The effects of thioamide backbone substitution on protein stability: a study in α-helical, β-sheet, and polyproline II helical contexts

Complementary Strategies for Installation of Thioimidates into Peptide Backbones

Thioimidates are a precursor and synthetic branch point to access either thioamide or amidine isosteres of the native amide (peptide bond). Previous syntheses of thioimidate-containing peptides were prone to side reactivity and required slow, cumbersome steps that were difficult to monitor. We describe a more efficient approach to directly couple thioimidates onto the growing peptide chain. This work also outlines optimal conditions for thioimidate formation on solid support and identifies potential off-target sites for alkylation that impact the choice of protecting group.

Total Syntheses of Streptamidine and Klebsazolicin Using Biomimetic On-Resin Ring-Closing Amidine Formation

Diketopiperazine (DKP) derived cyclic amidine structures widely exist in peptide natural products according to the genome mining result. The largely unknown bioactivity and mode of action are partially caused by the poor availability of the compounds via microbiological and chemical approaches. To tackle this challenge, in this work, we have developed the on-resin ring-closing amidine formation strategy to synthesize peptides containing N-terminal DKP derived cyclic amidine structure, in which the 6-exo-trig cyclization mediated by HgCl2 activation of thioamides was the key step. Leveraging from this new strategy, we finished the total syntheses of streptamidine and klebsazolicin. Meanwhile, eleven klebsazolicin analogues were synthesized for its structure-activity relationship study.

Electronic Control of Polyproline II Helix Stability via the Identity of Acyl Capping Groups: the Pivaloyl Group Particularly Promotes PPII

The type II polyproline helix (PPII) is a fundamental secondary structure of proteins, important in globular proteins, in intrinsically disordered proteins, and at protein-protein interfaces. PPII is stabilized in part by n→π* interactions between consecutive carbonyls, via electron delocalization between an electron-donor carbonyl lone pair (n) and an electron-acceptor carbonyl (π*) on the subsequent residue. We previously demonstrated that changes to the electronic properties of the acyl donor can predictably modulate the strength of n→π* interactions, with data from model compounds, in solution in chloroform, in the solid state, and computationally. Herein, we examined whether the electronic properties of acyl capping groups could modulate the stability of PPII in peptides in water. In X-PPGY-NH2 peptides (X=10 acyl capping groups), the effect of acyl group identity on PPII was quantified by circular dichroism and NMR spectroscopy. Electron-rich acyl groups promoted PPII relative to the standard acetyl (Ac-) group, with the pivaloyl and iso-butyryl groups most significantly increasing PPII. In contrast, acyl derivatives with electron-withdrawing substituents and the formyl group relatively disfavored PPII. Similar results, though lesser in magnitude, were also observed in X-APPGY-NH2 peptides, indicating that the capping group can impact PPII conformation at both proline and non-proline residues. The pivaloyl group was particularly favorable in promoting PPII. The effects of acyl capping groups were further analyzed in X-DfpPGY-NH2 and X-ADfpPGY-NH2 peptides, Dfp=4,4-difluoroproline. Data on these peptides indicated that acyl groups induced order Piv- > Ac- > For-. These results suggest that greater consideration should be given to the identity of acyl capping groups in inducing structure in peptides.

Beyond N-Alkylation: Synthesis, Structure, and Function of N-Amino Peptides

The growing list of physiologically important protein-protein interactions (PPIs) has amplified the need for compounds to target topologically complex biomolecular surfaces. In contrast to small molecules, peptide and protein mimics can exhibit three-dimensional shape complementarity across a large area and thus have the potential to significantly expand the "druggable" proteome. Strategies to stabilize canonical protein secondary structures without sacrificing side-chain content are particularly useful in the design of peptide-based chemical probes and therapeutics.Substitution of the backbone amide in peptides represents a subtle chemical modification with profound effects on conformation and stability. Studies focused on N-alkylation have already led to broad-ranging applications in peptidomimetic design. Inspired by nonribosomal peptide natural products harboring amide N-oxidations, we envisioned that main-chain hydrazide and hydroxamate bonds would impose distinct conformational preferences and offer unique opportunities for backbone diversification. This Account describes our exploration of peptide N-amination as a strategy for stabilizing canonical protein folds and for the structure-based design of soluble amyloid mimics.We developed a general synthetic protocol to access N-amino peptides (NAPs) on solid support. In an effort to stabilize β-strand conformation, we designed stitched peptidomimetics featuring covalent tethering of the backbone N-amino substituent to the preceding residue side chain. Using a combination of NMR, X-ray crystallography, and molecular dynamics simulations, we discovered that backbone N-amination alone could significantly stabilize β-hairpin conformation in multiple models of folding. Our studies revealed that the amide NH2 substituent in NAPs participates in cooperative noncovalent interactions that promote β-sheet secondary structure. In contrast to Cα-substituted α-hydrazino acids, we found that N-aminoglycine and its N'-alkylated derivatives instead stabilize polyproline II (PPII) conformation. The reactivity of hydrazides also allows for late-stage peptide macrocyclization, affording novel covalent surrogates of side-chain-backbone H-bonds.The pronounced β-sheet propensity of Cα-substituted α-hydrazino acids prompted us to target amyloidogenic proteins using NAP-based β-strand mimics. Backbone N-amination was found to render aggregation-prone lead sequences soluble and resistant to proteolysis. Inhibitors of Aβ and tau identified through N-amino scanning blocked protein aggregation and the formation of mature fibrils in vitro. We further identified NAP-based single-strand and cross-β tau mimics capable of inhibiting the prion-like cellular seeding activity of recombinant and patient-derived tau fibrils.Our studies establish backbone N-amination as a valuable addition to the peptido- and proteomimetic tool kit. α-Hydrazino acids show particular promise as minimalist β-strand mimics that retain side-chain information. Late-stage derivatization of hydrazides also provides facile entry into libraries of backbone-edited peptides. We anticipate that NAPs will thus find applications in the development of optimally constrained folds and modulators of PPIs.

Thioimidates provide general access to thioamide, amidine, and imidazolone peptide-bond isosteres

Thioamides, amidines, and heterocycles are three classes of modifications that can act as peptide-bond isosteres to alter the peptide backbone. Thioimidate protecting groups can address many of the problematic synthetic issues surrounding installation of these groups. Historically, amidines have received little attention in peptides due to limitations in methods to access them. The first robust and general procedure for the introduction of amidines into peptide backbones exploits the utility of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides. Further, amidines formed on-resin can be reacted to form (4H)-imidazolone heteorcycles which have recently been shown to act as cis-amide isosteres. General methods for heterocyclic installation capable of geometrically restricting peptide conformation are also under-developed. This work is significant because it describes a generally applicable and divergent approach to access unexplored peptide designs and architectures.

Probing effects of site-specific aspartic acid isomerization on structure and stability of GB1 through chemical protein synthesis

Chemical modifications of long-lived proteins, such as isomerization and epimerization, have been evoked as prime triggers for protein-damage related diseases. Deamidation of Asn residues, which results in formation of a mixture of l- and d-Asp and isoAsp via an intermediate aspartyl succinimide, can result in the disruption of cellular proteostasis and toxic protein depositions. In contrast to extensive data on the biological prevalence and functional implications of aspartyl succinimide formation, much less is known about the impact of the resulting altered backbone composition on properties of individual proteins at a molecular level. Here, we report the total chemical synthesis, biophysical characterization, and NMR structural analysis of a series of variants of the B1 domain of protein G from Streptococcal bacteria (GB1) in which all possible Asp isomers as well as an aspartyl succinimide were individually incorporated at a defined position in a solvent-exposed loop. Subtle local structural effects were observed; however, these were accompanied by notable differences in thermodynamic folded stability. Surprisingly, the noncanonical backbone connectivity of d-isoAsp led to a variant that exhibited enhanced stability relative to the natural protein.

Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection

Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.

Thioamide Analogues of MHC I Antigen Peptides

Short, synthetic peptides that are displayed by major histocompatibility complex I (MHC I) can stimulate CD8 T cells in vivo to destroy virus-infected or cancer cells. The development of such peptides as vaccines that provide protective immunity, however, is limited by rapid proteolytic degradation. Introduction of unnatural amino acid residues can suppress MHC I antigen proteolysis, but the modified peptides typically display lower affinity for MHC I and/or diminished ability to activate CD8 T cells relative to native antigen. Here, we report a new strategy for modifying MHC I antigens to enhance resistance to proteolysis while preserving MHC I affinity and T cell activation properties. This approach, replacing backbone amide groups with thioamides, was evaluated in two well-characterized antigens presented by HLA-A2, a common human MHC I. For each antigen, singly modified thioamide analogues retained affinity for HLA-A2 and activated T cells specific for the native antigen, as measured via interferon-γ secretion. In each system, we identified a highly potent triply substituted thioamide antigen ("thio-antigen") that displayed substantial resistance to proteolytic cleavage. Collectively, our results suggest that thio-antigens may represent a general and readily accessible source of potent vaccine candidates that resist degradation.

Structure-Activity Relationships of the Antimicrobial Peptide Natural Product Apidaecin

With the growing crisis of antimicrobial resistance, it is critical to continue to seek out new sources of novel antibiotics. This need has led to renewed interest in natural product antimicrobials, specifically antimicrobial peptides. Nonlytic antimicrobial peptides are highly promising due to their unique mechanisms of action. One such peptide is apidaecin (Api), which inhibits translation termination through stabilization of the quaternary complex of the ribosome-apidaecin-tRNA-release factor. Synthetic derivatives of apidaecin have been developed, but structure-guided modifications have yet to be considered. In this work, we have focused on modifying key residues in the Api sequence that are responsible for the interactions that stabilize the quaternary complex. We present one of the first examples of a highly modified Api peptide that maintains its antimicrobial activity and interaction with the translation complex. These findings establish a starting point for further structure-guided optimization of Api peptides.

Esterification of Thioamides via Selective N-C(S) Cleavage under Mild Conditions

Herein, we report an exceedingly mild method for the direct, transition-metal-free esterification of thioamides through the selective generation of tetrahedral intermediates. The method represents the first transition-metal-free approach to the thioamide to thionoester transformation in organic synthesis. This reactivity has been accomplished through N,N-Boc2-thioamides that engage in ground-state destabilization of the nN → π*C═S conjugation. The ground-state destabilization of "single-atom" bioisosteric thioamides will expand the arsenal of valuable amide bond functionalization reactions.

Evaluation of acyllysine isostere interactions with the aromatic pocket of the AF9 YEATS domain

Amide-π interactions, in which an amide interacts with an aromatic group, are ubiquitous in biology, yet remain understudied relative to other noncovalent interactions. Recently, we demonstrated that an electrostatically tunable amide-π interaction is key to recognition of histone acyllysine by the AF9 YEATS domain, a reader protein which has emerged as a therapeutic target due to its dysregulation in cancer. Amide isosteres are commonly employed in drug discovery, often to prevent degradation by proteases, and have proven valuable in achieving selectivity when targeting epigenetic proteins. However, like amide-π interactions, interactions of amide isosteres with aromatic rings have not been thoroughly studied despite widespread use. Herein, we evaluate the recognition of a series of amide isosteres by the AF9 YEATS domain using genetic code expansion to evaluate the amide isostere-π interaction. We show that compared to the amide-π interaction with the native ligand, each isostere exhibits similar electrostatic tunability with an aromatic residue in the binding pocket, demonstrating that the isosteres maintain similar interactions with the aromatic residue. We identify a urea-containing ligand that binds with enhanced affinity for the AF9 YEATS domain, offering a promising starting point for inhibitor development. Furthermore, we demonstrate that carbamate and urea isosteres of crotonyllysine are resistant to enzymatic removal by SIRT1, a protein that cleaves acyl post-translational modifications, further indicating the potential of amide isosteres in YEATS domain inhibitor development. These results also provide experimental precedent for interactions of these common drug discovery moieties with aromatic rings that can inform computational methods.

Structural impact of thioamide incorporation into a β-hairpin

The thioamide is a naturally-occurring single atom substitution of the canonical amide bond. The exchange of oxygen to sulfur alters the amide's physical and chemical characteristics, thereby expanding its functionality. Incorporation of thioamides in prevalent secondary structures has demonstrated that they can either have stabilizing, destabilizing, or neutral effects. We performed a systematic investigation of the structural impact of thioamide incorporation in a β-hairpin scaffold with nuclear magnetic resonance (NMR). Thioamides as hydrogen bond donors did not increase the foldedness of the more stable "YKL" variant of this scaffold. In the less stable "HPT" variant of the scaffold, the thioamide could be stabilizing as a hydrogen bond donor and destabilizing as a hydrogen bond acceptor, but the extent of the perturbation depended upon the position of incorporation. To better understand these effects we performed structural modelling of the macrocyclic folded HPT variants. Finally, we compare the thioamide effects that we observe to previous studies of both side-chain and backbone perturbations to this β-hairpin scaffold to provide context for our observations.

Chemoselective Transamidation of Thioamides by Transition-Metal-Free N-C(S) Transacylation

Thioamides represent highly valuable isosteric in the strictest sense "single-atom substitution" analogues of amides that have found broad applications in chemistry and biology. A long-standing challenge is the direct transamidation of thioamides, a process which would convert one thioamide bond (R-C(S)-NR¹ R² ) into another (R-C(S)-NR³ N⁴ ). Herein, we report the first general method for the direct transamidation of thioamides by highly chemoselective N-C(S) transacylation. The method relies on site-selective N-tert-butoxycarbonyl activation of 2° and 1° thioamides, resulting in ground-state-destabilization of thioamides, thus enabling to rationally manipulate nucleophilic addition to the thioamide bond. This method showcases a remarkably broad scope including late-stage functionalization (>100 examples). We further present extensive DFT studies that provide insight into the chemoselectivity and provide guidelines for the development of transamidation methods of the thioamide bond.

Ynamide-Mediated Synthetic Approach to Thioamide-Substituted Peptides

A novel synthetic approach to thioamide-substituted peptides is reported. It provides a practical tool for the chemical biology study of peptides and proteins by replacing a carbonyl oxygen atom of an amide bond by an sp²-hybridized sulfur atom to precisely introduce a thioamide bond Ψ[CS-NH] into a peptide backbone. The α-thioacyloxyenamide intermediates, originating from ynamide coupling reagent and proteinogenic amino monothioacids, are proved to be novel effective thioacylating reagents in both the solution and solid phase peptide syntheses. Herein, we describe the detailed synthesis protocol for site-specifically incorporating a thioamide bond at 19 of 20 proteinogenic amino acid residues (except for His) of a peptide backbone in a racemization/epimerization-free manner.

Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications

Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.

Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability

Amino acid side chains are key to fine-tuning the microenvironment polarity in proteins composed of polar amide bonds. Here, we report that substituting an oxygen atom of the backbone amide bond with sulfur atom desolvates the thioamide bond, thereby increasing its lipophilicity. The impact of such local desolvation by O to S substitution in proteins was tested by synthesizing thioamidated variants of Pin1 WW domain. We observe that a thioamide acts in synergy with nonpolar amino acid side chains to reduce the microenvironment polarity and increase protein stability by more than 14 °C. Through favorable van der Waals and hydrogen bonding interactions, this single atom substitution significantly stabilizes proteins without altering the amino acid sequence and structure of the native protein.

Folding and Unfolding of the Tryptophan Zipper in the Presence of Two Thioamide Substitutions

We studied the stability and folding and unfolding kinetics of the tryptophan zipper, containing different double thioamide subsitutions. Conformation change was triggered by photoisomerization of an integrated AMPP photoswitch in the turn region of the hairpin, and transient spectra were recorded in the deep UV and the mid-IR, covering the time window of the (un)folding transition from picoseconds to tens of microseconds. Thio-substitution of inward-pointing backbone carbonyls was found to strongly destabilize the β-hairpin structures, whereas molecules with two outward pointing thio-carbonyls showed similar or enhanced stability with respect to the unsubstituted sequence, which we attribute to stronger interstrand hydrogen bonding. Thiolation of the two Trp residues closest to the turn can even prevent the opening of the hairpin after cis-trans isomerization of the switch. The circular dichroism due to the two thioamide ππ* transitions is spectrally well-separated from the aromatic tryptophan signal. It changes upon photoswitching, reflecting a local change in coupling and geometry.

Opportunities and challenges in the synthesis of thioamidated peptides

Chemical modifications of peptides hold great promise for modulating their pharmacological properties. In the last few decades amide to thioamide substitution has been widely explored to modulate the conformation, non-covalent interactions, and proteolytic stability of peptides. Despite widespread utilization, there are some potential limitations including epimerization and degradation under basic and acidic conditions, respectively. In this chapter, we present the synthetic method to build thio-precursors, their site-specific incorporation onto a growing peptide chain, and troubleshooting during the elongation of thioamidated peptides. This highly efficient, rapid, and robust method can be used for positional scanning of the thioamide bond.

Incorporating thioamides into proteins by native chemical ligation

The thioamide is a versatile replacement of the peptide backbone with altered hydrogen bonding and conformational preferences, as well the ability participate in energy and electron transfer processes. Semi-synthetic incorporation of a thioamide into a protein can be used to study protein folding or protein/protein interactions using these properties. Semi-synthesis also provides the opportunity to study the role of thioamides in natural proteins. Here we outline the semi-synthesis of a model protein, the B1 domain of protein G (GB1) with a thioamide at the N-terminus or the C-terminus. The thioamide is synthetically incorporated into a fragment by solid-phase peptide synthesis, whereas the remainder of the protein is recombinantly expressed. Then, the two fragments are joined by native chemical ligation. The explicit protocol for GB1 synthesis is accompanied by examples of applications with GB1 and other proteins in structural biology and protein misfolding studies.

Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics

Recent years have seen a growing number of examples of designed oligomeric molecules with artificial backbone connectivity that are capable of adopting complex folded tertiary structures analogous to those seen in natural proteins. A range of experimental techniques from structural biology and biophysics have been brought to bear in the study of these proteomimetic agents. Here, we discuss some considerations encountered in the characterization of high-resolution folded structure as well as folding thermodynamics of protein-like artificial backbones. We provide an overview of the use of X-ray crystallography and NMR spectroscopy in such systems and review example applications of these methods in the primary literature. Further, we provide detailed protocols for two experiments that have proved useful in our prior and ongoing efforts to compare folding thermodynamics between natural protein domains and heterogeneous-backbone counterparts.

Doubling Förster Resonance Energy Transfer Efficiency in Proteins with Extrinsic Thioamide Probes: Implications for Thiomodified Nucleobases

Designing a potential protein-ligand pair is pivotal, not only to track the protein structure dynamics, but also to assist in an atomistic understanding of drug delivery. Herein, the potential of a small model thioamide probe being used to study albumin proteins is reported. By monitoring the Förster resonance energy transfer (FRET) dynamics with the help of fluorescence spectroscopic techniques, a twofold enhancement in the FRET efficiency of 2-thiopyridone (2TPY), relative to that of its amide analogue, is observed. Molecular dynamics simulations depict the relative position of the free energy minimum to be quite stable in the case of 2TPY through noncovalent interactions with sulfur, which help to enhance the FRET efficiency. Finally, its application is shown by pairing thiouracils with protein. It is found that the site-selective sulfur atom substitution approach and noncovalent interactions with sulfur can substantially enhance the FRET efficiency, which could be a potential avenue to explore in the design of FRET probes to study the structure and dynamics of biomolecules.

Side-chain thioamides as fluorescence quenching probes

Thioamides, single atom oxygen-to-sulfur substitutions of canonical amide bonds, can be valuable probes for protein folding and protease studies. Here, we investigate the fluorescence quenching properties of thioamides incorporated into the side-chains of amino acids. We synthesize and incorporate Fmoc-protected, solid-phase peptide synthesis building blocks for introducing Nε -thioacetyl-lysine and γ-thioasparagine. Using rigid model peptides, we demonstrate the distance-dependent fluorescence quenching of these thioamides. Furthermore, we describe attempts to incorporate of Nε -thioacetyl-lysine into proteins expressed in Escherichia coli using amber codon suppression.

Nickel-catalyzed C-alkylation of thioamide, amides and esters by primary alcohols through a hydrogen autotransfer strategy

A simple catalyst of Ni(OAc)2 and P(t-Bu)3 enables selective C-alkylation of thioacetamides and primary acetamides with alcohols for the first time. Monoalkylation of thioamides, amides and t-butyl esters occurs in excellent yields (>95%). Mechanistic studies reveal that the reaction proceeds via a hydrogen autotransfer pathway.

Non-conventional Hydrogen Bonding and Aromaticity: A Systematic Study on Model Nucleobases and Their Solvated Clusters

The conceptual development of aromaticity is essential to rationalize and understand the structure and behavior of aromatic heterocycles. This work addresses for the first time, the interconnection between aromaticity and sulfur/selenium centered hydrogen bonds (S/SeCHBs) involved in representative heterocycle models of canonical nucleobases (2-Pyridone; 2PY) and its sulfur (2-Thiopyridone; 2TPY) and selenium (2-Selenopyridone; 2SePY) analogs. The nucleus-independent chemical shift (NICS) and gauge induced magnetic current density (GIMIC) values suggested significant reduction of aromaticity upon replacement of exocyclic carbonyl oxygen with sulfur and selenium. However, we observed two-fold (57 %) and three-fold (80 %) enhancement in the aromaticity for 2TPY dimer, and 2SePY dimer, respectively which are connected through S/SeCHBs. Aromaticity enhancement was also noticed in 1 : 1 H-bonded complexes (heterodimers), micro hydrated clusters and for bulk hydration. It is expected that exocyclic S and Se incorporation into heterocycles without compromising aromatic loss would definitely reinforce to design new supramolecular building blocks via S/SeCH-bonded complexes.

The Prodigious Hydrogen Bonds with Sulfur and Selenium in Molecular Assemblies, Structural Biology, and Functional Materials

Hydrogen bonds (H-bonds) play important roles in imparting functionality to the basic molecules of life by stabilizing their structures and directing their interactions. Numerous studies have been devoted to understanding H-bonds involving highly electronegative atoms like nitrogen, oxygen, and halogens and consequences of those H-bonds in chemical reactions, catalysis, and structure and function of biomolecules; but the involvement of less electronegative atoms like sulfur and selenium in H-bond formation establishes the concept of noncanonical H-bonds. Initially belittled for the "weak" nature of their interactions, these perceptions have gradually evolved over time through dedicated efforts by several research groups. This has been facilitated by advancements in experimental methods for their detection through gas-phase laser spectroscopy and solution NMR spectroscopy, as well as through theoretical predictions from high level quantum chemical calculations.In this Account, we present insights into the versatility of the sulfur and selenium centered H-bonds (S/SeCHBs) by highlighting their multifarious applications in various fields from chemical reactions to optoelectronic properties to structural biology. Our group has highlighted the significance and strength of such H-bonds in natural and modified biomolecules. Here, we have reviewed several molecular assemblies, biomolecules, and functional materials, where the role of these H-bonds is pivotal in influencing biological functions. It is worth mentioning here that the precise experimental data obtained from gas-phase laser spectroscopy have contributed considerably to changing the existing perceptions toward S/SeCHBs. Thus, molecular beam experiments, though difficult to perform on smaller model thio- or seleno-substituted Molecules, etc. (amides, nucleobases, drug molecules), are inevitable to gather elementary knowledge and convincing concepts on S/SeCHBs that can be extended from a small four-atom sulfanyl dimer to a large 14 kDa iron-sulfur protein, ferredoxin. These H-bonds can also tailor a fascinating array of molecular frameworks and design supramolecular assemblies by inter- and intralinking of individual "molecular Lego-like" units.The discussion is indeed intriguing when it turns to the usage of S/SeCHBs in facile synthetic strategies like tuning regioselectivity in reactions, as well as invoking phenomena like dual phosphorescence and chemiluminescence. This is in addition to our investigations of the dispersive nature of the hydrogen bond between metal hydrides and sulfur or selenium as acceptor, which we anticipate would lead to progress in the areas of proton and hydride transfer, as well as force-field design. This Account demonstrates how ease of fabrication, enhanced efficiency, and alteration of physicochemical properties of several functional materials is facilitated owing to the presence of S/SeCHBs. Our efforts have been instrumental in the evaluation of various S/SeCHBs in flue gas capture, as well as design of organic energy harvesting materials, where dipole moment and polarizability have important roles to play. We hope this Account invokes newer perspectives with regard to how H-bonds with sulfur and selenium can be adequately adopted for crystal engineering, for more photo- and biophysical studies with different spectroscopic methods, and for developing next-generation field-effect transistors, batteries, superconductors, and organic thin-film transistors, among many other multifunctional materials for the future.

Designed Synthesis of a 1D Polymer in Twist-Stacked Topology via Single-Crystal-to-Single-Crystal Polymerization

To synthesize a fully organic 1D polymer in a novel twist-stacked topology, we designed a peptide monomer HC≡CCH₂ -NH-Ile-Leu-N₃ , which crystallizes with its molecules H-bonded along a six-fold screw axis. These H-bonded columns pack parallelly such that molecules arrange head-to-tail, forming linear non-covalent chains in planes perpendicular to the screw axis. The chains arrange parallelly to form molecular layers which twist-stack along the screw axis. Crystals of this monomer, on heating, undergo single-crystal-to-single-crystal (SCSC) topochemical azide-alkyne cycloaddition (TAAC) polymerization to yield an exclusively 1,4-triazole-linked polymer in a twist-stacked layered topology. This topologically defined polymer shows better mechanical strength and thermal stability than its unordered form, as evidenced by nanoindentation studies and thermogravimetric analysis, respectively. This work illustrates the scope of topochemical polymerizations for synthesizing polymers in pre-decided topologies.

The structure and properties of MFG-E8 and the In vitro assessment of its toxic effects on myoblast cells

Four high-molecular-weight protein fractions of milk fat globule membrane (MFGM) were isolated from bovine milk. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), MALDI-TOF/TOF™ and Liquid chromatography electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) were used to measure the molecular sizes of the MFGM. Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD) were performed to determine the conformations of the MFGM. The results showed that the main protein (98.33%) in MFGM protein fraction 2 was Milk fat globule epidermal growth factor-VIII (MFG-E8), with a molecular weight of 47.82 kDa. The secondary structural component measurements showed that the MFG-E8 consisted of 5% helix, 70% sheet and 25% random coil, and the results matched well with the prediction by SSPro 5.1 bioinformatic analysis. The thermograms analysis revealed that Td and△H of MFG-E8 were 60.50°Cand 132.29 kJ/mol. The in vitro digestibility of MFG-E8 showed that it can be enzymatically hydrolyzed in the stomach and relatively stable in the intestinal fluid. The in vitro C₂C₁₂ and Caco2 cell activity tests indicated that MFG-E8 promoted the proliferation of C₂C₁₂ myoblast cells without cytotoxicity. The biological functional properties of MFG-E8 may be related to the fact that MFG-E8 possesses a high level of β-sheet structure. Our results suggested that MFG-E8 possesses broad prospects not only for use in functional food products but also as a source of natural anti-sarcopenia drugs.

Increasing protein stability by engineering the n → π* interaction at the β-turn

Abundant n → π* interactions between adjacent backbone carbonyl groups, identified by statistical analysis of protein structures, are predicted to play an important role in dictating the structure of proteins. However, experimentally testing the prediction in proteins has been challenging due to the weak nature of this interaction. By amplifying the strength of the n → π* interaction via amino acid substitution and thioamide incorporation at a solvent exposed β-turn within the GB1 proteins and Pin 1 WW domain, we demonstrate that an n → π* interaction increases the structural stability of proteins by restricting the ϕ torsion angle. Our results also suggest that amino acid side-chain identity and its rotameric conformation play an important and decisive role in dictating the strength of an n → π* interaction.

Amino acid residues adopt a right-handed α-helical conformation with increasing strength of the n → π* interaction. We also demonstrate a direct consequence of n → π* interactions on enhancing the structural stability of proteins.

Developing bioorthogonal probes to span a spectrum of reactivities

Bioorthogonal chemistries enable researchers to interrogate biomolecules in living systems. These reactions are highly selective and biocompatible and can be performed in many complex environments. However, like any organic transformation, there is no perfect bioorthogonal reaction. Choosing the "best fit" for a desired application is critical. Correspondingly, there must be a variety of chemistries-spanning a spectrum of rates and other features-to choose from. Over the past few years, significant strides have been made towards not only expanding the number of bioorthogonal chemistries, but also fine-tuning existing reactions for particular applications. In this Review, we highlight recent advances in bioorthogonal reaction development, focusing on how physical organic chemistry principles have guided probe design. The continued expansion of this toolset will provide more precisely tuned reagents for manipulating bonds in distinct environments.

Peptide Folding and Binding Probed by Systematic Non-canonical Mutagenesis

Many proteins and peptides fold upon binding another protein. Mutagenesis has proved an essential tool in the study of these multi-step molecular recognition processes. By comparing the biophysical behavior of carefully selected mutants, the concert of interactions and conformational changes that occur during folding and binding can be separated and assessed. Recently, this mutagenesis approach has been radically expanded by deep mutational scanning methods, which allow for many thousands of mutations to be examined in parallel. Furthermore, these high-throughput mutagenesis methods have been expanded to include mutations to non-canonical amino acids, returning peptide structure-activity relationships with unprecedented depth and detail. These developments are timely, as the insights they provide can guide the optimization of de novo cyclic peptides, a promising new modality for chemical probes and therapeutic agents.

Convenient synthesis of thioamidated peptides and proteins

The unique physicochemical properties of a thioamide bond, which is an ideal isostere of an amide bond, have not been fully exploited because of the tedious synthesis of thionated amino acid building blocks. Here, we report a purification-free and highly efficient synthesis of thiobenzotriazolides of Fmoc-protected and orthogonally protected 20 naturally occurring amino acids including asparagine, glutamine, and histidine. The near-quantitative conversion to the respective thioamidated peptides on solid support demonstrates the robustness of the synthetic route. Furthermore, the unaltered incorporation efficiency of thiobenzotriazolides from their stock solution till 48 h suggests their compatibility toward automated peptide synthesis. Finally, utilizing an optimized cocktail of 2% DBU + 5% piperazine for fast Fmoc-deprotection, we report the synthesis of a thioamidated Pin1 WW domain and thioamidated GB1 directly on solid support.

Studies of Thioamide Effects on Serine Protease Activity Enable Two-Site Stabilization of Cancer Imaging Peptides

Thioamide substitutions in peptides can be used as fluorescence quenchers in protease sensors and as stabilizing modifications of hormone analogs. To guide these applications in the context of serine proteases, we here examine the cleavage of several model substrates, scanning a thioamide between the P3 and P3' positions, and identify perturbing positions for thioamide substitution. While all serine proteases tested were affected by P1 thioamidation, certain proteases were also significantly affected by other thioamide positions. We demonstrate how these findings can be applied by harnessing the combined P3/P1 effect of a single thioamide on kallikrein proteolysis to protect two key positions in a neuropeptide Y-based imaging probe, increasing its serum half-life to >24 h while maintaining potency for binding to Y1 receptor expressing cells. Such stabilized peptide probes could find application in imaging cell populations in animal models or even in clinical applications such as fluorescence-guided surgery.

Selenoamides modulate dipole-dipole interactions in hydrogen bonded supramolecular polymers of 1,3,5-substituted benzenes

We report the synthesis and self-assembly behavior of a chiral C₃-symmetrical benzene-tricarboselenoamide. The introduction of the selenoamide moiety enhances the dipolar character of the supramolecular interaction and confers a remarkable thermal stability to the supramolecular polymers obtained.

Intramolecular van der Waals Interactions Challenge Anion Binding in perthio-Bambusurils

Bambusurils (BUs) are known to be rigid cavitands that feature an extended, jigger-like conformation, and the BU[6]s strongly bind anions within their hydrophobic cavity. These features are not necessarily shared by the family of perthio-BUs. This study reveals that perthio-BUs assume a compact conformation and perthio-BU[6]s are poor anion binders, crystallizing as anion-free species from solutions containing halide salts. Computational studies show that the equatorial sulfur atoms compete against guest anions for binding with the glycoluril methine groups via strong van der Waals (vdW) attractive interactions. These competitive contacts not only account for the diminished anion-binding of perthio-BUs, but also explain their compact conformation. The semithio- and perthio-BU[4]s form linear coordination polymers with Hg^II in the solid-state regardless of their intrinsic molecular conformation. The strong involvement of sulfur atoms in intramolecular interactions differentiates the equatorial from the axial (peripheral) heteroatoms, thus offering chemoselective and regioselective transformations.

Broad-Band Ultraviolet CD Spectroscopy of Ultrafast Peptide Backbone Conformational Dynamics

The far-UV spectral window widely used for the conformational analysis of biomolecules is not easily covered with broad-band lasers. This has made it difficult to use circular dichroism (CD) spectroscopy to directly follow fast structure changes. By combining transient CD spectroscopy in the deep-UV with thioamide substitution, we demonstrate a method to overcome this difficulty. We investigated a dipeptide whose two carbonyl oxygen atoms were replaced by sulfur, red-shifting the strong lowest-lying ππ* transitions into the more accessible 250-370 nm spectral window. Coupling of the two thioamide units cannot be resolved by achiral 2D-UV spectroscopy, but it gives rise to a pronounced bisignate CD spectrum. The transient CD spectra reveal weakening of this coupling in the electronically excited state, where conformational constraints are released. Our results show that direct local probing of fast backbone conformational change via CD spectroscopy is possible in combination with site-selective thio substitution in peptides and proteins.

Biosynthesis and Chemical Applications of Thioamides

Thioamidation as a posttranslational modification is exceptionally rare, with only a few reported natural products and exactly one known protein example (methyl-coenzyme M reductase from methane-metabolizing archaea). Recently, there has been significant progress in elucidating the biosynthesis and function of several thioamide-containing natural compounds. Separate developments in the chemical installation of thioamides into peptides and proteins have enabled cell biology and biophysical studies to advance the current understanding of natural thioamides. This review highlights the various strategies used by Nature to install thioamides in peptidic scaffolds and the potential functions of this rare but important modification. We also discuss synthetic methods used for the site-selective incorporation of thioamides into polypeptides with a brief discussion of the physicochemical implications. This account will serve as a foundation for the further study of thioamides in natural products and their various applications.