Ultrafast scalable parallel algorithm for the radial distribution function histogramming using MPI maps

Kouetcha, Daniella Nguemalieu; Ramézani, Hamidréza; Cohaut, N.

doi:10.1007/s11227-016-1854-0

Cited by 16 publications

(3 citation statements)

References 49 publications

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“…For frame visualization at different nanoseconds, UCSF Chimera [47] and Discovery Studio v21.1.0.20298 [52] were utilized. Radial distribution function (RDF) plots were generated for chemical interactions that play a significant role in anchoring the compound at the docked site and increase intermolecular stability [35,63].…”

Section: Molecular Dynamics Simulation Studymentioning

confidence: 99%

Determination of Novel Anti-Cancer Agents by Targeting OGG1 Enzyme Using Integrated Bioinformatics Methods

Muhseen

Ali

Jaber

et al. 2021

IJERPH

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The 8-oxoguanine DNA glycosylase (OGG1) enzyme is a key DNA glycosylase mediating the excision of 7,8-dihydro-8-oxoguanine (8-oxoG) from DNA molecule to the start base excision repair pathway. The OGG1 glycosylase function depletion has been seen to obstruct pathological conditions such as inflammation, A3 T-cell lymphoblastic acute leukemia growth, and neurodegenerative diseases, thus warranting OGG1 as an attractive anti-cancer enzyme. Herein, we employed several drug libraries intending to screen non-toxic inhibitory molecules against the active pocket of the enzyme that achieved stable binding mode in dynamics. Two anti-cancer compounds ([O-]C1=C(CC2=CC=CC=C2)SC(=[N+]1CC(=O)NC3=NC=C(CC4=CC=CC=C4)S3)S and CCCN(CCC)[S]-(=O)(=O)C1=CC=C(C=C1)C(=O)NNC2=NC3=CC=C(Br)C=C3C(=N2)C4=CC=CC=C4) from Selleckchem.com were identified to occupy the active pocket of OGG1 and bind with greater affinity than Control TH5487. The binding affinity of Top-1 is −11.6 kcal/mol while that of Top-2 is −10.7 kcal/mol in contrast to TH5487 Control (−9 kcal/mol). During molecular dynamic simulations versus time, the said compounds are tightly held by the enzyme with no minor structural deviations reported except flexible loops in particular those present at the N and C-terminal. Both the compounds produced extensive hydrophobic interactions with the enzyme along with stable hydrogen bonding. The docking and molecular dynamics simulations predictions were further validated by molecular mechanics with generalized Born and surface area solvation (MM/GBSA) and Poisson Boltzmann surface area (MM/PBSA), and WaterSwap binding energies that validated strong binding of the compounds to the enzyme. The MM/GBSA binding free energy for Top-1 complex is −28.10 kcal/mol, Top-2 complex is −50.14 kcal/mol) and Control is −46.91 kcal/mol while MM/PBSA value for Top-1, Top-2 and Control is −23.38 kcal/mol, −35.29 kcal/mol and −38.20 kcal/mol, respectively. Computational pharmacokinetics support good druglike candidacy of the compounds with acceptable profile of pharmacokinetics and very little toxicity. All these findings support the notion that the compounds can be used in experiments to test their anti-cancer activities.

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Section: Molecular Dynamics Simulation Studymentioning

confidence: 99%

Determination of Novel Anti-Cancer Agents by Targeting OGG1 Enzyme Using Integrated Bioinformatics Methods

Muhseen

Ali

Jaber

et al. 2021

IJERPH

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“…The distribution and bonding pattern of intermolecular interactions of the MEPVC residues atom(s) with respect to the TLR3 were studied through radial distribution function (RDF) (Abbasi et al, 2016;Donohue, 1954;Kouetcha et al, 2017). RDF mainly describes distance 'r' between two entities and is represented by g(r).…”

Section: Radial Distribution Function and Inter Molecular Interactionsmentioning

confidence: 99%

Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine

Ismail

Ahmad

Azam

2020

Journal of Molecular Liquids

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“…2. The randomness issue has been perfectly achieved in the sense that the radial distribution function leads to the stochastic patterns in according to the condensed matter physics considerations [49][50][51][52][53] (see Figure 3d). To pursue the numerical modeling of the mortar specimens herein, one-eight symmetry assumption has been utilized in the sense that only 1/8 of model has been accounted for the computations.…”

Section: Geometrical Configurationsmentioning

confidence: 99%

Reactive transport numerical modeling of mortar carbonation: Atmospheric and accelerated carbonation

Jeong¹,

Ramézani

Chuta³

2019

Journal of Building Engineering

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Ultrafast scalable parallel algorithm for the radial distribution function histogramming using MPI maps

Cited by 16 publications

References 49 publications

Determination of Novel Anti-Cancer Agents by Targeting OGG1 Enzyme Using Integrated Bioinformatics Methods

Determination of Novel Anti-Cancer Agents by Targeting OGG1 Enzyme Using Integrated Bioinformatics Methods

Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine

Reactive transport numerical modeling of mortar carbonation: Atmospheric and accelerated carbonation

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