Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency

Protein–protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.     

A method to determine the kinetics of multiple proteins in human infants with respiratory distress syndrome

We report a method to measure in vivo turnover of four proteins from sequential tracheal aspirates obtained from human newborn infants with respiratory distress syndrome using targeted proteomics. We detected enrichment for all targeted proteins approximately 3 h from the start of infusion of [5,5,5-(2)H(3)] leucine, secretion times that varied from 1.2 to 2.5 h, and half lives that ranged between 10 and 21 h. Complement factor B, a component of the alternative pathway of complement activation, had an approximately twofold-longer half-life than the other three proteins. In addition, the kinetics of mature and carboxy-terminal tryptic peptides from the same protein (surfactant protein B) were not statistically different (p = 0.49).     

Antibiotic recognition by binuclear metallo-beta-lactamases revealed by X-ray crystallography

Metallo-beta-lactamases are zinc-dependent enzymes responsible for resistance to beta-lactam antibiotics in a variety of host bacteria, usually Gram-negative species that act as opportunist pathogens. They hydrolyze all classes of beta-lactam antibiotics, including carbapenems, and escape the action of available beta-lactamase inhibitors. Efforts to develop effective inhibitors have been hampered by the lack of structural information regarding how these enzymes recognize and turn over beta-lactam substrates. We report here the crystal structure of the Stenotrophomonas maltophilia L1 enzyme in complex with the hydrolysis product of the 7alpha-methoxyoxacephem, moxalactam. The on-enzyme complex is a 3'-exo-methylene species generated by elimination of the 1-methyltetrazolyl-5-thiolate anion from the 3'-methyl group. Moxalactam binding to L1 involves direct interaction of the two active site zinc ions with the beta-lactam amide and C4 carboxylate, groups that are common to all beta-lactam substrates. The 7beta-[(4-hydroxyphenyl)malonyl]-amino substituent makes limited hydrophobic and hydrogen bonding contacts with the active site groove. The mode of binding provides strong evidence that a water molecule situated between the two metal ions is the most likely nucleophile in the hydrolytic reaction. These data suggest a reaction mechanism for metallo-beta-lactamases in which both metal ions contribute to catalysis by activating the bridging water/hydroxide nucleophile, polarizing the substrate amide bond for attack and stabilizing anionic nitrogen intermediates. The structure illustrates how a binuclear zinc site confers upon metallo-beta-lactamases the ability both to recognize and efficiently hydrolyze a wide variety of beta-lactam substrates.     

An efficient, path-independent method for free-energy calculations

Classical free-energy methods depend on the definition of physical or nonphysical integration paths to calculate free-energy differences between states. This procedure can be problematic and computationally expensive when the states of interest do not overlap and are far apart in phase space. Here we introduce a novel method to calculate free-energy differences that is path-independent by transforming each end state into a reference state in which the vibrational entropy is the sole component of the total entropy, thus allowing direct computation of the relative free energy. We apply the method to calculate side-chain entropies of a beta-hairpin-forming peptide in a variety of backbone conformations, demonstrating its importance in determining structural propensities. We find that low-free-energy conformations achieve their stability through optimal trade off between enthalpic gains due to favorable interatomic interactions and entropic losses incurred by the same.     

Synthesis and Protonation Features of 24-, 27- and 32-membered Macrocyclic Polyamines

Three macrocyclic polyamines [24]ane-N₆ 1 , [32]ane-N₈ 2 and [27]ane-N₆O₃ 3 of ring size 24, 32 and 27, respectively, have been synthesized. They contain either trimethylenediamine of ethylenediamine units. The acyclic analog 4 , as the reference compound, was also prepared. Compounds 1–3 are macrocyclic analogs of natural polyamines and are potential ligands for metal cations as well as, when protonated, for anions. The protonation constants of compounds 1–4 have been determined. They are high enough for compounds 1–4 to be fully protonated in a pH-range close to neutrality, as required for binding of anions of weak acids. The effect of structural features on the protonation constants are briefly discussed in relation to the design of macrocyclic polyamine ligands.