Thermodynamics of the interaction between spike protein of severe acute respiratory syndrome-coronavirus-2 and the receptor of human angiotensin converting enzyme 2. Effects of possible ligands

Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 1000000 deaths all over the world and still lacks a medical treatment despite the attention of the whole scientific community. Human angiotensin-converting enzyme 2 (ACE2) was recently recognized as the transmembrane protein that serves as the point of entry of SARS-CoV-2 into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the protein complex. Moreover, the free energy of binding between ACE2 and the active receptor binding domain of the SARS-CoV-2 spike protein is evaluated quantitatively, providing for the first time the thermodynamics of virus?receptor recognition. Furthermore, the action of different ACE2 ligands is also examined in particular in their capacity to disrupt SARS-CoV-2 recognition, also providing via a free energy profile the quantification of the ligand-induced decreased affinity. These results improve our knowledge on molecular grounds of the SARS-CoV-2 infection and allow us to suggest rationales that could be useful for the subsequent wise molecular design for the treatment of COVID-19 cases

π‐Bridge Substitution in DASAs: The Subtle Equilibrium between Photochemical Improvements and Thermal Control

Donor-acceptor Stenhouse adducts (DASAs) are playing an outstanding role as innovative and versatile photoswitches. Until now, all the efforts have been spent on modifying the donor and acceptor moieties to modulate the absorption energy and improve the cyclization and reversion kinetics. However, there is a strong dependence on specific structural modifications and a lack of predictive behavior, mostly owing to the complex photoswitching mechanism. Here, by means of a combined experimental and theoretical study, the effect of chemical modification of the pi-bridge linking the donor and acceptor moieties is systematically explored, revealing the significant impact on the absorption, photocyclization, and relative stability of the open form. In particular, a position along the pi-bridge is found to be the most suited to redshift the absorption while preserving the cyclization. However, thermal back-reaction to the initial isomer is blocked. These effects are explained in terms of an increased acceptor capability offered by the pi-bridge substituent that can be modulated. This strategy opens the path toward derivatives with infra-red absorption and a potential anchoring point for further functionalization

Rational Design and Synthesis of Efficient Sunscreens to Boost the Solar Protection Factor

Skin cancer incidence has been increasing in the last decades, but most of the commercial formulations used as sunscreens are designed to protect only against solar erythema. Many of the active components present in sunscreens show critical weaknesses, such as low stability and toxicity. Thus, the development of more efficient components is an urgent health necessity and an attractive industrial target. We have rationally designed core moieties with increased photoprotective capacities and a new energy dissipation mechanism. Using these scaffolds, we have synthesized a series of compounds with tunable properties suitable for their use in sunscreens, and enhanced properties in terms of stability, light energy dissipation, and toxicity. Moreover, some representative compounds were included in final sunscreen formulations and a relevant solar protection factor boost was measured

Chiral Hydrogen Bond Environment Providing Unidirectional Rotation in Photoactive Molecular Motors

Generation of a chiral hydrogen bond environment in efficient molecular photoswitches is proposed as a novel strategy for the design of photoactive molecular motors. Here, the following strategy is used to design a retinal-based motor presenting singular properties: (i) a single excitation wavelength is needed to complete the unidirectional rotation process (360°); (ii) the absence of any thermal step permits the process to take place at low temperatures; and (iii) the ultrafast process permits high rotational frequencies.Ministerio de Economía y CompetitividadMinisterio de Ciencia e InnovaciónUniversidad de Alcal

A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement

In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the a-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible a-helix to a-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches

Structural Substituent Effect in the Excitation Energy of aChromophore: Quantitative Determination and Application toS-Nitrosothiols

A methodology for the prediction of excitation energies for substituted chromophores on the basis of ground state structures has been developed. The formalism introduces the concept of ?structural substituent excitation energy effect? for the rational prediction and quantification of the substituent effect in the excitation energy of a chromophore to an excited electronic state. This effect quantifies exclusively the excitation energy variation due to the structural changes of the chromophore induced by the substituent. Therefore, excitation bathochromic and hypsochromic shifts of substituted chromophores can be predicted on the basis of known ground and excited potential energy surfaces of a reference unsubstituted chromophore, together with the ground state minimum energy structure of the substituted chromophore. This formalism can be applied if the chemical substitution does not affect the nature of the electronic excitation, where the substituent effect can be understood as a force acting on the chromophore and provoking a structural change on it. The developed formalism provides a useful tool for quantitative and qualitative determination of the excitation energy of substituted chromophores and also for the analysis and determination of the structural changes affecting this energy. The proposed methodology has been applied to the prediction of the excitation energy to the first bright state of several S-nitrosothiols using the potential energy surfaces of methyl-S-nitrosothiol as a reference unsubstituted chromophore.Ministerio de Ciencia e InnovaciónUniversidad de Alcal

Reversible Light-Induced Dimerization of Secondary Face Azobenzene-Functionalized β-Cyclodextrin Derivatives

β-cyclodextrin (βCyD) derivatives equipped with aromatic appendages at the secondary face exhibit tailorable self-assembling capabilities. The aromatic modules can participate in inclusion phenomena and/or aromatic-aromatic interactions. Supramolecular species can thus form that, at their turn, can engage in further co-assembling with third components in a highly regulated manner; the design of nonviral gene delivery systems is an illustrative example. Endowing such systems with stimuli responsiveness while keeping diastereomeric purity and a low synthetic effort is a highly wanted advancement. Here, we show that an azobenzene moiety can be "clicked" to a single secondary O-2 position of βCyD affording 1,2,3-triazole-linked βCyD-azobenzene derivatives that undergo reversible light-controlled self-organization into dimers where the monomer components face their secondary rims. Their photoswitching and supramolecular properties have been thoroughly characterized by UV-vis absorption, induced circular dichroism, nuclear magnetic resonance, and computational techniques. As model processes, the formation of inclusion complexes between a water-soluble triazolylazobenzene derivative and βCyD as well as the assembly of native βCyD/βCyD-azobenzene derivative heterodimers have been investigated in parallel. The stability of the host-guest supramolecules has been challenged against the competitor guest adamantylamine and the decrease of the medium polarity using methanol-water mixtures. The collective data support that the E-configured βCyD-azobenzene derivatives, in aqueous solution, form dimers stabilized by the interplay of aromatic-aromatic and aromatic-βCyD cavity interactions after partial reciprocal inclusion. Photoswitching to the Z-isomer disrupts the dimers into monomeric species, offering opportunity for the spatiotemporal control of the organizational status by light.The authors thank MCIN/AEI/10.13039/501100011033 (PID2019-105858RB-I00, to C.O.M, PID2020-118403GB-I00; PID2020-118384GB-I00; 119130GB-I00), and PID2020-MCIN/AEI/10.13039/961 501100011033 and “ERDF A way of making Europe” (PID2021-124247OB-C21), the Junta de Andalucía (P20_00166, US-1380698), the CAM (CM/JIN/2021-022), the COST action GLYCONanoPROBES (CM18132), and the Booster program of ENS Paris-Saclay for financial support. We also acknowledge the CITIUS (Univ. Seville) for technical support. G.R.-B and M.C.P.-P. are FPU fellows (Grant numbers FPU18/02922 and FPU19/04361, respectively). T.N. is grateful to Junta de Andalucía for a post-doctoral fellowship (contract number P12-FQM-1467). C.F.-C. thanks the UAH collaboration grant awarded.Peer reviewe

Atomistic-Level Description of the Covalent Inhibition of SARS-CoV-2 Papain-like Protease

Inhibition of the papain-like protease (PLpro) of SARS-CoV-2 has been demonstrated to be a successful target to prevent the spreading of the coronavirus in the infected body. In this regard, covalent inhibitors, such as the recently proposed VIR251 ligand, can irreversibly inactivate PLpro by forming a covalent bond with a specific residue of the catalytic site (Cys111), through a Michael addition reaction. An inhibition mechanism can therefore be proposed, including four steps: (i) ligand entry into the protease pocket; (ii) Cys111 deprotonation of the thiol group by a Brønsted–Lowry base; (iii) Cys111-S− addition to the ligand; and (iv) proton transfer from the protonated base to the covalently bound ligand. Evaluating the energetics and PLpro conformational changes at each of these steps could aid the design of more efficient and selective covalent inhibitors. For this aim, we have studied by means of MD simulations and QM/MM calculations the whole mechanism. Regarding the first step, we show that the inhibitor entry in the PLpro pocket is thermodynamically favorable only when considering the neutral Cys111, that is, prior to the Cys111 deprotonation. For the second step, MD simulations revealed that His272 would deprotonate Cys111 after overcoming an energy barrier of ca. 32 kcal/mol (at the QM/MM level), but implying a decrease of the inhibitor stability inside the protease pocket. This information points to a reversible Cys111 deprotonation, whose equilibrium is largely shifted toward the neutral Cys111 form. Although thermodynamically disfavored, if Cys111 is deprotonated in close proximity to the vinylic carbon of the ligand, then covalent binding takes place in an irreversible way (third step) to form the enolate intermediate. Finally, due to Cys111-S− negative charge redistribution over the bound ligand, proton transfer from the initially protonated His272 is favored, finally leading to an irreversibly modified Cys111 and a restored His272. These results elucidate the selectivity of Cys111 to enable formation of a covalent bond, even if a weak proton acceptor is available, as His272

Fungal Light Emitter: Understanding Its Chemical Nature and pH-Dependent Emission in Water Solution

International audienc