The Use of MALDI-TOF-MS and In Silico Studies for Determination of Antimicrobial Peptides’ Affinity to Bacterial Cells

Abstract

Several methods have been proposed for determining the binding affinity of antimicrobial peptides (AMPs) to bacterial cells. Here the utilization of MALDI-TOF-MS was proposed as a reliable and efficient method for high throughput AMP screening. The major advantage of the technique consists of finding AMPs that are selective and specific to a wide range of Gramnegative and -positive bacteria, providing a simple reliable screening tool to determine the potential candidates for broad spectrum antimicrobial drugs. As a prototype, amp-1 and -2 were used, showing highest activity toward Gram-negative and -positive membranes respectively. In addition, in silico molecular docking studies with both peptides were carried out for the membranes. In silico results indicated that both peptides presented affinity for DPPG and DPPE phospholipids, constructed in order to emulate an in vivo membrane bilayer. As a result, amp-1 showed a higher complementary surface for Gram-negative while amp-2 showed higher affinity to Gram-positive membranes, corroborating MS analyses. In summary, results here obtained suggested that in vitro methodology using MALDI-TOF-MS in addition to theoretical studies may be able to improve AMP screening quality.

Synthesis,68Ga-Radiolabeling, and PreliminaryIn VivoAssessment of a Depsipeptide-Derived Compound as a Potential PET/CT Infection Imaging Agent

“…The bacterial concentration was kept at 1.5 × 10 8 colony forming units (CFU). Five different concentrations (20, 40, 60, 80, and 100 μ M) of the above-mentioned compounds were used for all experiments, following the described method [ 10 ]. The final reaction volume was 600 μ L. Bacteria and compound mixtures were incubated at 37°C in an orbital shaker at 100 rpm for 3 h. After incubation, the cells were centrifuged at 3000 ×g for 20 min and the supernatant was removed.…”

Peptides and Peptidomics: A Tool with Potential in Control of Plant Viral Diseases

“…Several strategies had been described to get peptides in function microbial agent's control, between them, peptides with target to bacterial membrane [8] or antifungal activity [9]. In some cases those molecules had gotten from specificity selection assays based in directly interaction between molecules as well as modification of bioactive peptides and de novo design reported previously in data base like PhytAMP [10]- [13], using combinatory chemistry and computational chemistry like tools to enhance the antimicrobial activity and develop and chose new peptides with a best biological activity [10].…”

Elucidating Novel Bacterial Targets and Designing Unusual Antimicrobial Peptides: Two Faces of the Same Proteomic Coin

“…Additionally, for easy AMP detection the primary structures of such compounds must be better understood [54,56]. On this specific point more knowledge is needed, since several AMPs are quite promiscuous, being able to act in different ways under different conditions but with almost identical sequences [79]. This specific property could make it difficult to predict the function by proteomics, although MS techniques have been applied as a reliable and effective method for high-throughput AMP screening [13], and more studies must be performed in order to clarify structure-functional relations.…”