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      Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics

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          Summary

          The chemical similarity of antibacterial cyclic peptides and peptidomimetics was studied in order to identify new promising cyclic scaffolds. A large descriptor space coupled with cluster analysis was employed to digitize known antibacterial structures and to gauge the potential of new peptidomimetic macrocycles, which were conveniently synthesized by acylbenzotriazole methodology. Some of the synthesized compounds were tested against an array of microorganisms and showed antibacterial activity against Bordetella bronchistepica, Micrococcus luteus, and Salmonella typhimurium.

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          Most cited references54

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          The relationship between peptide structure and antibacterial activity.

          Cationic antimicrobial peptides are a class of small, positively charged peptides known for their broad-spectrum antimicrobial activity. These peptides have also been shown to possess anti-viral and anti-cancer activity and, most recently, the ability to modulate the innate immune response. To date, a large number of antimicrobial peptides have been chemically characterized, however, few high-resolution structures are available. Structure-activity studies of these peptides reveal two main requirements for antimicrobial activity, (1) a cationic charge and (2) an induced amphipathic conformation. In addition to peptide conformation, the role of membrane lipid composition, specifically non-bilayer lipids, on peptide activity will also be discussed.
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            Molecular similarity: a key technique in molecular informatics.

            Molecular Informatics utilises many ideas and concepts to find relationships between molecules. The concept of similarity, where molecules may be grouped according to their biological effects or physicochemical properties has found extensive use in drug discovery. Some areas of particular interest have been in lead discovery and compound optimisation. For example, in designing libraries of compounds for lead generation, one approach is to design sets of compounds "similar" to known active compounds in the hope that alternative molecular structures are found that maintain the properties required while enhancing e.g. patentability, medicinal chemistry opportunities or even in achieving optimised pharmacokinetic profiles. Thus the practical importance of the concept of molecular similarity has grown dramatically in recent years. The predominant users are pharmaceutical companies, employing similarity methods in a wide range of applications e.g. virtual screening, estimation of absorption, distribution, metabolism, excretion and toxicity (ADME/Tox) and prediction of physicochemical properties (solubility, partitioning etc.). In this perspective, we discuss the representation of molecular structure (descriptors), methods of comparing structures and how these relate to measured properties. This leads to the concept of molecular similarity, its various definitions and uses and how these have evolved in recent years. Here, we wish to evaluate and in some cases challenge accepted views and uses of molecular similarity. Molecular similarity, as a paradigm, contains many implicit and explicit assumptions in particular with respect to the prediction of the binding and efficacy of molecules at biological receptors. The fundamental observation is that molecular similarity has a context which both defines and limits its use. The key issues of solvation effects, heterogeneity of binding sites and the fundamental problem of the form of similarity measure to use are addressed.
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              Diversity of antimicrobial peptides and their mechanisms of action.

              Antimicrobial peptides encompass a wide variety of structural motifs. Many peptides have alpha-helical structures. The majority of these peptides are cationic and amphipathic but there are also hydrophobic alpha-helical peptides which possess antimicrobial activity. In addition, some beta-sheet peptides have antimicrobial activity and even antimicrobial alpha-helical peptides which have been modified to possess a beta-structure retain part of their antimicrobial activity. There are also antimicrobial peptides which are rich in a certain specific amino acid such as Trp or His. In addition, antimicrobial peptides exist with thio-ether rings, which are lipopeptides or which have macrocyclic Cys knots. In spite of the structural diversity, a common feature of the cationic antimicrobial peptides is that they all have an amphipathic structure which allows them to bind to the membrane interface. Indeed, most antimicrobial peptides interact with membranes and may be cytotoxic as a result of disturbance of the bacterial inner or outer membranes. Alternatively, a necessary but not sufficient property of these peptides may be to be able to pass through the membrane to reach a target inside the cell. The interaction of these peptides with biological membranes is not just a function of the peptide but is also modulated by the lipid components of the membrane. It is not likely that this diverse group of peptides has a single mechanism of action, but interaction of the peptides with membranes is an important requirement for most, if not all, antimicrobial peptides.
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                Author and article information

                Contributors
                Role: Guest Editor
                Journal
                Beilstein J Org Chem
                Beilstein J Org Chem
                Beilstein Journal of Organic Chemistry
                Beilstein-Institut (Trakehner Str. 7-9, 60487 Frankfurt am Main, Germany )
                1860-5397
                2012
                24 July 2012
                : 8
                : 1146-1160
                Affiliations
                [1 ]Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
                [2 ]Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig-44519, Egypt
                [3 ]Department of Organic Chemistry, College of Pharmacy, Misr University for Science and Technology, Al-Motamayez District, P.O. Box: 77, Egypt
                [4 ]Department of Chemistry, Quaid i Azam University, Islamabad 45320, Pakistan
                [5 ]Department of Biochemistry, Quaid i Azam University, Islamabad 45320, Pakistan
                [6 ]Department of Chemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
                Article
                10.3762/bjoc.8.128
                3458733
                23019443
                b1879eb1-e2de-4d03-b708-d883650eadb0
                Copyright © 2012, Berhanu et al; licensee Beilstein-Institut.

                This is an Open Access article under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                The license is subject to the Beilstein Journal of Organic Chemistry terms and conditions: ( http://www.beilstein-journals.org/bjoc)

                History
                : 24 February 2012
                : 1 June 2012
                Categories
                Full Research Paper
                Chemistry
                Organic Chemistry

                Organic & Biomolecular chemistry
                antibacterial,cluster analysis,n-acylbenzotriazoles,peptidomimetics,similarity

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