Peptidomimetic Drug Design Research Articles

Exploring computational tools for improved structural design and stability of helical AApeptides

Peptidomimetics have garnered increased attention due to their unique structural properties and self-assembly, as well as their promising applications in material sciences and peptidomimetic drug design. N-acetylated-N-aminoethyl amino acid oligomers (AApeptides), a novel class of helical foldamer, have been effectively utilized to imitate protein helices and regulate protein-protein interactions. While the structures of a series of AApeptides have been determined experimentally, the chemical diversity of AApeptides is impeding the advancement of peptide inhibitor development and high-level architecture design through purely experimental methods. Consequently, there's an urgent need for effective computational tools to facilitate the structural design of more complex systems using AApeptides. While a general AMBER force field (GAFF) can be applied to simulate AApeptides, it is crucial to evaluate the accuracy of such a force field and consider alternatives to enhance accuracy. In this study, we employed molecular dynamics simulations (MD) to assess the stability of a helical AApeptide. Our findings indicate that GAFF alone is insufficient to stabilize the helical structure of our AApeptide. We suggest the use of restraints derived from experimentally determined structures to guide the simulation and maintain this helical structure. Although any set of restraint definitions used in this study can simulate helical packing, a minimum of three points per AApeptide building block restraint is necessary to accurately reproduce the hydrogen bonding pattern.

Re-evaluation of P-Chiral, N-Phosphoryl Sulfonamide Brønsted Acids in the Asymmetric Synthesis of 1,2,3,4-Tetrahydroquinoline-2-carboxylate Esters via Biomimetic Transfer Hydrogenation

AbstractEnantioenriched heterocyclic and rigidified bioisosteres of amino acids are valuable building blocks in drug discovery, particularly in the design of peptidomimetic drugs. The rigidified bioisostere of phenylalanine, 1,2,3,4-tetrahydroquinoline-2-carboxylic acid, is found in several biologically active compounds. However, only a small number of successful methodologies have been reported for its asymmetric synthesis. To develop an environmentally benign and metal-free organocatalytic process for the preparation of this compound, a number of novel P-chiral, N-phosphoryl sulfonamide Brønsted acids were synthesized and evaluated in a biomimetic transfer hydrogenation reaction of quinoline-2-carboxylates to give the (R)-1,2,3,4-tetrahydroquinoline-2-carboxylates.

δ-Azaproline and Its Oxidized Variants.

Peptides featuring backbone N-amino substituents exhibit unique conformational properties owing to additional electrostatic, hydrogen-bonding, and steric interactions. Here, we describe the synthesis and conformational analysis of three δ-azaproline derivatives as potential proline surrogates. Our studies demonstrate stereoelectronic tuning of heterocyclic ring pucker, cis/trans amide propensity, and amide isomerization barriers within a series of oxidation state variants. A combination of NMR, X-ray diffraction, and density functional theory calculations shows that electron density and hybridization at the δ position play a dominant role in the conformational preferences of each analogue. Both δ-azaproline and γ,δ-dehydro-δ-azaproline exhibit strong trans amide rotamer propensities irrespective of ring conformation, while a novel residue, γ-oxo-δ-azaproline, features rapid amide isomerization kinetics and isoenergetic amide bond geometries influenced by torsional strain and H-bonding interactions. The introduction of the δ heteroatom in each residue allows the decoupling of structural effects that are typically linked in proline and its pyrrolidine-substituted analogues. δ-Azaproline derivatives thus represent useful probes of prolyl amide isomerism with potential applications in peptidomimetic drug design and protein folding.

Diversity, evolution and medical applications of insect antimicrobial peptides.

Antimicrobial peptides (AMPs) are short proteins with antimicrobial activity. A large portion of known AMPs originate from insects, and the number and diversity of these molecules in different species varies considerably. Insect AMPs represent a potential source of alternative antibiotics to address the limitation of current antibiotics, which has been caused by the emergence and spread of multidrug-resistant pathogens. To get more insight into AMPs, we investigated the diversity and evolution of insect AMPs by mapping their phylogenetic distribution, allowing us to predict the evolutionary origins of selected AMP families and to identify evolutionarily conserved and taxon-specific families. Furthermore, we highlight the use of the nematode Caenorhabditis elegans as a whole-animal model in high-throughput screening methods to identify AMPs with efficacy against human pathogens, including Acinetobacter baumanii and methicillin-resistant Staphylococcus aureus. We also discuss the potential medical applications of AMPs, including their use as alternatives for conventional antibiotics in ectopic therapies, their combined use with antibiotics to restore the susceptibility of multidrug-resistant pathogens, and their use as templates for the rational design of peptidomimetic drugs that overcome the disadvantages of therapeutic peptides.The article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’.

Gram-Scale Synthesis of 3,5-Methanonipecotic Acid, a Nonchiral Bicyclic β-Amino Acid

A scalable synthesis was developed of 3,5-methanoni­pecotic acid (3-azabicyclo[3.1.1]heptane-1-carboxylic acid), a rare example of a conformationally constrained nonchiral β-amino acid, potentially useful in peptide engineering and peptidomimetic drug design. A retrosynthetic strategy based on disconnections exclusively within the symmetry planes of the target and the intermediate molecules was found to be useful and might deliver expedite syntheses in other similar cases.

C-terminal domain of p16INK4a is adequate in inducing cell cycle arrest, growth inhibition and CDK4/6 interaction similar to the full length protein in HT-1080 fibrosarcoma cells

The tumor suppressor p16(INK4a) has earned widespread attention in cancer studies since its discovery as an inhibitor of cyclin-dependent kinases (CDKs) 4/6. Structurally, it consists of four complete ankyrin repeats, believed to be involved in CDK4 interaction. According to the previous disparities concerning the importance of domains and inactivating mutations in p16, we aimed to search for the domain possessing the functional properties of the full length protein. Upon our in silico screening analyses followed by experimental assessments, we have identified the novel minimum functional domain of p16 to be the C-terminal half including ankyrin repeats III, IV and the C-terminal flanking region accompanied by loops 2 and 3. Transfection of this truncated form into HT-1080 human fibrosarcoma cells, lacking endogenous p16, revealed that it is able to inhibit cell growth and proliferation equivalent to p16(INK4a). The functional analysis showed that this fragment like p16 can interact with CDK4/6, block the entry into S phase of the cell cycle and suppress growth as indicated by colony formation assay. Identification of p16 minimum functional domain can be of benefit to the future peptidomimetic drug design as well as gene transfer for cancer therapy.

Study of MDM2 Binding to p53-Analogues: Affinity, Helicity, and Applicability to Drug Design

MDM2 is a key regulator of the p53 tumor-suppressor protein. Here we study the effect of modifications of a p53 N-terminal fragment on its binding to MDM2, using implicit-solvent MD and MM-GB/SA calculations. We provide interpretation of existing experimental data and predict the effect of mutations on binding. Notably 1) We analyze the effect of regulatory phosphorylations at Ser/Thr residues and suggest that a balance between favorable electrostatics and desolvation penalties determines the effect of phosphorylation; 2) We compare the helical stability in solution of p53 alanine mutants and propose a helix stabilizing role for several residues involved in hydrogen bonding and hydrophobic packing; 3) We obtain good correlations between calculated and experimental affinities for a set of peptidomimetic inhibitors, both alone and in combination with p53 analogues, demonstrating potential applicability to drug design. From the technical aspect, protocol optimization and selection of simulation tools are addressed in detail. To the best of our knowledge this is the first published example of MM-GB/SA calculations utilizing a conformational ensemble generated with implicit solvent MD. Our results suggest that this highly efficient variant of classical explicit-solvent MM-GB/SA may be used for studying protein-protein interactions and for the design of peptidomimetic drugs.

Peptidomimetic Therapeutic Agents Targeting the Protease Enzyme of the Human Immunodeficiency Virus and Hepatitis C Virus

During the past two decades, great strides have been made in the design of peptidomimetic drugs for the treatment of viral infections, despite the stigma of poor drug-like properties, low oral absorption, and high clearance associated with such compounds. This Account summarizes the progress made toward overcoming such liabilities and highlights the drug discovery efforts that have focused specifically on human immunodeficiency virus (HIV) and hepatitis C virus (HCV) protease inhibitors. The arsenal against the incurable disease AIDS, which is caused by HIV infection, includes peptidomimetic compounds that target the virally encoded aspartic protease enzyme. This enzyme is essential to the production of mature HIV particles and plays a key role in maintaining infectivity. However, because of the rapid genomic evolution of viruses, an inevitable consequence in the treatment of all viral infections is the emergence of resistance to the drugs. Therefore, the incomplete suppression of HIV in treatment-experienced AIDS patients will continue to drive the search for more effective therapeutic agents that exhibit efficacy against the mutants raised by the earlier generation of protease inhibitors. Currently, a number of substrate-based peptidomimetic agents that target the virally encoded HCV NS3/4A protease are in clinical development. Mechanistically, these inhibitors can be generally divided into activated carbonyls that are transition-state mimics or compounds that tap into the feedback mode of enzyme-product inhibition. In the HCV field, there is justified optimism that a number of these compounds will soon reach commercialization as therapeutic agents for the treatment of HCV infections. Structural research has guided the successful design of both HIV and HCV protease inhibitors. X-ray crystallography, NMR, and computational studies have provided valuable insight in to the free-state preorganization of peptidomimetic ligands and their enzyme-bound conformation. Researchers have designed a variety of novel bioisosteric replacements of amino acids and short peptides that contain all of the required pharmacophore moieties and play a key role in inducing conformational changes to the overall molecule. The knowledge gained from these studies will undoubtedly guide the future design of therapeutic agents and further contribute to the success of this field.

Molecular Mapping of the Recognition Interface between the Islet Amyloid Polypeptide and Insulin

Nature's route for amyloid prevention: Insulin is a natural inhibitor of amyloid formation by the islet amyloid polypeptide (IAPP). The interacting domains of both proteins were identified by using a reductionist approach (see scheme). An understanding of the molecular mechanism of this physiological interaction may lead to the design of peptidomimetic drugs for type II diabetes.

Utilizing the Intramolecular Fukuyama—Mitsunobu Reaction for a Flexible Synthesis of Novel Heterocyclic Scaffolds for Peptidomimetic Drug Design.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Utilizing the intramolecular Fukuyama–Mitsunobu reaction for a flexible synthesis of novel heterocyclic scaffolds for peptidomimetic drug design

We report the synthesis of the novel scaffolds pyrazino[1,2- b]isoquinoline and pyrrolo[1,2- a]pyrazine displaying the somatostatin pharmacophores. Both classes of compounds contain a pyrazine heterocycle, which can be prepared in a straightforward manner utilizing an intramolecular Fukuyama–Mitsunobu reaction. As both the families derive from amino acids, they can be accessed in high optical purity.

A strategy for designing inhibitors of alpha-synuclein aggregation and toxicity as a novel treatment for Parkinson's disease and related disorders.

Convergent biochemical and genetic evidence suggests that the formation of alpha-synuclein (alpha-syn) protein deposits is an important and, probably, seminal step in the development of Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). It has been reported that transgenic animals overexpressing human alpha-syn develop lesions similar to those found in the brain in PD, together with a progressive loss of dopaminergic cells and associated abnormalities of motor function. Inhibiting and/or reversing alpha-syn self-aggregation could, therefore, provide a novel approach to treating the underlying cause of these diseases. We synthesized a library of overlapping 7-mer peptides spanning the entire alpha-syn sequence, and identified amino acid residues 64-100 of alpha-syn as the binding region responsible for its self-association. Modified short peptides containing alpha-syn amino acid sequences from part of this binding region (residues 69-72), named alpha-syn inhibitors (ASI), were found to interact with full-length alpha-syn and block its assembly into both early oligomers and mature amyloid-like fibrils. We also developed a cell-permeable inhibitor of alpha-syn aggregation (ASID), using the polyarginine peptide delivery system. This ASID peptide was able to inhibit the DNA damage induced by Fe(II) in neuronal cells transfected with alpha-syn(A53T), a familial PD-associated mutation. ASI peptides without this delivery system did not reverse levels of Fe(II)-induced DNA damage. Furthermore, the ASID peptide increased (P<0.0005) the number of cells stained positive for Bcl-2, while significantly (P<0.05) decreasing the percentage of cells stained positive for BAX. These short peptides could serve as lead compounds for the design of peptidomimetic drugs to treat PD and related disorders.

New Reactions and Structures for Peptidomimetic Drug Design

AbstractFor Abstract see ChemInform Abstract in Full Text.

Clinically validated peptides as templates for de novo peptidomimetic drug design at G-protein-coupled receptors.

Recent advances in the development of potent and selective peptide and non-peptide ligands for peptidergic receptors are anticipated to help further unravel the roles of class I and II G-protein-coupled receptors in the pathogenesis of human diseases and to accelerate the clinical utility of small molecule peptidomimetics. Peptidomimetic drug discovery directed towards somatostatin agonists, urotensin II antagonists, gonadotropin-releasing hormone antagonists, neurotensin and complement C5a modulators, melanocortin-4 agonists and vasopressin V(2) agonists has achieved success through integration of conformational-based drug design, site-directed mutagenesis, screening, combinatorial chemistry and classical medicinal chemistry. Acceptance that discreet ensembles of secondary structural motifs underpin the interactions of peptides with their cognate receptors has enabled the development of molecules which mimic or stabilize such pharmacophores.

Design, synthesis, and NMR structure of linear and cyclic oligomers containing novel furanoid sugar amino acids.

Sugar Amino Acids (SAAs) are sugar moieties containing at least one amino and one carboxyl group. The straightforward synthesis of two furanoid SAAs, 3-amino-3-deoxy-1,2-isopropylidene-alpha-D-ribofuranoic acid (f-SAA1) and 3-amino-3-deoxy-1,2-isopropylidene-alpha-D-allofuranoic acid (f-SAA2) starting from diacetone glucose, is described. These SAAs were used as structural templates aiming at new structures for peptidomimetic drug design. f-SAA1 resembles a beta-amino acid, whereas f-SAA2 is a gamma-amino acid mimetic. Thus, for the synthesis of the mixed, linear and cyclic oligomers of f-SAA1, beta-homo-glycine (beta-hGly, also called beta-alanine) was chosen as an amino acid counterpart, while for the oligomer of f-SAA2 gamma-amino butyric acid (GABA) was chosen. Fmoc-[f-SAA1-beta-hGly](3)-OH (3) and cyclo[f-SAA1-beta-hGly](3) (5) resemble linear and cyclic beta-peptides with a very different substitution pattern, compared with the beta-peptides known so far in the literature, whereas Fmoc-[f-SAA2-GABA](3)-OH (4) resembles a gamma-peptide. The linear f-SAA oligomers 3 and 4 were synthesized on the solid-phase using Fmoc strategy. 23 unambiguous interresidue NOE contacts (from a total of 76 NOE values), obtained from extensive NMR studies in C(3)CN, were used in subsequent simulated annealing and MD calculations, to elucidate the 12/10/12-helical structure of oligomer 3 in CH(3)CN. The results indicate that f-SAA1 strongly induces a secondary structure. A characteristic CD curve for the linear oligomer 3 is observed up to 75 degrees C in both CH(3)CN and CH(3)CN/H(2)O, even though 3 contains beta-hGly, which is known to destabilize helices. By contrast, 4 does not seem to form a stable conformation in solution. The cyclic SAA containing oligomer cyclo [f-SAA1-beta-hGly](3) (5) exhibits a C(3) symmetric conformation on the NMR chemical shift time scale.

Defining minimal structural features in substrates of the H(+)/peptide cotransporter PEPT2 using novel amino acid and dipeptide derivatives.

The peptide transporter PEPT2, expressed in a variety of tissues, including kidney, lung, and the central nervous system, mediates the uphill transport of di- and tripeptides, as well as a variety of peptidomimetic drugs. To identify the essential molecular features of substrates that determine affinity and transport by PEPT2, we synthesized a series of amino acid derivatives as well as modified dipeptides. Kinetic constants for the interaction of test compounds with PEPT2 were obtained in a competition assay using Pichia pastoris yeast cells expressing mammalian PEPT2. The two-electrode voltage-clamp technique in Xenopus laevis oocytes was used to assess the substrate's electrogenic transport properties. Whereas omega bar-amino fatty acids showed no affinity for PEPT2, the introduction of a single carbonyl group into the backbone increased both affinity and transport currents more than 30-fold. omega bar-amino fatty acids, at their amino or carboxyl group coupled to an alanine residue, allowed us to determine the importance of the spatial position of functional groups within the molecule. Affinity and transport function declined by elongating the omega bar-amino acid chain when located in the N-terminal position, whereas the elongation in the carboxyl terminal with an N-terminal alanine caused less pronounced effects. The results clearly establish that a free N terminus, a correctly positioned backbone carbonyl group, and a carboxylic group that is in a suitable distance from the intramolecular carbonyl function and the amino terminal head group are the main features for substrate recognition and transport by PEPT2. This information provides the framework for a rational design of peptidomimetic drugs for delivery via PEPT2.

Phosphotyrosyl Peptides Block Stat3-mediated DNA Binding Activity, Gene Regulation, and Cell Transformation

Signal transducers and activators of transcription (STATs) comprise a family of cytoplasmic signaling proteins that participates in normal cellular responses to cytokines and growth factors. Frequently, however, constitutive activation of certain STAT family members, particularly Stat3, has accompanied a wide variety of human malignancies. To identify small molecule inhibitors of Stat3, we investigated the ability of the Stat3 SH2 domain-binding peptide, PY*LKTK (where Y* represents phosphotyrosine), to disrupt Stat3 activity in vitro. The presence of PY*LKTK, but not PYLKTK or PFLKTK, in nuclear extracts results in significant reduction in the levels of DNA binding activities of Stat3, to a lesser extent of Stat1, and with no effect on that of Stat5. Analyses of alanine scanning mutagenesis and deletion derivatives of PY*LKTK reveal that the Leu residue at the Y+1 position and a substituent at the Y-1 position (but not necessarily Pro) are essential for the disruption of active Stat3, thereby mapping the minimum active sequence to the tripeptide, XY*L. Studies involving bead-coupled PY*LKTK peptide demonstrate that this phosphopeptide directly complexes with Stat3 monomers in vitro, suggesting that PY*LKTK disrupts Stat3:Stat3 dimers. As evidence for the functional importance of peptide-directed inhibition of Stat3, PY*LKTK-mts (mts, membrane translocating sequence) selectively inhibits constitutive and ligand-induced Stat3 activation in vivo. Furthermore, PY*LKTK-mts suppresses transformation by the Src oncoprotein, which has been shown previously to require constitutive Stat3 activation. Altogether, we have identified a minimal peptide that inhibits Stat3 signaling and provides the conceptual basis for use of this peptide as a lead for novel peptidomimetic drug design.

Transport characteristics of peptides and peptidomimetics: II. Hydroxyethylamine bioisostere-containing peptidomimetics as substrates for the oligopeptide transporter and P-glycoprotein in the intestinal mucosa.

Peptide bond bioisosteres, such as hydroxyethylamine (Hea), have frequently been used to stabilize metabolically labile peptide bonds in peptidomimetic drug design in an effort to increase the oral bioavailability of drug candidates. However, the impact of the peptide bond bioisosteres on the cell permeation characteristics of peptidomimetics is not well understood, particularly with respect to the effects on the substrate activity for proteins that can restrict (e.g. P-glycoprotein, P-gp) or facilitate (e.g. the oligopeptide transporter, OPT) intestinal mucosal permeation of peptidomimetics. In this study, terminally free and terminally modified (N-acetylated and C-amidated) peptidomimetics of H-Ala-Phe-OH and H-Ala-Phe-Ala-OH with the Ala-Phe peptide bonds replaced by Hea bioisosteres were synthesized. Transport characteristics of these peptidomimetics were investigated using Caco-2 cell monolayers as an in vitro model of the intestinal mucosa. The study showed that the Hea bioisostere stabilized the peptidomimetics to protease metabolism in Caco-2 cells. All terminally free peptidomimetics showed significant affinity and substrate activity for OPT. The affinity and substrate activity for OPT were stereoselective for peptidomimetics containing an S,S-configuration for the two adjacent chiral centers related to the Hea bioisostere. Three of the four terminally modified peptidomimetics showed significant substrate activity for P-gp and, interestingly, the substrate activity for P-gp was also stereoselective; however, it was in favor of an R,R-configuration for the two adjacent chiral centers related to the Hea bioisostere.

Design criteria for molecular mimics of fragments of the beta-turn. 1. C alpha atom analysis.

Peptides represent an extensive class of biologically active molecules. They may be used as leads in the development of novel therapeutic agents provided the pharmacophoric information present within them can be translated into non-peptide analogs that lack the peptide backbone and are stable to proteolysis. This is the rationale for peptidomimetic drug design. Frequently, the beta-turn has been implicated as a conformation important for biological recognition of peptides. Empirical evidence from known peptidomimetics, coupled with a theoretical model of peptide binding and the observation that glycine and proline residues are common within the beta-turn, has suggested the design of molecules to mimic placement of between two and four of the side-chains. The moderate number of different beta-turn conformations, combined with the combinatoric nature of side-chain selection complicates the procedure. In this paper, cluster analysis has been used to classify the arrangement of C alpha atoms about the various fragments of the beta-turn. Recombination of the observed patterns provides a general model for the beta-turn which may be used as an effective screen for potential peptidomimetic scaffolds in chemical databases.