Piroxicam inhibits NMDA receptor-mediated excitotoxicity through allosteric inhibition of the GluN2B subunit: An in silico study elucidating a novel mechanism of action of the drug

In-silico studies on wild orange (Citrus macroptera Mont.) compounds against COVID-19 pro-inflammation targets

One-fifth of COVID-19 patients suffer a severe course of COVID-19 (SARS-CoV-2) infection; however, the specific causes remain unclear. Despite numerous papers that have been flooded in different scientific journals clear clinical picture of COVID-19 aftermath persists to remain fuzzy. The survivors of severe COVID-19infection having defeated the virus are just the starting of an uncharted recovery path. Currently, there is no drug available that is safe to consume to combat this pandemic. However, researchers still struggling to find specific therapeutic solutions. The present study employed an in silico approach to assessing the inhibitory potential of the phytochemicals obtained from GC-MS analysis of Citrus macroptera against inflammatory proteins like COX-2, NMDAR and VCAM-1 which remains in a hyperactive state even after a patient is fully cured of this deadly mRNA virus. An extensive molecular docking investigation of the phyto-compounds at the active binding pockets of the inflammatory proteins revealed the promising inhibitory potential of the phytochemicals. Reasonable physicochemical attributes of the compounds following Lipinski's rule of five, VEBER and PAINS analysis further established them as potential therapeutic candidates against aforesaid inflammatory proteins. MM-GBSA binding free energy estimation revealed that Limonene was the most promising candidate displaying the highest binding efficacy with the concerned VCAM-1 protein included in the present analysis. An interesting finding is the phytochemicals exhibited better binding energy scores with the concerned COX-2, VCAM-1 and NMDA receptor proteins than the conventional drugs that are specifically targeted against them. Our in silico results suggest that all the natural phyto-compounds derived from C. macroptera could be employed in Post covid inflammation complexities after appropriate pre-clinical and clinical trials for further scientific validation.Communicated by Ramaswamy H. Sarma.

Meloxicam Inhibits Apoptosis in Neurons by Deactivating Tumor Necrosis Factor Receptor Superfamily Member 25, Leading to the Decreased Cleavage of DNA Fragmentation Factor Subunit α in Alzheimer's Disease

Neuronal apoptosis is considered to be a critical cause of Alzheimer's disease (AD). Recently, meloxicam has shown neuroprotective effects; however, the inherent mechanisms are highly overlooked. Using APP/PS1 transgenic (Tg) mice as in vivo animal models, we found that meloxicam inhibits apoptosis in neurons by deactivating tumor necrosis factor receptor superfamily member 25 (TNFRSF25), leading to the suppression of the expression of fas-associated protein with death domain (FADD) and the cleavage of DNA fragmentation factor subunit α (DFFA) and cysteine aspartic acid protease-3 (caspase 3) via β-amyloid protein (Aβ)-depressing mechanisms. Moreover, the meloxicam treatment blocked the effects of β-amyloid protein oligomers (Aβo) on stimulating the synthesis of tumor necrosis factor α (TNF-α) and TNF-like ligand 1A (TL1A) in neuroblastoma (N) 2a cells. TNF-α and TL1A induce apoptosis in neurons via TNFR- and TNFRSF25-dependent caspase 3-activating mechanisms, respectively. Knocking down the expression of TNFRSF25 blocked the effects of TL1A on inducing apoptosis in neurons by deactivating the signaling cascades of FADD, caspase 3, and DFFA. Consistently, TNFRSF25 shRNA blocked the effects of Aβo on inducing neuronal apoptosis, which was corroborated by the efficacy of meloxicam in inhibiting Aβo-induced neuronal apoptosis. By ameliorating neuronal apoptosis, meloxicam improved memory loss in APP/PS1 Tg mice.

GPCR_LigandClassify.py; a rigorous machine learning classifier for GPCR targeting compounds

The current study describes the construction of various ligand-based machine learning models to be used for drug-repurposing against the family of G-Protein Coupled Receptors (GPCRs). In building these models, we collected > 500,000 data points, encompassing experimentally measured molecular association data of > 160,000 unique ligands against > 250 GPCRs. These data points were retrieved from the GPCR-Ligand Association (GLASS) database. We have used diverse molecular featurization methods to describe the input molecules. Multiple supervised ML algorithms were developed, tested and compared for their accuracy, F scores, as well as for their Matthews' correlation coefficient scores (MCC). Our data suggest that combined with molecular fingerprinting, ensemble decision trees and gradient boosted trees ML algorithms are on the accuracy border of the rather sophisticated deep neural nets (DNNs)-based algorithms. On a test dataset, these models displayed an excellent performance, reaching a ~ 90% classification accuracy. Additionally, we showcase a few examples where our models were able to identify interesting connections between known drugs from the Drug-Bank database and members of the GPCR family of receptors. Our findings are in excellent agreement with previously reported experimental observations in the literature. We hope the models presented in this paper synergize with the currently ongoing interest of applying machine learning modeling in the field of drug repurposing and computational drug discovery in general.

An in silico investigation on the inhibitory potential of the constituents of Pomegranate juice on antioxidant defense mechanism: Relevance to neurodegenerative diseases

Elevation in the levels of reactive oxygen and nitrogen species (RONS), and downregulation of cellular antixoidants, have ubiquitously been reported from studies in animal models of neurodegenerative diseases, including Parkinson’s disease (PD) and Alzheimer’s disease (AD). Thus, plant-derived compounds are widely being investigated for their beneficial effects in these models. However, while studies have reported antioxidant potentials of several phytochemicals, a large number of studies have demonstrated different phytochemicals to be rather pro-oxidant and exaggerate oxidative stress (OS). One such study aimed to investigate possible ameliorative effect of Pomegranate juice (PJ) in rat model of toxin-induced parkinsonism revealed that PJ exacerbates OS, inflammation and promotes neurodegeneration. Thus, it remains to be investigated whether different constituents and metabolites of PJ are pro-oxidant or anti-oxidant. Using computational modeling, we investigated possible inhibitory potential of different constituents of PJ and their metabolites viz. delphinidin-3-glucoside, dimethylellagic acid-glucuronide, ellagic acid, ellagitannin, gallic acid, gallotannin 23, pelargonidin, punicalagin, urolithin A, urolithin A-glucuronide and urolithin B, on anti-oxidant defense system of the brain. The results indicate that the constituents of PJ have the potential to inhibit five key enzymes of the neuronal antioxidant defense system, viz. catalase, superoxide dismutase, glutathione peroxidase 4, glutathione reductase and glutathione-S-transferase. Thus, it is surmised that the constituents of PJ may contribute to OS and neurodegeneration by way of affecting antioxidant defense mechanism. This may particularly be more pronounced in neurodegenerative diseases, since neurons are known to be more vulnerable to OS. Thus, the present findings caution the use of PJ in patients prone to OS, especially those suffering from neurodegenerative diseases, and warrant further experimental studies to unveil the effects of individual components and metabolites of PJ on antioxidant defense system of brain.

Tea polyphenols as multi-target therapeutics for Alzheimer's disease: An in silico study

Alzheimer's disease (AD) is the most common progressive neurodegenerative disease characterized by cognitive decline, dementia, and in later stages complete loss of feelings, sensation and death. The global prevalence of the disease is on the rise, and it affects 35-40% of the population above 80 years. The pathological hallmarks of the disease include extra-neuronal deposition of amyloid-β (Aβ) as plaques and intra-neuronal hyperphosphorylated tau protein as neurofibrillary tangles, which cause neurodegeneration and cerebral atrophy. Aβ deposition is catalyzed by β-secretase and γ-secretase, while tau hyperphosphorylation is catalyzed by glycogen synthase kinase - 3β (GSK-3β). With neurodegeneration, the level of the neurotransmitter acetylcholine (ACh), as well as acetylcholinesterase (AChE), decreases in the synaptic cleft, called cholinergic deficiency. This leads to the cardinal behavioural abnormalities of AD, which is referred to as cholinergic hypothesis of AD. The other enzyme which degrades ACh is the butyrylcholinesterase (BuChE). Thus, current treatment options of AD include symptomatic treatment to elevate the levels of ACh by inhibiting AChE. However, the currently used drugs cause several side effects, and the quest for novel drugs remains an interesting and essential venture. Since the disease has multiple pathophysiologies, there is an unrelenting need to develop novel drugs and lead molecules capable of inhibiting multiple pathways. The present study hypothesizes use of tea polyphenols against the key drug targets of AD, viz. β-Secretase, γ-Secretase, GSK-3β, AChE and BuChE. The hypothesis has been validated using molecular docking tools. The result indicates that the polyphenols may potentially inhibit these enzymes, similar to their known inhibitors. Thus, the findings are of immense significance in the therapeutic interventions of AD, using tea polyphenols as exciting multi-target drugs.

Disturbed purine nucleotide metabolism in chronic kidney disease is a risk factor for cognitive impairment

Chronic kidney disease (CKD) is an increasing global health burden. Disturbance in purine metabolism pathway and a higher level of serum uric acid, called hyperuricemia, is a risk factor of CKD, and it has been linked to increased prevalence and progression of the disease. In a recent study, it has been demonstrated that purine nucleotides and uric acid alter the activity of acetylcholinesterase (AChE). Thus, we hypothesize that adenine, hypoxanthine, xanthine, 2,8-dihydroxyadenine and uric acid may potentially interfere with the activity of AChE. The hypothesis has been tested using computational tools. Uric acid has been found to be the most potent inhibitor of AChE, with a binding affinity higher than the known inhibitors of the enzyme. Further, since depleted AChE activity is associated with dementia and cognitive impairment, the present study suggest that disturbed purine nucleotide metabolism in CKD is a risk factor for cognitive impairment.

Exploring neuroprotective potential of Withania somnifera phytochemicals by inhibition of GluN2B-containing NMDA receptors: An in silico study

N-methyl-d-aspartate receptors (NMDARs) mediated excitotoxicity has been implicated in multi-neurodegenerative diseases. Due to lack of efficacy and adverse effects of NMDA receptor antagonists, search for herbal remedies that may act as therapeutic agents is an active area of research to combat these diseases. Withania somnifera (WS) is being used for centuries as a nerve tonic and Nootropic agents. The present study targets the in silico evaluation of the neuroprotective efficacy of W. somnifera phytochemicals by inhibition of NMDA receptor-mediated excitotoxicity through allosteric inhibition of the GluN2B containing NMDARs. We predict Blood Brain Barrier (BBB) penetration, mutagenicity, drug-likeness and Human Intestinal Absorption properties of 25 WS phytochemicals. Further, molecular docking was performed to know whether these phytochemicals inhibit the GluN2B containing NMDARs or not. The results suggest that Anaferine, Beta-Sitosterol, Withaferin A, Withanolide A, Withanolide B and Withanolide D inhibit GluN2B containing NMDARs through allosteric mode similar to the well-known selective antagonist Ifenprodil. These phytochemicals have potential as an essentially useful oral drug to counter NMDARs mediated excitotoxicity and to treat multi-neurodegenerative diseases.

Piroxicam confer neuroprotection in Cerebral Ischemia by inhibiting Cyclooxygenases, Acid- Sensing Ion Channel-1a and Aquaporin-4: an in silico comparison with Aspirin and Nimesulide

Cerebral ischemia (CI), caused by the deprivation of oxygen and glucose to the brain, is the leading cause of permanent disability. Neuronal demise in CI has been linked to several pathways which include cyclooxygenases (COX) − mediated production of prostaglandins (PGs) and subsequently reactive oxygen species (ROS), aquaporin-4 (AQ-4) − mediated brain edema and acidsensing ion channel-1a (ASIC-1a) − mediated acidotoxicity, matrix remodeling, in addition to others. Several non-steroidal antiinflammatory drugs (NSAIDs) are presently in use to prevent these pathways. However, owing to the large number of processes involved, there is high drug load. So, identifying drugs with multimodal role has always been a frequently sought venture. The present in silico study has been performed to find out the relative efficacy of three different NSAIDs (Piroxicam, Aspirin and Nimesulide) in preventing neurodegeneration in CI, with respect to their inhibitory potential on COXs, AQ-4 and ASIC-1a. We find that piroxicam is the most potent inhibitor of these receptors as compared to the NSAIDs under investigation. Since piroxicam has already been reported to inhibit N-methyl-D-aspartate (NMDA) receptor and matrix metalloproteinases (MMPs), which are also linked to CI-induced neurodegeneration, we hereby propose piroxicam to be a gold-standard drug in preventing neurodegeneration in CI.