Molecular simulations of peptides: a useful tool for the development of new drugs and for the study of molecular recognition

DPD Simulation of Protein Conformations: From α-Helices to β-Structures

We suggest a coarse-grained model for DPD simulations of polypeptides in solutions. The model mimics hydrogen bonding that stabilizes α-helical and β-structures using dissociable Morse bonds between quasiparticles representing the peptide groups amenable to hydrogen bonding. We demonstrate the capabilities of the model by simulating transitions between coil-like, globular, α-helical, and β-hairpin configurations of model peptides, varying Morse potential parameters, the hydrophobicities of residue side chains, and pH, which determines the charges of residue side chains. We construct a model triblock polypeptide mimicking the sequence of residues α-synuclein at two different pHs. The conformations of this model polypeptide depend on pH similarly to the behavior observed experimentally. The suggested approach to accounting for hydrogen bond formation within the general DPD framework may make the DPD method a competitive alternative to CGMD for modeling equilibrium and dynamic properties of proteins and polypeptides, especially during their transport in confined environments.

Studying interactions by molecular dynamics simulations at high concentration

Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.

Disruption of Bcr-Abl coiled coil oligomerization by design

Oligomerization is an important regulatory mechanism for many proteins, including oncoproteins and other pathogenic proteins. The oncoprotein Bcr-Abl relies on oligomerization via its coiled coil domain for its kinase activity, suggesting that a designed coiled coil domain with enhanced binding to Bcr-Abl and reduced self-oligomerization would be therapeutically useful. Key mutations in the coiled coil domain of Bcr-Abl were identified that reduce homo-oligomerization through intermolecular charge-charge repulsion yet increase interaction with the Bcr-Abl coiled coil through additional salt bridges, resulting in an enhanced ability to disrupt the oligomeric state of Bcr-Abl. The mutations were modeled computationally to optimize the design. Assays performed in vitro confirmed the validity and functionality of the optimal mutations, which were found to exhibit reduced homo-oligomerization and increased binding to the Bcr-Abl coiled coil domain. Introduction of the mutant coiled coil into K562 cells resulted in decreased phosphorylation of Bcr-Abl, reduced cell proliferation, and increased caspase-3/7 activity and DNA segmentation. Importantly, the mutant coiled coil domain was more efficacious than the wild type in all experiments performed. The improved inhibition of Bcr-Abl through oligomeric disruption resulting from this modified coiled coil domain represents a viable alternative to small molecule inhibitors for therapeutic intervention.

Peptide-based Antifungal Therapies against Emerging Infections

Acquired drug resistance to mycotic infections is rapidly emerging as a major medical problem. Opportunistic fungal infections create therapeutic challenges, particularly in high risk immunocompromised patients with AIDS, cancer, and those undergoing transplantation. Higher mortality and/or morbidity rates due to invasive mycosis have been increasing over the last 20 years, and in light of growing resistance to commonly used antibiotics, novel antifungal drugs and approaches are required. Currently there is considerable interest in antifungal peptides that are ubiquitous in plant and animal kingdoms. These small cationic peptides may have specific targets or may be multifunctional in their mechanism of action. On the basis of recent advances in protein engineering and solid phase syntheses, the utility and potential of selected peptides as efficient antifungal drugs with acceptable toxicity profiles are being realized. This review will discuss recent advances in peptide therapy for opportunistic fungal infections.