model systems. For elements beyond the third row of the periodic table, corrections for relativistic effects are necessary when calculating NMR parameters. Such corrections may be necessary even for light atoms due to the shielding effect of a neighboring heavy atom. This work examines the extent to which non-relativistic DFT calculations are able to reproduce experimental 15N and 113Cd NMR chemical shift tensors in pyridine-metal coordination complexes. It is shown that while for the calculation of 15N NMR chemical shift tensors there is no real need to consider relativistic corrections, for 113Cd, on the contrary, none of the tested calculation methods could reproduce the experimentally obtained tensor to any extent correctly.

Edge Substitution Effects of Histidine Tautomerization Behaviors on the Structural Properties and Aggregation Properties of Aβ(1-42) Mature Fibril

Histidine behaviors play critical roles in folding and misfolding processes due to the changes in net charge and the various N/N-H orientations on imidazole rings. However, the effect of histidine tautomerization (HIE (Nε-H, ε) and HID (Nδ-H, δ) states) behaviors on the edge chain of Aβ mature fibrils remains inadequately understood, which is critical for finding a strategy to disturb fibril elongation and growth. In the current study, eight independent molecular dynamics simulations were conducted to investigate such impacts on the structural and aggregation properties. Our results from three different binding models revealed that the binding contributions of edge substitution effects are primarily located between chains 1 and 2. Histidine states significantly influence the secondary structure of each domain. Further analysis confirmed that the C1_H6//C1_E11 intrachain interaction is essential in maintaining the internal stability of chain 1, while the C1_H13//C2_H13 and C1_H14//C2_H13 interchain interactions are critical in maintaining the interchain stability of the fibril structure. Our subsequent analysis revealed that the current edge substitution leads to the loss of the C1_H13//C1_E11 intrachain and C1_H13//C2_H14 interchain interactions. The N-terminal regularity was significantly directly influenced by histidine states, particularly by the residue of C1_H13. Our study provides valuable insights into the effect of histidine behaviors on the edge chain of Aβ mature fibril, advancing our understanding of the histidine behavior hypothesis in misfolding diseases.

Application of in-silico drug discovery techniques to discover a novel hit for target-specific inhibition of SARS-CoV-2 Mpro's revealed allosteric binding with MAO-B receptor: A theoretical study to find a cure for post-covid neurological disorder

Several studies have revealed that SARS-CoV-2 damages brain function and produces significant neurological disability. The SARS-CoV-2 coronavirus, which causes COVID-19, may infect the heart, kidneys, and brain. Recent research suggests that monoamine oxidase B (MAO-B) may be involved in metabolomics variations in delirium-prone individuals and severe SARS-CoV-2 infection. In light of this situation, we have employed a variety of computational to develop suitable QSAR model using PyDescriptor and genetic algorithm-multilinear regression (GA-MLR) models (R2 = 0.800-793, Q2LOO = 0.734-0.727, and so on) on the data set of 106 molecules whose anti-SARS-CoV-2 activity was empirically determined. QSAR models generated follow OECD standards and are predictive. QSAR model descriptors were also observed in x-ray-resolved structures. After developing a QSAR model, we did a QSAR-based virtual screening on an in-house database of 200 compounds and found a potential hit molecule. The new hit's docking score (-8.208 kcal/mol) and PIC50 (7.85 M) demonstrated a significant affinity for SARS-CoV-2's main protease. Based on post-covid neurodegenerative episodes in Alzheimer's and Parkinson's-like disorders and MAO-B's role in neurodegeneration, the initially disclosed hit for the SARS-CoV-2 main protease was repurposed against the MAO-B receptor using receptor-based molecular docking, which yielded a docking score of -12.0 kcal/mol. This shows that the compound that inhibits SARS-CoV-2's primary protease may bind allosterically to the MAO-B receptor. We then did molecular dynamic simulations and MMGBSA tests to confirm molecular docking analyses and quantify binding free energy. The drug-receptor complex was stable during the 150-ns MD simulation. The first computational effort to show in-silico inhibition of SARS-CoV-2 Mpro and allosteric interaction of novel inhibitors with MAO-B in post-covid neurodegenerative symptoms and other disorders. The current study seeks a novel compound that inhibits SAR's COV-2 Mpro and perhaps binds MAO-B allosterically. Thus, this study will enable scientists design a new SARS-CoV-2 Mpro that inhibits the MAO-B receptor to treat post-covid neurological illness.

Insight into the degradation of amino substituted benzimidazo[1,2-a]quinolines via a combined experimental and density functional theory study

Heterocyclic compounds have been shown to be potential chemotherapeutic agents, especially the benzimidazole derivatives studied in this work. The ultimate goal in the search for biologically active and effective molecules is to commercialize a product whose stability must be reliable. Therefore, in the development of drugs, forced degradation experiments are performed under the environmental conditions to which they are subjected during transportation and storage to ensure quality and safety before marketing. Hydrolytic, thermal, photolytic, and degradation in the presence of hydrogen peroxide are experimental stress tests to which the newly synthesized compounds were subjected to gain insight into the degradation pathways of the analytes. Degradation of two benzimidazole derivatives was observed under all applied conditions while the major impact showed photolysis with ten and four degradation products, respectively. In total, eighteen major degradation products were detected and identified using high-resolution mass spectrometry. Computer models in the TEST program were applied to the proposed structures to evaluate the bioaccumulation factor, toxicity, and mutagenicity of the analyzed compounds, while density functional theory analysis (DFT) revealed factors affecting the vulnerability of systems towards exceeding acidic/basic conditions and H2O2.

Prion-like Aggregation of the Heptapeptide GNNQQNY into Amyloid Nanofiber Is Governed by Configuration Entropy

A major cause of prion infectivity is the early formation of small, fibril-like aggregates consisting of the heptapeptide GNNQQNY. The prion aggregates exhibit a unique stacking mode in which the hydrophobic tyrosine (Y) is exposed outward, forming a bilayer β-sheet-stacking zipper structure. This stacking mode of the prion peptides, termed "Y-outward" structure for convenience, goes against the common understanding that, for other amyloid-forming peptides, the hydrophobic residues should be hidden within the peptide fibril, referred to as "Y-inward" structure. To explore the extraordinary stacking behaviors of the prion GNNQQNY peptides, two fibril models are constructed in a fashion of "Y-outward" and "Y-inward" stackings and then studied in silico to examine their thermodynamic stabilities and disaggregation pathways. The "Y-inward" structure indeed exhibits stronger thermodynamic stability than the "Y-outward" structure, according to potential energy and stacking energy calculations. To show how the peptide fibrils dissociate, we illustrated two disaggregation pathways. A dihedral-based free energy landscape was then calculated to examine the conformational degrees of freedom of the GNNQQNY chains in the "Y-outward" and "Y-inward" structures. Peptide chains lose more configurational entropy in the "Y-inward" structure than in the "Y-outward" structure, indicating that the prion peptides are prone to aggregate in a fashion of "Y-outward" stacking pattern due to its low conformational constraints. The prion-like aggregation of the GNNQQNY peptides into amyloid fibrils is primarily governed by the configuration entropy.

Quinones as Neuroprotective Agents

Quinones can in principle be viewed as a double-edged sword in the treatment of neurodegenerative diseases, since they are often cytoprotective but can also be cytotoxic due to covalent and redox modification of biomolecules. Nevertheless, low doses of moderately electrophilic quinones are generally cytoprotective, mainly due to their ability to activate the Keap1/Nrf2 pathway and thus induce the expression of detoxifying enzymes. Some natural quinones have relevant roles in important physiological processes. One of them is coenzyme Q₁₀, which takes part in the oxidative phosphorylation processes involved in cell energy production, as a proton and electron carrier in the mitochondrial respiratory chain, and shows neuroprotective effects relevant to Alzheimer's and Parkinson's diseases. Additional neuroprotective quinones that can be regarded as coenzyme Q₁₀ analogues are idobenone, mitoquinone and plastoquinone. Other endogenous quinones with neuroprotective activities include tocopherol-derived quinones, most notably vatiquinone, and vitamin K. A final group of non-endogenous quinones with neuroprotective activity is discussed, comprising embelin, APX-3330, cannabinoid-derived quinones, asterriquinones and other indolylquinones, pyrroloquinolinequinone and its analogues, geldanamycin and its analogues, rifampicin quinone, memoquin and a number of hybrid structures combining quinones with amino acids, cholinesterase inhibitors and non-steroidal anti-inflammatory drugs.

Antioxidant activity of lidocaine, bupivacaine, and ropivacaine in aqueous and lipophilic environments: an experimental and computational study

Introduction: Local anesthetics are widely recognized pharmaceutical compounds with various clinical effects. Recent research indicates that they positively impact the antioxidant system and they may function as free radical scavengers. We hypothesize that their scavenging activity is influenced by the lipophilicity of the environment. Methods: We assessed the free radical scavenging capacity of three local anesthetics (lidocaine, bupivacaine, and ropivacaine) using ABTS, DPPH, and FRAP antioxidant assays. We also employed quantum chemistry methods to find the most probable reaction mechanism. The experiments were conducted in an aqueous environment simulating extracellular fluid or cytosol, and in a lipophilic environment (n-octanol) simulating cellular membranes or myelin sheets. Results: All local anesthetics demonstrated ABTS˙⁺ radical scavenging activity, with lidocaine being the most effective. Compared to Vitamin C, lidocaine exhibited a 200-fold higher half-maximal inhibitory concentration. The most thermodynamically favorable and only possible reaction mechanism involved hydrogen atom transfer between the free radical and the -C-H vicinal to the carbonyl group. We found that the antioxidant activity of all tested local anesthetics was negligible in lipophilic environments, which was further confirmed by quantum chemical calculations. Conclusion: Local anesthetics exhibit modest free radical scavenging activity in aqueous environments, with lidocaine demonstrating the highest activity. However, their antioxidant activity in lipophilic environments, such as cellular membranes, myelin sheets, and adipose tissue, appears to be negligible. Our results thus show that free radical scavenging activity is influenced by the lipophilicity of the environment.

Sesamol prevents mitochondrial impairment and pro-inflammatory alterations in the human neuroblastoma SH-SY5Y cells: role for Nrf2

Mitochondria are a primary source and a target of reactive oxygen species (ROS). Increased mitochondrial production of ROS is associated with bioenergetics decline, cell death, and inflammation. Here we investigated whether a pretreatment (for 24 h) with sesamol (SES; at 12.5-50 µM) would be efficient in preventing the mitochondrial collapse induced by hydrogen peroxide (H₂O₂, at 300 µM) in the human neuroblastoma SH-SY5Y cell line. We have found that a pretreatment with SES at 25 µM decreased the effects of H₂O₂ on lipid peroxidation, protein carbonylation, and protein nitration in membranes obtained from the mitochondria isolated from the SH-SY5Y cells. In this regard, SES pretreatment decreased the production of superoxide anion radical (O₂^-•) by the mitochondria of H₂O₂-treated cells. SES also prevented the mitochondrial dysfunction induced by H₂O₂, as assessed by analyzing the activity of the complexes I and V. The H₂O₂-induced reduction in the production of adenosine triphosphate (ATP) was also prevented by SES. The levels of the pro-inflammatory cytokines interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α), as well as the activity of the transcription factor nuclear factor-κB (NF-κB) were downregulated by the SES pretreatment in the H₂O₂-challenged cells. Silencing of the nuclear factor erythroid 2-related factor 2 (Nrf2) transcription factor abolished the protection induced by SES regarding mitochondrial function and inflammation. Thus, SES depends on Nrf2 to promote mitochondrial protection in cells facing redox impairment.

Carving the senescent phenotype by the chemical reactivity of catecholamines: An integrative review

Macromolecules damaged by covalent modifications produced by chemically reactive metabolites accumulate in the slowly renewable components of living bodies and compromise their functions. Among such metabolites, catecholamines (CA) are unique, compared with the ubiquitous oxygen, ROS, glucose and methylglyoxal, in that their high chemical reactivity is confined to a limited set of cell types, including the dopaminergic and noradrenergic neurons and their direct targets, which suffer from CA propensities for autoxidation yielding toxic quinones, and for Pictet-Spengler reactions with carbonyl-containing compounds, which yield mitochondrial toxins. The functions progressively compromised because of that include motor performance, cognition, reward-driven behaviors, emotional tuning, and the neuroendocrine control of reproduction. The phenotypic manifestations of the resulting disorders culminate in such conditions as Parkinson's and Alzheimer's diseases, hypertension, sarcopenia, and menopause. The reasons to suspect that CA play some special role in aging accumulated since early 1970-ies. Published reviews address the role of CA hazardousness in the development of specific aging-associated diseases. The present integrative review explores how the bizarre discrepancy between CA hazardousness and biological importance could have emerged in evolution, how much does the chemical reactivity of CA contribute to the senescent phenotype in mammals, and what can be done with it.

Prediction of the endocrine-disrupting ability of 49 per- and polyfluoroalkyl substances: In silico and epidemiological evidence

The toxic effects of per- and polyfluoroalkyl substances (PFASs) on humans are mediated by nuclear hormone receptors (NHRs). However, data on the interaction of PFASs and NHRs is limited. Endocrine Disruptome, an inverse docking tool, was used in this study to simulate the docking of 49 common PFASs with 14 different types of human NHRs. According to the findings, 25 PFASs have a high or moderately high probability of binding to more than five NHRs, with androgen receptor (AR) and mineralocorticoid receptor (MR) being the most likely target NHRs. Molecular docking analyses revealed that the binding modes of PFASs with the two NHRs were similar to those of their corresponding co-crystallized ligands. PFASs, in particular, may disrupt the endocrine system by binding to MR. This finding is consistent with epidemiological research that has linked PFASs to MR-related diseases. Our findings may contribute to a better understanding of the health risks posed by PFASs.

COVID-19 infection and neurodegeneration: Computational evidence for interactions between the SARS-CoV-2 spike protein and monoamine oxidase enzymes

Although COVID-19 has been primarily associated with pneumonia, recent data show that its causative agent, the SARS-CoV-2 coronavirus, can infect many vital organs beyond the lungs, including the heart, kidneys and the brain. The literature agrees that COVID-19 is likely to have long-term mental health effects on infected individuals, which signifies a need to understand the role of the virus in the pathophysiology of brain disorders that is currently unknown and widely debated. Our docking and molecular dynamics simulations show that the affinity of the spike protein from the wild type (WT) and the South African B.1.351 (SA) variant towards MAO enzymes is comparable to that for its ACE2 receptor. This allows for the WT/SA⋅⋅⋅MAO complex formation, which changes MAO affinities for their neurotransmitter substrates, thereby impacting their metabolic conversion and misbalancing their levels. Knowing that this fine regulation is strongly linked with the etiology of various brain pathologies, these results are the first to highlight the possibility that the interference with the brain MAO catalytic activity is responsible for the increased neurodegenerative illnesses following a COVID-19 infection, thus placing a neurobiological link between these two conditions in the spotlight. Since the obtained insight suggests that a more contagious SA variant causes even larger disturbances, and with new and more problematic strains likely emerging in the near future, we firmly advise that the presented prospect of the SARS-CoV-2 induced neurological complications should not be ignored, but rather requires further clinical investigations to achieve an early diagnosis and timely therapeutic interventions.

Antiradical Activity of Dopamine, L-DOPA, Adrenaline, and Noradrenaline in Water/Methanol and in Liposomal Systems

Catecholamines play a crucial role in signal transduction and are also expected to act as endogeneous antioxidants, but the mechanism of their antioxidant action is not fully understood. Here, we describe the impact of pH on the kinetics of reaction of four catecholamines (L-DOPA, dopamine, adrenaline, and noradrenaline) with model 2,2-diphenyl-1-picrylhydrazyl radical (dpph^•) in methanol/water. The increase in pH from 5.5 to 7.4 is followed by a 2 order of magnitude increase in the rate constant, e.g., for dopamine (DA) k^pH5.5 = 1,200 M^–1 s^–1 versus k^pH7.4 = 170,000 M^–1 s^–1, and such rate acceleration is attributed to a fast electron transfer from the DA anion to dpph^•. We also proved that at pH 7.0 DA breaks the peroxidation chain of methyl linoleate in liposomes assembled from neutral and negatively charged phospholipids. In contrast to no inhibitory effect during peroxidation in non-ionic emulsions, in bilayers one molecule of DA traps approximately four peroxyl radicals, with a rate constant k_inh >10³ M^–1 s^–1. Our results from a homogeneous system and bilayers prove that catecholamines act as effective, radical trapping antioxidants with activity depending on the ionization status of the catechol moiety, as well as microenvironment: organization of the lipid system (emulsions vs bilayers) and interactions of catecholamines with the biomembrane.

Insights into the Pathogenesis of Neurodegenerative Diseases: Focus on Mitochondrial Dysfunction and Oxidative Stress

As the population ages, the incidence of neurodegenerative diseases is increasing. Due to intensive research, important steps in the elucidation of pathogenetic cascades have been made and significantly implicated mitochondrial dysfunction and oxidative stress. However, the available treatment in Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis is mainly symptomatic, providing minor benefits and, at most, slowing down the progression of the disease. Although in preclinical setting, drugs targeting mitochondrial dysfunction and oxidative stress yielded encouraging results, clinical trials failed or had inconclusive results. It is likely that by the time of clinical diagnosis, the pathogenetic cascades are full-blown and significant numbers of neurons have already degenerated, making it impossible for mitochondria-targeted or antioxidant molecules to stop or reverse the process. Until further research will provide more efficient molecules, a healthy lifestyle, with plenty of dietary antioxidants and avoidance of exogenous oxidants may postpone the onset of neurodegeneration, while familial cases may benefit from genetic testing and aggressive therapy started in the preclinical stage.

The Air We Breathe: Air Pollution as a Prevalent Proinflammatory Stimulus Contributing to Neurodegeneration

Air pollution is regarded as an important risk factor for many diseases that affect a large proportion of the human population. To date, accumulating reports have noted that particulate matter (PM) is closely associated with the course of cardiopulmonary disorders. As the incidence of Alzheimer’s disease (AD), Parkinson’s disease (PD), and autoimmune disorders have risen and as the world’s population is aging, there is an increasing interest in environmental health hazards, mainly air pollution, which has been slightly overlooked as one of many plausible detrimental stimuli contributing to neurodegenerative disease onset and progression. Epidemiological studies have indicated a noticeable association between exposure to PM and neurotoxicity, which has been gradually confirmed by in vivo and in vitro studies. After entering the body directly through the olfactory epithelium or indirectly by passing through the respiratory system into the circulatory system, air pollutants are subsequently able to reach the brain. Among the potential mechanisms underlying particle-induced detrimental effects in the periphery and the central nervous system (CNS), increased oxidative stress, inflammation, mitochondrial dysfunction, microglial activation, disturbance of protein homeostasis, and ultimately, neuronal death are often postulated and concomitantly coincide with the main pathomechanisms of neurodegenerative processes. Other complementary mechanisms by which PM could mediate neurotoxicity and contribute to neurodegeneration remain unconfirmed. Furthermore, the question of how strong and proven air pollutants are as substantial adverse factors for neurodegenerative disease etiologies remains unsolved. This review highlights research advances regarding the issue of PM with an emphasis on neurodegeneration markers, symptoms, and mechanisms by which air pollutants could mediate damage in the CNS. Poor air quality and insufficient knowledge regarding its toxicity justify conducting scientific investigations to understand the biological impact of PM in the context of various types of neurodegeneration.

Monoamine Oxidase Inhibitors: A Review of Their Anti-Inflammatory Therapeutic Potential and Mechanisms of Action

Chronic inflammatory diseases are debilitating, affect patients' quality of life, and are a significant financial burden on health care. Inflammation is regulated by pro-inflammatory cytokines and chemokines that are expressed by immune and non-immune cells, and their expression is highly controlled, both spatially and temporally. Their dysregulation is a hallmark of chronic inflammatory and autoimmune diseases. Significant evidence supports that monoamine oxidase (MAO) inhibitor drugs have anti-inflammatory effects. MAO inhibitors are principally prescribed for the management of a variety of central nervous system (CNS)-associated diseases such as depression, Alzheimer's, and Parkinson's; however, they also have anti-inflammatory effects in the CNS and a variety of non-CNS tissues. To bolster support for their development as anti-inflammatories, it is critical to elucidate their mechanism(s) of action. MAO inhibitors decrease the generation of end products such as hydrogen peroxide, aldehyde, and ammonium. They also inhibit biogenic amine degradation, and this increases cellular and pericellular catecholamines in a variety of immune and some non-immune cells. This decrease in end product metabolites and increase in catecholamines can play a significant role in the anti-inflammatory effects of MAO inhibitors. This review examines MAO inhibitor effects on inflammation in a variety of in vitro and in vivo CNS and non-CNS disease models, as well as their anti-inflammatory mechanism(s) of action.

A multidimensional computational exploration of congenital myasthenic syndrome causing mutations in human choline acetyltransferase

Missense mutations of human choline acetyltransferase (CHAT) are mainly associated with congenital myasthenic syndrome (CMS). To date, several pathogenic mutations have been reported, but due to the rarity and genetic complexity of CMS and difficult genotype-phenotype correlations, the CHAT mutations, and their consequences are underexplored. In this study, we systematically sift through the available genetic data in search of previously unreported pathogenic mutations and use a dynamic in silico model to provide structural explanations for the pathogenicity of the reported deleterious and undetermined variants. Through rigorous multiparameter analyses, we conclude that mutations can affect CHAT through a variety of different mechanisms: by disrupting the secondary structure, by perturbing the P-loop through long-range allosteric interactions, by disrupting the domain connecting loop, and by affecting the phosphorylation process. This study provides the first dynamic look at how mutations affect the structure and catalytic activity in CHAT and highlights the need for further genomic research to better understand the pathology of CHAT.

Clinical Phenotypes of Parkinson's Disease Associate with Distinct Gut Microbiota and Metabolome Enterotypes

Parkinson’s disease (PD) is a clinically heterogenic disorder characterized by distinct clinical entities. Most studies on motor deficits dichotomize PD into tremor dominant (TD) or non-tremor dominant (non-TD) with akinetic-rigid features (AR). Different pathophysiological mechanisms may affect the onset of motor manifestations. Recent studies have suggested that gut microbes may be involved in PD pathogenesis. The aim of this study was to investigate the gut microbiota and metabolome composition in PD patients in relation to TD and non-TD phenotypes. In order to address this issue, gut microbiota and the metabolome structure of PD patients were determined from faecal samples using 16S next generation sequencing and gas chromatography–mass spectrometry approaches. The results showed a reduction in the relative abundance of Lachnospiraceae, Blautia, Coprococcus, Lachnospira, and an increase in Enterobacteriaceae, Escherichia and Serratia linked to non-TD subtypes. Moreover, the levels of important molecules (i.e., nicotinic acid, cadaverine, glucuronic acid) were altered in relation to the severity of phenotype. We hypothesize that the microbiota/metabolome enterotypes associated to non-TD subtypes may favor the development of gut inflammatory environment and gastrointestinal dysfunctions and therefore a more severe α-synucleinopathy. This study adds important information to PD pathogenesis and emphasizes the potential pathophysiological link between gut microbiota/metabolites and PD motor subtypes.

Influence of energy deficiency on the subcellular processes of Substantia Nigra Pars Compacta cell for understanding Parkinsonian neurodegeneration

Parkinson's disease (PD) is the second most prominent neurodegenerative disease around the world. Although it is known that PD is caused by the loss of dopaminergic cells in substantia nigra pars compacta (SNc), the decisive cause of this inexorable cell loss is not clearly elucidated. We hypothesize that "Energy deficiency at a sub-cellular/cellular/systems level can be a common underlying cause for SNc cell loss in PD." Here, we propose a comprehensive computational model of SNc cell, which helps us to understand the pathophysiology of neurodegeneration at the subcellular level in PD. The aim of the study is to see how deficits in the supply of energy substrates (glucose and oxygen) lead to a deficit in adenosine triphosphate (ATP). The study also aims to show that deficits in ATP are the common factor underlying the molecular-level pathological changes, including alpha-synuclein aggregation, reactive oxygen species formation, calcium elevation, and dopamine dysfunction. The model suggests that hypoglycemia plays a more crucial role in leading to ATP deficits than hypoxia. We believe that the proposed model provides an integrated modeling framework to understand the neurodegenerative processes underlying PD.

The benzene metabolite p-benzoquinone inhibits the catalytic activity of bovine liver catalase: A biophysical study

The current communication reports the inhibitory effect of para-benzoquinone (p-BQ) on the structure and function of bovine liver catalase (BLC), a vital antioxidant enzyme. Both BLC and p-BQ were dissolved in respective buffers and the biophysical interaction was studied at physiological concentrations. For the first time our data reveals an enthalpy-driven interaction between BLC and p-BQ which is due to hydrogen bonding and van der Waals interactions. The binding affinity of p-BQ with BLC is nearly 2.5 folds stronger in MOPS buffer than Phosphate buffer. Importantly, the binding affinity between BLC and p-BQ was weak in HEPES buffer as compared to other buffers being the strongest in Tris buffer. Molecular docking studies reveal that binding affinity of p-BQ with BLC differ depending upon the nature of buffers rather than on the participating amino acid residues of BLC. This is further supported by the differential changes in secondary structures of BLC. The p-BQ-induced conformational change in BLC was evident from the reduced BLC activity in presence of different buffers in the following order, Phosphate>MOPS>Tris>HEPES. The absorbance peak of BLC was gradually increased and fluorescence spectra of BLC were drastically decreased when BLC to p-BQ molar ratio was incrementally enhanced from 0 to 10,000 times in presence of all buffers. Nevertheless, the declined activity of BLC was positively correlated with the reduced fluorescence and negatively correlated with the enhanced absorbance. Electrochemical study with cyclic voltammeter also suggests a direct binding of p-BQ with BLC in presence of different buffers. Thus, p-BQ-mediated altered secondary structure in BLC results into compromised activity of BLC.

How Monoamine Oxidase A Decomposes Serotonin: An Empirical Valence Bond Simulation of the Reactive Step

The enzyme-catalyzed degradation of the biogenic amine serotonin is an essential regulatory mechanism of its level in the human organism. In particular, monoamine oxidase A (MAO A) is an important flavoenzyme involved in the metabolism of monoamine neurotransmitters. Despite extensive research efforts, neither the catalytic nor the inhibition mechanisms of MAO enzymes are currently fully understood. In this article, we present the quantum mechanics/molecular mechanics simulation of the rate-limiting step for the serotonin decomposition, which consists of hydride transfer from the serotonin methylene group to the N5 atom of the flavin moiety. Free-energy profiles of the reaction were computed by the empirical valence bond method. Apart from the enzymatic environment, the reference reaction in the gas phase was also simulated, facilitating the estimation of the catalytic effect of the enzyme. The calculated barrier for the enzyme-catalyzed reaction of 14.82 ± 0.81 kcal mol-1 is in good agreement with the experimental value of 16.0 kcal mol-1, which provides strong evidence for the validity of the proposed hydride-transfer mechanism. Together with additional experimental and computational work, the results presented herein contribute to a deeper understanding of the catalytic mechanism of MAO A and flavoenzymes in general, and in the long run, they should pave the way toward applications in neuropsychiatry.

A comprehensive review of monoamine oxidase inhibitors as Anti-Alzheimer's disease agents: A review

Monoamine oxidases (MAO-A and MAO-B) are mammalian flavoenzyme, which catalyze the oxidative deamination of several neurotransmitters like norepinephrine, dopamine, tyramine, serotonin, and some other amines. The oxidative deamination produces several harmful side products like ammonia, peroxides, and aldehydes during the biochemical reaction. The concentration of biochemical neurotransmitter alteration in the brain by MAO is directly related with several neurological disorders like Alzheimer's disease and Parkinson's disease (PD). Activated MAO also contributes to the amyloid beta (Aβ) aggregation by two successive cleft β-secretase and γ-secretase of amyloid precursor protein (APP). Additionally, activated MAO is also involved in aggregation of neurofibrillary tangles and cognitive destruction through the cholinergic neuronal damage and disorder of the cholinergic system. MAO inhibition has general anti-Alzheimer's disease effect as a consequence of oxidative stress reduction prompted by MAO enzymes. In this review, we outlined and addressed recent understanding on MAO enzymes such as their structure, physiological function, catalytic mechanism, and possible therapeutic goals in AD. In addition, it also highlights the current development and discovery of potential MAO inhibitors (MAOIs) from various chemical scaffolds.

Hydride Abstraction as the Rate-Limiting Step of the Irreversible Inhibition of Monoamine Oxidase B by Rasagiline and Selegiline: A Computational Empirical Valence Bond Study

Monoamine oxidases (MAOs) catalyze the degradation of a very broad range of biogenic and dietary amines including many neurotransmitters in the brain, whose imbalance is extensively linked with the biochemical pathology of various neurological disorders, and are, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. Still, despite this practical significance, the precise molecular mechanism underlying the irreversible MAO inhibition with clinically used propargylamine inhibitors rasagiline and selegiline is still not unambiguously determined, which hinders the rational design of improved inhibitors devoid of side effects current drugs are experiencing. To address this challenge, we present empirical valence bond QM/MM simulations of the rate-limiting step of the MAO inhibition involving the hydride anion transfer from the inhibitor α-carbon onto the N5 atom of the flavin adenin dinucleotide (FAD) cofactor. The proposed mechanism is strongly supported by the obtained free energy profiles, which confirm a higher reactivity of selegiline over rasagiline, while the calculated difference in the activation Gibbs energies of ΔΔG^‡ = 3.1 kcal mol^-1 is found to be in very good agreement with that from the measured literature k_inact values that predict a 1.7 kcal mol^-1 higher selegiline reactivity. Given the similarity with the hydride transfer mechanism during the MAO catalytic activity, these results verify that both rasagiline and selegiline are mechanism-based irreversible inhibitors and offer guidelines in designing new and improved inhibitors, which are all clinically employed in treating a variety of neuropsychiatric and neurodegenerative conditions.

Cyclization step of noradrenaline and adrenaline autoxidation: a quantum chemical study

Catecholamine autoxidation has been recognized as one of the potential trigger factors for catecholaminergic neuron loss characteristics of neurodegenerative diseases. The cyclization step with intramolecular Michael addition of catecholamine o-quinones has been shown to be the irreversible and rate limiting step of the autoxidation reaction across a broad pH range and has a complex pH dependence that has not yet been fully understood. Using quantum chemical calculations, we demonstrated that in the case of noradrenaline and adrenaline two catecholamine o-quinone species, one with an unprotonated and one with a protonated quinone group can participate in the cyclization reaction and that the mechanisms of these reactions significantly differ, emphasizing the importance of quinone group protonation states in the reaction mechanism. With a thorough exploration of the reaction kinetics, we further showed that at acidic pH the cyclization reaction rate is pH independent, while at alkaline pH the pH dependence is marked, explaining the experimentally observed complex pH dependence.

The quinone group protonation state determines the reaction mechanism of noradrenaline and adrenaline o-quinone cyclization.

Experimental and theoretical substantiation of differences of geometric isomers of copper(II) α-amino acid chelates in ATR-FTIR spectra

Stereo and structural isomerism of the copper(II) chelate complexes define their biological activity. At the same time, the identification of the geometric isomers of such complexes is a nontrivial task of modern coordination chemistry. In the presented work we have studied the trans- and cis-isomers of chelates bis(S-valinato)copper(II), (R,S-valinato)copper(II) and other mixed ligand copper(II) amino acid complexes with the joint use of experimental by ATR-FTIR spectroscopy and DFT simulations. Using DFT simulations (method M06/6 311+G(d)) the optimum conformers of the geometric isomers of copper(II) a-amino acid chelate complexes were found and their characteristic stretching vibrations were established in the mid-wave region of the IR spectra. The experimental ATR-FTIR bands of the compounds well agree with the theoretical estimates. Such a joint use allows to determine of cis- and trans-isomers of copper(II) N,O-amino acid chelates in the mid-wave region of the ATR-FTIR spectrum.

Path Integral Calculation of the Hydrogen/Deuterium Kinetic Isotope Effect in Monoamine Oxidase A-Catalyzed Decomposition of Benzylamine

Monoamine oxidase A (MAO A) is a well-known enzyme responsible for the oxidative deamination of several important monoaminergic neurotransmitters. The rate-limiting step of amine decomposition is hydride anion transfer from the substrate α–CH2 group to the N5 atom of the flavin cofactor moiety. In this work, we focus on MAO A-catalyzed benzylamine decomposition in order to elucidate nuclear quantum effects through the calculation of the hydrogen/deuterium (H/D) kinetic isotope effect. The rate-limiting step of the reaction was simulated using a multiscale approach at the empirical valence bond (EVB) level. We applied path integral quantization using the quantum classical path method (QCP) for the substrate benzylamine as well as the MAO cofactor flavin adenine dinucleotide. The calculated H/D kinetic isotope effect of 6.5 ± 1.4 is in reasonable agreement with the available experimental values.

Experimental and Computational Study of the Antioxidative Potential of Novel Nitro and Amino Substituted Benzimidazole/Benzothiazole-2-Carboxamides with Antiproliferative Activity

We present the synthesis of a range of benzimidazole/benzothiazole-2-carboxamides with a variable number of methoxy and hydroxy groups, substituted with nitro, amino, or amino protonated moieties, which were evaluated for their antiproliferative activity in vitro and the antioxidant capacity. Antiproliferative features were tested on three human cancer cells, while the antioxidative activity was measured using 1,1-diphenyl-picrylhydrazyl (DPPH) free radical scavenging and ferric reducing antioxidant power (FRAP) assays. Trimethoxy substituted benzimidazole-2-carboxamide 8 showed the most promising antiproliferative activity (IC₅₀ = 0.6–2.0 µM), while trihydroxy substituted benzothiazole-2-carboxamide 29 was identified as the most promising antioxidant, being significantly more potent than the reference butylated hydroxytoluene BHT in both assays. Moreover, the latter also displays antioxidative activity in tumor cells. The measured antioxidative capacities were rationalized through density functional theory (DFT) calculations, showing that 29 owes its activity to the formation of two [O•∙∙∙H–O] hydrogen bonds in the formed radical. Systems 8 and 29 were both chosen as lead compounds for further optimization of the benzazole-2-carboxamide scaffold in order to develop more efficient antioxidants and/or systems with the antiproliferative activity.

Computational Insight into the Mechanism of the Irreversible Inhibition of Monoamine Oxidase Enzymes by the Antiparkinsonian Propargylamine Inhibitors Rasagiline and Selegiline

Monoamine oxidases (MAOs) are flavin adenine dinucleotide containing flavoenzymes that catalyze the degradation of a range of brain neurotransmitters, whose imbalance is extensively linked with the pathology of various neurological disorders. This is why MAOs have been the central pharmacological targets in treating neurodegeneration for more than 60 years. Still, despite this practical importance, the precise chemical mechanisms underlying the irreversible inhibition of the MAO B isoform with clinical drugs rasagiline (RAS) and selegiline (SEL) remained unknown. Here we employed a combination of MD simulations, MM-GBSA binding free energy evaluations, and QM cluster calculations to show the MAO inactivation proceeds in three steps, where, in the rate-limiting first step, FAD utilizes its N5 atom to abstracts a hydride anion from the inhibitor α-CH₂ group to ultimately give the final inhibitor-FAD adduct matching crystallographic data. The obtained free energy profiles reveal a lower activation energy for SEL by 1.2 kcal mol^-1 and a higher reaction exergonicity by 0.8 kcal mol^-1, with the former being in excellent agreement with experimental ΔΔG^‡_EXP = 1.7 kcal mol^-1, thus rationalizing its higher in vivo reactivity over RAS. The calculated ΔG_BIND energies confirm SEL binds better due to its bigger size and flexibility allowing it to optimize hydrophobic C-H···π and π···π interactions with residues throughout both of enzyme's cavities, particularly with FAD, Gln206 and four active site tyrosines, thus overcoming a larger ability of RAS to form hydrogen bonds that only position it in less reactive orientations for the hydride abstraction. Offered results elucidate structural determinants affecting the affinity and rates of the inhibition reaction that should be considered to cooperate when designing more effective compounds devoid of untoward effects, which are of utmost significance and urgency with the growing prevalence of brain diseases.

Revisited Mechanism of Reaction between a Model Lysine Amino Acid Side Chain and 4-Hydroxynonenal in Different Solvent Environments

We revisit the mechanism of reaction between a model lysine side chain and reactive aldehyde 4-hydroxynonenal in different solvents with an increasing water content. We show by model organic reactions and qualitative spectrometric analysis that a nonpolar pyrrole adduct is dominantly formed in non-aqueous solvents dichloromethane and acetonitrile. On the other hand, in aqueous acetonitrile and neat water, other polar products are also isolated, including Michael adducts, hemiacetal adducts, and pyridinium salt adducts, at the same time as the ratio of nonpolar products to polar products is decreasing. The experiments are supported by detailed quantum chemical calculations of the reaction mechanism with different computational setups showing that the pyrrole adduct is the most thermodynamically stable product compared to Michael adducts and hemiacetal adducts and also indicating that water molecules released along the reaction pathway are catalyzing reaction steps involving proton transfer. Finally, we also identify the mechanism of the pyridinium salt adduct that is formed only in aqueous solutions.

Dopamine Autoxidation Is Controlled by Acidic pH

We studied the reaction mechanism of dopamine autoxidation using quantum chemical methods. Unlike other biogenic amines important in the central nervous system, dopamine and noradrenaline are capable of undergoing a non-enzymatic autoxidative reaction giving rise to a superoxide anion that further decomposes to reactive oxygen species. The reaction in question, which takes place in an aqueous solution, is as such not limited to the mitochondrial membrane where scavenging enzymes such as catalase and superoxide dismutase are located. With the experimental rate constant of 0.147 s⁻¹, the dopamine autoxidation reaction is comparably as fast as the monoamine oxidase B catalyzed dopamine decomposition with a rate constant of 1 s⁻¹. By using quantum chemical calculations, we demonstrated that the rate-limiting step is the formation of a hydroxide ion from a water molecule, which attacks the amino group that enters intramolecular Michael addition, giving rise to a pharmacologically inert aminochrome. We have shown that for dopamine stability on a time scale of days, it is essential that the pH value of the synaptic vesicle interior is acidic. The pathophysiologic correlates of the results are discussed in the context of Parkinson's disease as well as the pathology caused by long-term amphetamine and cocaine administration.

The inhibition of heme oxigenase-1 (HO-1) abolishes the mitochondrial protection induced by sesamol in LPS-treated RAW 264.7 cells

Redox impairment and mitochondrial dysfunction have been seen in inflammation. Thus, there is interest in studies aiming to find molecules that would exert mitochondrial protection in mammalian tissues undergoing inflammation. Sesamol (SES) is an antioxidant and anti-inflammatory molecule as demonstrated in both in vitro and in vivo experimental models. Nonetheless, it was not previously demonstrated whether and how SES would cause mitochondrial protection during inflammation. Thus, we investigated here whether a pretreatment (for 1 h) with SES (1-100 μM) would prevent mitochondrial impairment in lipopolysaccharide (LPS)-treated RAW 264.7 cells. It was also evaluated whether the heme oxigenase-1 (HO-1) would be involved in the effects on mitochondria induced by SES. We found that SES reduced the levels of lipid peroxidation and protein nitration in the membranes of mitochondria obtained from LPS-treated RAW 264.7 cells. SES also attenuated the production of superoxide anion radical (O₂^-•) and nitric oxide (NO^•) in this experimental model. SES suppressed the LPS-elicited mitochondrial dysfunction, as assessed through the analyses of the activities of the mitochondrial complexes I and V. SES also abrogated the LPS-induced decrease in the levels of adenosine triphosphate (ATP) and in the mitochondrial membrane potential (MMP). SES induced mitochondria-related anti-apoptotic effects in LPS-treated cells. Besides, SES pretreatment abrogated the LPS-triggered inflammation by decreasing the levels of pro-inflammatory proteins. The SES-induced mitochondria-associated protection was blocked by the specific inhibitor of HO-1, ZnPP IX (20 μM). Therefore, SES induced mitochondrial protection in LPS-treated cells by a mechanism involving HO-1.

Drosophila melanogaster has the enzymatic machinery to make the melanic component of neuromelanin

In Drosophila, the same set of genes that are used for cuticle pigmentation and sclerotization are present in the nervous system and are responsible for neurotransmitter recycling. In this study, we carried out biochemical analysis to determine whether insects have the enzymatic machinery to make melanic component of neuromelanin. We focused our attention on two key enzymes of melanogenesis, namely phenoloxidase and dopachrome decarboxylase/tautomerase. Activity staining of the proteins isolated from the Drosophila larval brain tissue, separated by native polyacrylamide gel electrophoresis, indicated the presence of these two enzymes. Mass spectral sequence analysis of the band also supported this finding. To best of our knowledge, this is the first report on the presence of the enzymatic machinery to make melanin part of neuromelanin in any insect brain.

Why does the Y326I mutant of monoamine oxidase B decompose an endogenous amphetamine at a slower rate than the wild type enzyme? Reaction step elucidated by multiscale molecular simulations

This work investigates the Y326I point mutation effect on the kinetics of oxidative deamination of phenylethylamine (PEA) catalyzed by the monoamine oxidase B (MAO B) enzyme. PEA is a neuromodulator capable of affecting the plasticity of the brain and is responsible for the mood enhancing effect caused by physical exercise. Due to a similar functionality, PEA is often regarded as an endogenous amphetamine. The rate limiting step of the deamination was simulated at the multiscale level, employing the Empirical Valence Bond approach for the quantum treatment of the involved valence states, whereas the environment (solvated protein) was represented with a classical force field. A comparison of the reaction free energy profiles delivered by simulation of the reaction in the wild type MAO B and its Y326I mutant yields an increase in the barrier by 1.06 kcal mol^-1 upon mutation, corresponding to a roughly 6-fold decrease in the reaction rate. This is in excellent agreement with the experimental kinetic studies. Inspection of simulation trajectories reveals possible sources of the point mutation effect, namely vanishing favorable electrostatic interactions between PEA and a Tyr326 side chain and an increased amount of water molecules at the active site due to the replacement of tyrosine by a less spacious isoleucine residue, thereby increasing the dielectric shielding of the catalytic environment provided by the enzyme.

Human dopamine transporter: the first implementation of a combined in silico/in vitro approach revealing the substrate and inhibitor specificities

Parkinson's disease (PD) is characterized by the loss of dopamine-generating neurons in the substantia nigra and corpus striatum. Current treatments alleviate PD symptoms rather than exerting neuroprotective effect on dopaminergic neurons. New drugs targeting the dopaminergic neurons by specific uptake through the human dopamine transporter (hDAT) could represent a viable strategy for establishing selective neuroprotection. Molecules able to increase the bioactive amount of extracellular dopamine, thereby enhancing and compensating a loss of dopaminergic neurotransmission, and to exert neuroprotective response because of their accumulation in the cytoplasm, are required. By means of homology modeling, molecular docking, and molecular dynamics simulations, we have generated 3D structure models of hDAT in complex with substrate and inhibitors. Our results clearly reveal differences in binding affinity of these compounds to the hDAT in the open and closed conformations, critical for future drug design. The established in silico approach allowed the identification of promising substrate compounds that were subsequently analyzed for their efficiency in inhibiting hDAT-dependent fluorescent substrate uptake, through in vitro live cell imaging experiments. Taken together, our work presents the first implementation of a combined in silico/in vitro approach enabling the selection of promising dopaminergic neuron-specific substrates.

B Vitamins and Ageing

Vitamin B contributes to the overall health and wellbeing, including that of energy metabolism, methylation, synthesis and DNA repair and proper immune function. Deficiency in B vitamins has been linked to neurocognitive disorders, mitochondrial dysfunction, immune dysfunction and inflammatory conditions. In ageing populations B vitamin deficiency has been linked to cardiovascular disorders, cognitive dysfunction, osteoporosis and methylation disorders and can increase the risk of developing degenerative diseases, particularly cardiovascular disease, cognitive diseases and osteoporosis. Optimization of B vitamin status in the elderly may prove beneficial in the prevention of degenerative diseases. Here we discuss broadly the role of B vitamins in ageing.

Free radicals and polyphenols: The redox chemistry of neurodegenerative diseases

The oxidation of bioorganic materials by air and, particularly, the oxidative stress involved in the cell loss and other pathologies associated with neurodegenerative diseases (NDs) are of enormous social and economic importance. NDs generally involve free radical reactions, beginning with the formation of an initiating radical by some redox, thermal or photochemical process, causing nucleic acid, protein and lipid oxidations and the production of harmful oxidative products. Physically, persons afflicted by NDs suffer progressive loss of memory and thinking ability, mood swings, personality changes, and loss of independence. Therefore, the development of antioxidant strategies to retard or minimize the oxidative degradation of bioorganic materials has been, and still is, of paramount importance. While we are aware of the importance of investigating the biological and medical aspects of the diseases, elucidation of the associated chemistry is crucial to understanding their progression, heading to intelligent chemical intervention to find more efficient therapies to prevent or delay the onset of the diseases. Accordingly, this review aims to provide the reader with a chemical base to understand the behavior and properties of the reactive oxygen species involved and of typical radical scavengers such as polyphenolic antioxidants. Some discussion on the structures of the various species, their formation, chemical reactivities and lifetimes is included. The ultimate goal is to understand how, when and where they form, how far they travel prior to react, which molecules are their targets, and how we can, eventually, control their activity to minimize their impact by means of chemical methods. Recent strategies explore chemical modifications of the hydrophobicity of potent, natural antioxidants to improve their efficiency by fine-tuning their concentrations at the reaction site.

What a Difference a Methyl Group Makes: The Selectivity of Monoamine Oxidase B Towards Histamine and N-Methylhistamine

Monoamine oxidase (MAO) enzymes catalyze the degradation of a very broad range of biogenic and dietary amines including many neurotransmitters in the brain, whose imbalance is extensively linked with the biochemical pathology of various neurological disorders. Although sharing around 70 % sequence identity, both MAO A and B isoforms differ in substrate affinities and inhibitor sensitivities. Inhibitors that act on MAO A are used to treat depression, due to their ability to raise serotonin concentrations, whereas MAO B inhibitors decrease dopamine degradation and improve motor control in patients with Parkinson disease. Despite this functional importance, the factors affecting MAO selectivity are poorly understood. Here, we used a combination of molecular dynamics (MD) simulations, molecular mechanics with Poisson-Boltzmann and surface area solvation (MM-PBSA) binding free energy evaluations, and quantum mechanical (QM) cluster calculations to address the unexpected, yet challenging MAO B selectivity for N-methylhistamine (NMH) over histamine (HIS), differing only in a single methyl group distant from the reactive ethylamino center. This study shows that a dominant selectivity contribution is offered by a lower activation free energy for NMH by 2.6 kcal mol^-1 , in excellent agreement with the experimental ΔΔG^≠_EXP =1.4 kcal mol^-1 , together with a more favorable reaction exergonicity and active-site binding. This study also confirms the hydrophobic nature of the MAO B active site and underlines the important role of Ile199, Leu171, and Leu328 in properly orienting substrates for the reaction.