A Fourier Transformation Based Method to Mine Peptide Space for Antimicrobial Activity

Background Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is possible to discover new candidate peptides using the available genomic and proteomic data. High throughput computational techniques could also be used to virtually scan the entire peptide space for discovering out new candidate antimicrobial peptides. Result We have identified a unique indexing method based on biologically distinct characteristic features of known antimicrobial peptides. Analysis of the entries in the antimicrobial peptide databases, based on our indexing method, using Fourier transformation technique revealed a distinct peak in their power spectrum. We have developed a method to mine the genomic and proteomic data, for the presence of peptides with potential antimicrobial activity, by looking for this distinct peak. We also used the Euclidean metric to rank the potential antimicrobial peptides activity. We have parallelized our method so that virtually any given protein space could be data mined, in search of antimicrobial peptides. Conclusion The results show that the Fourier transform based method with the property based coding strategy could be used to scan the peptide space for discovering new potential antimicrobial peptides

Protein Structure

Since the dawn of recorded history, and probably even before, men and women have been grasping at the mechanisms by which they themselves exist. Only relatively recently, did this grasp yield anything of substance, and only within the last several decades did the proteins play a pivotal role in this existence. In this expose on the topic of protein structure some of the current issues in this scientific field are discussed. The aim is that a non-expert can gain some appreciation for the intricacies involved, and in the current state of affairs. The expert meanwhile, we hope, can gain a deeper understanding of the topic

A computational study of cyclic peptides with vibrational circular dichroism

Cyclic peptides are a class of molecules that has shown antimicrobial potential. These are complex compounds to investigate with their large conformational space and multiple chiral centers. A technique that can be used to investigate both conformational preferences and absolute configuration (AC) is vibrational circular dichroism (VCD). To extract information from the experimental VCD spectra a comparison with calculated spectra is often needed and this is the focus of this thesis: the calculation of VCD spectra. The VCD spectra are very sensitive to small structural changes, and to accurately calculate the spectra, all important conformers need to be identified. The first part of this thesis has been to establish a reliable computational protocol using meta-dynamics to sample the conformational space and ab initio methods to calculate the spectra for cyclic peptides. Using our protocol, we have investigated if VCD alone can determine the AC of cyclic tetra- and hexapeptides. We show that it is possible to determine the AC of the cyclic peptides with two chiral centers while for the peptides with three and four chiral centers, VCD is at best able to reduce the number of possible ACs and further investigation with other techniques is needed. Further, we investigated four cyclic hexapeptides with antimicrobial potential. These peptides, in contrast to the ones used for validating the protocol, consist of several amino acids with long and positively charged side chains. For these peptides, a molecular dynamics based approach provided VCD spectra in better agreement with experiment than our protocol. Reasons for this may be the lack of atomistic detail in the solvent model used during the conformational search and insufficient description of dispersion interactions during the meta-dynamics simulation

Nanotechnology approaches to combat antimicrobial resistance: novel therapeutics and diagnostics

Antimicrobial resistance (AMR) is a global issue caused by misuse of antibiotics and a lack of new antibiotics coming to market. Combating the development of AMR requires the development of new antimicrobial agents to treat bacterial infections and better diagnostic tools for improved stewardship. This thesis describes novel approaches to address these issues using nanotechnology. The main technique employed in these studies was atomic force microscopy (AFM), used in both conventional imaging mode and in an innovative sensing capacity. From a therapeutic perspective, the mechanism of action of novel antimicrobial structures (protein / DNA) were studied, using real-time imaging on model membranes and live E. coli cells. Nanometre resolution was achieved on both systems, allowing rapid membrane poration and subsequent cell death to be observed for a de novo designed antimicrobial peptide and a pioneering antimicrobial DNA-lipid origami structure. In addition, this thesis describes the first visualisation of the Membrane Attack Complex (MAC) on live bacterial cells showing remarkable similarity with the recently solved cryo-EM structure. In working to develop novel phenotypic diagnostic tools for AMR, we report on a novel antibiotic susceptibility testing (AST) device. This device uses single cell optical interference to provide a rapid (∼45 min) and simple measure of the effect of antimicrobials on suspended bacterial cells. Homebuilt code was developed to analyse datasets, allowing antibiotic sensitivity to be systematically determined for lab and clinical strains of E. coli. This thesis provides insights into a number of potential avenues to pursue in the face of increasing AMR, with future work entailing moving the described from the lab closer to clinical use

Investigating antimicrobial resistance mechanisms in Neisseria gonorrhoeae using peptide probes

The continuing evolution of antibiotic resistance strains of Neisseria gonorrhoeae coupled with the paucity of new antimicrobial agents makes the treatment of gonococcal infections challenging. A major cause of resistance is the expression of a multidrug efflux pump termed MtrCDE, which exports a wide range of antimicrobial agents. Efflux pumps are membrane-bound systems and consequently challenging to study and target with drugs. The transcriptional regulator (MtrR) of the efflux pump, however, is a soluble protein and therefore more amenable to study and drug target validation investigations. This thesis serves to investigate the hypothesis that substrates for the MtrCDE efflux pump are also ligands for the regulator MtrR. Isothermal titration calorimetry (ITC) was used to show that MtrR binds commercial antibiotics and antimicrobial peptides. -lactam antibiotics not only bind MtrR but are hydrolysed by the multidrug protein. Evidence for this novel enzymatic activity is provided by ITC, mass spectrometric and microbiological techniques. A series of peptides derived from LL-37 were synthesised and screened for binding to MtrR. A key region of LL-37 with a higher affinity to MtrR than the natural product was then identified. The peptide binding site in MtrR was elucidated via a photoactivated peptide binding study. Electrophoresis mobility shift assays indicated that the peptides do not induce derepression of the genes controlled by MtrR, although the peptide derivatives of LL-37 were shown to be substrates for the MtrCDE efflux pump

Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society

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