Development of a Python-based electron ionization mass spectrometry amino acid and peptide fragment prediction model.

The increased fragmentation caused by harsher ionization methods used during mass spectrometry such as electron ionization can make interpreting the mass spectra of peptides difficult. Therefore, the development of tools to aid in this spectral analysis is important in utilizing these harsher ionization methods to study peptides, as these tools may be more accessible to some researchers. We have compiled fragmentation mechanisms described in the literature, confirmed them experimentally, and used them to create a Python-based fragment prediction model for peptides analyzed under direct exposure probe electron ionization mass spectrometry. This initial model has been tested using single amino acids as well as targeted libraries of short peptides. It was found that the model does well in predicting fragments of peptides composed of amino acids for which the model is well-defined, but several cases where additional mechanistic information needs to be incorporated have been identified.

Peptoid-Peptide Hybrid Analogs of the Enterococcus faecalis Fsr Auto-Inducing Peptide (AIP) Reveal Crucial Structure-Activity Relationships.

As multidrug-resistant bacteria become a more pressing risk to human health, alternate approaches to treating bacterial infections are being increasingly investigated. Enterococcus faecalis is an opportunistic pathogen responsible for a large percentage of secondary enterococci infections. Its pathogenicity has been shown to be largely dependent on a cell-density communication mechanism, termed quorum sensing. In this study, we conducted a systematic investigation of the lactone-containing macrocyclic signaling peptide used by E. faecalis for Fsr-mediated communication, termed gelatinase biosynthesis activating pheromone (GBAP). Specifically, through a combination of the on-resin sub-monomer and solution phase peptoid building block synthesis approaches, we successfully synthesized a library of peptoid-peptide hybrid analogs of GBAP and determined the biological effects associated with the introduction of the peptoid (N-alkyl glycine derivative) modifications. Within the macrocycle region of the peptide, as have been seen with other modifications, the F7 site was unusually tolerant toward peptoid modification, compared with other macrocyclic sites. Interestingly, within the exocyclic tail, peptoid modification at the N2 site completely abolished activity, a first for a single tail modification.

Development and utilization of peptide-based quorum sensing modulators in Gram-positive bacteria.

Quorum sensing (QS) is a mechanism by which bacteria regulate cell density-dependent group behaviors. Gram-positive bacteria generally rely on auto-inducing peptide (AIP)-based QS signaling to regulate their group behaviors. To develop synthetic modulators of these behaviors, the natural peptide needs to be identified and its structure-activity relationships (SARs) with its cognate receptor (either membrane-bound or cytosolic) need to be understood. SAR information allows for the rational design of peptides or peptide mimics with enhanced characteristics, which in turn can be utilized in studies to understand species-specific QS mechanisms and as lead scaffolds for the development of therapeutic candidates that target QS. In this review, we discuss recent work associated with the approaches used towards forwarding each of these steps in Gram-positive bacteria, with a focus on species that have received less attention.

N-Methylation of Amino Acids in Gelatinase Biosynthesis-Activating Pheromone Identifies Key Site for Stability Enhancement with Retention of the Enterococcus faecalis fsr Quorum Sensing Circuit Response.

The growing prevalence of multiantibiotic-resistant bacteria necessitates looking at potential alternative approaches for attenuating infections by bacteria while reducing the rate of antibiotic resistance development. Enterococcus faecalis is responsible for a large percentage of clinical enterococci infections, and its pathogenicity has been demonstrated to be influenced by quorum sensing (QS). In this study, we report the systematic study of the relationship between backbone hydrogens and the ability to activate the FsrC receptor. We demonstrate that N-methylation was particularly well-tolerated at one site (Phe7) and granted stability against protease digestion, increasing the peptide half-life relative to the native signal by more than 6-fold. The inclusion of the N-Me-Phe7 modification may be useful for improving the pharmacological properties of E. faecalis QS inhibitors as part of the development of future therapeutic candidates.

Rational Design of Potent Activators and Inhibitors of the Enterococcus faecalis Fsr Quorum Sensing Circuit.

The increasing rate of resistance development to conventional antibiotics by bacteria necessitates the identification of alternative treatment possibilities that can reduce the ability of bacteria to adapt. Enterococcus faecalis remains the leading cause of clinical enterococci infections and has exhibited quorum sensing (QS)-dependent pathogenicity. Here, we report the development of macrocyclic peptide-based activators and inhibitors of the E. faecalis Fsr QS circuitry. To this end, we developed, optimized, and compared three synthetic routes for lactone-containing macrocyclic peptide scaffolds. We then utilized previous and current structure-activity relationship (SAR) insights of the native QS signaling peptide to rationally design the most potent activators and inhibitors of the Fsr QS circuitry identified to date. The application of these peptides could provide a means to attenuate the pathogenicity of E. faecalis without introducing significant selective pressure on the bacteria to develop resistance.

Recent Advances in GLP-1 Receptor Agonists for Use in Diabetes Mellitus.

Preclinical Research Mimetics of Glucagon-like peptide 1 (GLP-1) represent a useful alternative or complementary treatment choice to insulin in the treatment of diabetes mellitus. The lack of hypoglycemia as a side effect when GLP-1 receptor agonists are used along with the tendency of these therapeutic agents to prevent or even reduce weight gain makes them valuable targets in therapy development. However, native GLP-1 and many of its early analogues have very short half-lives, requiring repeated treatment to maintain therapeutic levels. As all current treatments are injected subcutaneously, a large focus has been made on trying to extend the half-lives of GLP-1 analogues while retaining bioactivity. Most success in this regard has been achieved with the use of peptide-protein fusions, which are not as well suited for oral administration. However, recent work focused on the development of non-fusion peptides with increased half-lives that may be more appropriate for oral administration. This minireview discusses the structural characteristics of past and present analogues as well as the recent work conducted toward developing novel GLP-1 receptor agonists. Drug Dev Res 78 : 292-299, 2017. © 2017 Wiley Periodicals, Inc.

An Entirely Solid Phase Peptide Synthesis-Based Strategy for Synthesis of Gelatinase Biosynthesis-Activating Pheromone (GBAP) Analogue Libraries: Investigating the Structure-Activity Relationships of the Enterococcus faecalis Quorum Sensing Signal.

The development of an entirely solid-phase peptide synthesis (SPPS)-based synthesis of the quorum sensing signal gelatinase biosynthesis-activating pheromone (GBAP) from Enterococcus faecalis is reported. The method was used to prepare three libraries of analogues to investigate the structure-activity relationships (SARs) of the GBAP signal. The SAR studies revealed new characteristics of the GBAP signal and uncovered the most potent quorum sensing activator in E. faecalis known to date.