Rational design of antimicrobial peptides targeting Gram-negative bacteria

Membrane-targeting host antimicrobial peptides (AMPs) can kill or inhibit the growth of Gram-negative bacteria. However, the evolution of resistance among microbes poses a substantial barrier to the long-term utility of the host AMPs. Combining experiment and molecular dynamics simulations, we show that terminal carboxyl capping enhances both membrane insertion and antibacterial activity of an AMP called P1. Furthermore, we show that a bacterial strain with evolved resistance to this peptide becomes susceptible to P1 variants with either backbone capping or lysine-to-arginine substitutions. Our results suggest that cocktails of closely related AMPs may be useful in overcoming evolved resistance.     

Rational design of a ternary supramolecular system: self-assembly of pentanuclear lanthanide helicates

The self-assembly of the first pentanuclear helicate was predicted on the structural basis obtained for linear and tetranuclear parent supramolecular compounds. Accordingly, the designed ternary supramolecular system requires appropriate polytopic organic receptors, which were successfully synthesized. Indeed, the formation of pentanuclear complexes was experimentally evidenced with NMR and ESMS spectra that perfectly reflect the expected pattern. The structural features in the europium pentanuclear complex are highlighted with semiempirical molecular modeling. The present work validates the combinatorial approach leading to the thermodynamically driven formation of tower-like pentanuclear edifices.     

Rational design and functional evolution of targeted peptides for bioanalytical applications

The complicated, highly dynamic and diverse nature of biosystems brings great challenges to the specific analysis of molecular processes of interest. Nature provides antibodies for the specific recognition of antigens, which is a straight-forward way for targeted analysis. However, there are still limitations during the practical applications due to the big size of the antibodies, which accelerate the discovery of small molecular probes. Peptides built from various optional building blocks and easily achieved by chemical synthetic approaches with predictable conformations, are versatile and can act as tailor-made targeting vehicles. In this mini review, we summarize the recent developments in the discovery of novel peptides for bioanalytical and biomedical applications. Progresses in peptide-library design and selection strategies are presented. Recent achievements in the peptide-guided detection, imaging and disease treatment are also focused.     

Rational design of transglutaminase substrate peptides for rapid enzymatic formation of hydrogels

Short peptide substrates with high specificity toward transglutaminase (TGase) enzyme were designed, characterized, and coupled to a biocompatible polymer, allowing for rapid enzymatic cross-linking of peptide-polymer conjugates into hydrogels. Eight acyl acceptor Lys-peptide substrates and three acyl donor Gln-peptide substrates were rationally designed and synthesized. The kinetic constants of these peptides toward tissue transglutaminase were measured by enzyme assay using RP-HPLC analysis with the aid of LC-ESI/MS. Several acyl donor and acyl acceptor peptides with high specificities toward TGase were identified, including a few containing the unusual amino acid l-3,4-dihydroxylphenylalanine (DOPA), which is found in the adhesive proteins secreted by marine and freshwater mussels. Acyl donor and acyl acceptor peptides with high substrate specificities were separately coupled to branched poly(ethylene glycol) (PEG) polymer molecules. Equimolar solutions of these polymer-peptide conjugates rapidly formed hydrogels in less than 2 min in the presence of transglutaminase under physiological conditions. The use of biocompatible building blocks, their rapid solidification from a liquid precursor under physiologic conditions, and the ability to incorporate adhesive amino acid residues using biologically benign enzymatic cross-linking are advantageous properties for the use of such materials for tissue repair, drug delivery, and tissue engineering applications.     

Rational design of thioamide peptides as selective inhibitors of cysteine protease cathepsin L

Aberrant levels of cathepsin L (Cts L), a ubiquitously expressed endosomal cysteine protease, have been implicated in many diseases such as cancer and diabetes. Significantly, Cts L has been identified as a potential target for the treatment of COVID-19 due to its recently unveiled critical role in SARS-CoV-2 entry into the host cells. However, there are currently no clinically approved specific inhibitors of Cts L, as it is often challenging to obtain specificity against the many highly homologous cathepsin family cysteine proteases. Peptide-based agents are often promising protease inhibitors as they offer high selectivity and potency, but unfortunately are subject to degradation in vivo. Thioamide substitution, a single-atom O-to-S modification in the peptide backbone, has been shown to improve the proteolytic stability of peptides addressing this issue. Utilizing this approach, we demonstrate herein that good peptidyl substrates can be converted into sub-micromolar inhibitors of Cts L by a single thioamide substitution in the peptide backbone. We have designed and scanned several thioamide stabilized peptide scaffolds, in which one peptide, R^S_1A, was stabilized against proteolysis by all five cathepsins (Cts L, Cts V, Cts K, Cts S, and Cts B) while inhibiting Cts L with >25-fold specificity against the other cathepsins. We further showed that this stabilized R^S_1A peptide could inhibit Cts L in human liver carcinoma lysates (IC₅₀ = 19 μM). Our study demonstrates that one can rationally design a stabilized, specific peptidyl protease inhibitor by strategic placement of a thioamide and reaffirms the place of this single-atom modification in the toolbox of peptide-based rational drug design.

Information on the effects of sidechain and backbone modification on the activity of cathepsin (Cts) L, V, K, S, and B was used to design a thioamide peptide that is inert to all Cts and selectively inhibits Cts L.     

Rational design of allosteric ribozymes

Background: Efficient operation of cellular processes relies on the strict control that each cell exerts over its metabolic pathways. Some protein enzymes are subject to allosteric regulation, in which binding sites located apart from the enzyme's active site can specifically recognize effector molecules and alter the catalytic rate of the enzyme via conformational changes. Although RNA also performs chemical reactions, no ribozymes are known to operate as true allosteric enzymes in biological systems. It has recently been established that small-molecule receptors can readily be made of RNA, as demonstrated by the in vitro selection of various RNA aptamers that can specifically bind corresponding ligand molecules. We set out to examine whether the catalytic activity of an existing ribozyme could be brought under the control of an effector molecule by designing conjoined aptamer-ribozyme complexes.Results: By joining an ATP-binding RNA to a self-cleaving ribozyme, we have created the first example of an allosteric ribozyme that has a catalytic rate that can be controlled by ATP. A 180-fold reduction in rate is observed upon addition of either adenosine or ATP, but no inhibition is detected in the presence of dATP or other nucleoside triphosphates. Mutations in the aptamer domain that are expected to eliminate ATP binding or that increase the distance between aptamer and ribozyme domains result in a loss of ATP-specific allosteric control. Using a similar design approach, allosteric hammerhead ribozymes that are activated in the presence of ATP were created and another ribozyme that can be controlled by theophylline was created.Conclusions: The catalytic features of these conjoined aptamer-ribozyme constructs demonstrate that catalytic RNAs can also be subject to allosteric regulation — a key feature of certain protein enzymes. Moreover, by using simple rational design strategies, it is now possible to engineer new catalytic polynucleotides which have rates that can be tightly and specifically controlled by small effector molecules.     

Rational design of porous titanophosphates

To rationally design new nanoporous materials based on titanophosphates, a small library of titanium phosphate crystalline nanoporous compounds has been build up and its compounds have been investigated by X-ray diffraction and by in- and ex-situ NMR. The main trends of the unusual titanium solution chemistry, of the prenucleation building units and of their assembling have been established. The classical trial and error strategy can therefore be replaced by a better control of the steps leading to the final targeted network.     

Rational design of DNA nanoarchitectures

DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.     

Rational design of polymer colloids

Recent advances in understanding of the fundamental mechanistic events in emulsion polymerization give the potential for rational design of new materials based on polymer colloids. It is now possible to design a new industrial process from first principles, based on well‐understood mechanistic principles. An overview of recent developments in the fundamental science of emulsion polymerization is given, with examples of the application of this knowledge to topologically‐controlled synthesis of novel materials based on natural rubber and polybutadiene seed latexes.     

Material binding peptides for nanotechnology

Remarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.     

Quantum chemistry benchmarking of binding and selectivity for lanthanide extractants

Computer‐aided screening methods facilitate the discovery of new extractants for heavy and rare‐earth metal separations. In this work, we have benchmarked the accuracy of different quantum chemistry methods for calculating extractant binding energies and selectivities. Specifically, we compare calculated data from different exchange correlation functionals (B3LYP‐D3, ωB97X‐D3, and M06‐L) and different basis sets (including large‐core effective core potentials and all‐electron basis sets). We report aqueous‐phase binding energy and selectivity trends for 1:1 and 3:1 extractant/lanthanide models for the complexes. We find that binding selectivities are not particularly sensitive to model chemistry, but binding energies are sensitive. Furthermore, calculated trends in selectivity using 3:1 extractant/lanthanide models are in better agreement with available experimental trends than trends using 1:1 extractant/lanthanide models. Lastly, we find that the B3LYP‐D3/6‐31 + G* model chemistry with the Stuttgart large‐core relativistic effective core potentials on the lanthanide sufficiently reproduces results from larger basis set calculations and is confirmed as suitable for relatively fast and efficient screening of lanthanide binding energies and selectivities.     

Rational design of light-controllable polymer micelles

Amphiphilic block copolymer (BCP) micelles are nanocarriers that hold promise for controlled delivery applications. This account highlights our recent works on light-dissociable BCP micelles. We have designed and developed light-responsive amphiphilic BCPs whose micellar aggregates (core-shell micelles and vesicles) can be disrupted by light exposure. The basic strategy is to incorporate a chromophore into the structure of the hydrophobic block, whose photoreaction can result in a conformational or structural change that shifts the hydrophilic/hydrophobic balance toward the destabilization of the micelles. Using various chromophores including azobenzene, pyrene and nitrobenzene, we have achieved both reversible and irreversible dissociation of BCP micelles upon illumination with UV/visible or near infrared light. The demonstrated rational design principle based on light-changeable or light-switchable amphiphilicity is general and can be applied to many polymer/chromophore combinations. This opens the door to developing photocontrollable polymer nanocarriers offering control over when and where the release of loaded agents takes place.     

Rational design of a calcium-binding protein

Calcium ions play key roles as structural components in biomineralization and as a second messenger in signaling pathways. We have introduced a de novo designed calcium-binding site into the framework of a non-calcium-binding protein, domain 1 of CD2. The resulting protein selectively binds calcium over magnesium with calcium-binding affinity comparable to that of natural extracellular calcium-binding proteins (K(d) of 50 microM). This experiment is the first successful metalloprotein design that has a high coordination number (seven) metal-binding site constructed into a beta-sheet protein. Our results demonstrate the feasibility of designing a single calcium-binding site into a host protein, taking into account only local properties of a calcium-binding site obtained by a survey of natural calcium-binding proteins and chelators. The resulting site exhibits strong metal selectivity, suggesting that it should now be feasible to understand and manipulate signaling processes by designing novel calcium-modulated proteins with specifically desired functions and to affect their stability.     

Rational design of chiral nanoscale adamantanoids

[formula: see text] Utilizing coordination as a motif, the self-organization of six ditopic and four tritopic building blocks leads to the formation of nanoscale adamantanoid frameworks.     

Rational design of 0D, 1D, and 3D open frameworks based on tetranuclear lanthanide(III) sulfonate-phosphonate clusters

Hydrothermal reactions of lanthanide(III) salts with m-sulfophenylphosphonic acid (H3L1) and 1,10-phenanthroline (phen) or N,N'-piperazinebis(methylenephosphonic acid) (H4L2) afforded six novel lanthanide(III) sulfonate-phosphonates based on tetranuclear clusters, namely, [La(2)(L1)2(phen)4(H2O)].4.5H2O (1), [Ln2(L1)2(phen)2(H2O)5].3H2O (Ln = Nd, 2; Eu, 3; Er, 4), and [Ln2(HL1)(H2L2)2(H2O)4].8H2O (Ln = La, 5; Nd, 6). Compounds 2-4 contain discrete tetranuclear lanthanide(III) cluster units in which four lanthanide(III) ions are bridged by two tridentate and two tetradentate phosphonate groups. In compound 1, the tetranuclear clusters are further interconnected into a 1D chain through the coordination of the sulfonate groups. The structures of compounds 5 and 6 can be viewed as a 3D architecture based on a different types of tetranuclear cluster units that are interconnected by bridging H2L2 anions. In the tetranuclear clusters of compounds 5 and 6, the four lanthanide(III) centers are interconnected by only two HL1 ligands. Compound 2 is a luminescent material in the near-IR region, whereas compound 3 displays a strong luminescent emission band in the red-light region. Magnetic property measurements of compounds 2-4 and 6 indicate that there are strong antiferromagetic interactions between magnetic centers within the cluster units.     

Protein binding to lanthanide(III) complexes can reduce the water exchange rate at the lanthanide

The GdIII-based magnetic resonance imaging contrast agent MS-325 targets the blood protein serum albumin, resulting in an increased efficacy (relaxivity) as a relaxation agent. MS-325 showed different relaxivities when bound to serum albumin from different species, e.g., r1=30.5 mM-1 s-1 (rabbit) vs 46.3 mM-1 s-1 (human) at 35 degrees C and 0.47 T. To investigate the mechanism for this difference, surrogate complexes were prepared where the GdIII ion was replaced by other LnIII ions. Fluorescence lifetime measurements of the EuIII analogue indicated that the hydration number was q=1 and did not change when bound to either human, rat, rabbit, pig, or dog serum albumin. The YbIII analogue, YbL1, was prepared and characterized by 1H NMR. Line-shape analysis of the paramagnetic-shifted 1H NMR resonances in the presence of increasing amounts of human (HSA) or rabbit (RSA) serum albumin allowed estimation of the transverse relaxation rate, R2, of these resonances for the protein-bound YbL1. The rotational correlation time of YbL1 was calculated from R2, and the Yb-H distance and was tauR=8+/-1 ns when bound to HSA and 13+/-2 ns when bound to RSA. The water exchange rate at the DyIII analogue, DyL1, was determined from variable-temperature R2 measurements at 9.4 T when DyL1 was bound to either HSA or RSA. At 37 degrees C, water exchange at DyL1 was (31+/-5)x10(6) s-1 when bound to HSA but (3.8+/-0.2)x10(6) s-1 when bound to RSA. Slower water exchange upon RSA binding explains the differences in relaxivity observed. The approach of using surrogate lanthanides to identify specific molecular parameters influencing relaxivity is applicable to other protein-targeted GdIII contrast agents.     

Advances in anion binding and sensing using luminescent lanthanide complexes

Luminescent lanthanide complexes have been actively studied as selective anion receptors for the past two decades. Ln(iii) complexes, particularly of europium(iii) and terbium(iii), offer unique photophysical properties that are very valuable for anion sensing in biological media, including long luminescence lifetimes (milliseconds) that enable time-gating methods to eliminate background autofluorescence from biomolecules, and line-like emission spectra that allow ratiometric measurements. By careful design of the organic ligand, stable Ln(iii) complexes can be devised for rapid and reversible anion binding, providing a luminescence response that is fast and sensitive, offering the high spatial resolution required for biological imaging applications. This review focuses on recent progress in the development of Ln(iii) receptors that exhibit sufficiently high anion selectivity to be utilised in biological or environmental sensing applications. We evaluate the mechanisms of anion binding and sensing, and the strategies employed to tune anion affinity and selectivity, through variations in the structure and geometry of the ligand. We highlight examples of luminescent Ln(iii) receptors that have been utilised to detect and quantify specific anions in biological media (e.g. human serum), monitor enzyme reactions in real-time, and visualise target anions with high sensitivity in living cells.

This minireview highlights advances in anion binding and sensing using luminescent lanthanide(iii) complexes.