MD Simulation of AEDG Peptide Complexes with New K2R Dendrimer and Dendrigraft

Biocompatible peptide dendrimers and dendrigrafts have useful properties for application in biomedicine. In previous papers the computational approach for study lysine dendrimers and dendrigrafts as well as their complexes with various medical peptides was used. In this paper the comparison of complex formation between molecules of therapeutic AEDG tetrapeptide and novel K2R peptide dendrimer or DG2 dendrigraft of near the same size and charge was fulfilled. The systems consisting of 16 therapeutic AEDG tetrapeptide molecules and one dendrimer or one dendrigraft were studied by molecular dynamics simulation. Full atomic models of these molecules in water with explicit counterions were used for this goal. First of all, the process of complex formation was studied. It was obtained that peptide molecules were attracted by both branched molecules and were quickly adsorbed by them. Times of complexes formation as well as size, anisotropy and structure of each complex were calculated. It was demonstrated that both K2R dendrimer and DG2 dendrigraft are effective for complexation of these peptide molecules but new dendrimer complex is more stable than dendrigraft complex because it has almost twice more hydrogen bonds with peptide molecules and 33% more ion pairs with their charged groups.

Peptide Dendrimers: From Enzyme Models to Antimicrobials and Transfection Reagents

Aiming at studying cooperativity effects between amino acids in easily accessible protein models, we have explored the chemistry of peptide dendrimers, which we obtain as pure products by solid-phase peptide synthesis using a branching diamino acid such as lysine at every second or third position in a peptide sequence, followed by reverse-phase HPLC purification. This article reviews discoveries driven by combinatorial library synthesis and screening, including enantioselective esterase and aldolase enzyme models, cobalamin binding and peroxidase dendrimers, glycopeptide dendrimer biofilm inhibitors and their X-ray crystal structures as complexes with lectins, antimicrobial peptide dendrimers active against multidrug resistant Gram-negative bacteria, and transfection reagents for siRNA and CRISPR-Cas9 plasmid DNA. Latest developments include cheminformatics and artificial intelligence for exploring the peptide chemical space, and the principle of stereorandomization to understand the role of peptide chirality in activity.

Antimicrobial Peptide Dendrimers and Quorum-Sensing Inhibitors in Formulating Next-Generation Anti-Infection Cell Therapy Dressings for Burns

Multidrug resistance infections are the main cause of failure in the pro-regenerative cell-mediated therapy of burn wounds. The collagen-based matrices for delivery of cells could be potential substrates to support bacterial growth and subsequent lysis of the collagen leading to a cell therapy loss. In this article, we report the development of a new generation of cell therapy formulations with the capacity to resist infections through the bactericidal effect of antimicrobial peptide dendrimers and the anti-virulence effect of anti-quorum sensing MvfR (PqsR) system compounds, which are incorporated into their formulation. Anti-quorum sensing compounds limit the pathogenicity and antibiotic tolerance of pathogenic bacteria involved in the burn wound infections, by inhibiting their virulence pathways. For the first time, we report a biological cell therapy dressing incorporating live progenitor cells, antimicrobial peptide dendrimers, and anti-MvfR compounds, which exhibit bactericidal and anti-virulence properties without compromising the viability of the progenitor cells.

Super-Cationic Peptide Dendrimers—Synthesis and Evaluation as Antimicrobial Agents

Microbial infections are a major public health concern. Antimicrobial peptides (AMPs) have been demonstrated to be a plausible alternative to the current arsenal of drugs that has become inefficient due to multidrug resistance. Herein we describe a new AMP family, namely the super-cationic peptide dendrimers (SCPDs). Although all members of the series exert some antibacterial activity, we propose that special attention should be given to (KLK)2KLLKLL-NH2 (G1KLK-L2KL2), which shows selectivity for Gram-negative bacteria and virtually no cytotoxicity in HepG2 and HEK293. These results reinforce the validity of the SCPD family as a valuable class of AMP and support G1KLK-L2KL2 as a strong lead candidate for the future development of an antibacterial agent against Gram-negative bacteria.

Developments in Treatment Methodologies Using Dendrimers for Infectious Diseases

Dendrimers comprise a specific group of macromolecules, which combine structural properties of both single molecules and long expanded polymers. The three-dimensional form of dendrimers and the extensive possibilities for use of additional substrates for their construction creates a multivalent potential and a wide possibility for medical, diagnostic and environmental purposes. Depending on their composition and structure, dendrimers have been of interest in many fields of science, ranging from chemistry, biotechnology to biochemical applications. These compounds have found wide application from the production of catalysts for their use as antibacterial, antifungal and antiviral agents. Of particular interest are peptide dendrimers as a medium for transport of therapeutic substances: synthetic vaccines against parasites, bacteria and viruses, contrast agents used in MRI, antibodies and genetic material. This review focuses on the description of the current classes of dendrimers, the methodology for their synthesis and briefly drawbacks of their properties and their use as potential therapies against infectious diseases.

A Study with Peptide Dendrimers Reveals an Extreme pH Dependence of Antibiotic Activity Above pH 7.4

The presence of ionizable groups in antimicrobial peptides (AMPs) often induces a pH-dependent activity. Herein we report that removing eight low p<i>K</i>_a amino termini in antimicrobial peptide dendrimer (AMPD) <b>G3KL</b> provides dendrimer <b>XC1</b> with a broader pH-activity range. Furthermore, raising the pH to 8.0 reveals strong activities against <i>Klebsiella pneumoniae</i> and methicillin resistant <i>Staphylococcus aureus</i> (MRSA) against which these AMPDs are inactive at pH 7.4. We observe a similar effect with polymyxin B on MRSA. Binding experiments with a fluorescent AMPD and the effect of high salt concentration suggest that the activity increase reflects stronger electrostatic binding to the bacteria at high pH. pH-profiling of other polycationic antimicrobials (polymers, peptidomimetics, foldamers, dendrimers) might similarly enhance their activity range, with possible use for topical treatments.

A Study with Peptide Dendrimers Reveals an Extreme pH Dependence of Antibiotic Activity Above pH 7.4

The presence of ionizable groups in antimicrobial peptides (AMPs) often induces a pH-dependent activity. Herein we report that removing eight low p<i>K</i>_a amino termini in antimicrobial peptide dendrimer (AMPD) <b>G3KL</b> provides dendrimer <b>XC1</b> with a broader pH-activity range. Furthermore, raising the pH to 8.0 reveals strong activities against <i>Klebsiella pneumoniae</i> and methicillin resistant <i>Staphylococcus aureus</i> (MRSA) against which these AMPDs are inactive at pH 7.4. We observe a similar effect with polymyxin B on MRSA. Binding experiments with a fluorescent AMPD and the effect of high salt concentration suggest that the activity increase reflects stronger electrostatic binding to the bacteria at high pH. pH-profiling of other polycationic antimicrobials (polymers, peptidomimetics, foldamers, dendrimers) might similarly enhance their activity range, with possible use for topical treatments.