Combinatorial Chemistry & High Throughput Screening

ISSN: 1386-2073 - Volume 9, 10 Issues, 2006

Combinatorial Chemistry & High Throughput Screening
Volume 8, Number 3, May 2005

Contents

Antimicrobial Peptides
Guest Editor: Alexander Cole


Editorial Pp. 207-208


Defensins and Other Antimicrobial Peptides: A Historical Perspective and an Update Pp. 209-217
Tomas Ganz
[Abstract] [Purchase Article]


Improving on Nature’s Defenses: Optimization & High Throughput Screening of Antimicrobial Peptides Pp. 219-233
D. Raventos, O. Taboureau, P.H. Mygind, J.D. Nielsen, C.P. Sonksen and H.-H. Kristensen
[Abstract] [Purchase Article]


Peptoids As Source of Compounds Eliciting Antibacterial Activity Pp. 235-239
Isabel Masip, Enrique Perez-Paya and Angel Messeguer
[Abstract] [Purchase Article]


Molecular Mechanisms of Membrane Perturbation by Antimicrobial Peptides and the Use of Biophysical Studies in the Design of Novel Peptide Antibiotics Pp. 241-256
K. Lohner and S.E. Blondelle
[Abstract] [Purchase Article]


Design of Host Defence Peptides for Antimicrobial and Immunity Enhancing Activities Pp. 257-272
Joseph B. McPhee, Monisha G. Scott and Robert E.W. Hancock
[Abstract] [Purchase Article]


Cathelicidins – Nature's Attempt at Combinatorial Chemistry Pp. 273-280
Ole E. Sørensen and Niels Borregaard
[Abstract] [Purchase Article]


Meet the Guest Editor Pp. 281-281
Alexander M. Cole
[Abstract] [Purchase Article]




Abstracts

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Editorial

The urgent need to develop new antibiotics has been a major force behind the advancement of antimicrobial peptides as therapeutics and preventatives. Over the last decade, there have been significant improvements in methodology that are essential to drive the evolution of peptides into marketable drugs. The development of sensitive, high-throughput tools to screen libraries of peptide compounds has enabled the discovery of next-generation molecules active against a broad spectrum of microbes. By looking at the effect that peptide compounds have on the protein expression of both the host and the pathogen, the fields of genomics and proteomics have been invaluable resources in the discovery process. More recently, combinatorial chemistry has played an increasing role in the design of next-generation peptides. Much like current combination antibiotic treatments, ‘designer peptides’ could likely emerge, whereby antimicrobial peptide cocktails would be formulated specific to each pathogen. However, the convergence of the aforementioned technologies is still in its infancy, and thus it may still be too soon to know how antimicrobial peptides come to meeting the specifications of agents for topical or systemic administration.

In this special issue of Combinatorial Chemistry and High Throughput Screening, we have included contributions from scientists with diverse perspectives on developing antimicrobial peptide-based drugs. The first article by Ganz provides an introduction and historical overview of the discovery of defensins and other antimicrobial peptides. This perspective offers an elegant interpretation of seminal discoveries from visionaries such as Ehrlich and Metchnikoff, and proceeds to trace other important contributions that shaped modern innate immunology. Other topics that set the stage for this issue are also discussed, including the mechanism of antimicrobial activity, microbial resistance, and structure-function considerations that are essential in the development of therapeutics. Kristensen and colleagues follow with a detailed account of high-throughput screening systems that have been developed to optimize antimicrobial peptides. The advantages and disadvantages of two approaches are discussed in depth: computational in silico-based screening systems and cell-based in vivo screening systems.

Peptidomimetics called “peptoids” are unique, non-natural N-alkylglycine oligomers that can be easily adapted to combinatorial chemistry approaches. The paper by Masip, Perez-Paya, and Messeguer discusses properties of peptoids that render these molecules suitable antibacterial agents. Importantly, lead compounds (“hits”) against diverse pharmaceutical targets have been discovered through iterative screening of peptoid libraries.
The next article describes studies of the mechanism of action of antimicrobial peptides utilizing membrane model systems for the rational design of novel peptide antibiotics. Lohner and Blondelle provide an in-depth review of the use of biophysical studies in the engineering of peptide antibiotics with improved therapeutic indices. In this article, models of membrane perturbation are discussed, with particular focus on the role of membrane lipid composition in membrane disruption by, and translocation of, antimicrobial peptides.

In designing peptide-based antimicrobial agents, it is imperative to investigate the host’s response to infection and the effect of antimicrobial peptides on this process. McPhee, Scott and Hancock examine the role of structure in the design of cationic antimicrobial peptides that also confer enhancement of the host’s natural immunity. This report pursues the design and characterization of select prototypical cationic peptides, their modulating effects on the host immune system, and how certain bacteria mount strategies to evade peptide action. While the primary target of cationic antimicrobial peptides is thought to be the microbial membrane, this group also discusses an emerging concept: non-membrane targets for antimicrobial peptides. The report is rounded out by an honest delineation of hurdles in peptide development, and how we are attempting to overcome these obstacles.

The last article in the series by Sørensen and Borregaard reminds us that combinatorial chemistry was not just an invention by humankind – indeed, nature has evolved a unique family of antimicrobial peptides called “cathelicidins”, an extremely diverse group of peptides released by mammalian epithelia and neutrophils. Several properties of cathelicidins are discussed, which render them ideal templates for advanced combinatorial approaches. The authors conclude by commenting on an important, but frequently overlooked, facet of antibiotic design – screens for efficacy must include biologically relevant systems that reflect the environment(s) in which the antimicrobial peptides are designed to function.


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Defensins and Other Antimicrobial Peptides: A Historical Perspective and an Update
Tomas Ganz

Antimicrobial peptides are effectors of innate immunity in phagocytes, body fluids and epithelia. In mammals, defensins, peptides with a characteristic six-cysteine framework, are particularly abundant and widely distributed in various animal species and tissues. The first part of this review provides a historical overview of the ideas that led to the current state-of-the-art in antimicrobial peptides, and the second part is an update on mammalian defensins and their role in host defense to infections.


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Improving on Nature’s Defenses: Optimization & High Throughput Screening of Antimicrobial Peptides
D. Raventos, O. Taboureau, P.H. Mygind, J.D. Nielsen, C.P. Sonksen and H.-H. Kristensen

Antimicrobial peptides (AMPs) are ubiquitous in nature where they play important roles in host defense and microbial control. Despite their natural origin, antimicrobial spectrum and potency, the lead peptide candidates that so far have entered pharmaceutical development have all been further optimized by rational or semi-rational approaches.

In recent years, several high throughput screening (HTS) systems have been developed to specifically address optimization of AMPs. These include a range of computational in silico systems and cell-based in vivo systems.

The in silico-based screening systems comprise several computational methods such as Quantitative Structure/Activity Relationships (QSAR) as well as simulation methods mimicking peptide/membrane interactions. The in vivo-based systems can be divided in cis-acting and trans-acting screening systems. The cis-acting pre-screens, where the AMP exerts its antimicrobial effect on the producing cell, allow screening of millions or even billions of lead candidates for their basic antimicrobial or membrane-perturbating activity. The trans-acting screens, where the AMP is secreted or actively liberated from the producing cell and interacts with cells different from the producing cell, allow for screening under more complex and application-relevant conditions.

This review describes the application of HTS systems employed for AMPs and lists advantages as well as limitations of these systems.


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Peptoids As Source of Compounds Eliciting Antibacterial Activity
Isabel Masip, Enrique Perez-Paya and Angel Messeguer

N-Alkylglycine oligomers (peptoids) constitute a family of non-natural peptidomimetics attractive for the early drug discovery process because of their physicochemical features, easy of adaptation to combinatorial chemistry approaches and their proteolytic stability. Consequently, peptoid libraries have found application for discovering hits against a wide diversity of pharmaceutical targets, among which different examples of antibacterials are found. In the present work, research efforts addressed towards the identification of peptoids as antibacterial agents are discussed.


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Molecular Mechanisms of Membrane Perturbation by Antimicrobial Peptides and the Use of Biophysical Studies in the Design of Novel Peptide Antibiotics
K. Lohner and S.E. Blondelle

Antibiotic resistant bacterial strains represent a global health problem with a strong social and economic impact. Thus, there is an urgent need for the development of antibiotics with novel mechanisms of action. There is currently an extensive effort to understand the mode of action of antimicrobial peptides which are considered as one alternative to classical antibiotics. The main advantage of this class of substances, when considering bacterial resistance, is that they rapidly, within minutes, kill bacteria. Antimicrobial peptides can be found in every organism and display a wide spectrum of activity. Hence, the goal is to engineer peptides with an improved therapeutic index, i.e. high efficacy and target specificity. For the rational design of such novel antibiotics it is essential to elucidate the molecular mechanism of action. Biophysical studies have been performed using to a large extent membrane model systems demonstrating that there are distinctive different mechanisms of bacterial killing by antimicrobial peptides. One can distinguish between peptides that permeabilize and/or disrupt the bacterial cell membrane and peptides that translocate through the cell membrane and interact with a cytosolic target. Lantibiotics exhibit specific mechanisms, e.g. binding to lipid II, a precursor of the peptidoglycan layer, either resulting in membrane rupture by pore formation or preventing cell wall biosynthesis. The classical models of membrane perturbation, pore formation and carpet mechanism, are discussed and related to other mechanisms that may lead to membrane dysfunction such as formation of lipid-peptide domains or membrane disruption by formation of non-lamellar phases. Emphasis is on the role of membrane lipid composition in these processes and in the translocation of antimicrobial peptides.


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Design of Host Defence Peptides for Antimicrobial and Immunity Enhancing Activities
Joseph B. McPhee, Monisha G. Scott and Robert E. W. Hancock

Host defense peptides are a vital component of the innate immune systems of humans, other mammals, amphibians, and arthropods. The related cationic antimicrobial peptides are also produced by many species of bacteria and function as part of the antimicrobial arsenal to help the producing organism reduce competition for resources from sensitive species. The antimicrobial activities of many of these peptides have been extensively characterized and the structural requirements for these activities are also becoming increasingly clear. In addition to their known antimicrobial role, many host defense peptides are also involved in a plethora of immune functions in the host. In this review, we examine the role of structure in determining antimicrobial activity of certain prototypical cationic peptides and ways that bacteria have evolved to usurp these activities. We also review recent literature on what structural components are related to these immunomodulatory effects. It must be stressed however that these studies, and the area of peptide research, are still in their infancy.


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Cathelicidins – Nature's Attempt at Combinatorial Chemistry
Ole E. Sørensen and Niels Borregaard

Cathelicidins are a family of diverse antimicrobial peptides found in granules of mammalian neutrophils. Cathelicidins are active against a broad range of microbes in different environments. Aside from their antimicrobial activity, cathelicidins possess other biological properties including cytotoxic activity towards mammalian cells. Several studies have shown that the amino acid sequence of cathelicidins can be modified to temper undesired properties, such as hemolytic and cytotoxic activity, and at the same time maintain antimicrobial activity. These properties make cathelicidins ideal templates in combinatorial chemistry for designing de novo antimicrobial peptides for therapeutic use. However, one of the major challenges will be to screen these peptides in experimentally relevant models that reflect the environments in which the peptides should be therapeutically active.


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Meet the Guest Editor
Alexander M. Cole

Alexander Cole has been investigating two aspects of innate host defense. The first area examines the natural ability of human airway secretions to prevent pathogenic bacterial colonization and aims to identify the host substances that mediate the innate resistance to colonization. His group is examining the host defense of the airways of donors who are healthy and donors who are persistent nasal carriers of Staphylococcus aureus. Their studies to date suggest that a defect exists in the nasal fluid of carriers that permits the colonization of S. aureus in their nasal passages. Ongoing studies to resolve the molecular determinants of S. aureus nasal carriage include a proteomic approach to identify molecules that are dysregulated in S. aureus carrier fluid. Their second focus is based on the reconstruction (from an expressed pseudogene) of a human antimicrobial peptide, called “retrocyclin”, homologous to rhesus monkey circular minidefensins. The peptide had a remarkable ability to inhibit proviral DNA formation and to protect immortalized and primary human CD4+ lymphocytes from in vitro infection by both X4 and R5 strains of HIV-1. Current goals include characterizing retrocyclin’s antiretroviral mechanism of action, testing the activity, stability and toxicity of retrocyclin in human fluids, and constructing next-generation analogs for use as antimicrobial therapeutics and preventatives.