NMR structure and activity relationship of defensin-analogous peptides
In recent years, strains of bacteria with resistance to conventional antibiotics have been emerging at an alarming rate leading to the urgency of designing a new generation of antimicrobials. One of the promising avenues has been antimicrobial peptides and peptoids. Despite intensive research, detai...
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| Other Authors: | |
| Format: | Thesis |
| Language: | English |
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2014
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| Online Access: | https://hdl.handle.net/10356/56137 |
| _version_ | 1824453555627491328 |
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| author | Bai, Yang |
| author2 | Roger W. Beuerman |
| author_facet | Roger W. Beuerman Bai, Yang |
| author_sort | Bai, Yang |
| collection | NTU |
| description | In recent years, strains of bacteria with resistance to conventional antibiotics have been emerging at an alarming rate leading to the urgency of designing a new generation of antimicrobials. One of the promising avenues has been antimicrobial peptides and peptoids. Despite intensive research, detailed bactericidal and cytotoxic mechanisms of AMPs are still largely unknown. In this thesis, molecular template evolution based on the peptide sequence modifications, biophysical studies using fluorescence labeling and NMR spectroscopy, virtual screening utilizing large scale molecular dynamics simulations are exploited for rational antimicrobial drug discovery. Two main classes of drug candidates are studied, human β-defensin-3 derived linear as well as branched peptides targeting Gram-negative bacteria and peptide mimetics synthesized from cationic charge-modified alpha-mangostin predominantly active against Gram-positive bacteria. The results show that the binding affinity, partitioning into the lipid bilayer, the ability to oligomerize and form well defined structures upon interactions with biological phases (e.g. bacterial membranes, peptidoglycans and LPS layers) may contribute to condensation of positive charges in AMP macrostructures resulting in membrane remodeling and eventual lysis of bacteria. The interactions between AMPs and negatively charged lipids characteristic to the composition of the bacterial inner membranes can cause redistribution of membrane lipids, which in turn may result in increased membrane permeability and bacterial lysis. In the case of branched peptide targeting Gram-negative bacteria, a progressive structure accretion is observed in water, LPS, and lipid environments. Despite inducing rapid aggregation of outer membrane lipopolysaccharides, AMPs remain highly mobile in the aggregated lattice. These findings suggest that AMPs possessing both enhanced mobility in the bacterial outer membrane and spatial structure facilitating its interactions with the membrane-water interface may provide excellent structural motifs for developing broad-spectrum new antimicrobials. For peptoids targeting Gram-positive bacteria, large oligomers formed by strong hydrophobic interactions between xanthone groups were observed in aqueous solution, lipid micelles and liposomes. The peptoid-induced graded leakage of the content of the lipid liposomes used to model bacterium was monitored by both florescence study as well as solution state NMR using bacterial membrane mimicking liposomes incorporating florescence reporter or paramagnetic molecules inside. A novel AMP membrane targeting mechanism, a patch model, was proposed. Once approaching bacterial membrane, an incoming individual peptoid molecule does not directly bind to the peptoid-free lipid surface but rather preferentially interacts with growing peptoid oligomers (patches) already assembled on the surface. This creates a significant concentration buildup of the disruptors in the limited surface area resulting in the vesicle disruptions only in those liposomes where a sufficiently large patch of AMPs has been formed hence a graded leakage phenomenon in overall liposome ensembles. Fast growing large peptoid patches built on bacterial membrane eventually lead to lipid bilayer deformation and bacterial lysis. Our novel patch model provides explanation for graded leakage observed for many AMPs, inspiring new direction for antimicrobial drug design. |
| first_indexed | 2025-02-19T03:08:17Z |
| format | Thesis |
| id | ntu-10356/56137 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-02-19T03:08:17Z |
| publishDate | 2014 |
| record_format | dspace |
| spelling | ntu-10356/561372023-02-28T18:48:46Z NMR structure and activity relationship of defensin-analogous peptides Bai, Yang Roger W. Beuerman Konstantin Pervushin School of Biological Sciences Singapore Eye Research Institute DRNTU::Science::Biological sciences In recent years, strains of bacteria with resistance to conventional antibiotics have been emerging at an alarming rate leading to the urgency of designing a new generation of antimicrobials. One of the promising avenues has been antimicrobial peptides and peptoids. Despite intensive research, detailed bactericidal and cytotoxic mechanisms of AMPs are still largely unknown. In this thesis, molecular template evolution based on the peptide sequence modifications, biophysical studies using fluorescence labeling and NMR spectroscopy, virtual screening utilizing large scale molecular dynamics simulations are exploited for rational antimicrobial drug discovery. Two main classes of drug candidates are studied, human β-defensin-3 derived linear as well as branched peptides targeting Gram-negative bacteria and peptide mimetics synthesized from cationic charge-modified alpha-mangostin predominantly active against Gram-positive bacteria. The results show that the binding affinity, partitioning into the lipid bilayer, the ability to oligomerize and form well defined structures upon interactions with biological phases (e.g. bacterial membranes, peptidoglycans and LPS layers) may contribute to condensation of positive charges in AMP macrostructures resulting in membrane remodeling and eventual lysis of bacteria. The interactions between AMPs and negatively charged lipids characteristic to the composition of the bacterial inner membranes can cause redistribution of membrane lipids, which in turn may result in increased membrane permeability and bacterial lysis. In the case of branched peptide targeting Gram-negative bacteria, a progressive structure accretion is observed in water, LPS, and lipid environments. Despite inducing rapid aggregation of outer membrane lipopolysaccharides, AMPs remain highly mobile in the aggregated lattice. These findings suggest that AMPs possessing both enhanced mobility in the bacterial outer membrane and spatial structure facilitating its interactions with the membrane-water interface may provide excellent structural motifs for developing broad-spectrum new antimicrobials. For peptoids targeting Gram-positive bacteria, large oligomers formed by strong hydrophobic interactions between xanthone groups were observed in aqueous solution, lipid micelles and liposomes. The peptoid-induced graded leakage of the content of the lipid liposomes used to model bacterium was monitored by both florescence study as well as solution state NMR using bacterial membrane mimicking liposomes incorporating florescence reporter or paramagnetic molecules inside. A novel AMP membrane targeting mechanism, a patch model, was proposed. Once approaching bacterial membrane, an incoming individual peptoid molecule does not directly bind to the peptoid-free lipid surface but rather preferentially interacts with growing peptoid oligomers (patches) already assembled on the surface. This creates a significant concentration buildup of the disruptors in the limited surface area resulting in the vesicle disruptions only in those liposomes where a sufficiently large patch of AMPs has been formed hence a graded leakage phenomenon in overall liposome ensembles. Fast growing large peptoid patches built on bacterial membrane eventually lead to lipid bilayer deformation and bacterial lysis. Our novel patch model provides explanation for graded leakage observed for many AMPs, inspiring new direction for antimicrobial drug design. DOCTOR OF PHILOSOPHY (SBS) 2014-04-03T08:40:52Z 2014-04-03T08:40:52Z 2014 2014 Thesis Bai, Y. (2013). NMR structure and activity relationship of defensin-analogous peptides. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/56137 10.32657/10356/56137 en 199 p. application/pdf |
| spellingShingle | DRNTU::Science::Biological sciences Bai, Yang NMR structure and activity relationship of defensin-analogous peptides |
| title | NMR structure and activity relationship of defensin-analogous peptides |
| title_full | NMR structure and activity relationship of defensin-analogous peptides |
| title_fullStr | NMR structure and activity relationship of defensin-analogous peptides |
| title_full_unstemmed | NMR structure and activity relationship of defensin-analogous peptides |
| title_short | NMR structure and activity relationship of defensin-analogous peptides |
| title_sort | nmr structure and activity relationship of defensin analogous peptides |
| topic | DRNTU::Science::Biological sciences |
| url | https://hdl.handle.net/10356/56137 |
| work_keys_str_mv | AT baiyang nmrstructureandactivityrelationshipofdefensinanalogouspeptides |