The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective

Exploring Membrane Cholesterol Binding to the CB1 Receptor: A Computational Perspective

Cholesterol (CHOL) is a potential allosteric modulator of the CB1 receptor. In this work, we use atomistic molecular dynamics simulations to study how CHOL interacts with CB1 and to identify its binding sites (BS) and residence times on specific receptor zones. Our results evince minimal changes in CB1 conformational dynamics and secondary structure due to CHOL. We report five BSs, three of which coincide with previously described interaction regions (BS1, BS2, and BS3), while BS4 and BS5 are proposed as new BSs. Quantum descriptors of bonding such as Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM), and Noncovalent Interactions (NCI) analyses are employed to characterize the CHOL-BS interactions. The results show an exponential correlation between the strength of the interactions (mainly hydrogen bonds and hydrophobic contacts) and the residence time at the BSs. Although other approaches exist to identify high-affinity protein sites, our methodology integrates classical and quantum descriptions to better characterize BSs and predict ligand residence times in CB1, distinguishing persistent from transitory contacts. Since CHOL has been suggested as a potential endogenous allosteric ligand, our flexible strategy allows studying interactions that stabilize CHOL in CB1, could be extended to cannabinoid binding, and contribute to designing improved receptor ligands.

Encapsulation of charged halogens by the 512 water cage

This study focuses on the encapsulation of the entire series of halides by the 512 cage of twenty water molecules and on the characterization of water to water and water to anion interactions. State-of-the-art computations are used to determine equilibrium geometries, energy related quantities, and thermal stability towards dissociation and to dissect the nature and strength of intermolecular interactions holding the clusters as stable units. Two types of structures are revealed: heavily deformed cages for F- indicating a preference for microsolvation, and slightly deformed cages for the remaining anions indicating a preference for encapsulation. The primary variable dictating the properties of the clusters is the charge density of the central halide, with the most severe effects observed for the F- case. For the remaining halides, the anion may be safely viewed as a sort of "big electron" with little local disruptive power, enough to affect the network of non-covalent hydrogen bonds in the cage, but not enough to break it. Gibbs energies for dissociation either into cavity and halide or into water molecules and halide suggest that, in a similar way as to methane clathrate, a more weakly bonded complex that has been detected in the gas phase, all halide containing clathrate-like structures should be amenable to experimental detection in the gas phase at moderate temperature and pressure conditions.

A Computational Workflow to Predict Biological Target Mutations: The Spike Glycoprotein Case Study

The biological target identification process, a pivotal phase in the drug discovery workflow, becomes particularly challenging when mutations affect proteins' mechanisms of action. COVID-19 Spike glycoprotein mutations are known to modify the affinity toward the human angiotensin-converting enzyme ACE2 and several antibodies, compromising their neutralizing effect. Predicting new possible mutations would be an efficient way to develop specific and efficacious drugs, vaccines, and antibodies. In this work, we developed and applied a computational procedure, combining constrained logic programming and careful structural analysis based on the Structural Activity Relationship (SAR) approach, to predict and determine the structure and behavior of new future mutants. "Mutations rules" that would track statistical and functional types of substitutions for each residue or combination of residues were extracted from the GISAID database and used to define constraints for our software, having control of the process step by step. A careful molecular dynamics analysis of the predicted mutated structures was carried out after an energy evaluation of the intermolecular and intramolecular interactions using the HINT (Hydrophatic INTeraction) force field. Our approach successfully predicted, among others, known Spike mutants.

Water Maintains the UV-Vis Spectral Features During the Insertion of Anionic Naproxen and Ibuprofen into Model Cell Membranes

UV-vis spectra of anionic ibuprofen and naproxen in a model lipid bilayer of the cell membrane are investigated using computational techniques in combination with a comparative analysis of drug spectra in purely aqueous environments. The simulations aim at elucidating the intricacies behind the negligible changes in the maximum absorption wavelength in the experimental spectra. A set of configurations of the systems constituted by lipid, water, and drugs or just water and drugs are obtained from classical Molecular Dynamics simulations. UV-vis spectra are computed in the framework of atomistic Quantum Mechanical/Molecular Mechanics (QM/MM) approaches together with Time-Dependent Density Functional Theory (TD-DFT). Our results suggest that the molecular orbitals involved in the electronic transitions are the same, regardless of the chemical environment. A thorough analysis of the contacts between the drug and water molecules reveals that no significant changes in UV-vis spectra are a consequence of ibuprofen and naproxen molecules being permanently microsolvated by water molecules, despite the presence of lipid molecules. Water molecules microsolvate the charged carboxylate group as expected but also microsolvate the aromatic regions of the drugs.

Microsolvation versus Encapsulation in Mono, Di, and Trivalent Cations

The effects of the formal charge in the stability and bonding of water cavities when solvating a cation are studied here using [X(H₂ O)₂₀ ]^q+ clusters starting with the well known 5¹² isomer of (water)₂₀ , placing a single mono, di, or trivalent X^q+ cation at the interior, and then optimizing and characterizing the resulting clusters. Highly correlated interaction and deformation energies are calculated using the CCSD(T)-DLPNO formalism. Bonding interactions are characterized using the tools provided by the quantum theory of atoms in molecules, natural bond orbitals, and non-covalent surfaces. Our results indicate that water to water hydrogen bonds are sensibly strengthened resulting in strong cooperative effects, which amount to ≈ 2 ${ \approx 2}$  kcal/mol per hydrogen bond in the bare cavity and to larger values for the systems including the cations. Approximate encapsulation, that is, surrounding the cation by a network of hydrogen bonds akin to the well known methane clathrate seems to be preferred by cations with smaller charge densities while microsolvation, that is, cluster structures having explicit X⋯O contacts seem to be preferred by cations with larger charge densities which severely deform the cavity.

Microsolvation of electrons by a handful of ammonia molecules

Microsolvation of electrons in ammonia is studied here via anionic NH_{3 n} ^- clusters with n = 2-6. Intensive samplings of the corresponding configurational spaces using second-order perturbation theory with extended basis sets uncover rich and complex energy landscapes, heavily populated by many local minima in tight energy windows as calculated from highly correlated coupled cluster methods. There is a marked energetical preference for structures that place the excess electron external to the molecular frame, effectively coordinating it with the three protons from a single ammonia molecule. Overall, as the clusters grow in size, the lowest energy dimer serves as the basic motif over which additional ammonia molecules are attached via unusually strong charge-assisted hydrogen bonds. This is a priori quite unexpected because, on electrostatic grounds, the excess electron would be expected to be in contact with as many protons as possible. Accordingly, a full quantum mechanical treatment of the bonding interactions under the tools provided by the quantum theory of atoms in molecules is carried out in order to dissect and understand the nature of intermolecular contacts. Vertical detachment energies reveal bound electrons even for n = 2.

Perspective Chapter: Bioinformatics Study of the Evolution of SARS-CoV-2 Spike Protein

SARS-CoV-2 belongs to the family of coronaviruses, which are characterized by spikes that sit densely on the surface of the virus. The spike protein (Spro) is responsible for the attachment of the virus to the host cell via the ACE2 receptor on the surface of the host cell. The strength of the interaction between the receptor-binding domain (RBD) of the highly glycosylated spike protein of the virus and the host cell ACE2 receptor represents the key determinant of the infectivity of the virus. The SARS-CoV-2 virus has mutated since the beginning of the outbreak, and the vast majority of mutations has been detected in the spike protein or its RBD. Since specific mutations significantly affect the ability of the virus to transmit and to evade immune response, studies of these mutations are critical. We investigate GISAID data to show how viral spike protein mutations evolved during the pandemic. We further present the interactions of the viral Spro RBD with the host ACE2 receptor. We have performed a large-scale mutagenesis study of the Spro RBD-ACE2 interface by performing point mutations in silico and identifying the ambiguous interface stabilization by the most common point mutations in the viral variants of interest (beta, gamma, delta, omicron).

Analysis of Conformational Preferences in Caffeine

High level DLPNO−CCSD(T) electronic structure calculations with extended basis sets over B3LYP−D3 optimized geometries indicate that the three methyl groups in caffeine overcome steric hindrance to adopt uncommon conformations, each one placing a C−H bond on the same plane of the aromatic system, leading to the C−H bonds eclipsing one carbonyl group, one heavily delocalized C−N bond constituent of the fused double ring aromatic system, and one C−H bond from the imidazole ring. Deletion of indiscriminate and selective non-Lewis orbitals unequivocally show that hyperconjugation in the form of a bidirectional −CH3 ⇆ aromatic system charge transfer is responsible for these puzzling conformations. The structural preferences in caffeine are exclusively determined by orbital interactions, ruling out electrostatics, induction, bond critical points, and density redistribution because the steric effect, the allylic effect, the Quantum Theory of Atoms in Molecules (QTAIM), and the non-covalent interactions (NCI), all predict wrong energetic orderings. Tiny rotational barriers, not exceeding 1.3 kcal/mol suggest that at room conditions, each methyl group either acts as a free rotor or adopts fluxional behavior, thus preventing accurate determination of their conformations. In this context, our results supersede current experimental ambiguity in the assignation of methyl conformation in caffeine and, more generally, in methylated xanthines and their derivatives.

Ring Vibrations to Sense Anionic Ibuprofen in Aqueous Solution as Revealed by Resonance Raman

We unravel the potentialities of resonance Raman spectroscopy to detect ibuprofen in diluted aqueous solutions. In particular, we exploit a fully polarizable quantum mechanics/molecular mechanics (QM/MM) methodology based on fluctuating charges coupled to molecular dynamics (MD) in order to take into account the dynamical aspects of the solvation phenomenon. Our findings, which are discussed in light of a natural bond orbital (NBO) analysis, reveal that a selective enhancement of the Raman signal due to the normal mode associated with the C-C stretching in the ring, νC=C, can be achieved by properly tuning the incident wavelength, thus facilitating the recognition of ibuprofen in water samples.

To be or not to be? that is the entropic, enthalpic, and molecular interaction dilemma in the formation of (water)20 clusters and methane clathrate

A detailed analysis under a comprehensive set of theoretical and computational tools of the thermodynamical factors and of the intermolecular interactions behind the stabilization of a well known set of (water)20 cavities and of the methane clathrate is offered in this work. Beyond the available reports of experimental characterization at extreme conditions of most of the systems studied here, all clusters should be amenable to experimental detection at 1 atm and moderate temperatures since 280 K marks the boundary at which, ignoring reaction paths, formation of all clusters is no longer spontaneous from the 20H2O → (H2O)20 and CH4 + 20H2O → CH4@512 processes. As a function of temperature, a complex interplay leading to the free energy of formation occurs between the destabilizing entropic contributions, mostly due to cluster vibrations, and the stabilizing enthalpic contributions, due to intermolecular interactions and the PV term, is best illustrated by the highly symmetric 512 cage consistently showing signs of stronger intermolecular bonding despite having smaller binding energy than the other clusters. A fluxional wall of attractive non-covalent interactions, arising because of the cumulative effect of a large number of tiny individual charge transfers to the interstitial region, plays a pivotal role stabilizing the CH4@512 clathrate.