Nikhil Maroli

Bio: Nikhil Maroli is an academic researcher from Indian Institute of Science. The author has contributed to research in topics: Molecular beacon & Aptamer. The author has an hindex of 7, co-authored 17 publications receiving 105 citations. Previous affiliations of Nikhil Maroli include Defence Research and Development Organisation & Bharathiar University.

The Potential role of Procyanidin as a Therapeutic Agent against SARS-CoV-2: A Text Mining, Molecular Docking and Molecular Dynamics Simulation Approach

Abstract: A novel coronavirus (SARS-CoV-2) has caused a major outbreak in human all over the world. There are several proteins interplay during the entry and replication of this virus in human. Here, we have used text mining and named entity recognition method to identify co-occurrence of the important COVID 19 genes/proteins in the interaction network based on the frequency of the interaction. Network analysis revealed a set of genes/proteins, highly dense genes/protein clusters and sub-networks of Angiotensin-converting enzyme 2 (ACE2), Helicase, spike (S) protein (trimeric), membrane (M) protein, envelop (E) protein, and the nucleocapsid (N) protein. The isolated proteins are screened against procyanidin-a flavonoid from plants using molecular docking. Further, molecular dynamics simulation of critical proteins such as ACE2, Mpro and spike proteins are performed to elucidate the inhibition mechanism. The strong network of hydrogen bonds and hydrophobic interactions along with van der Waals interactions inhibit receptors, which are essential to the entry and replication of the SARS-CoV-2. The binding energy which largely arises from van der Waals interactions is calculated (ACE2=-50.21 ± 6.3, Mpro=-89.50 ± 6.32 and spike=-23.06 ± 4.39) through molecular mechanics Poisson-Boltzmann surface area also confirm the affinity of procyanidin towards the critical receptors. Communicated by Ramaswamy H. Sarma.

The neurotoxicity of environmental aluminum is still an issue - eScholarship

Abstract: NeuroToxicology 31 (2010) 575–581 Contents lists available at ScienceDirect NeuroToxicology Review The neurotoxicity of environmental aluminum is still an issue Stephen C. Bondy * Program in Environmental Toxicology, Division Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA 92697-1825, USA A R T I C L E I N F O A B S T R A C T Article history: Received 18 September 2009 Received in revised form 24 March 2010 Accepted 10 May 2010 Available online 27 May 2010 Evidence for the neurotoxicity of extended exposure to low levels of aluminum salts is described using an animal model treated with aluminum at low levels reflecting those found in some water supplies. Emphasis is given to the potential role of aluminum in acceleration and promotion of some indices characteristic of brain aging. These hallmarks include the appearance of excess levels of inflammation in specific brain areas. Aluminum salts can increase levels of glial activation, inflammatory cytokines and amyloid precursor protein within the brain. Both normal brain aging and to a greater extent, Alzheimer’s disease are associated with elevated basal levels of markers for inflammation. These are not attributable to obvious exogenous stimuli and may reflect the lifespan history of the organism’s immune responses. It is possible that aluminum salts can act as a subtle promoter of such apparently unprovoked responses. s 2010 Elsevier Inc. All rights reserved. Keywords: Aluminum Drinking water brain aging Alzheimer’s disease Contents Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Aluminum is environmentally prevalent and ingested by humans. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . There is an epidemiological relation between chronic aluminum exposure and the incidence of Alzheimer’s disease . . . . . . . . . . . Aluminum exposure may also promote the onset of Parkinson’s disease. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Acute exposure to aluminum can cause clinical neurotoxicity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Elevated levels of intrinsic inflammation are associated with neural aging and this is exacerbated in several neurodegenerative diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Low levels of aluminum in drinking water of experimental animals, elevate basal levels of inflammatory activity within the CNS Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1. Introduction This review on the potential neurotoxic hazard posed by aluminum focuses on distinguishing between those aspects of aluminum neurotoxicity that are widely accepted and not controversial, and those aspects that are suggestive but not fully established. The work of this laboratory over the past 12 years is described and this falls into the latter classification, adding to the body of evidence increasingly implicating aluminum as a potentially hazardous environmental agent. The most accepted facts relating to aluminum include: (i) it’s widespread prevalence and level of human consumption, (ii) the * Correspondence address: Department of Community and Environmental Medicine, University of California at Irvine, Irvine, CA 92697-1825, USA. Tel.: +1 949 824 8077; fax: +1 949 824 2793. E-mail address: scbondy@uci.edu. 0161-813X/$ – see front matter s 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.neuro.2010.05.009 known neurotoxicity of high levels of aluminum, and (iii) a repeated epidemiological correlation between ingested aluminum and the incidence of Alzheimer’s disease. Another relevant area of widespread consensus is the tendency of the aging brain to express elevated levels of inflammation and the further exacerbation of this state in several neurodegenerative diseases. Less accepted is the evidence that aluminum can be a causal factor in promoting Alzheimer’s disease. This area has been handicapped by earlier erroneous reports of heightened levels of aluminum in amyloid plaques. Tissue aluminum levels are notoriously difficult to determine and later more reliable findings leading to similar conclusions have been overshadowed by these original reports. The main objective of our more recent studies has been to study the effects of extended exposure of experimental animals to levels of aluminum that have relevance for the human population. Demon- stration that these can provoke cerebral inflammatory responses resembling those that are found with brain senescence, can provide a mechanistic link to epidemiological reports.

Artificial Intelligence in the Battle against Coronavirus (COVID-19): A Survey and Future Research Directions

Abstract: Artificial intelligence (AI) has been applied widely in our daily lives in a variety of ways with numerous successful stories. AI has also contributed to dealing with the coronavirus disease (COVID-19) pandemic, which has been happening around the globe. This paper presents a survey of AI methods being used in various applications in the fight against the COVID-19 outbreak and outlines the crucial roles of AI research in this unprecedented battle. We touch on a number of areas where AI plays as an essential component, from medical image processing, data analytics, text mining and natural language processing, the Internet of Things, to computational biology and medicine. A summary of COVID-19 related data sources that are available for research purposes is also presented. Research directions on exploring the potentials of AI and enhancing its capabilities and power in the battle are thoroughly discussed. We highlight 13 groups of problems related to the COVID-19 pandemic and point out promising AI methods and tools that can be used to solve those problems. It is envisaged that this study will provide AI researchers and the wider community an overview of the current status of AI applications and motivate researchers in harnessing AI potentials in the fight against COVID-19.

Review on Nanoparticles and Nanostructured Materials: Bioimaging, Biosensing, Drug Delivery, Tissue Engineering, Antimicrobial, and Agro-Food Applications

Abstract: In the last few decades, the vast potential of nanomaterials for biomedical and healthcare applications has been extensively investigated. Several case studies demonstrated that nanomaterials can offer solutions to the current challenges of raw materials in the biomedical and healthcare fields. This review describes the different nanoparticles and nanostructured material synthesis approaches and presents some emerging biomedical, healthcare, and agro-food applications. This review focuses on various nanomaterial types (e.g., spherical, nanorods, nanotubes, nanosheets, nanofibers, core-shell, and mesoporous) that can be synthesized from different raw materials and their emerging applications in bioimaging, biosensing, drug delivery, tissue engineering, antimicrobial, and agro-foods. Depending on their morphology (e.g., size, aspect ratio, geometry, porosity), nanomaterials can be used as formulation modifiers, moisturizers, nanofillers, additives, membranes, and films. As toxicological assessment depends on sizes and morphologies, stringent regulation is needed from the testing of efficient nanomaterials dosages. The challenges and perspectives for an industrial breakthrough of nanomaterials are related to the optimization of production and processing conditions.

ACE2 Interaction Networks in COVID-19: A Physiological Framework for Prediction of Outcome in Patients with Cardiovascular Risk Factors.

Abstract: Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (coronavirus disease 2019; COVID-19) is associated with adverse outcomes in patients with cardiovascular disease (CVD). The aim of the study was to characterize the interaction between SARS-CoV-2 and Angiotensin-Converting Enzyme 2 (ACE2) functional networks with a focus on CVD. Methods: Using the network medicine approach and publicly available datasets, we investigated ACE2 tissue expression and described ACE2 interaction networks that could be affected by SARS-CoV-2 infection in the heart, lungs and nervous system. We compared them with changes in ACE-2 networks following SARS-CoV-2 infection by analyzing public data of human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). This analysis was performed using the Network by Relative Importance (NERI) algorithm, which integrates protein-protein interaction with co-expression networks. We also performed miRNA-target predictions to identify which miRNAs regulate ACE2-related networks and could play a role in the COVID19 outcome. Finally, we performed enrichment analysis for identifying the main COVID-19 risk groups. Results: We found similar ACE2 expression confidence levels in respiratory and cardiovascular systems, supporting that heart tissue is a potential target of SARS-CoV-2. Analysis of ACE2 interaction networks in infected hiPSC-CMs identified multiple hub genes with corrupted signaling which can be responsible for cardiovascular symptoms. The most affected genes were EGFR (Epidermal Growth Factor Receptor), FN1 (Fibronectin 1), TP53, HSP90AA1, and APP (Amyloid Beta Precursor Protein), while the most affected interactions were associated with MAST2 and CALM1 (Calmodulin 1). Enrichment analysis revealed multiple diseases associated with the interaction networks of ACE2, especially cancerous diseases, obesity, hypertensive disease, Alzheimer’s disease, non-insulin-dependent diabetes mellitus, and congestive heart failure. Among affected ACE2-network components connected with the SARS-Cov-2 interactome, we identified AGT (Angiotensinogen), CAT (Catalase), DPP4 (Dipeptidyl Peptidase 4), CCL2 (C-C Motif Chemokine Ligand 2), TFRC (Transferrin Receptor) and CAV1 (Caveolin-1), associated with cardiovascular risk factors. We described for the first time miRNAs which were common regulators of ACE2 networks and virus-related proteins in all analyzed datasets. The top miRNAs regulating ACE2 networks were miR-27a-3p, miR-26b-5p, miR-10b-5p, miR-302c-5p, hsa-miR-587, hsa-miR-1305, hsa-miR-200b-3p, hsa-miR-124-3p, and hsa-miR-16-5p. Conclusion: Our study provides a complete mechanistic framework for investigating the ACE2 network which was validated by expression data. This framework predicted risk groups, including the established ones, thus providing reliable novel information regarding the complexity of signaling pathways affected by SARS-CoV-2. It also identified miRNAs that could be used in personalized diagnosis in COVID-19.