De Novo Design and Synthesis of Ultra-Short Peptidomimetic Antibiotics Having Dual Antimicrobial and Anti-Inflammatory Activities

Ravichandran N. Murugan, Mija Ahn, Eunha Hwang, Ji-Hyung Seo, Chaejoon Cheong, Jeong Kyu Bang, Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of KoreaBinu Jacob, Song Yub Shin, Department of Bio-Materials, Graduate School and Department of Cellular and Molecular Medicine, School of Medicine, Chosun University, Gwangju, Republic of KoreaHoik Sohn, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, United States of AmericaHyo-Nam Park, Jae-Kyung Hyun, Division of Electron Microscopic Research, Korea Basic Science Institute, Daejeon, Republic of KoreaEunjung Lee, Ki-Woong Jeong, Yangmee Kim, Department of Bioscience and Biotechnology, Institute of SMART Biotechnology, Konkuk University, Seoul, Republic of KoreaKy-Youb Nam, Bioinformatics and Molecular Design Research Center, Yonsei University Research Complex, Seoul, Republic of KoreaBackground: Much attention has been focused on the design and synthesis of potent, cationic antimicrobial peptides (AMPs) that possess both antimicrobial and anti-inflammatory activities. However, their development into therapeutic agents has been limited mainly due to their large size (12 to 50 residues in length) and poor protease stability.-- Methodology/Principal Findings: In an attempt to overcome the issues described above, a set of ultra-short, His-derived antimicrobial peptides (HDAMPs) has been developed for the first time. Through systematic tuning of pendant hydrophobic alkyl tails at the N(π)- and N(τ)-positions on His, and the positive charge of Arg, much higher prokaryotic selectivity was achieved, compared to human AMP LL-37. Additionally, the most potent HDAMPs showed promising dual antimicrobial and anti-inflammatory activities, as well as anti–methicillin-resistant Staphylococcus aureus (MRSA) activity and proteolytic resistance. Our results from transmission electron microscopy, membrane depolarization, confocal laser-scanning microscopy, and calcein-dye leakage experiments propose that HDAMP-1 kills microbial cells via dissipation of the membrane potential by forming pore/ion channels on bacterial cell membranes. -- Conclusion/Significance: The combination of the ultra-short size, high-prokaryotic selectivity, potent anti-MRSA activity, anti-inflammatory activity, and proteolytic resistance of the designed HDAMP-1, -3, -5, and -6 makes these molecules promising candidates for future antimicrobial therapeutics.This work was supported in part by the Korea Basic Science Institute's research program grants T33418 (J.K.B) and T33518 (J-k.H.), and the Korea Research Foundation, funded by the Korean Government (KRF-2011-0009039 to S.Y.S.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.ChemistryBiochemistryEmail: [email protected] (JKB)Email: [email protected] (SYS

AA mismatched DNAs with a single base difference exhibit a large structural change and a propensity for the parallel-stranded conformation

AA mismatches in DNA with different nearest-neighbor sequences were studied to understand the structural changes that accompany base-pair mismatches and the associated thermodynamics. Two synthesized duplexes, , 5' -d(CGACAATTGACG) (called AA1) and 5' -d(CGAGAATTCACG) (called AA2) as a palindrome sequences, had different nearest-neighbor sequences to the AA mismatches. This study focused on elucidating the structural and thermodynamic differences between these two molecules. A hydrogen bond between the mismatched adenines in AA1 was found, while no hydrogen bond in AA2. Both of the mismatched adenines in AA1 were stacked in the helix, while the mismatched adenine in AA2 surrounded by guanines was partially out of the helix and the other mismatched adenine surrounded by cytosines was stacked in the helix. Thermodynamically, AA1 was more stable than AA2. The melting temperature of the internal bases of AA1 was about 7 degree higher than that of AA2. The standard Gibbs free energy change for the duplex formation of AA1 was 1.30 Kcal/mol smaller than that of AA2. These thermal properties could be ascribed to the formation of the hydrogen bond. The conformational changes of these molecules at low pH were also investigated and compared. AA1 unambiguously assumed a parallel-stranded duplex at pH 4, while AA2 existed as a mixture of anti-parallel and parallel duplexes below pH 5

Structure of AQEE-30 of VGF Neuropeptide in Membrane-Mimicking Environments

AQEE-30 is one of the VGF peptides, which are derived from the VGF polypeptide precursor, and related to various physiological phenomena including neuroprotective effects in Huntington′s disease and amyotrophic lateral sclerosis (ALS). Although various functions of AQEE-30 have been reported so far, the structure of this peptide has not been reported yet. In this study, the structure of human AQEE-30 was investigated in hexafluoroisopropanol (HFIP) and dodecyl phosphocholine (DPC) micelle solutions, using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. CD results showed that AQEE-30 had a partial helical structure in aqueous buffer, and the helical structure was stabilized in the HFIP and DPC micelle solutions. The 3D structures determined by NMR spectroscopy showed that AQEE-30 adopted mainly α-helical structure in both the HFIP and DPC micelle solutions. The surface of AQEE-30 showed that it was predominantly negatively charged. The residues from 601 to 611 in both the HFIP and DPC micelle solutions showed amphiphilicity with four negatively charged residues, glutamate. The C-terminal consecutive arginine residues formed a partial positively charged surface. These results suggest an α-helical active structure of AQEE-30 in the cell-membrane environment

A Quick Method to Measure Hydroxyl Ion Contents in Bone Mineral Crystals Using Solid State NMR

A 31P CP MAS technique with a pre-saturation pulse was developed to measure OH- contents of bone quickly. This technique could save experimental time at least 128 times compared with a 2D 1H-31P HetCor technique. It also yielded higher signal to noise ratio (SNR), which decreased measurement error. The OH- content in bovine bone was 66.1 mol%