Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein

One of the entry mechanisms of the SARS-CoV-2 coronavirus into host cells involves endosomal acidification. It has been proposed that under acidic conditions, the fusion peptide proximal region (FPPR) of the SARS-CoV-2 spike glycoprotein acts as a pH-dependent switch, modulating immune response accessibility by influencing the positioning of the receptor binding domain (RBD). This would provide indirect coupling of RBD opening to the environmental pH. Here, we explored this possible pH-dependent conformational equilibrium of the FPPR within the SARS-CoV-2 spike glycoprotein. We analyzed hundreds of experimentally determined spike structures from the Protein Data Bank and carried out pH-replica exchange molecular dynamics to explore the extent to which the FPPR conformation depends on pH and the positioning of the RBD. A meta-analysis of experimental structures identified alternate conformations of the FPPR among structures in which this flexible regions was resolved. However, the results did not support a correlation between the FPPR conformation and either RBD position or the reported pH of the cryo-EM experiment. We calculated pKa values for titratable side chains in the FPPR region using PDB structures, but these pKa values showed large differences between alternate PDB structures that otherwise adopt the same FPPR conformation type. This hampers the comparison of pKa values in different FPPR conformations to rationalize a pH-dependent conformational change. We supplemented these PDB-based analyses with all-atom simulations and used constant-pH replica exchange molecular dynamics to estimate pKa values in the context of flexibility and explicit water. The resulting titration curves show good reproducibility between simulations, but they also suggest that the titration curves of the different FPPR conformations are the same within the error bars. In summary, we were unable to find evidence supporting the previously published hypothesis of an FPPR pH-dependent equilibrium: neither from existing experimental data nor from constant-pH MD simulations. The study underscores the complexity of the spike system and opens avenues for further exploration into the interplay between pH and SARS-CoV-2 viral entry mechanisms.

Accurate Computation of Aqueous pKas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

The use of static electronic structure calculations to compute solution-phase pKas offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pKas of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pKas of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pKa units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pKas are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid-base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.

The aug-cc-pVTZ-J basis set for the p-block fourth-row elements Ga, Ge, As, Se, and Br

The aug-cc-pVTZ-J basis set family is extended to include the fourth-row p-block elements Ga, Ge, As, Se, and Br. We use the established approach outlined by Sauer and coworkers (J. Chem. Phys. 115, 1324 [2001], J. Chem. Phys. 133, 054308 [2010], J. Chem. Theory Comput. 7, 4070 [2011], and J. Chem. Theory Comput. 7, 4077 [2011]) where the completely uncontracted aug-cc-pVTZ basis set is saturated with tight s-, p-, d-, and f-functions to form the aug-cc-pVTZ-Juc basis set for the tested elements. The saturation is carried out on the simplest hydrides possible for the tested elements GaH, GeH₄ , AsH₃ , H₂ Se, and HBr until an improvement is less than 0.01% for all s-, p-, and d-functions added. f-Functions are added to an improvement less than or equal to 1.0% due to the computational expense these functions add. The saturated aug-cc-pVTZ-Juc (26s16p12d5f) is then recontracted using the molecular orbital coefficients from self-consistent field calculations on the simple hydrides to improve computational efficiency. During contraction of the basis set, we observe that the linear hydrogen bromide molecule has a slower convergence than the other tested molecules which sets a limit on the accuracy obtained. All calculations with the contracted aug-cc-pVTZ-J [17s10p7d5f] gives results that are within 1.0% of the uncontracted results at considerable computational savings.

Interplay between Ionization and Tautomerism in Bioactive β-Enamino Ester-Containing Cyclic Compounds: Study of Annulated 1,2,3,6-Tetrahydroazocine Derivatives

Depending on the chemical scaffold, a bioactive species could reflect the interplay between ionization and tautomerism, which is often complicated by the possibility of populating different conformational states, in the case of flexible ligands. In this context, theoretical methods can be valuable to discern the role of these factors, as shown here for β-enamino esters of 1,2,3,6-tetrahydroazocino-fused ring systems, some of which had proven to be suitable scaffolds for designing novel acetylcholinesterase inhibitors. The compounds investigated herein form two clusters with distinctive experimental pK_a values (i.e., α,β-diesters and β-esters ranging within 6.1-7.3 and 8.2-9.0 pK_a intervals, respectively), which implies a drastic difference in the most populated species at physiological conditions. While chemoinformatic tools did not provide a consistent description of the actual pK_a values, the theoretical analysis performed for the protonated and neutral species of these compounds revealed a marked change in the tautomeric preference of the tetrahydroazocine moiety upon (de)protonation. Excellent agreement between the calculated and experimental pK_a values was found when the tautomeric preference of the protonated and neutral species was considered. Overall, this study highlights the potential use of high-level computational methods to disclose the mutual influence between ionization, tautomerism, and conformational preferences in multifunctional (bio)organic compounds.

RPA(D) and HRPA(D): Two new models for calculations of NMR indirect nuclear spin-spin coupling constants

In this article, the RPA(D) and HRPA(D) models for the calculation of linear response functions are presented. The performance of the new RPA(D) and HRPA(D) models is compared to the performance of the established RPA, HRPA, and SOPPA models in calculations of indirect nuclear spin-spin coupling constants using the CCSD model as a reference. The doubles correction offers a significant improvement on both the RPA and HRPA models; however, the improvement is more dramatic in the case of the RPA model. For all coupling types investigated in this study, the results obtained using the HRPA(D) model are comparable in accuracy to those given by the SOPPA model, while requiring between 30% and 90% of the calculation time needed for SOPPA. The RPA(D) model, while of slightly lower accuracy compared to the CCSD model than HRPA(D), offered calculation times of only approximately 25% of those required for SOPPA for all the investigated molecules. © 2018 Wiley Periodicals, Inc.

Furanosyl Oxocarbenium Ion Conformational Energy Landscape Maps as a Tool to Study the Glycosylation Stereoselectivity of 2-Azidofuranoses, 2-Fluorofuranoses and Methyl Furanosyl Uronates

The 3D shape of glycosyl oxocarbenium ions determines their stability and reactivity and the stereochemical course of SN 1 reactions taking place on these reactive intermediates is dictated by the conformation of these species. The nature and configuration of functional groups on the carbohydrate ring affect the stability of glycosyl oxocarbenium ions and control the overall shape of the cations. We herein map the stereoelectronic substituent effects of the C2-azide, C2-fluoride and C4-carboxylic acid ester on the stability and reactivity of the complete suite of diastereoisomeric furanoses by using a combined computational and experimental approach. Surprisingly, all furanosyl donors studied react in a highly stereoselective manner to provide the 1,2-cis products, except for the reactions in the xylose series. The 1,2-cis selectivity for the ribo-, arabino- and lyxo-configured furanosides can be traced back to the lowest-energy 3 E or E3 conformers of the intermediate oxocarbenium ions. The lack of selectivity for the xylosyl donors is related to the occurrence of oxocarbenium ions adopting other conformations.

Cooperation of the Neutral and the Cationic Leaving Group Pathways in Acid-Catalyzed O-Benzylation of TriBOT

The reaction profile of acid-catalyzed O-benzylation with 2,4,6-tris(benzyloxy)-1,3,5-triazine (TriBOT) was analyzed to study the reaction kinetics. The first-order kinetic constant for the formation of benzyl cation species from N-protonated TriBOT (neutral leaving group pathway) was estimated and compared with that of the model compound for TriBOT. Since rapid consumption of TriBOT in the late stage could not be explained solely by this pathway, cooperation of another reaction mechanism, the cationic leaving group pathway, was proposed to rationalize the rate acceleration.

On the nature of the electronic effect of multiple hydroxyl groups in the 6-membered ring - the effects are additive but steric hindrance plays a role too

Research during the last two decades has shown a remarkable directional component of the substituent effects of hydroxy groups, which has a profound effect on the properties of hydroxylated compounds such as carbohydrates. While the epimerisation of a single hydroxyl function is well studied the consequence of multiple epimerisations is more speculative. In this work the effect of three epimerisations was investigated. To this end epimeric 2-phenyl iminoxylitols that have a phenyl group as a conformational anchor and thus hydroxyl groups in the axial or equatorial position, respectively, were synthesized and their pK_a and conformation were studied. The results show that the large difference in the electronic effect between the axial and equatorial hydroxyls is partially cancelled by counteracting steric hindrance from 1,3-diaxial interactions. Hydrogen bonding does not appear to play any role in the electronic influence of the hydroxyl groups.