Diptool—A Novel Numerical Tool for Membrane Interactions Analysis, Applying to Antimicrobial Detergents and Drug Delivery Aids

The widespread problem of resistance development in bacteria has become a critical issue for modern medicine. To limit that phenomenon, many compounds have been extensively studied. Among them were derivatives of available drugs, but also alternative novel detergents such as Gemini surfactants. Over...

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Autores principales:	Mateusz Rzycki, Sebastian Kraszewski, Marta Gładysiewicz-Kudrawiec
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	surfactants numerical tool drug delivery free energy calculation molecular dynamics lipid membranes Technology T Electrical engineering. Electronics. Nuclear engineering TK1-9971 Engineering (General). Civil engineering (General) TA1-2040 Microscopy QH201-278.5 Descriptive and experimental mechanics QC120-168.85
Acceso en línea:	https://doaj.org/article/d58de226a50e4dd4b43a38008ee39c2d
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spelling	oai:doaj.org-article:d58de226a50e4dd4b43a38008ee39c2d2021-11-11T18:01:55ZDiptool—A Novel Numerical Tool for Membrane Interactions Analysis, Applying to Antimicrobial Detergents and Drug Delivery Aids10.3390/ma142164551996-1944https://doaj.org/article/d58de226a50e4dd4b43a38008ee39c2d2021-10-01T00:00:00Zhttps://www.mdpi.com/1996-1944/14/21/6455https://doaj.org/toc/1996-1944The widespread problem of resistance development in bacteria has become a critical issue for modern medicine. To limit that phenomenon, many compounds have been extensively studied. Among them were derivatives of available drugs, but also alternative novel detergents such as Gemini surfactants. Over the last decade, they have been massively synthesized and studied to obtain the most effective antimicrobial agents, as well as the most selective aids for nanoparticles drug delivery. Various protocols and distinct bacterial strains used in Minimal Inhibitory Concentration experimental studies prevented performance benchmarking of different surfactant classes over these last years. Motivated by this limitation, we designed a theoretical methodology implemented in custom fast screening software to assess the surfactant activity on model lipid membranes. Experimentally based QSAR (quantitative structure-activity relationship) prediction delivered a set of parameters underlying the Diptool software engine for high-throughput agent-membrane interactions analysis. We validated our software by comparing score energy profiles with Gibbs free energy from the Adaptive Biasing Force approach on octenidine and chlorhexidine, popular antimicrobials. Results from Diptool can reflect the molecule behavior in the lipid membrane and correctly predict free energy of translocation much faster than classic molecular dynamics. This opens a new venue for searching novel classes of detergents with sharp biologic activity.Mateusz RzyckiSebastian KraszewskiMarta Gładysiewicz-KudrawiecMDPI AGarticlesurfactantsnumerical tooldrug deliveryfree energy calculationmolecular dynamicslipid membranesTechnologyTElectrical engineering. Electronics. Nuclear engineeringTK1-9971Engineering (General). Civil engineering (General)TA1-2040MicroscopyQH201-278.5Descriptive and experimental mechanicsQC120-168.85ENMaterials, Vol 14, Iss 6455, p 6455 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	surfactants numerical tool drug delivery free energy calculation molecular dynamics lipid membranes Technology T Electrical engineering. Electronics. Nuclear engineering TK1-9971 Engineering (General). Civil engineering (General) TA1-2040 Microscopy QH201-278.5 Descriptive and experimental mechanics QC120-168.85
spellingShingle	surfactants numerical tool drug delivery free energy calculation molecular dynamics lipid membranes Technology T Electrical engineering. Electronics. Nuclear engineering TK1-9971 Engineering (General). Civil engineering (General) TA1-2040 Microscopy QH201-278.5 Descriptive and experimental mechanics QC120-168.85 Mateusz Rzycki Sebastian Kraszewski Marta Gładysiewicz-Kudrawiec Diptool—A Novel Numerical Tool for Membrane Interactions Analysis, Applying to Antimicrobial Detergents and Drug Delivery Aids
description	The widespread problem of resistance development in bacteria has become a critical issue for modern medicine. To limit that phenomenon, many compounds have been extensively studied. Among them were derivatives of available drugs, but also alternative novel detergents such as Gemini surfactants. Over the last decade, they have been massively synthesized and studied to obtain the most effective antimicrobial agents, as well as the most selective aids for nanoparticles drug delivery. Various protocols and distinct bacterial strains used in Minimal Inhibitory Concentration experimental studies prevented performance benchmarking of different surfactant classes over these last years. Motivated by this limitation, we designed a theoretical methodology implemented in custom fast screening software to assess the surfactant activity on model lipid membranes. Experimentally based QSAR (quantitative structure-activity relationship) prediction delivered a set of parameters underlying the Diptool software engine for high-throughput agent-membrane interactions analysis. We validated our software by comparing score energy profiles with Gibbs free energy from the Adaptive Biasing Force approach on octenidine and chlorhexidine, popular antimicrobials. Results from Diptool can reflect the molecule behavior in the lipid membrane and correctly predict free energy of translocation much faster than classic molecular dynamics. This opens a new venue for searching novel classes of detergents with sharp biologic activity.
format	article
author	Mateusz Rzycki Sebastian Kraszewski Marta Gładysiewicz-Kudrawiec
author_facet	Mateusz Rzycki Sebastian Kraszewski Marta Gładysiewicz-Kudrawiec
author_sort	Mateusz Rzycki
title	Diptool—A Novel Numerical Tool for Membrane Interactions Analysis, Applying to Antimicrobial Detergents and Drug Delivery Aids
title_short	Diptool—A Novel Numerical Tool for Membrane Interactions Analysis, Applying to Antimicrobial Detergents and Drug Delivery Aids
title_full	Diptool—A Novel Numerical Tool for Membrane Interactions Analysis, Applying to Antimicrobial Detergents and Drug Delivery Aids
title_fullStr	Diptool—A Novel Numerical Tool for Membrane Interactions Analysis, Applying to Antimicrobial Detergents and Drug Delivery Aids
title_full_unstemmed	Diptool—A Novel Numerical Tool for Membrane Interactions Analysis, Applying to Antimicrobial Detergents and Drug Delivery Aids
title_sort	diptool—a novel numerical tool for membrane interactions analysis, applying to antimicrobial detergents and drug delivery aids
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/d58de226a50e4dd4b43a38008ee39c2d
work_keys_str_mv	AT mateuszrzycki diptoolanovelnumericaltoolformembraneinteractionsanalysisapplyingtoantimicrobialdetergentsanddrugdeliveryaids AT sebastiankraszewski diptoolanovelnumericaltoolformembraneinteractionsanalysisapplyingtoantimicrobialdetergentsanddrugdeliveryaids AT martagładysiewiczkudrawiec diptoolanovelnumericaltoolformembraneinteractionsanalysisapplyingtoantimicrobialdetergentsanddrugdeliveryaids
_version_	1718431971197059072

Diptool—A Novel Numerical Tool for Membrane Interactions Analysis, Applying to Antimicrobial Detergents and Drug Delivery Aids

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