Energetics of an n --> pi interaction that impacts protein structure

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.

Pseudodiproline (Pro-Cyp) Oligomers Fold into Helical Polyproline Type secondary structures

The synthesis and conformational properties of oligo-proline mimetics composed of dimeric and tetrameric Pro-Cyp constructs linked by a hydroxymethylene unit are reported. Oligomers were studied both in the solid state and in solution, unveiling right-handed helical conformation depending on the configuration of the vicinally substituted trans-cyclopentane carboxylic acid unit (Cyp). Unlike polyproline oligomers, the alternating synthetic Pro-Cyp counterparts are not stabilized by n-π* interactions but rely instead on the steric demands of the extended backbone conformation within the hydroxymethylene-linked Pro-Cyp repeating units.

Probing Non-Covalent Interactions through Molecular Balances: A REG-IQA Study

The interaction energies of two series of molecular balances (1-X with X = H, Me, OMe, NMe2 and 2-Y with Y = H, CN, NO2, OMe, NMe2) designed to probe carbonyl…carbonyl interactions were analysed at the B3LYP/6-311++G(d,p)-D3 level of theory using the energy partitioning method of Interacting Quantum Atoms/Fragments (IQA/IQF). The partitioned energies are analysed by the Relative Energy Gradient (REG) method, which calculates the correlation between these energies and the total energy of a system, thereby explaining the role atoms have in the energetic behaviour of the total system. The traditional "back-of-the-envelope" open and closed conformations of molecular balances do not correspond to those of the lowest energy. Hence, more care needs to be taken when considering which geometries to use for comparison with the experiment. The REG-IQA method shows that the 1-H and 1-OMe balances behave differently to the 1-Me and 1-NMe2 balances because the latter show more prominent electrostatics between carbonyl groups and undergoes a larger dihedral rotation due to the bulkiness of the functional groups. For the 2-Y balance, REG-IQA shows the same behaviour across the series as the 1-H and 1-OMe balances. From an atomistic point of view, the formation of the closed conformer is favoured by polarisation and charge-transfer effects on the amide bond across all balances and is counterbalanced by a de-pyramidalisation of the amide nitrogen. Moreover, focusing on the oxygen of the amide carbonyl and the α-carbon of the remaining carbonyl group, electrostatics have a major role in the formation of the closed conformer, which goes against the well-known n-π* interaction orbital overlap concept. However, REG-IQF shows that exchange-correlation energies overtake electrostatics for all the 2-Y balances when working with fragments around the carbonyl groups, while they act on par with electrostatics for the 1-OMe and 1-NMe2. REG-IQF also shows that exchange-correlation energies in the 2-Y balance are correlated to the inductive electron-donating and -withdrawing trends on aromatic groups. We demonstrate that methods such as REG-IQA/IQF can help with the fine-tuning of molecular balances prior to the experiment and that the energies that govern the probed interactions are highly dependent on the atoms and functional groups involved.

Molecular orbital and topological electron density study of n → π* interactions: amides and thioamides cases

The n → π* interactions were studied in amides and thioamides systems models, through the analysis of the electron density topology along with the Natural Bonding Orbital (NBO) approach. The effect of the dispersion terms was assessed using different DFT functionals. The NBO, independent gradient model (IGM), and the analysis of the reduced density gradient outcomes show that dispersion forces play a significant role in the strength of n → π* interactions. The IGM results indicate that δg height values for n → π* interactions do not extend beyond 0.025. All the methods used in this work predict that n → π* interaction between pairs of thioamides is stronger than those between amides. However, the electron density topology-based methods were not able to replicate the trends in the relative force of this interaction found in the experimental and NBO results.

An Inherent Difference between Serine and Threonine Phosphorylation: Phosphothreonine Strongly Prefers a Highly Ordered, Compact, Cyclic Conformation

Phosphorylation and dephosphorylation of proteins by kinases and phosphatases are central to cellular responses and function. The structural effects of serine and threonine phosphorylation were examined in peptides and in proteins, by circular dichroism, NMR spectroscopy, bioinformatics analysis of the PDB, small-molecule X-ray crystallography, and computational investigations. Phosphorylation of both serine and threonine residues induces substantial conformational restriction in their physiologically more important dianionic forms. Threonine exhibits a particularly strong disorder-to-order transition upon phosphorylation, with dianionic phosphothreonine preferentially adopting a cyclic conformation with restricted ϕ (ϕ ∼ -60°) stabilized by three noncovalent interactions: a strong intraresidue phosphate-amide hydrogen bond, an n → π* interaction between consecutive carbonyls, and an n → σ* interaction between the phosphate Oγ lone pair and the antibonding orbital of C-Hβ that restricts the χ2 side-chain conformation. Proline is unique among the canonical amino acids for its covalent cyclization on the backbone. Phosphothreonine can mimic proline's backbone cyclization via noncovalent interactions. The preferred torsions of dianionic phosphothreonine are ϕ,ψ = polyproline II helix > α-helix (ϕ ∼ -60°); χ1 = g-; χ2 ∼ +115° (eclipsed C-H/O-P bonds). This structural signature is observed in diverse proteins, including in the activation loops of protein kinases and in protein-protein interactions. In total, these results suggest a structural basis for the differential use and evolution of threonine versus serine phosphorylation sites in proteins, with serine phosphorylation typically inducing smaller, rheostat-like changes, versus threonine phosphorylation promoting larger, step function-like switches, in proteins.

Cyclic peptides target the aromatic cage of a PHD-finger reader domain to modulate epigenetic protein function

Plant homeodomain fingers (PHD-fingers) are a family of reader domains that can recruit epigenetic proteins to specific histone modification sites. Many PHD-fingers recognise methylated lysines on histone tails and play crucial roles in transcriptional regulation, with their dysregulation linked to various human diseases. Despite their biological importance, chemical inhibitors for targeting PHD-fingers are very limited. Here we report a potent and selective de novo cyclic peptide inhibitor (OC9) targeting the Nε-trimethyllysine-binding PHD-fingers of the KDM7 histone demethylases, developed using mRNA display. OC9 disrupts PHD-finger interaction with histone H3K4me3 by engaging the Nε-methyllysine-binding aromatic cage through a valine, revealing a new non-lysine recognition motif for the PHD-fingers that does not require cation-π interaction. PHD-finger inhibition by OC9 impacted JmjC-domain mediated demethylase activity at H3K9me2, leading to inhibition of KDM7B (PHF8) but stimulation of KDM7A (KIAA1718), representing a new approach for selective allosteric modulation of demethylase activity. Chemoproteomic analysis showed selective engagement of OC9 with KDM7s in T cell lymphoblastic lymphoma SUP T1 cells. Our results highlight the utility of mRNA-display derived cyclic peptides for targeting challenging epigenetic reader proteins to probe their biology, and the broader potential of this approach for targeting protein-protein interactions.

Skeletal Ring Contractions via I(I)/I(III) Catalysis: Stereoselective Synthesis of cis-α,α-Difluorocyclopropanes

The clinical success of α,α-difluorocyclopropanes, combined with limitations in the existing synthesis portfolio, inspired the development of an operationally simple, organocatalysis-based strategy to access cis-configured derivatives with high levels of stereoselectivity (up to >20:1 cis:trans). Leveraging an I(I)/I(III)-catalysis platform in the presence of an inexpensive HF source, it has been possible to exploit disubstituted bicyclobutanes (BCBs) as masked cyclobutene equivalents for this purpose. In situ generation of this strained alkene, enabled by Brønsted acid activation, facilitates an unprecedented 4 → 3 fluorinative ring contraction, to furnish cis-α,α-difluorinated cyclopropanes in a highly stereoselective manner (up to 88% yield). Mechanistic studies are disclosed together with conformational analysis (X-ray crystallography and NMR) to validate cis-α,α-difluorocyclopropanes as isosteres of the 1,4-dicarbonyl moiety. Given the importance of this unit in biology and the foundational n_o → π* interactions that manifest themselves in this conformation (e.g., collagen), it is envisaged that the title motif will find application in focused molecular design.

Understanding the n → π* non-covalent interaction using different experimental and theoretical approaches

Herein, a perspective on the recent understanding of weak n → π* interaction obtained using different experimental and theoretical approaches is presented. This interaction is purely an orbital interaction that involves the delocalization of the lone pair electrons (n) on nitrogen, oxygen, and sulfur to the π* orbitals of CO, CN, and aromatic rings. The n → π* interaction has been found to profoundly influence the stabilization of peptides, proteins, drugs, and various small molecules. Although the functional properties of this non-covalent interaction are still quite underestimated, there are recent demonstrations of applying this interaction to the regulation of synthetic chemistry, catalysis, and molecular recognition. However, the identification and quantification of the n → π* interaction remain a demanding task as this interaction is quite weak and based on the electron delocalization between the two orbitals, while hyperconjugation interactions between neighboring atoms and the group involved in the n → π* interaction are simultaneously present. This review provides a comprehensive picture of understanding the n → π* interaction using different experimental approaches such as the X-ray diffraction technique, and electronic, NMR, microwave, and IR spectroscopy, in addition to quantum chemistry calculations. A detailed understanding of the n → π* interaction can help in modulating the strength of this interaction, which will be further helpful in designing efficient drugs, synthetic peptides, peptidomimetics, etc.

Solvation stabilizes intercarbonyl n→π* interactions and polyproline II helix

n→π* interactions between consecutive carbonyls stabilize the α-helix and polyproline II helix (PPII) conformations in proteins. n→π* interactions have been suggested to provide significant conformational biases to the disordered states of proteins. To understand the roles of solvation on the strength of n→π* interactions, computational investigations were conducted on a model n→π* interaction, the twisted-parallel-offset formaldehyde dimer, as a function of explicit solvation of the donor and acceptor carbonyls, using water and HF. In addition, the effects of urea, thiourea, guanidinium, and monovalent cations on n→π* interaction strength were examined. Solvation of the acceptor carbonyl significantly strengthens the n→π* interaction, while solvation of the donor carbonyl only modestly weakens the n→π* interaction. The n→π* interaction strength was maximized with two solvent molecules on the acceptor carbonyl. Urea stabilized the n→π* interaction via simultaneous engagement of both oxygen lone pairs on the acceptor carbonyl. Solvent effects were further investigated in the model peptides Ac-Pro-NMe₂, Ac-Ala-NMe₂, and Ac-Pro₂-NMe₂. Solvent effects in peptides were similar to those in the formaldehyde dimer, with solvation of the acceptor carbonyl increasing n→π* interaction strength and resulting in more compact conformations, in both the proline endo and exo ring puckers, as well as a reduction in the energy difference between these ring puckers. Carbonyl solvation leads to an energetic preference for PPII over both the α-helix and β/extended conformations, consistent with experimental data that protic solvents and protein denaturants both promote PPII. Solvation of the acceptor carbonyl weakens the intraresidue C5 hydrogen bond that stabilizes the β conformation.

Leveraging the n→π* Interaction in Alkene Isomerization by Selective Energy Transfer Catalysis

Examples of geometric alkene isomerization in nature are often limited to the net exergonic direction (ΔG°<0), with the antipodal net endergonic processes (ΔG°>0) comparatively under-represented. Inspired by the expansiveness of the maleate to fumarate (Z→E) isomerization in biochemistry, we investigated the inverse E→Z variant to validate nO →πC=O * interactions as a driving force for contra-thermodynamic isomerization. A general protocol involving selective energy transfer catalysis with inexpensive thioxanthone as a sensitizer (λmax =402 nm) is disclosed. Whilst in the enzymatic process nO →πC=O * interactions commonly manifest themselves in the substrate, these same interactions are shown to underpin directionality in the antipodal reaction by shortening the product alkene chromophore. The process was validated with diverse fumarate derivatives (>30 examples, up to Z:E>99:1), including the first examples of tetrasubstituted alkenes, and the involvement of nO →πC=O * interactions was confirmed by X-ray crystallography.

Facile synthesis of eight-membered cyclic(ester-amide)s and their organocatalytic ring-opening polymerizations

Facile modular synthesis of eight-membered cyclic(ester-amide)s based on phthalic anhydride and β-amino alcohols and organocatalitic ROP of the monomers to afford degradable semi-aromatic poly(ester-amides)s with tunable thermal properties.

Deciphering the Backbone Noncovalent Interactions that Stabilize Polyproline II Conformation and Reduce cis Proline Abundance in Polyproline Tracts

Proline (Pro) has a higher propensity to adopt cis amide geometry than the other natural amino acids, and a poly-Pro (poly-P) tract can adopt either a polyproline I (PPI, all cis amide) or a polyproline II (PPII, all trans amide) helical conformation. Recent studies have revealed a reduced abundance of cis amide geometry among the inner Pro residues of a poly-P tract. However, the forces that stabilize the polyproline helices and the reason for the higher trans amide propensity of the inner Pro residues of a poly-P tract are poorly understood. Herein, we have studied both Pro and non-Pro PPII helical sequences and identified the backbone noncovalent interactions that are crucial to the higher stability of the trans Pro-amide geometry and the preference for a PPII helical conformation. We show the presence of reciprocal CO···CO interactions that extend over the whole PPII helical region. Interestingly, the CO···CO interactions strengthen with the increase in the PPII helical chain length and the inner CO groups possess stronger CO···CO interactions, which could explain the reduced cis abundance of the inner Pro residues of a poly-P tract. We also identified a much stronger (∼0.9 kcal·mol^-1) n_O → σ*_Cα-Cβ interaction between the N-terminal CO oxygen lone pair and the antibonding orbital (σ*) of their C_α-C_β bonds. As the n_O → σ*_Cα-Cβ interaction is possible only in the trans isomers of Pro, this interaction should be crucial for the stabilization of a PPII helix. Finally, an unusual n_N(amide) → σ*_C-N interaction (∼0.3 kcal·mol^-1) was observed between the peptidic nitrogen lone pair (n_N) and the antibonding orbital (σ*_C-N) of the subsequent C-terminal peptide C-N bond. We propose a cumulative effect of these interactions in the stabilization of a PPII helix.

Magnetically Recyclable Graphene Oxide Demulsifier Adapting Wide pH Conditions on Detachment of Oil in the Crude Oil-in-Water Emulsion

In the present work, an amphiphilic and magnetically recyclable graphene oxide (MR-GO) demulsifier was devised and synthesized by graft of magnetic nanoparticles (Fe₃O₄@SiO₂-APTES) and ethylenediamine on the GO surface. The wettability and surface charges of MR-GO under various pH conditions can be regulated via adjusting the contents and species of surface functional groups (such as amino, carboxyl, and hydroxyl). In the demulsificaition test, MR-GO displayed favorable demulsification performance for crude oil-in-water (O/W) emulsion under pH of 2.0-10.0, thusly greatly improving the application scope of common demulsifier. The optimal dosage of MR-GO was 200 mg/L and the demulsification efficiency attained a maximum value of 99.7% for crude O/W emulsion with pH of 6.0. What's more, owing to its magnetic response performance, the MR-GO can be reused and the demulsification efficiency remained above 91.0% after six cycles. Based on the strong interfacial activity, MR-GO can arrive to the crude oil-water interface. With the synergy effects of interfacial adsorption (π-π/n-π) interactions and electrostatic attraction of demulsifier and interfacial films, and the aid of external mechanical forces, the interfacial films stabilized the emulsion were disrupted. Therefore, the oil droplets coated on the water droplets were gathered rapidly to form oily flocs and then migrated to the water surface to accomplish the demulsification of crude O/W emulsion.

Spectroscopic evidence of n → π* interactions involving carbonyl groups

n → π* has emerged as an important noncovalent interaction that can affect the conformations of both small- and macromolecules including peptides and proteins. Carbonyl-carbonyl (COCO) n → π* interactions involving CO groups are well studied. Recent studies have shown that the COCO n → π* interactions are the most abundant secondary interactions in proteins with a frequency of 33 interactions per 100 residues and, among the various secondary interactions, n → π* interactions are expected to provide the highest enthalpic contributions to the conformational stability of globular proteins. However, n → π* interactions are relatively weak and provide an average stabilization of about 0.25 kcal mol-1 per interaction in proteins. The strongest n → π* interaction could be as strong as a moderate hydrogen bond. Therefore, it is challenging to detect and quantify these weak interactions, especially in solution in the presence of perturbation from other intermolecular interactions. Accordingly, spectroscopic investigations that can provide direct evidence of n → π* interaction are limited, and the majority of papers published in this area have relied on X-ray crystallography and/or theoretical calculations to establish the presence of this interaction. The aim of this perspective is to discuss the studies where a spectroscopic signature in support of n → π* interaction was observed. As the "n → π* interaction" is a relatively new terminology, there remains the possibility of there being earlier studies where spectroscopic evidence for n → π* interactions was obtained but it was not discussed in light of the n → π* terminology. We noticed several such studies and, as can be expected, these studies were often overlooked in the discussion of n → π* interactions in the recent literature. In this perspective, we have also discussed these studies and provided computational support for the presence of n → π* interaction.

Therapeutic peptides for the treatment of cystic fibrosis: Challenges and perspectives

Cystic fibrosis (CF) is the most common amongst rare genetic diseases, affecting more than 70.000 people worldwide. CF is characterized by a dysfunctional chloride channel, termed cystic fibrosis conductance regulator (CFTR), which leads to the production of a thick and viscous mucus layer that clogs the lungs of CF patients and traps pathogens, leading to chronic infections and inflammation and, ultimately, lung damage. In recent years, the use of peptides for the treatment of respiratory diseases, including CF, has gained growing interest. Therapeutic peptides for CF include antimicrobial peptides, inhibitors of proteases, and modulators of ion channels, among others. Peptides display unique features that make them appealing candidates for clinical translation, like specificity of action, high efficacy, and low toxicity. Nevertheless, the intrinsic properties of peptides, together with the need of delivering these compounds locally, e.g. by inhalation, raise a number of concerns in the development of peptide therapeutics for CF lung disease. In this review, we discuss the challenges related to the use of peptides for the treatment of CF lung disease through inhalation, which include retention within mucus, proteolysis, immunogenicity and aggregation. Strategies for overcoming major shortcomings of peptide therapeutics will be presented, together with recent developments in peptide design and optimization, including computational analysis and high-throughput screening.

Quantifying Interactions and Solvent Effects Using Molecular Balances and Model Complexes

Where the basic units of molecular chemistry are the bonds within molecules, supramolecular chemistry is based on the interactions that occur between molecules. Understanding the "how" and "why" of the processes that govern molecular self-assembly remains an open challenge to the supramolecular community. While many interactions are readily examined in silico through electronic structure calculations, such insights may not be directly applicable to experimentalists. The practical limitations of computationally accounting for solvation is perhaps the largest bottleneck in this regard, with implicit solvation models failing to comprehensively account for the specific nature of solvent effects and explicit models incurring a prohibitively high computational cost. Since molecular recognition processes usually occur in solution, insight into the nature and effect of solvation is imperative not only for understanding these phenomena but also for the rational design of systems that exploit them.Molecular balances and supramolecular complexes have emerged as useful tools for the experimental dissection of the physicochemical basis of various noncovalent interactions, but they have historically been underexploited as a platform for the evaluation of solvent effects. Contrasting with large biological complexes, smaller synthetic model systems enable combined experimental and computational analyses, often facilitating theoretical analyses that can work in concert with experiment.Our research has focused on the development of supramolecular systems to evaluate the role of solvents in molecular recognition, and further characterize the underlying mechanisms by which molecules associate. In particular, the use of molecular balances has provided a framework to measure the magnitude of solvent effects and to examine the accuracy of solvent models. Such approaches have revealed how solvation can modulate the electronic landscape of a molecule and how competitive solvation and solvent cohesion can provide thermodynamic driving forces for association. Moreover, the use of simple model systems facilitates the interrogation and further dissection of the physicochemical origins of molecular recognition. This tandem experimental/computational approach has married less common computational techniques, like symmetry adapted perturbation theory (SAPT) and natural bonding orbital (NBO) analysis, with experimental observations to elucidate the influence of effects that are difficult to resolve experimentally (e.g., London dispersion and electron delocalization).

Reconciling Electrostatic and n→π* Orbital Contributions in Carbonyl Interactions

Interactions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance-dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short-range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O⋅⋅⋅C=O interactions.

Electronic and Steric Control of n→π* Interactions: Stabilization of the α-Helix Conformation without a Hydrogen Bond

The preferred conformations of peptides and proteins are dependent on local interactions that bias the conformational ensemble. The n→π* interaction between consecutive carbonyls promotes compact conformations, including the α-helix and polyproline II helix. In order to further understand the n→π* interaction and to develop methods to promote defined conformational preferences through acyl N-capping motifs, a series of peptides was synthesized in which the electronic and steric properties of the acyl group were modified. Using NMR spectroscopy, van't Hoff analysis of enthalpies, X-ray crystallography, and computational investigations, we observed that more electron-rich donor carbonyls (pivaloyl, iso-butyryl, propionyl) promote stronger n→π* interactions and more compact conformations than acetyl or less electron-rich donor carbonyls (methoxyacetyl, fluoroacetyl, formyl). X-ray crystallography indicates a strong, electronically tunable preference for the α-helix conformation, as observed directly on the φ and ψ torsion angles. Electron-donating acyl groups promote the α-helical conformation, even in the absence of the hydrogen bonding that stabilizes the α-helix. In contrast, electron-withdrawing acyl groups led to more extended conformations. More sterically demanding groups can promote trans amide bonds independent of the electronic effect on n→π* interactions. Chloroacetyl groups additionally promote n→π* interactions through the interaction of the chlorine lone pair with the proximal carbonyl π*. These data provide additional support for an important role of n→π* interactions in the conformational ensemble of disordered or unfolded proteins. Moreover, this work suggests that readily incorporated acyl N-capping motifs that modulate n→π* interactions may be employed rationally to promote conformational biases in peptides, with potential applications in molecular design and medicinal chemistry.

Conformational Analysis of n→π* Interactions in Collagen Triple Helix Models

Ab initio calculations of three models of collagen at positions Pro-Pro-Gly (1), Pro-Gly-Pro (2), and Gly-Pro-Pro (3) were performed to assess the conformational variation of n→π* contributions to the stability of the collagen triple helix. Full conformational analyses by relaxed potential-energy scans of the Ψ dihedral angle of the central residue in models 1, 2, and 3 revealed the presence of several n→π* interactions. In model 2, with Gly as the central residue, both the Φ and Ψ dihedral angles of Gly were scanned. Most minima of each model contained one or two n→π* interactions, with pyramidalization at the π* carbon. We also observed pyramidalization at the n→π* donor amide nitrogens. Minima with hydrogen-bond or non-native n→π* interactions compete with the collagen stabilizing n→π* interactions. The collagen-like n→ re-π* conformation was found as the global minimum only in model 3. The global minimum of 1 had a 5-membered ring hydrogen bond with an additional weak n→ si-π* interaction. The global minimum of 2 was in the extended conformation. We predict that the n→π* interactions found in native collagen, while individually small, cumulatively contribute to the stability of the triple helix conformation of collagen.

Interplay between hydrogen bonding and n→π* interaction in an analgesic drug salicin

The competition and cooperation between weak intermolecular interactions are important in determining the conformational preferences of molecules. Understanding the relative strengths of these effects in the context of potential drug candidates is therefore essential. We use a combination of gas-phase spectroscopy and quantum-chemical calculations to elucidate the nature of such interactions for the analgesic salicin [2-(hydroxymethyl)phenyl β-d-glucopyranoside], an analog of aspirin found in willow bark. Of several possible conformers, only three are observed experimentally, and these are found to correspond with the three lowest energy conformers obtained from density functional theory calculations and simulated Franck-Condon spectra. Natural bond orbital analyses show that these are characterized by a subtle interplay between weak n→π* interaction and conventional strong hydrogen bond, with additional insights into this interaction provided by analysis of quantum theory of atoms in molecules and symmetry-adapted perturbation theory calculations. In contrast, the higher energy conformers, which are not observed experimentally, are mostly stabilized by the hydrogen bond with negligible contribution of n→π* interaction. The n→π* interaction results in a preference for the benzyl alcohol group of salicin to adopt a gauche conformation, a characteristic also found when salicin is bound to the β-glucosidase enzyme. As such, understanding the interplay between these weak interactions has significance in the rationalization of protein structures.

Peptide Solubility Limits: Backbone and Side-Chain Interactions

We calculate the solubility limit of pentapeptides in water by simulating the phase separation in an oversaturated aqueous solution. The solubility limit order followed by our model peptides (GGRGG > GGDGG > GGGGG > GGVGG > GGQGG > GGNGG > GGFGG) is found to be the same as that reported for amino acid monomers from experiment (R > D > G > V > Q > N > F). Investigation of dynamical properties of peptides shows that the higher the solubility of a peptide is, the lower the time spent by the peptide in the aggregated cluster is. We also demonstrate that fluctuations in conformation and hydration number of peptide in monomeric form are correlated with the solubility of the peptide. We considered energetic mechanisms and dynamical properties of interbackbone CO-CO and CO···HN interactions. Our results confirm that CO-CO interactions more than the interbackbone H-bonds are important in peptide self-assembly and association. Further, we find that the stability of H-bonded peptide pairs arises mainly from coexisting CO-CO and CO···HN interactions.

Characterization of the short OC⋯OC π-hole tetrel bond in the solid state

An in-depth structure database investigation and experimental charge density analysis of the OC⋯OC π-hole tetrel bonds.

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

Fluorinated moieties are highly valuable to chemists due to the sensitive NMR detectability of the 19F nucleus. Fluorination of molecular scaffolds can also selectively influence a molecule's polarity, conformational preferences and chemical reactivity, properties that can be exploited for various chemical applications. A powerful route for incorporating fluorine atoms in biomolecules is last-stage fluorination of peptide scaffolds. One of these methods involves esterification of the C-terminus of peptides using a diazomethane species. Here, we provide an investigation of the physicochemical consequences of peptide esterification with partially fluorinated ethyl groups. Derivatives of N-acetylproline are used to model the effects of fluorination on the lipophilicity, hydrolytic stability and on conformational properties. The conformational impact of the 2,2-difluoromethyl ester on several neutral and charged oligopeptides was also investigated. Our results demonstrate that partially fluorinated esters undergo variable hydrolysis in biologically relevant buffers. The hydrolytic stability can be tailored over a broad pH range by varying the number of fluorine atoms in the ester moiety or by introducing adjacent charges in the peptide sequence.

The n→π* Interaction

The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group. Mixing of these orbitals releases energy, resulting in an attractive interaction. Hints of such interactions were evident in small-molecule crystal structures as early as the 1970s, but not until 2001 was the role of such interactions articulated clearly. These non-covalent interactions were first discovered during investigations into the thermostability of the proline-rich protein collagen, which achieves a robust structure despite a relatively low potential for hydrogen bonding. It was found that by modulating the distance between two carbonyl groups in the peptide backbone, one could alter the conformational preferences of a peptide bond to proline. Specifically, only the trans conformation of a peptide bond to proline allows for an attractive interaction with an adjacent carbonyl group, so when one increases the proximity of the two carbonyl groups, one enhances their interaction and promotes the trans conformation of the peptide bond, which increases the thermostability of collagen. More recently, attention has been paid to the nature of these interactions. Some have argued that rather than resulting from electron donation, carbonyl interactions are a particular example of dipolar interactions that are well-approximated by classical mechanics. However, experimental evidence has demonstrated otherwise. Numerous examples now exist where an increase in the dipole moment of a carbonyl group decreases the strength of its interactions with other carbonyl groups, demonstrating unequivocally that a dipolar mechanism is insufficient to describe these interactions. Rather, these interactions have important quantum-mechanical character that can be evaluated through careful experimental analysis and judicious use of computation. Although individual n→π* interactions are relatively weak (∼0.3-0.7 kcal/mol), the ubiquity of carbonyl groups across chemistry and biology gives the n→π* interaction broad impact. In particular, the n→π* interaction is likely to play an important role in dictating protein structure. Indeed, bioinformatics analysis suggests that approximately one-third of residues in folded proteins satisfy the geometric requirements to engage in an n→π* interaction, which is likely to be of particular importance for the α-helix. Other carbonyl-dense polymeric materials like polyesters and peptoids are also influenced by n→π* interactions, as are a variety of small molecules, some with particular medicinal importance. Research will continue to identify molecules whose conformation and activity are affected by the n→π* interaction and will clarify their specific contributions to the structures of biomacromolecules.

Influence of Hofmeister Ions on the Structure of Proline-Based Peptide Models: A Combined Experimental and Molecular Modeling Study

The influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The anions preferentially interact with the cis conformers of the peptide models, which is rationalized by the respective electrostatic potential surfaces. These preferred interactions have a strong impact on the thermodynamics of the cis/trans equilibria, leading to a higher population of the cis conformers. In distinct cases, these equilibria are nearly independent of temperature, showing that the salts are also able to stabilize the conformers over wide temperature ranges.

α-Aminoxy Peptoids: A Unique Peptoid Backbone with a Preference for cis-Amide Bonds

α-Peptoids, or N-substituted glycine oligomers, are an important class of peptidomimetic foldamers with proteolytic stability. Nevertheless, the presence of cis/trans-amide bond conformers, which contribute to the high flexibility of α-peptoids, is considered as a major drawback. A modified peptoid backbone with an improved control of the amide bond geometry could therefore help to overcome this limitation. Herein, we have performed the first thorough analysis of the folding propensities of α-aminoxy peptoids (or N-substituted 2-aminoxyacetic acid oligomers). To this end, the amide bond geometry and the conformational properties of a series of model α-aminoxy peptoids were investigated by using 1D and 2D NMR experiments, X-ray crystallography, natural bond orbital (NBO) analysis, circular dichroism (CD) spectroscopy, and molecular dynamics (MD) simulations revealing a unique preference for cis-amide bonds even in the absence of cis-directing side chains. The conformational analysis based on the MD simulations revealed that α-aminoxy peptoids can adopt helical conformations that can mimic the spatial arrangement of peptide side chains in a canonical α-helix. Given their ease of synthesis and conformational properties, α-aminoxy peptoids represent a new member of the peptoid family capable of controlling the amide isomerism while maintaining the potential for side-chain diversity.

Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structures

In this study, the solution structures of the homooligomers of a conformationally constrained bicyclic proline-type β-amino acid were studied by means of molecular dynamics (MD) calculations in explicit methanol and water using the umbrella sampling method. The ratio of trans-amide and cis-amide was estimated by NMR and the rotational barrier of the amide of acetylated bicyclic amino acid monomer was estimated by two-dimensional (2D) exchange spectroscopy (EXSY) or line-shape analysis. A bias potential was introduced with respect to the amide torsion angle ω to enhance conformational exchange including isomerization of amide bonds by lowering the rotation energy barrier. After determination of reweighting parameters to best reproduce the experimental results of the monomer amide, the free energy profile around the amide torsion angle ω was obtained from the MD trajectory by reweighting of the biased probability density. The MD simulation results support the existence of invertomers of nitrogen-pyramidalized amide. Furthermore, extended structures with a high fraction of trans-amide conformation appear to be increasingly stabilized as the oligomer is elongated, both in methanol and in water. Our conformational analysis of natural and non-natural tertiary-amide-based peptide oligomers indicates that these oligomers preferentially adopt a limited number of conformations.

Phosphorylation Increases Persistence Length and End-to-End Distance of a Segment of Tau Protein

Intrinsically disordered regions of proteins, which lack unique tertiary structure under physiological conditions, are enriched in phosphorylation sites and in significant local bias toward the polyproline II conformation. The overrepresented coincidence of this posttranslational regulatory signal and local conformational bias within unstructured regions raises a question: can phosphorylation serve to manipulate the conformational preferences of a disordered protein? In this study, we use time-resolved fluorescence resonance energy transfer and a, to our knowledge, novel data analysis method to directly measure the end-to-end distance distribution of a phosphorylatable peptide derived from the human microtubule associated protein tau. Our results show that phosphorylation at threonine or serine extends the end-to-end distance and increases the effective persistence length of the tested model peptides. Unexpectedly, the extension is independent of salt concentration, suggestive of a nonelectrostatic origin. The phosphorylation extension and stiffening effect provides a peptide-scale physical interpretation for the posttranslational regulation of the highly abundant protein-protein interactions found in disordered proteins, as well as a potential insight into the regulatory mechanism of the tau protein's microtubule binding activity.

4-ketoproline: An electrophilic proline analog for bioconjugation

Installing an electrophilic amino-acid residue can engender a peptide or protein with chemoselective reactivity. Such a modification to collagen, which is the most abundant protein in animals, could facilitate the development of new biomaterials. Collagen has an abundance of proline-like residues. Here, we report on the incorporation of an electrophilic proline congener, (2S)-4-ketoproline (Kep), into a collagen-mimetic peptide (CMP). An ab initio conformational analysis of Kep revealed its potential to be accommodated within a collagen triple helix. A synthetic CMP containing a Kep residue was indeed able to form a stable triple helix. Moreover, the condensation of its carbonyl group with aminooxy-biotin did not compromise the conformational stability of the triple helix. These data encourage the use of 4-ketoproline as an electrophilic congener of proline.

On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures

Protein structures are stabilized by a variety of noncovalent interactions (NCIs), including the hydrophobic effect, hydrogen bonds, electrostatic forces and van der Waals’ interactions. Our knowledge of the contributions of NCIs, and the interplay between them remains incomplete. This has implications for computational modeling of NCIs, and our ability to understand and predict protein structure, stability, and function. One consideration is the satisfaction of the full potential for NCIs made by backbone atoms. Most commonly, backbone‐carbonyl oxygen atoms located within α‐helices and β‐sheets are depicted as making a single hydrogen bond. However, there are two lone pairs of electrons to be satisfied for each of these atoms. To explore this, we used operational geometric definitions to generate an inventory of NCIs for backbone‐carbonyl oxygen atoms from a set of high‐resolution protein structures and associated molecular‐dynamics simulations in water. We included more‐recently appreciated, but weaker NCIs in our analysis, such as n→π* interactions, Cα‐H bonds and methyl‐H bonds. The data demonstrate balanced, dynamic systems for all proteins, with most backbone‐carbonyl oxygen atoms being satisfied by two NCIs most of the time. Combinations of NCIs made may correlate with secondary structure type, though in subtly different ways from traditional models of α‐ and β‐structure. In addition, we find examples of under‐ and over‐satisfied carbonyl‐oxygen atoms, and we identify both sequence‐dependent and sequence‐independent secondary‐structural motifs in which these reside. Our analysis provides a more‐detailed understanding of these contributors to protein structure and stability, which will be of use in protein modeling, engineering and design.

The n → π* interaction: a rapidly emerging non-covalent interaction

This perspective describes the current status of a recently discovered non-covalent interaction named as the n → π* interaction, which is very weak and counterintuitive in nature. In this review, we have provided a brief overview of the widespread presence of this interaction in biomacromolecules, small biomolecules and materials, as well as the physical nature of this interaction explored using various experimental and theoretical techniques. It has been found that this interaction is equally important to other non-covalent interactions for the stability and specific structures of biomolecules and materials. An in-depth understanding of this interaction can help in designing more efficient functional materials as well as drugs. The review also provides a future outlook in terms of exploring the detailed functional role of this interaction in biological processes and its direct spectroscopic evidence, which other commonly known non-covalent interactions (conventional hydrogen bonding, π-hydrogen bonding, π-stacking, etc.) have.

Mechanism for the enhanced reactivity of 4-mercaptoprolyl thioesters in native chemical ligation

Ring-strain-precluded strategy benefiting from entropy effects and n → π* orbital interaction, enhances the reactivity of C-terminal prolyl thioesters in NCL.

Energetic contribution to both acidity and conformational stability in peptide models

The acidity difference of the amide rotamers has been revised for a large set ofN-acetyl amino acids.

Sequence Programmable Peptoid Polymers for Diverse Materials Applications

Polymer sequence programmability is required for the diverse structures and complex properties that are achieved by native biological polymers, but efforts towards controlling the sequence of synthetic polymers are, by comparison, still in their infancy. Traditional polymers provide robust and chemically diverse materials, but synthetic control over their monomer sequences is limited. The modular and step-wise synthesis of peptoid polymers, on the other hand, allows for precise control over the monomer sequences, affording opportunities for these chains to fold into well-defined nanostructures. Hundreds of different side chains have been incorporated into peptoid polymers using efficient reaction chemistry, allowing for a seemingly infinite variety of possible synthetically accessible polymer sequences. Combinatorial discovery techniques have allowed the identification of functional polymers within large libraries of peptoids, and newly developed theoretical modeling tools specifically adapted for peptoids enable the future design of polymers with desired functions. Work towards controlling the three-dimensional structure of peptoids, from the conformation of the amide bond to the formation of protein-like tertiary structure, has and will continue to enable the construction of tunable and innovative nanomaterials that bridge the gap between natural and synthetic polymers.

Applications of Fluorine in Medicinal Chemistry

The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties associated with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a molecule can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addition, (18)F has been established as a useful positron emitting isotope for use with in vivo imaging technology that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compounds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compounds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug molecules and applications in positron emission tomography.

Aldehyde capture ligation for synthesis of native peptide bonds

Chemoselective reactions for amide bond formation have transformed the ability to access synthetic proteins and other bioconjugates through ligation of fragments. In these ligations, amide bond formation is accelerated by transient enforcement of an intramolecular reaction between the carboxyl and the amine termini of two fragments. Building on this principle, we introduce an aldehyde capture ligation that parlays the high chemoselective reactivity of aldehydes and amines to enforce amide bond formation between amino acid residues and peptides that are difficult to ligate by existing technologies.

Competition between n → π(Ar)* and conventional hydrogen bonding (N-H···N) interactions: an ab initio study of the complexes of 7-azaindole and fluorosubstituted pyridines

In this work, we have investigated a subtle competition between a very weak n → π(Ar)* interaction and a very strong hydrogen bond (N-H···N) interaction present in the complexes of 7-azaindole with a series of 2,6-substituted fluoropyridines and observed how the weak interaction modulates the overall structural motif of these complexes in the presence of the strong interaction. We have studied the structures and binding energies of these complexes using MP2 as well as dispersion-corrected DFT calculations. It has been found that the strength of the N-H···N interaction in these complexes decreases with increasing fluorination in the fluoropyridine ring while the proximity between the nitrogen atom in 7-azaindole and the aromatic ring of fluoropyridine increases through n → π(Ar)* interaction. Comparison of the binding energy values as well as structural parameters of these complexes calculated at the B3LYP level with those obtained at the MP2, M05-2X, and B97-D levels of theory clearly indicates that the dispersion effect is mostly responsible for this attractive n → π(Ar)* interaction. This conclusion is also supported by localized molecular orbital-energy decomposition analysis (LMO-EDA). The current investigation is the first theoretical study on the n → π(Ar)* interaction in the presence of a conventional strong hydrogen bonding interaction in the molecular system. Thus the present study has great significance for understanding the structures of the biomolecules as well as materials, as these interactions are very often present there simultaneously.