Proline-rich antimicrobial peptides (PrAMPs) are promising candidates to treat bacterial infections. The designer peptide ARV-1502 exhibits strong antimicrobial effects against Enterobacteriaceae both in vitro and in vivo. Since the inhibitory effects of ARV-1502 reported for the 70 kDa heat-shock protein DnaK do not fully explain the antimicrobial activity of its 176 substituted analogs, we further studied their effect on the bacterial 70S ribosome of Escherichia coli, a known target of PrAMPs. ARV-1502 analogues, substituted in positions 3, 4, and 8 to 12 (underlined) of the binding motif D3KPRPYLPRP12 with aspartic acid, lysine, serine, phenylalanine or leucine, were tested in a competitive fluorescence polarization (FP) binding screening assay using 5(6)-carboxyfluoresceinlabeled (Cf-) ARV-1502 and the 70S ribosome isolated from E. coli BW25113. While their effect on ribosomal protein expression was studied for green fluorescent protein (GFP) in a cell-free expression system (in vitro translation), the importance of known PrAMP transporters SbmA and MdtM was investigated using E. coli BW25113 and the corresponding knockout mutants. The dissociation constant (Kd) of 201 16 nmol/L obtained for Cf-ARV-1502 suggests strong binding to the E. coli 70S ribosome. An inhibitory binding assay indicated that the binding site overlaps with those of other PrAMPs including Onc112 and pyrrhocoricin as well as the non-peptidic antibiotics erythromycin and chloramphenicol. All these drugs and drug candidates bind to the exit-tunnel of the 70S ribosome. Substitutions of the C-terminal fragment of the binding motif YLPRP reduced binding. At the same time, inhibition of GFP expression increased with net peptide charge. Interestingly, the MIC values of wild-type and DsbmA and DmdtM knockout mutants indicated that substitutions in the ribosomal binding motif altered also the bacterial uptake, which was generally improved by incorporation of hydrophobic residues. In conclusion, most substituted ARV-1502 analogs bound weaker to the 70S ribosome than ARV-1502 underlining the importance of the YLPRP binding motif. The weaker ribosomal binding correlated well with decreased antimicrobial activity in vitro. Substituted ARV-1502 analogs with a higher level of hydrophobicity or positive net charge improved the ribosome binding, inhibition of translation, and bacterial uptake.

The antimicrobial peptide (AMP) ARV-1502 was designed based on naturally occurring short proline-rich AMPs, including pyrrhocoricin and drosocin. Identification of chaperone DnaK as a therapeutic target in Escherichia coli triggered intense research on the ligand- DnaK-interactions using fluorescence polarization and X-ray crystallography to reveal the binding motif and characterize the influence of the chaperone on protein refolding activity, especially in stress situations. In continuation of this research, 182 analogs of ARV-1502 were designed by substituting residues involved in antimicrobial activity against Gramnegative pathogens. The peptides synthesized on solid-phase were examined for their binding to E. coli and S. aureus DnaK providing 15 analogs with improved binding characteristics for at least one DnaK. These 15 analogs were distinguished from the original sequence by their increased hydrophobicity parameters. Additionally, the influence of the entire DnaK chaperone system, including co-chaperones DnaJ and GrpE on refolding and ATPase activity, was investigated. The increasingly hydrophobic peptides showed a stronger inhibitory effect on the refolding activity of E. coli chaperones, reducing protein refolding by up to 64%. However, these more hydrophobic peptides had only a minor effect on the ATPase activity. The most dramatic changes on the ATPase activity involved peptides with aspartate substitutions. Interestingly, these peptides resulted in a 59% reduction of the ATPase activity in the E. coli chaperone system whereas they stimulated the ATPase activity in the S. aureus system up to 220%. Of particular note is the improvement of the antimicrobial activity against S. aureus from originally >128 μg/mL to as low as 16 μg/mL. Only a single analog exhibited improved activity over the original value of 8 μg/mL against E. coli. Overall, the various moderate-throughput screenings established here allowed identifying (un)favored substitutions on 1) DnaK binding, 2) the ATPase activity of DnaK, 3) the refolding activity of DnaK alone or together with co-chaperones, and 4) the antimicrobial activity against both E. coli and S. aureus.

Anti-microbial proteins (AMP) are the key effector arm of the innate immune system. The prevalence of AMP in single-celled eukaryotes to humans shows its importance during the course of evolution. The first report for the role of the anti-microbial peptide in clearing infection was given by Alexander Fleming in 1990’s through the discovery of Penicillin and Lysozyme. The search for antimicrobial agents in human granulocytes was begun by Ehrlich in 1870’s but the first successful isolation of an antimicrobial agent from rabbit neutrophils was done by Zeya and Spitznagel in 1969. Later work by Peter Elshbach and his group on AMPs in rabbit neutrophils brought to light an AMP that can increase the permeability of the bacterial membrane. This AMP named as Bactericidal/permeability-increasing protein (BPI) was further isolated from human neutrophils. Since then many studies have been carried out to understand the mode of action of BPI, which culminated in understanding the new functional activity of this protein viz opsonisation, LPS neutralization and anti-angiogenic function. Knowing to the role of BPI as an anti-inflammatory agent, multiple studies have tried to use BPI for treating endotoxic shock. Dysregulation of BPI expression is associated with various inflammatory diseases like Crohn’s Disease (CD), Ulcerative colitis (UC) and Infectious enteritis’s. Mutations in BPI are also linked to susceptibility to various infections. Even though there are several studies focusing on the functional aspects of BPI, the regulation of BPI expression is poorly understood. Knowing the clinical importance of dysregulation of BPI, it is vital to understand the regulation of BPI expression during the course of bacterial infection. The Thesis is divided into four chapters. As the main aim of this study is to understand the regulation of BPI expression, in Chapter 1 we introduce the known facts about the protein. A brief overview of the mode of action and regulation of BPI is discussed in this chapter. The subsequent sections describe the diseases associated with Dysregulation of BPI and the use of BPI as a therapeutic agent in various diseases. Towards the end, the objective of the present study is discussed. BPI is primarily known to be expressed in human neutrophils and epithelial cells. Previous studies have shown that among innate immune cells, murine BPI is expressed only in dendritic cells and neutrophils, but not in macrophages. Based on these results, it was presumed that BPI is not expressed in human macrophages. In Chapter 2, we report the presence of BPI in human macrophages. Our studies revealed increased expression of BPI in human macrophages stimulated with various PAMPs (Pathogen-associated molecular patterns) viz., LPS, flagellin as well as during bacterial infection. Further, during the course of an infection, BPI interacted with Gram-negative bacteria, resulting in enhanced phagocytosis and subsequent control of the bacterial replication. However, it was observed that bacteria which can maintain an active replicating niche (Salmonella Typhimurium) avoid the interaction with BPI during later stages of infection. On the other hand Salmonella mutants, which cannot maintain a replicating niche, as well as Shigella flexneri, which quit the endosomal vesicle, showed interaction with BPI. BPI was induced in both M1 and M2 differentiated macrophages suggesting its role in limiting Gram-negative bacteria and parasitic infection. These results propose an active role of BPI in Gram-negative bacterial clearance by human macrophages. This chapter concludes with a discussion on the importance of BPI expression in human but not murine macrophages. The importance of maintaining an active replicating niche by STM to evade interaction with BPI is also discussed. As the first line of defense against invading pathogens, intestinal epithelium produces various antimicrobial proteins (AMP) that help with clearance of pathogen. The precise mechanism of AMP regulation in intestinal epithelium is not clear. Intestinal epithelium being a primary entry point for various pathogens, we tried to understand the regulation of BPI expression in the intestine during the course of bacterial infection. In Chapter 3, we report a direct correlation between intestinal damage and BPI expression. In Caco-2 cells, we see a significant increase in BPI levels upon membrane damage mediated by S.aureus infection and pore-forming toxins (Streptolysin and Listeriolysin). Cells detect changes in potassium levels as a Danger-associated molecular pattern (DAMP) associated with cell damage and induce BPI expression in a p38 dependent manner. These results are further supported by in vivo findings that BPI expression in the murine intestinal epithelium is induced upon infection with bacteria which cause intestinal damage (Salmonella Typhimurium & Shigella flexneri) whereas mutants which don’t cause intestinal damage (STM fliC & STM invC), didn’t induce BPI expression. These findings have a huge impact on our current understanding of AMP response during inflammatory bowel diseases (IBD). Our results suggest that dysregulation of BPI expression might be an effect rather than a cause of IBD. This chapter concludes with a discussion on the importance of potassium efflux associated with membrane damage as an important signal that helps in discriminating the invading pathogen from the pool of gut microflora. Bactericidal/permeability-increasing protein had been shown to possess anti-inflammatory and endotoxin neutralizing activity by interacting with LPS of Gram-negative bacteria. Even though rBPI (recombinant BPI) has cleared phase III clinical trials for treating endotoxemia, the high cost of purified BPI provided by pharmaceutical companies makes it inaccessible or unavailable for the common man. In Chapter 4, we examined the feasibility of using murine BPI (mBPI) expressed on halophilic Archaeal gas vesicle nanoparticles (GVNPs) for the treatment of endotoxemia in high-risk patients, using a murine model of D-galactosamine-induced endotoxic shock. Halobacterium sp. NRC-1 was used to express the N-terminal 199 amino acid residues of mBPI fused to the GVNP GvpC protein, and bound to the surface of the haloarchaeal GVNPs. Our results indicate that delivery of mBPIN-GVNPs increase the survival rate of mice challenged with lethal concentrations of lipopolysaccharide (LPS) and D-galactosamine. Additionally, the mBPIN-GVNP-treated mice displayed reduced symptoms of inflammation including inflammatory anemia, recruitment of neutrophils, liver apoptosis and pro-inflammatory serum cytokine levels. This chapter concludes with a discussion of the advantages of using mBPIN-GVNPs over purified protein in treating endotoxic shock.