Unnatural Amino Acid Substitutions Research Articles

Synthesis and Evaluation of Clickable Block Copolymers for Targeted Nanoparticle Drug Delivery

Polymeric nanoparticles with multifunctional capabilities, including surface functionalization, hold great promise to address challenges in targeted drug delivery. Here, we describe a concise, robust synthesis of a heterofunctional polyethylene glycol (PEG), HO-PEG-azide. This macromer was used to synthesize polylactide (PLA)-PEG-azide, a functional diblock copolymer. Rapid precipitation of this copolymer with a hydrophobic cargo resulted in the generation of monodisperse nanoparticles with azides in the surface corona. To demonstrate conjugation to these nanoparticles, a regioselectively modified alkyne-folate was employed as a model small molecule ligand, and the artificial protein A1 with an alkyne moiety introduced by unnatural amino acid substitution was selected as a model macromolecular ligand. Using the copper-catalyzed azide-alkyne ligation reaction, both ligands exhibited good conjugation efficiency even when low concentrations of ligands were used.

Optimization of co‐agonism at GLP‐1 and glucagon receptors to safely maximize weight reduction in DIO‐rodents

The ratio of GLP-1/glucagon receptor (GLP1R/GCGR) co-agonism that achieves maximal weight loss without evidence of hyperglycemia was determined in diet-induced obese (DIO) mice chronically treated with GLP1R/GCGR co-agonist peptides differing in their relative receptor agonism. Using glucagon-based peptides, a spectrum of receptor selectivity was achieved by a combination of selective incorporation of GLP-1 sequences, C-terminal modification, backbone lactam stapling to stabilize helical structure, and unnatural amino acid substitutions at the N-terminal dipeptide. In addition to α-amino-isobutyric acid (Aib) substitution at position two, we show that α,α'-dimethyl imidazole acetic acid (Dmia) can serve as a potent replacement for the highly conserved histidine at position one. Selective site-specific pegylation was used to further minimize enzymatic degradation and provide uniform, extended in vivo duration of action. Maximal weight loss devoid of any sign of hyperglycemia was achieved with a co-agonist comparably balanced for in vitro potency at murine GLP1R and GCGR. This peptide exhibited superior weight loss and glucose lowering compared to a structurally matched pure GLP1R agonist, and to co-agonists of relatively reduced GCGR tone. Any further enhancement of the relative GCGR agonist potency yielded increased weight loss but at the expense of elevated blood glucose. We conclude that GCGR agonism concomitant with GLP1R agonism constitutes a promising approach to treatment of the metabolic syndrome. However, the relative ratio of GLP1R/GCGR co-agonism needs to be carefully chosen for each species to maximize weight loss efficacy and minimize hyperglycemia.

Testing Models for the Slow Inactivated State using Unnatural Amino Acid Mutagenesis

K+ channels undergo a gating process called slow inactivation in which the selectivity filter changes conformation from a conductive state to a non-conductive state. Models for the structure of the selectivity filter in the slow inactivated state have been proposed based on structural studies of the KcsA K+ channel at low K+ or in the open state. Here, we experimentally evaluate the models for the slow inactivated state by using unnatural amino acid mutagenesis to precisely modify the selectivity filter. We have used the KcsA channel and the voltage gated K+ channel KvAP in our investigations. We will present the semisynthetic approaches used and describe the consequences of the unnatural amino acid substitutions on slow inactivation in the KcsA and KvAP channels.

Probing Intein-Catalyzed Thioester Formation by Unnatural Amino Acid Substitutions in the Active Site

Inteins are single-turnover catalysts that splice themselves out of a precursor polypeptide chain. For most inteins, the first step of protein splicing is the formation of a thioester through an N-S acyl shift at the upstream splice junction. However, the mechanism by which this reaction is achieved and the impact of mutations in and close to the active site remain unclear on the atomic level. To investigate these questions, we have further explored a split variant of the Ssp DnaB intein by introducing substitutions with unnatural amino acids within the short synthetic N-terminal fragment. A previously reported collapse of the oxythiazolidine anion intermediate into a thiazoline ring was found to be specificially dependent on the methyl side chain of the flanking Ala(-1). The stereoisomer d-Ala and the constitutional isomers β-Ala and sarcosine did not lead to this side reaction but rather supported splicing. Substitution of the catalytic Cys1 with homocysteine strongly inhibited protein splicing; however, thioester formation was not impaired. These results argue against the requirement of a base to deprotonate the catalytic thiol group prior to the N-S acyl shift, because it should be misaligned for optimal proton abstraction. A previously described mutant intein evolved for more general splicing in different sequence contexts could even rather efficiently splice with this homocysteine. Our findings show the large impact of some subtle structural changes on the protein splicing pathway, but also the remarkable tolerance toward other changes. Such insights will also be important for the biotechnological exploitation of inteins.

Unnatural Amino Acid Substitution as a Probe of the Allosteric Coupling Pathway in a Mycobacterial Cu(I) Sensor

The Cu(I) sensor Mycobacterium tuberculosis CsoR is a founding member of a new metalloregulatory protein family. Here we show that two "atom" substitutions of the Nepsilon2 face of a Cu(I) coordinating histidine-61 allosterically uncouple Cu(I) and DNA binding, with no effect on Cu(I) binding affinity and coordination structure. A model analogous to the allosteric switch mechanism in Staphylococcus aureus CzrA, a zinc sensor protein with a completely different fold, is proposed.

Differential cardiovascular effects of synthetic peptides derived from endomorphin-1 in anesthetized rats

Previously, five synthetic peptides derived from endomorphin-1 (Tyr1-Pro2-Trp3-Phe4-NH2, EM-1), including Tyr-D-Ala-Trp-p-Cl-Phe-NH2 (HDAPC), Tyr-D-Ala-Trp-Phe-NH2 (HDADC), Nalpha-amidino-Tyr-D-Ala-Trp-p-Cl-Phe-NH2 (GDAPC), Nalpha-amidino-Tyr-D-Ala-Trp-Phe-NH2 (GDADC) and Nalpha-amidino-Tyr-D-Pro-Gly-Trp-p-Cl-Phe-NH2 (GBDPC), were described to elicit analgesia by subcutaneous administration with enhanced metabolic stabilities. To further our knowledge of the influences of particular modification on the pharmacological activities of EM-1, the present study was undertaken to investigate cardiovascular effects of these peptides in anesthetized rats by intravenous injection. Our results showed that the four D-Ala-containing peptides decreased the systemic arterial pressure (SAP) and heart rate (HR) through a naloxone-sensitive mechanism. Different patterns, potencies and durations of cardiovascular effects were observed among these peptides. When compared to EM-1, the hemodynamic responses to these four tetrapeptides were significantly lower in magnitude but much longer in duration. Surprisingly, intravenous administration of the only pentapeptide GBDPC produced fairly prolonged hypertensive and tachycardiac effects, which was naloxone-insensitive, thus providing evidence that changes in the primary structure of a peptide can profoundly affect its pharmacological activity. Comparisons of the cardiovascular effects between these peptides showed that each modification introduced into EM-1, including N-amidination, chloro-halogenation and unnatural amino acid substitution, played a role in the influence on the cardiovascular regulation of these peptides.

Single-Walled Carbon Nanotube Binding Peptides: Probing Tryptophan's Importance by Unnatural Amino Acid Substitution

Peptides selected from phage-displayed libraries have been found to exhibit high-affinity binding to carbon nanotubes including single-walled carbon nanotubes (SWNTs), multi-walled carbon nanotubes, and single-walled carbon nanohorns. One unique feature of these peptides is that their amino acid sequences are rich in tryptophan and histidine residues. The aim of this study was to investigate the importance of the tryptophan residue in a newly identified SWNT-binding peptide, UW-1, which contains the motif, XTHXXPWTX, where X is any amino acid. Tryptophan was altered in the following ways: mutation to alanine or substitution with three unnatural tryptophan analogues, i.e., 5-fluorotryptophan, 5-hydroxytryptophan, and 7-azatryptophan. Analysis of experimental and computational data suggests that the highest occupied molecular orbital of the tryptophan residue in the peptide interacts with the lowest unoccupied molecular orbital from the SWNT. This information should be important in permitting modulation of peptide affinities to these nanomaterials.

Unnatural Amino Acid-Substituted (Hydroxyethyl)urea Peptidomimetics Inhibit γ-Secretase and Promote the Neuronal Differentiation of Neuroblastoma Cells

Gamma-secretase, exhibiting characteristics of aspartyl protease, mediates the intramembranous proteolysis of beta-amyloid precursor protein (APP) and Notch, and it is considered to be a prime pharmacological target in the development of therapeutics for Alzheimer's disease (AD). To identify compounds that block gamma-secretase-mediated proteolysis, we used a highly sensitive cell-based reporter gene assay for gamma-secretase in which Gal4/VP16-tagged C99-APP was expressed as the immediate substrate of gamma-secretase, and Gal4/VP16-tagged APP intracellular domain released by the gamma-secretase cleavage then activated the expression of the Gal4-driven luciferase reporter gene. Using this reporter assay, we demonstrated that the newly synthesized (hydroxyethyl)urea peptidomimetics, which contain unnatural amino acid moieties at positions P1' and/or P3', can effectively inhibit gamma-secretase activity and significantly reduce Abeta production. The gamma-secretase-dependent S3 cleavage of Notch was also consistently blocked by these (hydroxyethyl)ureas as evidenced by the decreased generation of the Notch intracellular domain, a prerequisite for the activation of Notch signaling. The inhibition of Notch signaling by active Jia compounds efficiently promotes the neuronal differentiation of neuroblastoma cells, intervening in tumorigenesis and the malignancy of neuroblastomas. Our results suggest that (hydroxyethyl)urea peptidomimetics containing unnatural amino acid substitutions could represent a novel class of gamma-secretase inhibitors with enhanced stability, providing the basis for the further development of effective therapeutics for AD and neuroblastomas.

Utilization of Combined Chemical Modifications to Enhance the Blood-Brain Barrier Permeability and Pharmacological Activity of Endomorphin-1

The endogenous mu-opioid receptor agonist, endomorphin (EM)-1, cannot be delivered into the central nervous system (CNS) in sufficient quantity to elicit analgesia when given systemically because it is severely restricted by the blood-brain barrier (BBB). To improve the physicochemical characteristics of EM-1 and subsequently achieve greater BBB permeation, we synthesized a series of EM-1 analogs by combining successful chemical modifications, including N-terminal cationization, C-terminal chloro-halogenation, and unnatural amino acid (d-Ala, Sar, and d-Pro-Gly) substitutions in position 2. Presently, their binding and bioassay activity, lipophilicity, stability, and antinociceptive activity were determined and compared. Guanidino-addition and chloro-halogenation attenuated the mu-receptor affinity to some extent, but they demonstrated differences in the influence on stability. It appeared that guanidino-addition contributed to brain stability enhancement for the greater part, whereas chloro-halogenation together with amino acid substitutions in position 2 was of more importance for the stability enhancement in serum than in brain. Determination of the octanol/buffer coefficient revealed that chloro-halogenation did compromise the decreased lipophilicity caused by guanidino-addition, and introduction of d-Ala as well as d-Pro-Gly, but not Sar, in place of l-Pro(2), also increased the overall lipophilicity to some extent. Among the peptides tested, intracerebroventricular injection of guanidino-[d-Ala(2), p-Cl-Phe(4)]EM-1 showed the strongest analgesia, being 3 times more potent than the parent peptide. We also found that in comparison with EM-1, the four d-Ala-containing tetrapeptides and the chloro-halogenated d-Pro-Gly-containing pentapeptide elicited significant and prolonged central-mediated analgesia upon subcutaneous administration, indicating that more peptides reached the CNS, eliciting greater analgesic effect.

Switching DNA-binding specificity by unnatural amino acid substitution

The specificity of protein–nucleic acid recognition is believed to originate largely from hydrogen bonding between protein polar atoms, primarily side-chain and polar atoms of nucleic acid bases. One way to design new nucleic acid binding proteins of novel specificity is by structure-guided alterations of the hydrogen bonding patterns of a nucleic acid–protein complex. We have used cI repressor of bacteriophage λ as a model system. In the λ-repressor–DNA complex, the ɛ-NH2 group (hydrogen bond donor) of lysine-4 of λ-repressor forms hydrogen bonds with the amide carbonyl atom of asparagine-55 (acceptor) and the O6 (acceptor) of CG6 of operator site OL1. Substitution of lysine-4 (two donors) by iso-steric S-(2-hydroxyethyl)-cysteine (one donor and one acceptor), by site-directed mutagenesis and chemical modification, leads to switch of binding specificity of λ-repressor from C:G to T:A at position 6 of OL1. This suggests that unnatural amino acid substitutions could be a simple way of generating nucleic acid binding proteins of altered specificity.