WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures

Kasam, Vinod; Salzemann, Jean; Botha, Marli; Dacosta, Ana; Degliesposti, Gianluca; Isea, Raúl; Kim, Doman; Maaß, Astrid; Kenyon, Colin; Rastelli, Giulio; Hofmann‐Apitius, Martin; Breton, Vincent

doi:10.1186/1475-2875-8-88

Cited by 38 publications

(33 citation statements)

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“…More than 46 million molecular structures were computer examined to find candidates with potential bioactivity. Grid based technology is now also being applied to manage databases of cancer patients which will help in assessing their treatment (Kasam et al, 2009).…”

Section: Q Applications Involving the Handling And Analysis Of Very mentioning

confidence: 99%

Particle and nuclear physics instrumentation and its broad connections

et al. 2016

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Section: Q Applications Involving the Handling And Analysis Of Very mentioning

confidence: 99%

Particle and nuclear physics instrumentation and its broad connections

et al. 2016

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“…The WPE platform [2], developed by the LPC Laboratory in Clermont-Ferrand, France, was successfully used in the WISDOM-I (2005) and WISDOM-II (2006) projects as a layer between users and grid resources. It facilitates the massive submission of jobs to the grid.…”

Section: The Wpe Platformmentioning

confidence: 99%

On the Performance Enhancement of WISDOM Production Environment

Bui¹,

Doan²,

Nguyen³

et al. 2012

Proceedings of the International Symposium on Grids and Clouds (ISGC) 2012 — PoS(ISGC 2012)

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The WPE (WISDOM Production Environment) is a job management system on the grid, which is successfully used in several virtual screening projects for malaria, such as WISDOM-I (2005) and WISDOM-II (2006). The experience using WPE showed however that there are still challenges to address such as agents massively killed when the Task Manager is empty, or the status monitoring module noticeably slowing down after a long execution time. We carried out tests to measure WPE performances and compare them to DIRAC's, a similar job management system. The obtained results confirm the problems encountered. To improve WPE performances, we discuss the reasons and propose corrective plans. This paper describes the scenario and results of the performance tests for the WPE before and after the corrections.

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“…Many experimental peptidic and nonpeptidic plm inhibitors exist and have been described in detail, along with their Ki values and often the steps of their synthesis, in a number of papers [37], . Some of these inhibitors were identified by high-throughput screening [61,67,68,69,70], by computational analysis of the plm's active site [56,62], or in natural products [57,71,72], though most are the result of rational drug design.…”

Section: Introductionmentioning

confidence: 99%

In-silico Antimalarial Study of Monocarbonyl Curcumin Analogs and Their 2,4-Dinitro Phenylhydrazones Using the Inhibition of Plasmepsin II as Test Model

Fadare¹,

Iwalewa²,

Obafemi³

et al. 2017

AJPS

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A well-known component of the Indian spice turmeric, curcumin, has received a lot of attention in recent years as a potential antimalarial agent but the inherent problems associated with low bioavailabilty tends to limit its applicability. The bioavailability is linked to its low solubility in water and its rapid break down in the blood plasma. In this study, we have proposed the use of synthetic analogs of curcumin and their derivatives which are expected to be less prone to degradation in the blood plasma as possible antimalarials. The binding affinity of monocarbonyl analogs of curcumin and their 2,4-dinitrophenylhydrazone derivatives for the chain A domain of plasmepsin II, one of the key enzymes involved in hemoglobin digestion in the food vacuole of the malaria parasite was determined by computational docking analysis, performed using Auto Dock Vina 1.1.2, pymol and Chem 3D ultra 12.0. The binding energies of the 20 compounds studied was compared with that of pepstatin A (a known inhibitor of plasmepsin II), curcumin and chloroquine. The 3D structure of the protein was obtained from the protein data bank (PDB ID:1M43), the compounds' 3D structure was generated with the Chem 3D ultra 12.0 and visualization done with pymol. Out of the 20 compounds docked with plasmepsin II, 17 had binding energies higher than that of pep A (-32.6, kJ/mol) and 19 of the compounds had binding energies higher than that of curcumin (30.96, kJ/mol). The docked compounds, 5b, 6b and 7b had the highest binding energies (-44.73 kJ/mol, -42.64 kJ/mol and -41.80 kJ/mol respectively). It is expected that the compounds with binding energies higher than that of pep A may be considered for further antimalarial studies in-vitro and in-vivo.

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WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures

Cited by 38 publications

References 50 publications

Particle and nuclear physics instrumentation and its broad connections

Particle and nuclear physics instrumentation and its broad connections

On the Performance Enhancement of WISDOM Production Environment

In-silico Antimalarial Study of Monocarbonyl Curcumin Analogs and Their 2,4-Dinitro Phenylhydrazones Using the Inhibition of Plasmepsin II as Test Model

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