Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids

Bolt, H. L.; Williams, C. E. J.; Brooks, R. V.; Zuckermann, R. N.; Cobb, S. L.; Bromley, E. H. C.

doi:10.1002/bip.23014

Title: Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids

Abstract

Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as determined by RP-HPLC retention time) may not always provide an effective predictive tool for rational design. Herein, we report the first ever application of partitioning experiments to determine the log D values for a series of peptoids. By comparing log D and average hydrophobicities we highlight the potential advantage of employing the former as a predictive tool in the rational design of biologically active peptoids.

Authors:

Bolt, H. L. ^[1]; Williams, C. E. J. ^[2]; Brooks, R. V. ^[2]; Zuckermann, R. N. ^[3]; Cobb, S. L. ^[1]; Bromley, E. H. C. ^[2]

Department of Chemistry, Durham University, South Road Durham DH1 3LE United Kingdom
Department of Physics, Durham University, South Road Durham DH1 3LE United Kingdom
Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley California

Publication Date:: Mon Jan 09 00:00:00 EST 2017

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1366313

Alternate Identifier(s):: OSTI ID: 1366314; OSTI ID: 1409436

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Published Article

Journal Name:: Biopolymers

Additional Journal Information:: Journal Name: Biopolymers Journal Volume: 108 Journal Issue: 4; Journal ID: ISSN 0006-3525

Publisher:: Wiley

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats


                    Bolt, H. L., Williams, C. E. J., Brooks, R. V., Zuckermann, R. N., Cobb, S. L., and Bromley, E. H. C. Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids.  United States: N. p., 2017. 
Web.  doi:10.1002/bip.23014.

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                    Bolt, H. L., Williams, C. E. J., Brooks, R. V., Zuckermann, R. N., Cobb, S. L., & Bromley, E. H. C. Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids.  United States.  https://doi.org/10.1002/bip.23014

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                    Bolt, H. L., Williams, C. E. J., Brooks, R. V., Zuckermann, R. N., Cobb, S. L., and Bromley, E. H. C. Mon .  
"Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids".  United States.  https://doi.org/10.1002/bip.23014.

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@article{osti_1366313,

  title        = {Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids},

  author       = {Bolt, H. L. and Williams, C. E. J. and Brooks, R. V. and Zuckermann, R. N. and Cobb, S. L. and Bromley, E. H. C.},

  abstractNote = {Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as determined by RP-HPLC retention time) may not always provide an effective predictive tool for rational design. Herein, we report the first ever application of partitioning experiments to determine the log D values for a series of peptoids. By comparing log D and average hydrophobicities we highlight the potential advantage of employing the former as a predictive tool in the rational design of biologically active peptoids.},

  doi          = {10.1002/bip.23014},

  journal      = {Biopolymers},

  number       = 4,

  volume       = 108,

  place        = {United States},

  year         = {Mon Jan 09 00:00:00 EST 2017},

  month        = {Mon Jan 09 00:00:00 EST 2017}

}

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Title: Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids

Abstract

Citation Formats

Free-floating ultrathin two-dimensional crystals from sequence-specific peptoid polymers journal, April 2010

Peptoid helicity modulation: precise control of peptoid secondary structures via position-specific placement of chiral monomers journal, January 2014

A Comparison of Linear and Cyclic Peptoid Oligomers as Potent Antimicrobial Agents journal, September 2011

Investigating the Anti-leishmanial Effects of Linear Peptoids journal, December 2014

Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides journal, February 2008

Amphiphilic Cyclic Peptoids That Exhibit Antimicrobial Activity by Disrupting Staphylococcus aureus Membranes : Amphiphilic Cyclic Peptoids journal, April 2013

Peptoid Polymers: A Highly Designable Bioinspired Material journal, May 2013

Peptoid Oligomers with α-Chiral, Aromatic Side Chains: Sequence Requirements for the Formation of Stable Peptoid Helices journal, July 2001

Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles journal, March 2016

“Bridged” n →π* Interactions Can Stabilize Peptoid Helices journal, October 2013

Lipitoids — novel cationic lipids for cellular delivery of plasmid DNA in vitro journal, June 1998

LogD: Lipophilicity for ionisable compounds journal, August 2008

Enlarging the chemical space of anti-leishmanials: a structure–activity relationship study of peptoids against Leishmania mexicana, a causative agent of cutaneous leishmaniasis journal, January 2016

New Peptidomimetic Polymers for Antifouling Surfaces journal, June 2005

Structure-Activity Relationship Study of Novel Peptoids That Mimic the Structure of Antimicrobial Peptides journal, May 2015

Antimicrobial, Hemolytic, and Cytotoxic Activities of β-Peptoid-Peptide Hybrid Oligomers: Improved Properties Compared to Natural AMPs journal, May 2010

Efficient method for the preparation of peptoids [oligo(N-substituted glycines)] by submonomer solid-phase synthesis journal, December 1992

Biomimetic Nanostructures: Creating a High-Affinity Zinc-Binding Site in a Folded Nonbiological Polymer journal, July 2008

Novel Peptoid Building Blocks: Synthesis of Functionalized Aromatic Helix-Inducing Submonomers journal, February 2010

Folding a Nonbiological Polymer into a Compact Multihelical Structure journal, August 2005

Efficacy of Antimicrobial Peptoids against Mycobacterium tuberculosis journal, April 2011

Peptoid transporters: effects of cationic, amphipathic structure on their cellular uptake journal, January 2012

The design, synthesis, and evaluation of molecules that enable or enhance cellular uptake: Peptoid molecular transporters journal, November 2000

Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure journal, April 1998

NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains journal, April 1998

Sequence Programmable Peptoid Polymers for Diverse Materials Applications journal, April 2015

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Peptoids: Synthesis, Characterization, and Nanostructures book, January 2011

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Synthesis and Characterization of Nitroaromatic Peptoids: Fine Tuning Peptoid Secondary Structure through Monomer Position and Functionality journal, February 2009

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Tuning Peptoid Secondary Structure with Pentafluoroaromatic Functionality: A New Design Paradigm for the Construction of Discretely Folded Peptoid Structures journal, November 2006

Free-floating ultrathin two-dimensional crystals from sequence-specific peptoid polymers
journal, April 2010

Peptoid helicity modulation: precise control of peptoid secondary structures via position-specific placement of chiral monomers
journal, January 2014

A Comparison of Linear and Cyclic Peptoid Oligomers as Potent Antimicrobial Agents
journal, September 2011

Investigating the Anti-leishmanial Effects of Linear Peptoids
journal, December 2014

Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides
journal, February 2008

Amphiphilic Cyclic Peptoids That Exhibit Antimicrobial Activity by Disrupting Staphylococcus aureus Membranes : Amphiphilic Cyclic Peptoids
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Peptoid Polymers: A Highly Designable Bioinspired Material
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journal, July 2001

Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles
journal, March 2016

“Bridged” n →π* Interactions Can Stabilize Peptoid Helices
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Lipitoids — novel cationic lipids for cellular delivery of plasmid DNA in vitro
journal, June 1998

LogD: Lipophilicity for ionisable compounds
journal, August 2008

Enlarging the chemical space of anti-leishmanials: a structure–activity relationship study of peptoids against Leishmania mexicana, a causative agent of cutaneous leishmaniasis
journal, January 2016

New Peptidomimetic Polymers for Antifouling Surfaces
journal, June 2005

Structure-Activity Relationship Study of Novel Peptoids That Mimic the Structure of Antimicrobial Peptides
journal, May 2015

Antimicrobial, Hemolytic, and Cytotoxic Activities of β-Peptoid-Peptide Hybrid Oligomers: Improved Properties Compared to Natural AMPs
journal, May 2010

Efficient method for the preparation of peptoids [oligo(N-substituted glycines)] by submonomer solid-phase synthesis
journal, December 1992

Biomimetic Nanostructures: Creating a High-Affinity Zinc-Binding Site in a Folded Nonbiological Polymer
journal, July 2008

Novel Peptoid Building Blocks: Synthesis of Functionalized Aromatic Helix-Inducing Submonomers
journal, February 2010

Folding a Nonbiological Polymer into a Compact Multihelical Structure
journal, August 2005

Efficacy of Antimicrobial Peptoids against Mycobacterium tuberculosis
journal, April 2011

Peptoid transporters: effects of cationic, amphipathic structure on their cellular uptake
journal, January 2012

The design, synthesis, and evaluation of molecules that enable or enhance cellular uptake: Peptoid molecular transporters
journal, November 2000

Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure
journal, April 1998

NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains
journal, April 1998

Sequence Programmable Peptoid Polymers for Diverse Materials Applications
journal, April 2015

Peptoid nanosheets exhibit a new secondary-structure motif
journal, October 2015

Peptoids: Synthesis, Characterization, and Nanostructures
book, January 2011

Structural and Spectroscopic Studies of Peptoid Oligomers with α-Chiral Aliphatic Side Chains
journal, November 2003

Synthesis and Characterization of Nitroaromatic Peptoids: Fine Tuning Peptoid Secondary Structure through Monomer Position and Functionality
journal, February 2009

A Threaded Loop Conformation Adopted by a Family of Peptoid Nonamers
journal, February 2006

Hydrophobicity and helicity of membrane-interactive peptides containing peptoid residues
journal, October 2002

Cell-penetrating peptoids: Introduction of novel cationic side chains
journal, May 2014

In Vivo, In Vitro, and In Silico Characterization of Peptoids as Antimicrobial Agents
journal, February 2016

Tuning Peptoid Secondary Structure with Pentafluoroaromatic Functionality: A New Design Paradigm for the Construction of Discretely Folded Peptoid Structures
journal, November 2006