α-Helical Structures of Oligopeptides with an Alternating l-Leu-Aib Segment

Red Fluorescence from Organic Microdots: Leveraging Foldamer-Linked Azobenzene for Enhanced Stability and Intensity in Bioimaging Applications

Azobenzene, while relevant, has faced constraints in biological system applications due to its suboptimal quantum yield and short-wavelength emission. This study presents a pioneering strategy for fabricating organic microdots by coupling foldamer-linked azobenzene, resulting in robust fluorescence intensity and stability, especially in aggregated states, thereby showing promise for bioimaging applications. Comprehensive experimental and computational examinations elucidate the mechanisms underpinning enhanced photostability and fluorescence efficacy. In vitro and in vivo evaluations disclose that the external layer of cis-azo-foldamer microdots performs a self-sacrificial function during photo-bleaching. Consequently, these red-fluorescent microdots demonstrate extraordinary structural and photochemical stabilities over extended periods. The conjugation of a β-peptide foldamer to the azobenzene chromophore through a glycine linker instigates a blue-shifted and amplified π*-n transition. Molecular dynamics simulations reveal that the aggregated state of cis-azo-foldamers fortifies the stability of cis isomers, thereby augmenting fluorescence efficiency. This investigation furnishes crucial insights into conceptualizing novel, biologically inspired materials, promising stable and enduring imaging applications, and carries implications for diverse arenas such as medical diagnostics, drug delivery, and sensing technologies.

Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions

A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.

On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model. II. Evaluation of the properties in an infinite crystal

The previously reported exact potential and multipole moment (EP/MM) method for fast and precise evaluation of the intermolecular electrostatic interaction energies in molecular crystals using the pseudoatom representation of the electron density [Nguyen, Macchi & Volkov (2020), Acta Cryst. A76, 630-651] has been extended to the calculation of the electrostatic potential (ESP), electric field (EF) and electric field gradient (EFG) in an infinite crystal. The presented approach combines an efficient Ewald-type summation (ES) of atomic multipoles up to the hexadecapolar level in direct and reciprocal spaces with corrections for (i) the net polarization of the sample (the `surface term') due to a net dipole moment of the crystallographic unit cell (if present) and (ii) the short-range electron-density penetration effects. The rederived and reported closed-form expressions for all terms in the ES algorithm have been augmented by the expressions for the surface term available in the literature [Stenhammar, Trulsson & Linse (2011), J. Chem. Phys. 134, 224104] and the exact potential expressions reported in a previous study [Volkov, King, Coppens & Farrugia (2006), Acta Cryst. A62, 400-408]. The resulting algorithm, coded using Fortran in the XDPROP module of the software package XD, was tested on several small molecular crystal systems (formamide, benzene, L-dopa, paracetamol, amino acids etc.) and compared with a series of EP/MM-based direct-space summations (DS) performed within a certain number of unit cells generated along both the positive and negative crystallographic directions. The EP/MM-based ES technique allows for a noticeably more precise determination of the EF and EFG and significantly better precision of the evaluated ESP when compared with the DS calculations, even when the latter include contributions from an array of symmetry-equivalent atoms generated within four additional unit cells along each crystallographic direction. In terms of computational performance, the ES/EP/MM method is significantly faster than the DS calculations performed within the extended unit-cell limits but trails the DS calculations within the reduced summation ranges. Nonetheless, the described EP/MM-based ES algorithm is superior to the direct-space summations as it does not require the user to monitor continuously the convergence of the evaluated properties as a function of the summation limits and offers a better precision-performance balance.

Synthesis and Structural Stability of α-Helical Gold(I)-Metallopeptidesy

The synthesis of hexa- and dodecapeptides functionalized with two Au(I)–phosphine complexes is reported. The high stability of the Au(I)–phosphine bond allowed orthogonal peptide-protecting-group chemistry, even when using hard Lewis acids like boron tribromide. This enabled the preparation of an Fmoc-protected lysine derivative carrying the Au(I) complex in a side chain, which was used in standard Fmoc-based solid-phase peptide synthesis protocols. Alanine and leucine repeats in the metallododecapeptide formed α-helical secondary structures in 2,2,2-trifluoroethanol–H2O and 1,1,1,3,3,3-hexafluoroisopropanol–H2O mixtures with high thermal stability, as shown by temperature-dependent CD spectroscopy studies.

Helical Antimicrobial Peptide Foldamers Containing Non-proteinogenic Amino Acids

Antimicrobial peptides (AMPs) are potential novel therapeutic drugs against microbial infections. Most AMPs function by disrupting microbial membranes because of their amphipathic properties and ordered secondary structures. In this minireview, we describe recent efforts to develop helical AMP foldamers containing non-proteinogenic amino acids, such as α,α-disubstituted α-amino acids, β-amino acids, γ-amino acids, side-chain stapling and N-alkyl glycines.

Structure–mechanical property relationship of a pentapeptide crystal

A peptide having miniature (P)310/α-helix conformation, forms intermolecular H-bonded supramolecular helical bundle structure which further self-assembled to interdigited supramolecular sheet-like structure that eventually from the brittle crystal.

Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methods

The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170-175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536; Nguyen & Volkov (2019). Acta Cryst. A75, 448-464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, L-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283-4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10^-5 kJ mol^-1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28-64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.

Alternative binding sites at the vitamin D receptor and their ligands

In recent decades, the majority of ligands developed for the vitamin D receptor (VDR) bind at its deeply buried genomic ligand binding pocket. Theses ligands can be categorized into agonists and partial agonists/antagonists. A limited number of ligands, most of them peptides, bind the VDR‒coactivator binding site that is formed in the presence of an agonist and inhibit coactivator recruitment, and therefore transcription. Another solvent exposed VDR‒ligand binding pocket was identified for lithocholic acid, improving the overall stability of the VDR complex. Additional proposed interactions with VDR are discussed herein that include the alternative VDR‒ligand binding pocket that may mediate both non-genomic cellular responses and binding function 3 that was identified for the androgen receptor. Many VDR ligands increase blood calcium levels at therapeutic concentrations in vivo, thus the identification of alternative VDR‒ligand binding pockets might be crucial to develop non-calcemic and potent ligands for VDR to treat cancer and inflammatory disease.

Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. I. The Löwdin α-function method

The previously reported [Volkov et al. (2004). Chem. Phys. Lett. 391, 170-175] exact potential and multipole moment (EP/MM) method for evaluation of intermolecular electrostatic interaction energies using the nuclei-centered pseudoatom representation of electron densities is significantly improved in terms of both speed and accuracy by replacing the numerical quadrature integration of the exact potential with a fully analytical technique. The resulting approach, incorporated in the XDPROP module of the software package XD, has been tested on several molecular systems ranging in size from water-water to dodecapeptide-dodecapeptide dimers using electron densities constructed via the University at Buffalo Aspherical Atom Databank. The improved hybrid method provides electrostatic interaction energies within the uncertainty of ≤0.2 kJ mol^-1 for all benchmark systems. The running time for a dimer of a sizable, 225-atom dodecapeptide is under 4 s on a 2012 central processing unit (2.8 GHz AMD Opteron 6348) and under 3 s on a relatively modern processor (2.8 GHz Intel Xeon E3-1505M v5).

Extent of Helical Induction Caused by Introducing α-Aminoisobutyric Acid into an Oligovaline Sequence

The preferred conformations of a dodecapeptide composed of l-valine (l-Val) and α-aminoisobutyric acid (Aib) residues, Boc-(l-Val-l-Val-Aib)₄-OMe (3), were analyzed in solution and in the crystalline state. Peptide 3 predominantly folded into a mixture of α- and 3₁₀-(P) helical structures in solution and a (P) α helix in the crystalline state.