Conformation and Biological Activity of Cyclic Peptides

Recommended Tool Compounds for the Melanocortin Receptor (MCR) G Protein-Coupled Receptors (GPCRs)

The melanocortin receptors are a centrally and peripherally expressed family of Class A GPCRs with physiological roles, including pigmentation, steroidogenesis, energy homeostasis, and others yet to be fully characterized. There are five melanocortin receptor subtypes that, apart from the melanocortin-2 receptor (MC2R), are stimulated by a shared set of endogenous agonists. Until 2020, X-ray crystallographic and cryo-electron microscopic (cryo-EM) structures of these receptors were unavailable, and the investigation of their mechanisms of action and putative ligand-receptor interactions was driven by site-directed mutagenesis studies of the receptors and targeted structure-activity relationship (SAR) studies of the endogenous and derivative synthetic ligands. Synthetic derivatives of the endogenous agonist ligand α-MSH have evolved into a suite of powerful ligands such as NDP-MSH (melanotan I), melanotan II (MTII), and SHU9119. This suite of tool compounds now enables the study of the melanocortin receptors and serves as scaffolds for FDA-approved drugs, means of validating stably expressing melanocortin receptor cell lines, core ligands in assessing cryo-EM structures of active and inactive receptor complexes, and essential references for high-throughput discovery and mechanism of action studies. Herein, we review the history and significance of a finite set of these essential tool compounds and discuss how they are being utilized to further the field's understanding of melanocortin receptor physiology and greater druggability.

Ultra-Fast-Healing Glassy Hyperbranched Plastics Capable of Restoring 26.4 MPa Tensile Strength within One Minute at Room Temperature

The growing concern regarding widespread plastic pollution has propelled the development of sustainable self-healing plastics. Although considerable efforts have been dedicated to fabricating self-healing plastics, achieving rapid healing at room temperature is extremely challenging. Herein, we have developed an ultra-fast-healing glassy polyurethane (UGPU) by designing a hyperbranched molecular structure with a high density of multiple hydrogen bonds (H-bonds) on compliant acyclic heterochains and introducing trace water to form water bridge across the fractured surfaces. The compliant acyclic heterochains allow the dense multiple hydrogen bonds to form a frozen network, enabling tensile strength of up to 70 MPa and storage modulus of 2.5 GPa. The hyperbranched structure can drive the reorganization of the H-bonding network through the high mobility of the branched chains and terminals, thereby leading to self-healing ability at room temperature. Intriguingly, the presence of trace water vapor facilitates the formation of activated layers and the rearrangement of networks across the fractured UGPU sections, thereby enabling ultra-fast self-healing at room temperature. Consequently, the restored tensile strength after healing for 1 minute achieves a historic-record of 26.4 MPa. Furthermore, the high transparency (>90 %) and ultra-fast healing property of UGPU make it an excellent candidate for advanced optical and structural materials.

Conformational modulation and polymerization-induced folding of proteomimetic peptide brush polymers

Peptide-brush polymers generated by graft-through living polymerization of peptide-modified monomers exhibit high proteolytic stability, therapeutic efficacy, and potential as functional tandem repeat protein mimetics. Prior work has focused on polymers generated from structurally disordered peptides that lack defined conformations. To obtain insight into how the structure of these polymers is influenced by the folding of their peptide sidechains, a set of polymers with varying degrees of polymerization was prepared from peptide monomers that adopt α-helical secondary structure for comparison to those having random coil structures. Circular dichroism and nuclear magnetic resonance spectroscopy confirm the maintenance of the secondary structure of the constituent peptide when polymerized. Small-angle X-ray scattering (SAXS) studies reveal the solution-phase conformation of PLPs in different solvent environments. In particular, X-ray scattering shows that modulation of solvent hydrophobicity, as well as hydrogen bonding patterns of the peptide sidechain, plays an important role in the degree of globularity and conformation of the overall polymer, with polymers of helical peptide brushes showing less spherical compaction in conditions where greater helicity is observed. These structural insights into peptide brush folding and polymer conformation inform the design of these proteomimetic materials with promise for controlling and predicting their artificial fold and morphology.

Identification of "Structural Pin" Interactions and their Significance for the Conformational Control of Macrocyclic Scaffolds

While peptide macrocycles with rigidified conformations have proven to be useful in the design of chemical probes of protein targets, conformational flexibility and rapid interconversion can be equally vital for biological activity and favorable physicochemical properties. This study introduces the concept of "structural pin", which describes a hydrogen bond that is largely responsible for stabilizing the entire macrocycle backbone conformation. Structural analysis of macrocycles using nuclear magnetic resonance (NMR), molecular modelling and X-ray diffraction indicates that disruption of the structural pin can drastically influence the conformation of the entire ring, resulting in novel states with increased flexibility. This finding provides a new tool to interrogate dynamic behaviour of macrocycles. Identification of structural pins offers a useful conceptual framework to understand positions that can either be modified to give flexible structures or retained to maintain the rigidity of the scaffold.

Recent Advances in the Field of Amino Acid-Conjugated Aminoferrocenes-A Personal Perspective

The development of turn-based inhibitors of protein-protein interactions has attracted considerable attention in medicinal chemistry. Our group has synthesized a series of peptides derived from an amino-functionalized ferrocene to investigate their potential to mimic protein turn structures. Detailed DFT and spectroscopic studies (IR, NMR, CD) have shown that, for peptides, the backbone chirality and bulkiness of the amino acid side chains determine the hydrogen-bond pattern, allowing tuning of the size of the preferred hydrogen-bonded ring in turn-folded structures. However, their biological potential is more dependent on their lipophilicity. In addition, our pioneering work on the chiroptical properties of aminoferrocene-containing peptides enables the correlation of their geometry with the sign of the CD signal in the absorption region of the ferrocene chromophore. These studies have opened up the possibility of using aminoferrocene and its derivatives as chirooptical probes for the determination of various chirality elements, such as the central chirality of amino acids and the helicity of peptide sequences.

Insights on Structure-Passive Permeability Relationship in Pyrrole and Furan-Containing Macrocycles

Macrocycles have recognized therapeutic potential, but their limited cellular permeability can hinder their development as oral drugs. To better understand the structure-permeability relationship of heterocycle-containing, semipeptidic macrocycles, a library was synthesized. These compounds were created by developing two novel reactions described herein: the reduction of activated oximes by LiBH4 and the aqueous reductive mono-N-alkylation of aldehydes using catalytic SmI2 and stoichiometric Zn. The permeability of the macrocycles was evaluated through a parallel artificial membrane permeability assay (PAMPA), and the results indicated that macrocycles with a furan incorporated into the structure have better passive permeability than those with a pyrrole moiety. Compounds bearing a 2,5-disubstituted pyrrole (endo orientation) were shown to be implicated in intramolecular H-bonds, enhancing their permeability. This study highlighted the impact of heterocycles moieties in semipeptides, creating highly permeable macrocycles, thus showing promising avenues for passive diffusion of drugs beyond the rule-of-five chemical space.

Contemporary Applications of Thioamides and Methods for Their Synthesis

Thioamides are naturally occurring isosteres of amide bonds in which the chalcogen atom of the carbonyl is changed from oxygen to sulfur. This substitution gives rise to altered nucleophilicity and hydrogen bonding properties with importance for both chemical reactivity and non-covalent interactions. As such, thioamides have been introduced into biologically active compounds to achieve improved target affinity and/or stability towards hydrolytic enzymes but have also been applied as probes of protein and peptide folding and dynamics. Recently, a series of new methods have been developed for the synthesis of thioamides as well as their utilization in peptide chemistry. Further, novel strategies for the incorporation of thioamides into proteins have been developed, enabling both structural and functional studies to be performed. In this Review, we highlight the recent developments in the preparation of thioamides and their applications for peptide modification and study of protein function.

Turn-Mimic Hydantoin-Based Loops Constructed by a Sequential Multicomponent Reaction

A collection of peptidomimetics characterized by having an aspartic acid motif embedded in a rigid hydantoin heterocycle are synthesized through a sequential multicomponent domino process followed by standard regioselective deprotection/coupling reactions based on acid-base liquid/liquid purification protocols. 1H nuclear magnetic resonance experiments, molecular modeling, and X-ray analysis showed that the resulting hydantoin-based loops I (in particular) and II (to a lesser extent) can be considered novel β-turn inducer motifs being able to project two peptide-like strands in a U-shaped conformation driven by the formation of intermolecular hydrogen bonds.

Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides

Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.

β-Turn Induction by a Diastereopure Azepane-Derived Quaternary Amino Acid

β-Turns are one of the most common secondary structures found in proteins. In the interest of developing novel β-turn inducers, a diastereopure azepane-derived quaternary amino acid has been incorporated into a library of simplified tetrapeptide models in order to assess the effect of the azepane position and peptide sequence on the stabilization of β-turns. The conformational analysis of these peptides by molecular modeling, NMR spectroscopy, and X-ray crystallography showed that this azepane amino acid is an effective β-turn inducer when incorporated at the i + 1 position. Moreover, the analysis of the supramolecular self-assembly of one of the β-turn-containing peptide models in the solid state reveals that it forms a supramolecular helical arrangement while maintaining the β-turn structure. The results here presented provide the basis for the use of this azepane quaternary amino acid as a strong β-turn inducer in the search for novel peptide-based bioactive molecules, catalysts, and biomaterials.

Proximity-Induced Ligation and One-Pot Macrocyclization of 1,4-Diketone-Tagged Peptides Derived from 2,5-Disubstituted Furans upon Release from the Solid Support

1,4-Dione-containing peptides are generated during the cleavage of 2,5-disubstituted furan-containing systems. The generated electrophilic systems then react with α-effect nucleophiles, following a Paal-Knorr-like mechanism, for the generation of macrocyclic peptides, occurring after simple resuspension of the crude peptide in water. Conveniently, the in situ generation of the electrophile from a stable furan ring avoids the complications associated with the synthesis of carbonyl-containing peptides. Detailed investigation of the reaction characteristics was first performed on supramolecular coiled-coil systems.

Photochemistry of phthalimidoadamantane dipeptides: effect of amino acid side chain on photocyclization

A series of dipeptides 1 was synthesized that at the N-site contained 3-(N-phthalimidoadamantane-1-carboxylic acid and at the C-site different aliphatic or aromatic L- or D-amino acids. The photochemical reaction of dipeptides 1 under acetone-sensitized conditions gave simple decarboxylation products 6, and decarboxylation-induced cyclization products 7, as well as some secondary products 8 and 9 formed by elimination of H2O or ring enlargement, respectively. Molecules 9 undergo secondary photoinduced H-abstractions by the phthalimide chromophore, delivering more complex polycycles 11. The photodecarboxylation-induced cyclization to 7 was observed only with phenylalanine (Phe), proline (Pro), leucine (Leu) and isoleucine (Ile). Contrary to dipeptides with Phe, the cyclization takes place with almost complete racemization at the amino acid chiral center, but diastereoselectively giving only one pair of enantiomers. The conducted investigation is important as it provides the breath and the scope of dipeptide cyclizations activated by phthalimides.

Synthesis and Conformational Analysis of Hydantoin-Based Universal Peptidomimetics

The synthesis of a collection of enantiomerically pure, systematically substituted hydantoins as structural privileged universal mimetic scaffolds is presented. It relies on a chemoselective condensation/cyclization domino process between isocyanates of quaternary or unsubstituted α-amino esters and N-alkyl aspartic acid diesters followed by standard hydrolysis/coupling reactions with amines, using liquid-liquid acid/base extraction protocols for the purification of the intermediates. Besides the nature of the α carbon on the isocyanate moiety, either a quaternary carbon or a more flexible methylene group, conformational studies in silico (molecular modeling), in solution (NMR, circular dichroism (CD), Fourier transform infrared (FTIR)), and in solid state (X-ray) showed that the presented hydantoin-based peptidomimetics are able to project their substituents in positions superimposable to the side chains of common protein secondary structures such as α-helix and β-turn, being the open α-helix conformation slightly favorable according to molecular modeling, while the closed β-turn conformation preferred in solution and in solid state.

Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds

The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d₆ ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d₆ and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.

Multimeric RGD-Based Strategies for Selective Drug Delivery to Tumor Tissues

RGD peptides have received a lot of attention over the two last decades, in particular to improve tumor therapy through the targeting of the αVβ3 integrin receptor. This review focuses on the molecular design of multimeric RGD compounds, as well as the design of suitable linkers for drug delivery. Many examples of RGD-drug conjugates have been developed, and we show the importance of RGD constructs to enhance binding affinity to tumor cells, as well as their drug uptake. Further, we also highlight the use of RGD peptides as theranostic systems, promising tools offering dual modality, such as tumor diagnosis and therapy. In conclusion, we address the challenging issues, as well as ongoing and future development, in comparison with large molecules, such as monoclonal antibodies.

Interaction of Positively Charged Oligopeptides with Blood Plasma Proteins

In this project, we combine two areas of research, experimental characterization and molecular docking studies of the interaction of positively charged oligopeptides with crucial blood plasma proteins. The investigated peptides are rich in NH₂ groups of amino acid side chains from Dap, Orn, Lys, and Arg residues, which are relevant in protein interaction. The peptides are 9- and 11-mer with the following sequences: (Lys-Dab-Dab-Gly-Orn-Pro-His-Lys-Arg-Lys-Dbt), (Lys-Dab-Ala-Gly-Orn-Pro-His-Lys-Arg), and (Lys-Dab-Dab-Gly-Orn-Pro-Phe(2-F)-Lys-Arg). The net charge of the compound strongly depends on the pH environment and it is an important aspect of protein binding. The studied oligopeptides exhibit therapeutic properties: anti-inflammatory activity and the capacity to diminish reactive oxygen species (ROS). Therefore, the mechanism of potential binding with blood plasma components is the next challenge. The binding interaction has been investigated under pseudo-physiological conditions with the main blood plasma proteins: albumin (BSA), α1-acid glycoprotein (AAG), and γ-globulin fraction (GGF). The biomolecular quenching constant (k_q) and binding constant (K_b) were obtained by fluorescence spectroscopy at various temperatures. Simultaneously, the changes in the secondary structure of proteins were monitored by circular dichroism (CD) and infrared spectroscopy (IR) by quantity analysis. Moreover, molecular docking studies were conducted to estimate the binding affinity, the binding domain, and the chemical nature of these interactions. The results show that the investigated oligopeptides could be mainly transported by albumin, and the binding domain I is the most favored cavity. The BSA and GGF are able to form stable complexes with the studied compounds as opposed to AAG. The binding reactions are spontaneous processes. The highest binding constants were determined for Lys-Dab-Dab-Gly-Orn-Pro-His-Lys-Arg-Lys-Dbt peptide, in which the values of the binding constants K_b to BSA and GGF were 10.1 × 10⁴ dm³mol^-1 and 3.39 × 10³ dm³mol^-1, respectively. The positively charged surface of peptides participated in salt bridge interaction with proteins; however, hydrogen bonds were also formed. The secondary structure of BSA and GGF after contact with peptides was changed. A reduction in the α-helix structure was observed with an increase in the β-sheet and β-turn and random coil structures.

Single Atom Ring Contraction of Peptide Macrocycles Using Cornforth Rearrangement

Site-selective transformations of densely functionalized scaffolds have been a topic of intense interest in chemical synthesis. Herein we have repurposed the rarely used Cornforth rearrangement as a tool to effect a single-atom ring contraction in cyclic peptide backbones. Investigations into the kinetics of the rearrangement were carried out to understand the impact of electronic factors, ring size, and linker type on the reaction efficiency. Conformational analysis was undertaken and showed how subtle differences in the peptide backbone result in substrate-dependent reaction profiles. This methodology can now be used to perform conformation-activity studies. The chemistry also offers an opportunity to install building blocks that are not compatible with traditional C-to-N iterative synthesis of macrocycle precursors.

Nonlinear Effects in Asymmetric Catalysis by Design: Concept, Synthesis, and Applications

Asymmetric synthesis constitutes a key technology for the preparation of enantiomerically pure compounds as well as for the selective control of individual stereocenters in the synthesis of complex compounds. It is thus of extraordinary importance for the synthesis of chiral drugs, dietary supplements, flavors, and fragrances, as well as novel materials with tunable and reconfigurable chiroptical properties or the assembly of complex natural products. Typically, enantiomerically pure catalysts are used for this purpose. To prepare enantiomerically pure ligands or organocatalysts, one can make use of the natural chiral pool. Ligands and organocatalysts with an atropisomeric biphenyl and binaphthyl system have become popular, as they are configurationally stable and contain a C2-symmetric skeleton, which has been found to be particularly privileged. For catalysts with opposite configurations, both product enantiomers can be obtained. Configurationally flexible biphenyl systems initially appeared to be unsuitable for this purpose, as they racemize after successful enantiomer separation and thus are neither storable nor afford a reproducible enantioselectivity. However, there are strategies that exploit the dynamics of such ligands to stereoconvergently enrich one of the catalyst enantiomers. This can be achieved, for example, by coordinating an enantiomerically pure additive to a ligand-metal complex, which results in deracemization of the configurationally flexible biphenyl system, thereby enriching the thermodynamically preferred diastereomer. In this Account, we present our strategy to design stereochemically flexible catalysts that combine the properties of supramolecular recognition, stereoconvergent alignment, and catalysis. Such systems are capable to recognize the chirality of the target product, leading to an increase in enantioselectivity during asymmetric catalysis. We have systematically developed and investigated these smart catalyst systems and have found ways to specifically design and synthesize them for various applications. In addition to (i) reaction product-induced chiral amplification, we have developed systems with (ii) intermolecular and (iii) intramolecular recognition, and successfully applied them in asymmetric catalysis. Our results pave the way for new applications such as temperature-controlled enantioselectivity, controlled inversion of enantioselectivity with the same chirality of the recognition unit, generation of positive nonlinear effects, and targeted design of autocatalytic systems through dynamic formation of transient catalysts. Understanding such systems is of enormous importance for catalytic processes leading to symmetry breaking and amplification of small imbalances of enantiomers and offer a possible explanation of homochirality of biological systems. In addition, we are learning how to target supramolecular interactions to enhance enantioselectivities in asymmetric catalysis through secondary double stereocontrol. Configurationally flexible catalysts will enable future resource-efficient development of asymmetric syntheses, as enantioselectivities can be fully switched by stereoselective alignment of the stereochemically flexible ligand core on demand.

Modeling of Biological Activity of PEO-Coated Titanium Implants with Conjugates of Cyclic RGD Peptide with Amino Acid Bisphosphonates

Titanium is considered to be the most essential metal in the field of implantology. The main factors determining metal biocompatibility, among others, include the morphology and chemical composition of the titanium surface. Therefore, the aim of this work was to develop approaches to control the biological activity of the titanium surface by creating coatings that combine both an inorganic phase with a given morphology and organic molecules containing an integrin-selective peptide that regulate cell adhesion and proliferation. As such, we synthesized new c(RGDfC) derivatives of amino acid bisphosphonates (four examples) with different bisphosphonate anchors and maleimide linkers. These molecules were deposited on a highly developed porous surface obtained via the plasma electrolytic oxidation (PEO) of coarse-grained and nanostructured titanium. In vitro studies demonstrated the increase in the viability degree of mesenchymal stem cells and fibroblasts on the surface of coarse-grained or nanostructured titanium modified with PEO and a c(RGDfC) derivative of ε-aminocaproic acid bisphophonate with an SMCC linker. As a result, the use of conjugates of amino acid bisphosphonates with a cyclic RGD peptide for the modification of PEO-coated titanium opens the ways for the effective control of the biological activity of the metal implant surface.

Anticancer peptides mechanisms, simple and complex

Peptide therapy has started since 1920s with the advent of insulin application, and now it has emerged as a new approach in treatment of diseases including cancer. Using anti-cancer peptides (ACPs) is a promising way of cancer therapy as ACPs are continuing to be approved and arrived at major pharmaceutical markets. Traditional cancer treatments face different problems like intensive adverse effects to patient's body, cell resistance to conventional chemical drugs and in some worse cases the occurrence of cell multidrug resistance (MDR) of cancerous tissues against chemotherapy. On the other hand, there are some benefits conceived for peptides usage in treatment of diseases specifically cancer, as these compounds present favorable characteristics such as smaller size, high activity, low immunogenicity, good biocompatibility in vivo, convenient and rapid way of synthesis, amenable to sequence modification and revision and there is no limitation for the type of cargo they carry. It is possible to achieve an optimum molecular and functional structure of peptides based on previous experience and bank of peptide motif data which may result in novel peptide design. Bioactive peptides are able to form pores in cell membrane and induce necrosis or apoptosis of abnormal cells. Moreover, recent researches have focused on the tumor recognizing peptide motifs with the ability to permeate to cancerous cells with the aim of cancer treatment at earlier stages. In this strategy the most important factors for addressing cancer are choosing peptides with easy accessibility to tumor cell without cytotoxicity effect towards normal cells. The peptides must also meet acceptable pharmacokinetic requirements. In this review, the characteristics of peptides and cancer cells are discussed. The various mechanisms of peptides' action proposed against cancer cells make the next part of discussion. It will be followed by giving information on peptides application, various methods of peptide designing along with introducing various databases. Future aspects of peptides for employing in area of cancer treatment come as conclusion at the end.

The redox-active Cu-FomA complex: the mode that provides coordination of CuII/CuI ions during the reduction/oxidation cycle

Colorectal cancer (CRC) is the third most commonly diagnosed form of cancer worldwide. Recent studies have indicated a strong correlation between microbial imbalance and the development of CRC. An abundance of Fusobacterium nucleatum, an anaerobic Gram-negative bacterium, has been considered a biomarker of CRC progression. Several investigations have also proposed that binding copper ions to various bacterial proteins enhances the Cu^II + e^- ⇄ Cu^I redox cycle, which consequently promotes uncontrolled production of reactive oxygen species (ROS) and propels colorectal carcinogenesis. In this work, a multidisciplinary approach was applied to study the molecular relation of copper with the peptide models of FomA, a protein expressed by Fusobacterium nucleatum. The main goal was to investigate all the factors that tune the Cu^II + e^- ⇄ Cu^I equilibrium. A linear peptide Fom1 (Ac-KGHGNGEEGTPTVHNE-NH₂) and cyclic peptide Fom2 (cyclo-(KGHGNGEEGTPTVHNE)) were used as ligands. The coordination of Cu^I was deduced from the NMR data. The conditional dissociation constants KcondD defined the stability of Cu^I complexes. The electrochemical activity of Cu^II and Cu^I compounds was analysed using cyclic voltammetry. A quasi-reversible redox conversion Cu^II-peptide + e^- ⇄ Cu^I-peptide was revealed for all studied systems. In the presence of ascorbic acid (HAsc), Cu^II complexes were immediately reduced to Cu^I species; however, their re-oxidation was kinetically sluggish. The HAsc-induced redox cycle provoked the metal-catalyzed oxidation (MCO) effect. That in the end prevented coordination of the re-appearing Cu^II ion to its initial binding site. The toxicity of the FomA-Cu^II/Cu^I complexes and their role in CRC progression were briefly discussed.

Sortase A-mediated cyclization of novel polycyclic RGD peptides for ανβ3 integrin targeting

Cyclic arginine-glycine-aspartic (RGD) peptides that specifically bind to integrin α_νβ₃ have been developed for drug delivery, tracers, and imaging for tumor diagnosis and treatment. Herein, a series of polycyclic RGD peptides containing dual, tri, and tetra rings were designed and synthesized through sortase A-mediated ligation. An in vitro test on cell adhesion inhibition indicated that the RGD peptide containing tricylic structure exhibited outstanding potency and selectivity for α_νβ₃ integrin.

Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch

Benenodin-1 is a thermally actuated lasso peptide rotaxane switch with two primary translational isomers that differ in the relative position of the residue Gln15. The conversion from one conformer to the other involves substantial enthalpy-entropy compensation: one conformer is energetically favored and the other is entropically favored. Here, we take a multi-scale quantum mechanical (QM) and classical molecular dynamic (MD) approach to reveal residue-specific sources of these differences in stability. QM reveals that the two benenodin-1 conformers involve distinct hydrogen bonding networks, with the enthalpically favored conformer having more intra-peptide hydrogen bonds between the Gln15 side chain and nearby residues. The evaluation of configurational entropy over the MD-sampled geometries reveals that the entropically favored conformer has enhanced conformational flexibility. By computing the by-residue-sum entropies, we identify the role of Gln15 and neighboring Glu14 in mediating the entropic variation during the switching process. These computational insights help explain the effects of Glu14Ala and Gln15Ala mutations on the conformational population of benenodin-1 observed experimentally.

An Integrated Strategy for Assessing the Metabolic Stability and Biotransformation of Macrocyclic Peptides in Drug Discovery toward Oral Delivery

Macrocyclic peptides (MCPs) are an emerging class of promising drug modalities that can be used to interrogate hard-to-drug ("undruggable") targets. However, their poor intestinal stability is one of the major liabilities or obstacles for oral drug delivery. We therefore investigated the metabolic stability and biotransformation of MCPs via a systematic approach and established an integrated in vitro assay strategy to facilitate MCP drug discovery, with a focus on oral delivery liabilities. A group of diverse MCPs were incubated with representative matrices, including simulated intestinal fluid with pancreatin (SIFP), human enterocytes, liver S9 fractions, liver lysosomes, plasma, and recombinant enzymes. The results revealed that the stability and biotransformation of MCPs varied, with the major metabolic pathways identified in different matrices. Under the given conditions, the selected MCPs generally showed better stability in plasma compared to that in SIFP. Our data suggest that pancreatic enzymes act as the primary metabolic barrier for the oral delivery of MCPs, mainly through hydrolysis of their backbone amide bonds. Whereas in enterocytes, multiple metabolic pathways appeared to be involved and resulted in metabolic reactions such as oxidation and reduction in addition to hydrolysis. Further studies suggested that lysosomal peptidase cathepsin B could be a major enzyme responsible for the cleavage of side-chain amide bonds in lysosomes. Collectively, we developed and implemented an integrated assay for assessing the metabolic stability and biotransformation of MCPs for compound screening in the discovery stage toward oral delivery. The proposed question-driven assay cascade can provide biotransformation insights that help to guide and facilitate lead candidate selection and optimization.

Navigating complex peptide structures using macrocycle conformational maps

Identification of turn motifs that are stabilized by intramolecular hydrogen bonds can be useful in describing the conformation of peptide systems. However, this approach is somewhat insufficient for cyclic peptides because peptide regions that are not positioned within a hydrogen bond can be left with no description. Furthermore, non-regular secondary structures and other rarely-observed conformations can be left without detailed evaluation. Herein, we describe “higher-order” ϕ/ψ plots termed macrocycle conformational maps (MCMs) as a tool for evaluating and comparing the conformations of a series of structurally related macrocyclic peptides.

Identification of turn motifs that are stabilized by hydrogen bonds can be useful in describing the conformation of peptides. Herein, we describe “higher-order” ϕ/ψ plots termed macrocycle conformational maps (MCMs) as a tool to evaluate and compare the conformations of related macrocycles.

Conformational Preferences and Antiproliferative Activity of Peptidomimetics Containing Methyl 1'-Aminoferrocene-1-carboxylate and Turn-Forming Homo- and Heterochiral Pro-Ala Motifs

The concept of peptidomimetics is based on structural modifications of natural peptides that aim not only to mimic their 3D shape and biological function, but also to reduce their limitations. The peptidomimetic approach is used in medicinal chemistry to develop drug-like compounds that are more active and selective than natural peptides and have fewer side effects. One of the synthetic strategies for obtaining peptidomimetics involves mimicking peptide α-helices, β-sheets or turns. Turns are usually located on the protein surface where they interact with various receptors and are therefore involved in numerous biological events. Among the various synthetic tools for turn mimetic design reported so far, our group uses an approach based on the insertion of different ferrocene templates into the peptide backbone that both induce turn formation and reduce conformational flexibility. Here, we conjugated methyl 1'-aminoferrocene-carboxylate with homo- and heterochiral Pro-Ala dipeptides to investigate the turn formation potential and antiproliferative properties of the resulting peptidomimetics 2-5. Detailed spectroscopic (IR, NMR, CD), X-ray and DFT studies showed that the heterochiral conjugates 2 and 3 were more suitable for the formation of β-turns. Cell viability study, clonogenic assay and cell death analysis showed the highest biological potential of homochiral peptide 4.

Macrocyclic Tetramers-Structural Investigation of Peptide-Peptoid Hybrids

Outstanding affinity and specificity are the main characteristics of peptides, rendering them interesting compounds for basic and medicinal research. However, their biological applicability is limited due to fast proteolytic degradation. The use of mimetic peptoids overcomes this disadvantage, though they lack stereochemical information at the α-carbon. Hybrids composed of amino acids and peptoid monomers combine the unique properties of both parent classes. Rigidification of the backbone increases the affinity towards various targets. However, only little is known about the spatial structure of such constrained hybrids. The determination of the three-dimensional structure is a key step for the identification of new targets as well as the rational design of bioactive compounds. Herein, we report the synthesis and the structural elucidation of novel tetrameric macrocycles. Measurements were taken in solid and solution states with the help of X-ray scattering and NMR spectroscopy. The investigations made will help to find diverse applications for this new, promising compound class.

Mutanobactin D from the Human Microbiome: Total Synthesis, Configurational Assignment, and Biological Evaluation

Mutanobactin D is a non-ribosomal, cyclic peptide isolated from Streptococcus mutans and shows activity reducing yeast-to-hyphae transition as well as biofilm formation of the pathogenic yeast Candida albicans. We report the first total synthesis of this natural product, which relies on enantioselective, zinc-mediated 1,3-dipolar cycloaddition and a sequence of cascading reactions, providing the key lipidated γ-amino acid found in mutanobactin D. The synthesis enables configurational assignment, determination of the dominant solution-state structure, and studies to assess the stability of the lipopeptide substructure found in the natural product. The information stored in the fingerprint region of the IR spectra in combination with quantum chemical calculations proved key to distinguishing between epimers of the α-substituted β-keto amide. Synthetic mutanobactin D drives discovery and analysis of its effect on growth of other members of the human oral consortium. Our results showcase how total synthesis is central for elucidating the complex network of interspecies communications of human colonizers.

Single- and Multiple-Dose Pharmacokinetics and Pharmacodynamics of PN-943, a Gastrointestinal-Restricted Oral Peptide Antagonist of α4β7, in Healthy Volunteers

PN‐943 is an orally stable, gastrointestinal‐restricted peptide that binds specifically to α4ß7 integrin on leukocytes, blocking leukocyte trafficking to and activation in the gut, inhibiting colon inflammation and reducing signs and symptoms of active ulcerative colitis. Two pharmacokinetic/pharmacodynamic studies were conducted in healthy volunteers. Study 1 was a first‐in‐human study with 40 male subjects receiving PN‐943, 100 to 1400 mg or placebo, as single doses and 57 male subjects receiving PN‐943, 100 to 1000 mg or placebo, as multiple doses. Study 2 was a randomized, crossover study comparing multiple doses of 450‐mg PN‐943 twice daily as a liquid solution and as an immediate‐release tablet in 10 subjects. No subjects discontinued due to treatment‐emergent adverse events. Consistent with the gastrointestinal‐restricted nature of the peptide, systemic exposure was minimal; there was an approximate dose‐proportional increase in area under the plasma concentration–time curve. There was minimal accumulation with once‐daily dosing and an absence of time‐dependent changes in pharmacokinetics. Administration of PN‐943 after a high‐fat meal reduced peak plasma concentration and area under the plasma concentration–time curve. There was minimal (<0.1%) urinary excretion of intact drug, and there was a dose‐related increase in fecal excretion of intact PN‐943. Dose‐dependent increases in blood receptor occupancy and reduction in blood receptor expression were observed, supporting target engagement. Twice‐daily dosing resulted in sustained receptor occupancy with low plasma fluctuations (143%). PN‐943 was generally well tolerated following single and multiple oral doses with low systemic exposure. Twice‐daily dosing resulted in sustained pharmacokinetics and pharmacodynamics, supporting further investigation in efficacy studies.

Modular Approaches to Synthesize Activity- and Affinity-Based Chemical Probes

Combinatorial and modular methods to synthesize small molecule modulators of protein activity have proven to be powerful tools in the development of new drug-like molecules. Over the past decade, these methodologies have been adapted toward utilization in the development of activity- and affinity-based chemical probes, as well as in chemoproteomic profiling. In this review, we will discuss how methods like multicomponent reactions, DNA-encoded libraries, phage displays, and others provide new ways to rapidly screen novel chemical probes against proteins of interest.

Determination of the Rituximab Binding Site to the CD20 Epitope Using SPOT Synthesis and Surface Plasmon Resonance Analyses

Antibodies not only play a major role in clinical diagnostics and biopharmaceutical analysis but also are a class of drugs that are regularly used to treat numerous diseases. The identification of antibody-epitope binding sites is then of great interest to many emerging medical and bioanalytical applications, particularly to design monoclonal antibodies (mAb) mimics taking advantage of amino acid residues involved in the binding. Among relevant antibodies, the monoclonal antibody rituximab has received significant attention as it is exploited to treat several cancers including non-Hodgkin's lymphoma and chronic lymphocytic leukemia, as well as some autoimmune disorders such as rheumatoid arthritis. The binding of rituximab to the targeted cells occurs via the recognition of the CD20 epitope. A crystallographic study has shown that the binding area, named paratope, is located at the surface of rituximab. Combining the SPOT method and the complementary surface plasmon resonance technique allowed us to detect an extended recognition domain buried in the pocket of the rituximab Fab formed by four β-sheets. More generally, the present study offers a comprehensive approach to identify antibody-epitope binding sites.

Sulfur Oxidation Increases the Rate of HIRE-Type [1.4]Thiazepinone Ring Expansion and Influences the Conformation of a Medium-Sized Heterocyclic Scaffold

The hydrated imidazoline ring expansion (HIRE-type) reaction was investigated for a series of di(hetero)arene-fused [1.4]thiazepinones in comparison with their sulfone counterparts. The sulfones were found to undergo ring expansion at a much higher rate compared to the thioethers, much in line with the current mechanistic understanding of the process. Moreover, the amide bond cis- and trans-isomers of the ring-expanded products were found, in the case of sulfones, to be stabilized through an intramolecular hydrogen bond. The latter phenomenon was studied in detail by NMR experiments and corroborated by X-ray crystallographic information.

Two-Dimensional Barriers for Probing Conformational Shifts in Macrocycles

We describe the development and use of composite two-dimensional barriers in macrocyclic backbones. These tunable constructs derive their mode of action from heterocyclic rearrangements. The Boulton-Katritzky reaction has been identified as a particularly versatile means to effect a composite barrier, allowing the examination of the influence of heterocycle translocation on conformation. Kinetic studies using ¹H NMR have revealed that the in-plane atom movement is fast in 17, 18, 19-membered rings but slows down in 16-membered rings. The analysis by NMR and MD simulation experiments is consistent with the maintenance of rare cis-amide motifs during conformational interconversion. Taken together, our investigation demonstrates that heterocyclic rearrangement reactions can be used to control macrocyclic backbones and provides fundamental insights that may be applicable to the development of a wide range of other conformational control elements.

RGD-Binding Integrins Revisited: How Recently Discovered Functions and Novel Synthetic Ligands (Re-)Shape an Ever-Evolving Field

Integrins have been extensively investigated as therapeutic targets over the last decades, which has been inspired by their multiple functions in cancer progression, metastasis, and angiogenesis as well as a continuously expanding number of other diseases, e.g., sepsis, fibrosis, and viral infections, possibly also Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). Although integrin-targeted (cancer) therapy trials did not meet the high expectations yet, integrins are still valid and promising targets due to their elevated expression and surface accessibility on diseased cells. Thus, for the future successful clinical translation of integrin-targeted compounds, revisited and innovative treatment strategies have to be explored based on accumulated knowledge of integrin biology. For this, refined approaches are demanded aiming at alternative and improved preclinical models, optimized selectivity and pharmacological properties of integrin ligands, as well as more sophisticated treatment protocols considering dose fine-tuning of compounds. Moreover, integrin ligands exert high accuracy in disease monitoring as diagnostic molecular imaging tools, enabling patient selection for individualized integrin-targeted therapy. The present review comprehensively analyzes the state-of-the-art knowledge on the roles of RGD-binding integrin subtypes in cancer and non-cancerous diseases and outlines the latest achievements in the design and development of synthetic ligands and their application in biomedical, translational, and molecular imaging approaches. Indeed, substantial progress has already been made, including advanced ligand designs, numerous elaborated pre-clinical and first-in-human studies, while the discovery of novel applications for integrin ligands remains to be explored.

Co-occurring Congeners Reveal the Position of Enantiomeric Amino Acids in Nonribosomal Peptides

The absolute configuration of the constituent amino acids in microbial nonribosomal peptides is typically determined by Marfey's method after total hydrolysis of the peptide. A challenge to structure elucidation arises when both d and l enantiomeric configurations of an amino acid are present. Determining the actual position of each amino acid enantiomer within the peptide sequence typically requires laborious approaches based on peptide partial hydrolysis or even total synthesis of the possible diastereomers. Herein, an alternative solution is discussed based on the homogeneous backbone chirality that governs all peptides biosynthesized by a common nonribosomal peptide synthetase. The information on configuration provided by Marfey's analysis of co-occurring minor congeners can reveal unequivocally the stereochemical sequence of the whole peptide family.

Chemically Diverse Multifunctional Peptide Platforms with Antimicrobial and Cell Adhesive Properties

Bacterial infections and incomplete biomaterial integration are major problems that can lead to the failure of medical implants. However, simultaneously addressing these two issues remains a challenge. Here, we present a chemical peptide library based on a multifunctional platform containing the antimicrobial peptide LF1-11 and the cell-adhesive motif RGD. The scaffolds were customized with catechol groups to ensure straightforward functionalization of the implant surface, and linkers of different length to assess the effect of peptide accessibility on the biological response. The peptidic platforms significantly improved the adhesion of mesenchymal stem cells and showed antimicrobial effects against Staphylococcus aureus. Of note is that peptides bearing spacers that were too long displayed the lowest efficiency. Subsequently, we designed a platform replacing linear RGD by cyclic RGD; this further enhanced eukaryotic cell adhesion while retaining excellent antimicrobial properties, thus being a suitable candidate for tissue engineering applications.

Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins

Macrocycles and cyclic peptides are increasingly attractive therapeutic modalities as they often have improved affinity, are able to bind to extended protein surfaces, and otherwise have favorable properties. Macrocyclization of a known binder may stabilize its bioactive conformation and improve its metabolic stability, cell permeability, and in certain cases oral bioavailability. Herein, we present implementation and application of an approach that automatically generates, evaluates, and proposes cyclizations utilizing a library of well-established chemical reactions and reagents. Using the three-dimensional (3D) conformation of the linear molecule in complex with a target protein as the starting point, this approach identifies attachment points, generates linkers, evaluates their geometric compatibility, and ranks the resulting molecules with respect to their predicted conformational stability and interactions with the target protein. As we show here with prospective and retrospective case studies, this procedure can be applied for the macrocyclization of small molecules and peptides and even PROteolysis TArgeting Chimeras (PROTACs) and proteins.

Tryptophan Analogues with Fixed Side-Chain Orientation: Expanding the Scope

A generalized synthetic strategy is proposed here for the synthesis of asymmetric β‐indoylated amino acids by 8‐aminoquinoline (8AQ)‐directed C(sp³)‐H functionalization of suitably protected precursors. Peptides containing one of the four stereoisomers of (indol‐3‐yl)‐3‐phenylalanine at position 2 of the parent peptide KwFwLL‐NH₂ (w=d‐Trp) cover a wide range of activities as ghrelin receptor inverse agonists, among them the most active described until now. This application exemplarily shows how β‐indoylated amino acids can be used for the systematic variation of the position of an indole group in a bioactive peptide.

Strategies for Fine-Tuning the Conformations of Cyclic Peptides

Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.

Design, Synthesis, and Characterization of the Macrocyclic Tetrapeptide cyclo[Pro-Sar-Phe-d-Phe]: A Mixed Opioid Receptor Agonist-Antagonist Following Oral Administration

Substance abuse remains a serious public health crisis, affecting millions of people worldwide. Macrocyclic tetrapeptides like CJ-15,208 and [d-Trp]CJ-15,208 demonstrate opioid activity shown to attenuate the rewarding effects of cocaine in conditioned place preference assays in mice, making them promising lead compounds for treating substance abuse. In the present study, we report the rational design, synthesis, conformational analysis, and continued pharmacological evaluation of the novel macrocyclic tetrapeptide cyclo[Pro-Sar-Phe-d-Phe] to further explore this unique molecular scaffold. This peptide was rationally designed based on X-ray and NMR structures of related macrocyclic tetrapeptides. Following synthesis, its solution-phase conformations were determined by NMR and molecular modeling. The peptide adopted multiple conformations in polar solvents, but a single conformation in chloroform that is stabilized by intramolecular hydrogen bonding. The peptide is orally bioavailable, producing antinociception and antagonism of kappa opioid receptor (KOR) stimulation following oral administration in a mouse 55 °C warm-water tail-withdrawal assay. Notably, cyclo[Pro-Sar-Phe-d-Phe] blocked both stress- and drug-induced reinstatement of cocaine and morphine conditioned place preference in mice following oral administration, and displayed a decreased side-effect profile compared to morphine. Thus, cyclo[Pro-Sar-Phe-d-Phe] is a promising lead compound for the treatment of substance abuse.

A Comparative Synthetic Strategy Perspective on α-Amino Acid- and Non-Amino Acid-Derived Synthons towards Total Syntheses of Selected Natural Macrolides

Macrocyclic alkaloids (macrolides) and cyclopeptides have an immense range of applications in drug discovery research because of their natural abundance and potential biological and physicochemical properties. Presently, more than 100 approved drugs or clinical drug candidates contain macrocyclic scaffolds as the biologically active component. This review provides an interesting perspective about the use of amino acid-derived chiral pools versus other methods derived from miscellaneous synthons towards the total synthesis of non-peptidic macrolides. The synthetic routes and the key strategies involved in the total syntheses of ten natural macrolides have been discussed. Both the amino acid-derived and non-amino acid-derived synthetic routes have been illustrated to present a comparative study between the two approaches.