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This study focuses on investigating the use of β-cyclodextrin (β-CyD) derivatives as additives in continuous flow peptide synthesis, with particular emphasis on challenging sequences such as the Jung-Redemann decapeptide and the 42-residue amyloid β polypeptide [Aβ(1-42)]. The efficacy of the OH-free β-CyD and two of its derivatives (Ac-β-CyD and HP-β-CyD) is compared with alternative, state-of-the-art synthetic methods, including the widely used and recently improved pseudoproline monomer technique, e.g., Ser(ΨPro). Our results show that the use of β-CyD as an additive results in a significant (8-19%) increase in the purity of the crude polypeptide compared to that determined by our reference method. The chromatograms determined by LC-MS were deconvoluted to estimate the more precise purity of the crude products, and we found that the improvement is greater when the free OH β-CyD is used and moderate when the acetyl-β-CyD or the 2-hydroxypropyl-β-CyD derivatives are used. We have found that the free CyD gives an improvement comparable to that achieved with the Ser(ΨPro) derivative.

Covalent drugs might bear electrophiles to chemically modify their targets and have the potential to target previously undruggable proteins with high potency. Covalent binding of drug-size molecules includes a noncovalent recognition provided by secondary interactions and a chemical reaction leading to covalent complex formation. Optimization of their covalent mechanism of action should involve both types of interactions. Noncovalent and covalent binding steps can be characterized by an equilibrium dissociation constant ( K I ) and a reaction rate constant ( k inact ), respectively, and they are affected by both the warhead and the scaffold of the ligand. The relative contribution of these two steps was investigated on a prototypic drug target KRAS G12C , an oncogenic mutant of KRAS. We used a synthetically more accessible nonchiral core derived from ARS-1620 that was equipped with four different warheads and a previously described KRAS-specific basic side chain. Combining these structural changes, we have synthesized novel covalent KRAS G12C inhibitors and tested their binding and biological effect on KRAS G12C by various biophysical and biochemical assays. These data allowed us to dissect the effect of scaffold and warhead on the noncovalent and covalent binding event. Our results revealed that the atropisomeric core of ARS-1620 is not indispensable for KRAS G12C inhibition, the basic side chain has little effect on either binding step, and warheads affect the covalent reactivity but not the noncovalent binding. This type of analysis helps identify structural determinants of efficient covalent inhibition and may find use in the design of covalent agents.

The increasing role of the DNA-encoded library technology in early phase drug discovery represents a significant demand for DNA-compatible synthetic methods for therapeutically relevant heterocycles. Herein, we report the first on-DNA synthesis of multisubstituted indoles via a cascade reaction of Sonogashira coupling and intramolecular ring closure. Further functionalization by Suzuki coupling at the third position exploits a diverse chemical space. The high fidelity of the method also enabled the construction of an indole-based mock library.

Traumatic spinal cord injury (SCI) results in disruption of tissue integrity and loss of function. We hypothesize that glycosylation has a role in determining the occurrence of regeneration and that biomaterial treatment can influence this glycosylation response. We investigated the glycosylation response to spinal cord transection in Xenopus laevis and rat. Transected rats received an aligned collagen hydrogel. The response compared regenerative success, regenerative failure, and treatment in an established nonregenerative mammalian system. In a healthy rat spinal cord, ultraperformance liquid chromatography (UPLC) N-glycoprofiling identified complex, hybrid, and oligomannose N-glycans. Following rat SCI, complex and outer-arm fucosylated glycans decreased while oligomannose and hybrid structures increased. Sialic acid was associated with microglia/macrophages following SCI. Treatment with aligned collagen hydrogel had a minimal effect on the glycosylation response. In Xenopus , lectin histochemistry revealed increased levels of N -acetyl-glucosamine (GlcNAc) in premetamorphic animals. The addition of GlcNAc is required for processing complex-type glycans and is a necessary foundation for additional branching. A large increase in sialic acid was observed in nonregenerative animals. This work suggests that glycosylation may influence regenerative success. In particular, loss of complex glycans in rat spinal cord may contribute to regeneration failure. Targeting the glycosylation response may be a promising strategy for future therapies.

MASP-1 and MASP-2 are key activator proteases of the complement lectin pathway. The first specific mannose-binding lectin-associated serine protease (MASP) inhibitors had been developed from the 14-amino-acid sunflower trypsin inhibitor (SFTI) peptide by phage display, yielding SFTI-based MASP inhibitors, SFMIs. Here, we present the crystal structure of the MASP-1/SFMI1 complex that we analyzed in comparison to other existing MASP-1/2 structures. Rigidified backbone structure has long been accepted as a structural prerequisite for peptide inhibitors of proteases. We found that a hydrophobic cluster organized around the P2 Thr residue is essential for the structural stability of wild-type SFTI. We also found that the same P2 Thr prevents binding of the rigid SFTI-like peptides to the substrate-binding cleft of both MASPs as the cleft is partially blocked by large gatekeeper enzyme loops. Directed evolution removed this obstacle by replacing the P2 Thr with a Ser, providing the SFMIs with high-degree structural plasticity, which proved to be essential for MASP inhibition. To gain more insight into the structural criteria for SFMI-based MASP-2 inhibition, we systematically modified MASP-2-specific SFMI2 by capping its two termini and by replacing its disulfide bridge with varying length thioether linkers. By doing so, we also aimed to generate a versatile scaffold that is resistant to reducing environment and has increased stability in exopeptidase-containing biological environments. We found that the reduction-resistant disulfide-substituted l-2,3-diaminopropionic acid (Dap) variant possessed near-native potency. As MASP-2 is involved in the life-threatening thrombosis in COVID-19 patients, our synthetic, selective MASP-2 inhibitors could be relevant coronavirus drug candidates.

The synthesis of new cyclic peptides comprising the 9-22 epitope (9)LKMADPNRFRGKDL(22) sequence derived from HSV gD-1 is reported. In addition, we describe procedures for the preparation of cyclic peptide dimers and conjugates with an oligotuftsin derivative carrier. The binding of a monoclonal antibody, Mab A16, to the synthesized compounds was determined by enzyme-linked immunosorbent assay. It was demonstrated that cyclization decreased the binding activity of the antibody to the epitope. However, dimerization and conjugation could significantly increase the binding capacity of the cyclic epitope peptides. The attachment site in dimers and conjugates, as well as the topology of the construct, had a significant influence on the antibody recognition, while replacement of Met in position 11 by Nle had no marked effect.

The 6-coordinate dioximatomanganese(II) complex [Mn(HL)(CH3OH)]+ (2, where H2L is [HON=C(CH3)C(CH3)=NCH2CH2]2NH), formed by instant solvolysis of [Mn2(HL)2](BPh4)2 (1) in methanol, accelerates the triethylamine (TEA)-catalyzed oxidation of 3,5-di-tert-butylcatechol (H2dtbc) by O2 to the corresponding o-benzoquinone. Significantly, 2 alone has no catalytic effect. The observed rate increase can be explained by the interaction of 2 with the hydroperoxo intermediate HdtbcO2- formed from Hdtbc- and O2 in the TEA-catalyzed oxidation. The kinetics of the TEA-catalyzed and Mn-enhanced reaction has been studied by gas-volumetric monitoring of the amount of O2 consumed. The initial rate of O2 uptake (V(in)) shows a first-order dependence on the concentration of 2 and O2 and saturation kinetics with respect to both H2dtbc and TEA. The observed kinetic behavior is consistent with parallel TEA-catalyzed and Mn-enhanced oxidation paths. The 3,5-di-tert-butylsemiquinone anion radical is an intermediate detectable by electron spin resonance (ESR) spectroscopy. The dimeric catalyst precursor has been characterized by X-ray diffraction and electrospray ionization mass spectrometry and the monomeric catalyst by ESR spectroscopy.

The recently discovered homochiral serine octamer has been a focus of interest because of its possible implications for the origin of homochirality in living systems. Electrospray ionization (ESI) and sonic spray ionization (SSI) tandem mass spectrometry have been used to generate this unusually stable magic number cluster. Several structures have been suggested for the serine octamer, based on tandem mass spectrometry, ion mobility measurements, and quantum mechanical calculations. We now report experimental hydrogen/deuterium (H/D) exchange data, which demonstrate the existence of two different structures for the serine octamer. These forms undergo exchange at significantly different rates. One form may correspond to solution-phase assembled clusters and the other to octamers formed during the ionization process. Experiments done at higher resolution confirm that the experimental observations made here apply to the serine octamer without interference from metaclusters, namely, higher order clusters (Ser(16) + 2H)(+2), etc., the (12)C isotopes of which have mass-to-charge ratios identical to the protonated octamers. H/D exchange of racemic serine shows predominantly the extensively exchanged ion population, as well as providing evidence that racemic serine generates abundant metaclusters. The evidence presented here shows that one type of serine octamer is responsible for the strong chiral effects associated with the formation of these magic number clusters. These slowly exchanging more fragile clusters are the octamers that might have played a role in homochirogenesis.

A novel ion source based on the principle of sonic spray ionization has been built and used to optimize mass spectrometric conditions for generating amino acid clusters. The ion source employs a simple pneumatic spray operated at extremely high nebulizing gas flow rates. Several factors that affect the performance of the cluster source are identified, and information from these observations provides insights into the mechanisms of gas phase ion formation. Serine is used as a model system in optimizing instrumental and sample parameters to maximize cluster ion formation. The sonic spray results for this oligomer compare favorably with electrospray data, showing an order of magnitude better signal intensity and excellent signal-to-noise ratios. The performance of the system for the protonated serine octamer includes a limit of detection of 10 nM and a linear dynamic range of 4 orders of magnitude. Ion formation was observed to go into saturation above 1 mM. This result and data on pH, electrolyte concentration, and solvent composition are interpreted as supporting a charge residue model of sonic spray ionization. Other amino acids can be substituted for serine in the octamer, with a strong chiral preference in favor of homochiral cluster formation in the cases of threonine and cysteine. These amino acids show a preference for substitution of more than two serine molecules. Phenylalanine, asparagine, tryptophan, and tyrosine also substitute into the serine octamer; however, the process yields only two incorporations and only small chiral effects.