Publication Information Koehbach, J,O'Brien, M,Muttenthaler, M,Miazzo, M,Akcan, M,Elliott, AG,Daly, NL,Harvey, PJ,Arrowsmith, S,Gunasekera, S,Smith, TJ,Wray, S,Goransson, U,Dawson, PE,Craik, DJ,Freissmuth, M,Gruber, CW (2013) 'Oxytocic plant cyclotides as templates for peptide G protein-coupled receptor ligand design'. Proceedings Of The National Academy Of Sciences Of The United States Of America, 110 (52):21183-21188.
Disulfide bonds play a decisive role in the folding and stability in most classes of extra-cellular bioactive peptides including hormones, neurotransmitters, growth factors, enzyme inhibitors, antimicrobial peptides and venom toxins. Controlling the folding of disulfide-rich peptides is not trivial and often determines the rate and the success of their synthesis. This work introduces an alternative strategy to direct disulfide formation by substituting cysteine by the nearly isosteric selenocysteine. It describes a novel methodology that allows efficient access to conopeptide libraries via an on-resin oxidation approach and furthermore analyzes disulfide bridge mimetics of increased stability of oxytocin, involving new synthetic routes and revealing an interesting functional selectivity switch for the human oxytocin receptor. Chapter 1 & 2 serve as an overall introduction with the main focus on the chemical aspects of the 21st proteinogenic amino acid selenocysteine in peptides and proteins. It describes the physicochemical properties of selenium/sulfur and selenocysteine/cysteine based on comprehensive structural (X-ray, NMR, CD) and biological data, and illustrates why selenocysteine is considered the most conservative substitution for cysteine. The synthetic methods on selenocysteine incorporation into peptides and proteins were reviewed, including an overview of the selenocysteine building block syntheses for Boc- and Fmoc- solid phase peptide synthesis. Selenocysteine-mediated reactions are addressed such as native chemical ligation and dehydroalanine formation towards peptide conjugation. Selenopeptides have very interesting and distinct properties, which led to a diverse range of applications such as structural, functional and mechanistic probes, robust scaffolds, enzyme engineering, peptide conjugation and folding tools, all discussed in this review. Chapter 3 contains the core work of the thesis and describes how selenocysteine was used to control regioselective folding of an important class of disulfide -rich peptides, the α−conotoxins. Driven by the physicochemical differences of cysteine and selenocysteine such as lower pKa, lower redox potential and higher nucleophilicity, it was possible to direct the peptides into desired folds by replacing pairs of cysteine residues with isosteric selenocysteine residues. Selective access to the globular and ribbon isoforms of α-AuIB, α-MI, α-[A10L]-PnIA, α-RgIA and α-ImI was achieved through oxidative folding in situ in less than ten minutes. CD and NMR analysis confirmed the isosteric character of the α-selenoconotoxins and comparison of the crystal structures of α-PnIA and Sec[2,4]-[A10L]-PnIA (1.4 A) showed an increase of bond length of only 0.3 A and Se-Se torsion angles within 4-6o of the corresponding Cys analogue. The α-selenoconotoxins exhibited comparable or more potent inhibition of acetylcholine-evoked currents mediated by nAChR subtypes (α3β2, α7, α1β1δγ) expressed in Xenopus oocytes and on rat hemi-diaphragm contraction assays. Studies in rat plasma and in equimolar glutathione solutions showed increased stability to scrambling of the selenocysteine isoforms. Chapter 4 describes the development of resin-supported chemistry using Boc-SPPS that leads directly to correctly folded α-conotoxins on resin. Drug lead optimization, high-throughput screening and structure-activity relationship studies often require easy synthetic access to a large number of analogues. This has been hampered by tedious and time-consuming folding and purification processes. The use of a safety-catch acid labile linker on a water compatible, amphiphilic polyethyleneglycol support (ChemMatrix) allows side-chain deprotection and subsequent oxidation on-resin in aqueous phosphate buffer solution at pH 8.4. A selection of small to medium sized peptides, including the α-conotoxins MI, Vc1.1 and PnIA, were synthesized and oxidized on resin. The solid support had an effect on the isomer formation of α-MI and α-Vc1.1, yielding all three possible isomers. Control over the isomer formation in Sec[3,8]-MI was obtained by replacing a pair of cysteine residues with a pair of isosteric selenocysteine residues, showing that seleno-chemistry is compatible with on-resin chemistry. Peptide cleavage was achieved by reductive acidolysis and peptides were obtained in >90% purity either by individual cleavage and RP-HPLC purification using labeled solvent-permeable resin bags, or by an efficient ‘one-pot’ cleavage and RP-HPLC-purification step. Chapter 5 investigates structure-activity relationships of more stable disulfide bond mimetics of oxytocin (lanthionine, cystathionine and selenium analogues) for the human oxytocin and vasopressin V1a receptor. A new on-resin thioether formation and two novel selenocysteine building blocks (Nα−tert-butyloxycarbonyl-acetamidomethyl-L-seleno-cysteine (Boc-L-Sec(Acm)-OH) and Nα−tert-butyloxycarbonyl-4-nitrobenzyl-L-selenocysteine (Boc-L-Sec(pNB)-OH)) were developed for analogue synthesis. The cystathionine and selenylsulfur analogues retained full binding and functional activity, while the lanthionine analogues surprisingly abolished activity. Metabolic stability in rat and human plasma was improved over oxytocin (12h) in the selenium analogues (20-25h), and in the all-D-, N-to C-terminal-cyclized- and all-D-retroinverse-oxytocin (> 48h). Substitution of the C-terminal carboxylic amide to a carboxylic acid in the selenium analogue [C1,6U]-Oxytocin-OH revealed an interesting 2600-fold functional selectivity switch for the human oxytocin receptor. The chemistry introduced in this study facilitates access to analogues with enhanced metabolic stability that retained full activity and has the potential to be applied to other important classes of disulfide-rich peptides.
TFF1 is a protective peptide of the Trefoil Factor Family (TFF), which is co-secreted with the mucin MUC5AC, gastrokine 2 (GKN2), and IgG Fc binding protein (FCGBP) from gastric surface mucous cells. Tff1-deficient mice obligatorily develop antropyloric adenoma and about 30% progress to carcinomas, indicating that Tff1 is a tumor suppressor. As a hallmark, TFF1 contains seven cysteine residues with three disulfide bonds stabilizing the conserved TFF domain. Here, we systematically investigated the molecular forms of TFF1 in the human gastric mucosa. TFF1 mainly occurs in an unusual monomeric form, but also as a homodimer. Furthermore, minor amounts of TFF1 form heterodimers with GKN2, FCGBP, and an unknown partner protein, respectively. TFF1 also binds to the mucin MUC6 in vitro, as shown by overlay assays with synthetic 125I-labeled TFF1 homodimer. The dominant presence of a monomeric form with a free thiol group at Cys-58 is in agreement with previous studies in Xenopus laevis and mouse. Cys-58 is likely highly reactive due to flanking acid residues (PPEEEC58EF) and might act as a scavenger for extracellular reactive oxygen/nitrogen species protecting the gastric mucosa from damage by oxidative stress, e.g., H2O2 generated by dual oxidase (DUOX).
Despite the increasing number of GPCR structures and recent advances in peptide design, the development of efficient technologies allowing rational design of high-affinity peptide ligands for single GPCRs remains an unmet challenge. Here, we develop a computational approach for designing conjugates of lariat-shaped macrocyclized peptides and a small molecule opioid ligand. We demonstrate its feasibility by discovering chemical scaffolds for the kappa-opioid receptor (KOR) with desired pharmacological activities. The designed De Novo Cyclic Peptide (DNCP)-β-naloxamine (NalA) exhibit in vitro potent mixed KOR agonism/mu-opioid receptor (MOR) antagonism, nanomolar binding affinity, selectivity, and efficacy bias at KOR. Proof-of-concept in vivo efficacy studies demonstrate that DNCP-β-NalA(1) induces a potent KOR-mediated antinociception in male mice. The high-resolution cryo-EM structure (2.6 Å) of the DNCP-β-NalA-KOR-Gi1 complex and molecular dynamics simulations are harnessed to validate the computational design model. This reveals a network of residues in ECL2/3 and TM6/7 controlling the intrinsic efficacy of KOR. In general, our computational de novo platform overcomes extensive lead optimization encountered in ultra-large library docking and virtual small molecule screening campaigns and offers innovation for GPCR ligand discovery. This may drive the development of next-generation therapeutics for medical applications such as pain conditions.
G protein-coupled receptors (GPCRs) are considered to represent the most promising drug targets; it has been repeatedly said that a large fraction of the currently marketed drugs elicit their actions by binding to GPCRs (with cited numbers varying from 30-50%). Closer scrutiny, however, shows that only a modest fraction of (∼60) GPCRs are, in fact, exploited as drug targets, only ∼20 of which are peptide-binding receptors. The vast majority of receptors in the humane genome have not yet been explored as sites of action for drugs. Given the drugability of this receptor class, it appears that opportunities for drug discovery abound. In addition, GPCRs provide for binding sites other than the ligand binding sites (referred to as the “orthosteric site”). These additional sites include (i) binding sites for ligands (referred to as “allosteric ligands”) that modulate the affinity and efficacy of orthosteric ligands, (ii) the interaction surface that recruits G proteins and arrestins, (iii) the interaction sites of additional proteins (GIPs, GPCR interacting proteins that regulate G protein signaling or give rise to G protein-independent signals). These sites can also be targeted by peptides. Combinatorial and natural peptide libraries are therefore likely to play a major role in identifying new GPCR ligands at each of these sites. In particular the diverse natural peptide libraries such as the venom peptides from marine cone-snails and plant cyclotides have been established as a rich source of drug leads. High-throughput screening and combinatorial chemistry approaches allow for progressing from these starting points to potential drug candidates. This will be illustrated by focusing on the ligand-based drug design of oxytocin (OT) and vasopressin (AVP) receptor ligands using natural peptide leads as starting points. Keywords: GPCR, drug, ligand-based design, peptide, cyclotide, conotoxin, oxytocin, vasopressin
Neurohypophysial peptides are ancient and evolutionarily highly conserved neuropeptides that regulate many crucial physiological functions in vertebrates and invertebrates. The human neurohypophysial oxytocin/vasopressin (OT/VP) signaling system with its four receptors has become an attractive drug target for a variety of diseases, including cancer, pain, cardiovascular indications, and neurological disorders. Despite its promise, drug development faces hurdles, including signaling complexity, selectivity and off-target concerns, translational interspecies differences, and inefficient drug delivery. In this review we dive into the complexity of the OT/VP signaling system in health and disease, provide an overview of relevant pharmacological probes, and discuss the latest trends in therapeutic lead discovery and drug development.