Irreversible electroporation in the curative treatment of Ewing's sarcoma

Steinbrecher, Kacie L.; Arslan, Bülent; Nassin, Michele L.; Kent, Paul

doi:10.1136/bcr-2016-216585

Cited by 4 publications

(3 citation statements)

References 14 publications

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“…2,[28][29] Since this time, a number of applications in both academia and industry have been reported. [30][31][32][33][34][35][36][37][38][39][40][41][42][43] However, to more reliably drive decisions in lead optimization, there are two major issues that alchemical methods should deal with, namely, adequate sampling of relevant configurations and force field accuracy. 3 To address the sampling issues methods like Hamiltonian exchange and replica exchange have been developed, [44][45][46] while improvements in force fields, like CGenFF, 47 AMOEBA, 48 OPLS 49 and AMBER/GAFF, [50][51] have been an ongoing effort and will continue to be for the foreseeable future.…”

Section: Introductionmentioning

confidence: 99%

Using AMBER18 for Relative Free Energy Calculations

Song

Zhu

et al. 2019

J. Chem. Inf. Model.

183

251

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With renewed interest in free energy methods in contemporary structure-based drug design there is a pressing need to validate against multiple targets and force fields to assess the overall ability of these methods to accurately predict relative binding free energies. We computed relative binding free energies using GPU accelerated Thermodynamic Integration (GPU-TI) on a dataset originally assembled by Schrödinger, Inc.. Using their GPU free energy code (FEP+) and the OPLS2.1 force field combined with the REST2 enhanced sampling approach, these authors obtained an overall MUE of 0.9 kcal/mol and an overall RMSD of 1.14 kcal/mol. In our study using GPU-TI from AMBER with the AMBER14SB/GAFF1.8 force field but without enhanced sampling, we obtained an overall MUE of 1.17 kcal/mol and an overall RMSD of 1.50 kcal/mol for the 330 perturbations contained in this data set. A more detailed analyses of our results suggested that the observed differences between the two studies arise from differences in sampling protocols along with differences in the force fields employed. Future work should address the problem of establishing benchmark quality results with robust statistical error bars obtained through multiple independent runs and enhanced sampling, which is possible with the GPU-accelerated features in AMBER.

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Section: Introductionmentioning

confidence: 99%

Using AMBER18 for Relative Free Energy Calculations

Song

Zhu

et al. 2019

J. Chem. Inf. Model.

183

251

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“…IRE has gained popularity for the treatment of multiple solid organ malignancies, including liver, kidney, prostate, bone, and locally advanced pancreatic tumors [3] , [7] . Its advantages over thermal modalities include an absence of a heat sink and less potential injury to adjacent vital structures.…”

Section: Discussionmentioning

confidence: 99%

Case report: Irreversible electroporation for locally advanced pancreatic cancer

Orcutt

Kis

Malafa

2017

International Journal of Surgery Case Reports

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“…Irreversible electroporation is gaining momentum as a nonthermal tissue ablation technique in treating sarcomas. 40,41 Steinbrecher et al 42 report about using IRE as a curative treatment for Ewing's sarcoma. In this case, the patient, a 9 year old girl could not undergo surgery or radiation due to the high risk of sacral nerve plexus destruction and paralysis.…”

Section: Ire For Sarcomasmentioning

confidence: 99%

Electro-therapies for sarcomas

Sundararajan¹,

Poompavai²,

Sree³

et al. 2019

JCPCR

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Sarcomas are cancers that occur in soft tissues and bones that mostly affect teenagers and young adults. Although its occurrence is rare, the affect is huge-metastatic and deaths are imminent. This mini review reports the various aspects of sarcomas, including Ewing's sarcoma and also discussed is the use of electrical pulse-based therapies, such as electrochemotherapy (ECT) and irreversible electroporation (IRE) for those patients who could not benefit from the standard therapies. Typically, 1200V/cm or 1000V/cm, 100µs, eight pulses are used for ECT and bleomycin and cisplatin are the two most commonly administered drugs. Lately calcium and other bio-compounds, such as mint are explored as anticancer drugs. In IRE, 80 pulses of 1000-1500V/cm, 100µs are used. In general electrotherapies offer an attractive alternative to current standard therapies when they are refractive.

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Irreversible electroporation in the curative treatment of Ewing's sarcoma

Cited by 4 publications

References 14 publications

Using AMBER18 for Relative Free Energy Calculations

Using AMBER18 for Relative Free Energy Calculations

Case report: Irreversible electroporation for locally advanced pancreatic cancer

Electro-therapies for sarcomas

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