Text mining and network analysis to find functional associations of genes in high altitude diseases

Bhasuran, Balu; Subramanian, Devika; Natarajan, Jeyakumar

doi:10.1016/j.compbiolchem.2018.05.002

Cited by 11 publications

(5 citation statements)

References 40 publications

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“…The current study employs a frequency-based co-occurrence approach and its aggregation to find the biological interlinks between important COVID 19 genes/proteins by text mining the CORD-19 corpus. To identify and extract the genes/proteins and interactions we have adapted our previous methodology(Bhasuran et al., 2018 ).…”

Section: Methodsmentioning

confidence: 99%

The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach

Maroli

Bhasuran

Natarajan

et al. 2020

Journal of Biomolecular Structure and Dynamics

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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.

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Section: Methodsmentioning

confidence: 99%

The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach

Maroli

Bhasuran

Natarajan

et al. 2020

Journal of Biomolecular Structure and Dynamics

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“…The text mining methods were used to retrieve the information related to AQP4 and T-2 toxins. Here, our previously proposed co-occurrence methodology was adapted to retrieve and analyze the data . The entries of proteins/genes associated with T-2 toxins were harvested from PubMed and PMC databases and text mining was performed over a set of parameters using a self-made javascript.…”

Section: Methodsmentioning

confidence: 99%

“…Here, our previously proposed co-occurrence methodology was adapted to retrieve and analyze the data. 114 The entries of proteins/genes associated with T-2 toxins were harvested from PubMed and PMC databases and text mining was performed over a set of parameters using a self-made javascript. We used two seed terms for querying aquaporin such as "aquaporin-4" and "AQP4" in both PubMed and PMC, respectively, for collecting all reported articles on aquaporin-4.…”

Section: Journal Of Chemical Information and Modelingmentioning

confidence: 99%

Molecular Mechanism of T-2 Toxin-Induced Cerebral Edema by Aquaporin-4 Blocking and Permeation

Maroli¹,

Kalagatur²,

Bhasuran³

et al. 2019

J. Chem. Inf. Model.

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The present study aimed to reveal the molecular mechanism of T-2 toxin-induced cerebral edema by aquaporin-4 (AQP4) blocking and permeation. AQP4 is a class of aquaporin channels that is mainly expressed in the brain, and its structural changes lead to life-threatening complications such as cardio-respiratory arrest, nephritis, and irreversible brain damage. We employed molecular dynamics simulation, text mining, and in vitro and in vivo analysis to study the structural and functional changes induced by the T-2 toxin on AQP4. The action of the toxin leads to disrupted permeation of water and permeation coefficients are found to be affected, from the native (2.49 ± 0.02 × 10–14 cm3/s) to toxin-treated AQP4 (7.68 ± 0.15 × 10–14 cm3/s) channels. Furthermore, the T-2 toxin forms strong electrostatic interactions at the binding site and pushes the key residues (Ala210, Phe77, Arg216, and His201) outward at the selectivity filter. Also, the role of a histidine residue in the AQP4 channel was identified by alchemical transformation and umbrella sampling methods. Alchemical free-energy perturbation energy for H201A ↔ A201H, which was found to be 3.07 ± 0.18 kJ/mol, indicates the structural importance of the histidine residue at 201. In addition, histopathology and expression of AQP4 in the Mus musculus brain tissues show the damaged and altered expression of the protein. Text mining reveals the co-occurrence of genes/proteins associated with the AQP4 expression and T-2 toxin-induced cell apoptosis, which leads to cerebral edema.

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“…The current study employs a frequency based co-occurrence approach and its aggregation to find the biological interlinks between important COVID 19 genes/proteins by text mining the CORD-19 corpus. To identify and extract the genes/proteins and interactions we have adapted our previous methodology [40].…”

Section: Identification and Co-occurrence Extraction Of Covid-19genesmentioning

confidence: 99%

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

Maroli

Bhasuran²,

Natarajan³

et al. 2020

Preprint

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<p>A novel coronavirus (SARS-CoV-2) has caused a major outbreak in the 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 andnamed 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 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.</p>

show abstract

Text mining and network analysis to find functional associations of genes in high altitude diseases

Cited by 11 publications

References 40 publications

The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach

The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach

Molecular Mechanism of T-2 Toxin-Induced Cerebral Edema by Aquaporin-4 Blocking and Permeation

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

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