General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides

Five Hypotheses on the Origins of Temperature Dependence of 77Se NMR Shifts in Diselenides

Notable thermal shifts in diselenides have been documented in 77Se NMR for more than 50 years, but no satisfactory explanation has been found. Here, five hypotheses are considered as possible explanations for the large temperature dependence of the 77Se chemical shifts of diaryl and dialkyl diselenides compared to monoselenides and selenols. Density functional theory calculations are provided to bolster hypotheses and better understand the effects of barrier height and dipole energies. It is proposed that the temperature dependence of diselenide 77Se NMR chemical shifts is due to rotation around the Se-Se bond and sampling of twisted conformers at higher temperatures. The molecular twisting is solvent dependent; here, DMSO-d6 and toluene-d8 were evaluated. No correlation was established between para-substituents on diaryl diselenides and the magnitude of the change in the 77Se NMR shift (Δδ) with temperature.

Differential molecular mechanisms of substrate recognition by selenium methyltransferases, INMT and TPMT, in selenium detoxification and excretion

It is known that the recommended dietary allowance of selenium (Se) is dangerously close to its tolerable upper intake level. Se is detoxified and excreted in urine as trimethylselenonium ion (TMSe) when the amount ingested exceeds the nutritional level. Recently, we demonstrated that the production of TMSe requires two methyltransferases: thiopurine S-methyltransferase (TPMT) and indolethylamine N-methyltransferase (INMT). In this study, we investigated the substrate recognition mechanisms of INMT and TPMT in the Se-methylation reaction. Examination of the Se-methyltransferase activities of two paralogs of INMT, namely, nicotinamide N-methyltransferase and phenylethanolamine N-methyltransferase, revealed that only INMT exhibited Se-methyltransferase activity. Consistently, molecular dynamics simulations demonstrated that dimethylselenide was preferentially associated with the active center of INMT. Using the fragment molecular orbital method, we identified hydrophobic residues involved in the binding of dimethylselenide to the active center of INMT. The INMT-L164R mutation resulted in a deficiency in Se- and N-methyltransferase activities. Similarly, TPMT-R152, which occupies the same position as INMT-L164, played a crucial role in the Se-methyltransferase activity of TPMT. Our findings suggest that TPMT recognizes negatively charged substrates, whereas INMT recognizes electrically neutral substrates in the hydrophobic active center embedded within the protein. These observations explain the sequential requirement of the two methyltransferases in producing TMSe.

Synergistic effect of lecithin and alginate, CMC, or PVP in stabilizing curcumin and its potential mechanism

This work aims to advance the understanding of the synergistic mechanism of lecithin and polymers (alginate, CMC, and PVP) in stabilizing curcumin, with a major focus on understanding the nanocomplex formation process and the main binding energy between molecules. It is demonstrated that lecithin and polymers have a synergistic effect in increasing the thermal acid, light, and digestion stability of curcumin. The potential mechanism is that the hydrophobic parts of curcumin molecules are first anchored at the region of the hydrophobic cavity of lecithin by van der Waals, while the hydrophilic parts are outward and are further encapsulated by hydrophilic polymers by van der Waals and electrostatic interaction to form a protective shell. This study contributes to our understanding of the synergistic mechanism of lecithin, polymers, and hydrophobic compounds, which can promote the synergistic use of lecithin and polymers to prepare nanocomplexes as an important tool for delivering bioactive compounds.

Diphenyl Diselenide and SARS-CoV-2: in silico Exploration of the Mechanisms of Inhibition of Main Protease (Mpro) and Papain-like Protease (PLpro)

The SARS-CoV-2 pandemic has prompted global efforts to develop therapeutics. The main protease of SARS-CoV-2 (M^pro) and the papain-like protease (PL^pro) are essential for viral replication and are key targets for therapeutic development. In this work, we investigate the mechanisms of SARS-CoV-2 inhibition by diphenyl diselenide (PhSe)₂ which is an archetypal model of diselenides and a renowned potential therapeutic agent. The in vitro inhibitory concentration of (PhSe)₂ against SARS-CoV-2 in Vero E6 cells falls in the low micromolar range. Molecular dynamics (MD) simulations and density functional theory (DFT) calculations [level of theory: SMD-B3LYP-D3(BJ)/6-311G(d,p), cc-pVTZ] are used to inspect non-covalent inhibition modes of both proteases via π-stacking and the mechanism of covalent (PhSe)₂ + M^pro product formation involving the catalytic residue C145, respectively. The in vitro CC₅₀ (24.61 μM) and EC₅₀ (2.39 μM) data indicate that (PhSe)₂ is a good inhibitor of the SARS-CoV-2 virus replication in a cell culture model. The in silico findings indicate potential mechanisms of proteases' inhibition by (PhSe)₂; in particular, the results of the covalent inhibition here discussed for M^pro, whose thermodynamics is approximatively isoergonic, prompt further investigation in the design of antiviral organodiselenides.

Preserving the Integrity of Empirical Force Fields

Generalized force fields (FFs) act as extensions to biomolecular FFs to provide a wide coverage of organic molecules. However, their precise application to an arbitrary molecule presents a separate challenge. We show that MATCH assigns different atom types and bonded and nonbonded parameters than CGenFF, and the AM1-BCC charge model, commonly used with GAFF/GAFF2, does not exactly reproduce the performance of the RESP charge model. The results indicate the need for caution when employing FFs to ensure their integrity with respect to their implementation and validation.

Simulating chalcogen bonding using molecular mechanics: a pseudoatom approach to model ebselen

The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19; however, efforts to model ebselen in silico have been hampered by the lack of an efficient and accurate method to assess its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to simulate the σ-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach is justified using an energy decomposition analysis of a number of density functional theory–optimized structures, which shows that the σ-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting molecular dynamics simulations on a number of simple complexes, as well as the clinically relevant enzyme SOD1 (superoxide dismutase), which is known to bind to ebselen.

Graphical Abstract

Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS

We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. We determined these parameters based on quantum mechanical (QM) calculations involving geometry optimization at the HF6-31G* level of theory. For each molecule we provide a coordinate file of the three-dimensional molecular structure, the topology and the parameter file. The applicability of these parameters was demonstrated by MD simulations of these molecules bound to the active site of the main protease of the coronavirus SARS-CoV-2, 3CLpro, which is a main player during viral replication causing COVID-19.

Dissecting Dynamic and Hydration Contributions to Sequence-Dependent DNA Minor Groove Recognition

Sequence selectivity is a critical attribute of DNA-binding ligands and underlines the need for detailed molecular descriptions of binding in representative sequence contexts. We investigated the binding and volumetric properties of DB1976, a model bis(benzimidazole)-selenophene diamidine compound with emerging therapeutic potential in acute myeloid leukemia, debilitating fibroses, and obesity-related liver dysfunction. To sample the scope of cognate DB1976 target sites, we evaluated three dodecameric duplexes spanning >10³-fold in binding affinity. The attendant changes in partial molar volumes varied substantially, but not in step with binding affinity, suggesting distinct modes of interactions in these complexes. Specifically, whereas optimal binding was associated with loss of hydration water, low-affinity binding released more hydration water. Explicit-atom molecular dynamics simulations showed that minor groove binding perturbed the conformational dynamics and hydration at the termini and interior of the DNA in a sequence-dependent manner. The impact of these distinct local dynamics on hydration was experimentally validated by domain-specific interrogation of hydration with salt, which probed the charged axial surfaces of oligomeric DNA preferentially over the uncharged termini. Minor groove recognition by DB1976, therefore, generates dynamically distinct domains that can make favorable contributions to hydration release in both high- and low-affinity binding. Because ligand binding at internal sites of DNA oligomers modulates dynamics at the termini, the results suggest both short- and long-range dynamic effects along the DNA target that can influence their effectiveness as low-MW competitors of protein binding.

Effect of Molecular Structure in the Chain Mobility of Dichalcogenide-Based Polymers with Self-Healing Capacity

Recently, it has been shown that the reaction mechanism in self-healing diphenyl dichalcogenide-based polymers involves the formation of sulfenyl and selenyl radicals. These radicals are able to attack a neighbouring dichalcogenide bond via a three-membered transition state, leading to the interchange of chalcogen atoms. Hence, the chain mobility is crucial for the exchange reaction to take place. In this work, molecular dynamics simulations have been performed in a set of disulfide- and diselenide-based materials to analyze the effect of the molecular structure in the chain mobility. First of all, a validation of the computational protocol has been carried out, and different simulation parameters like initial guess, length of the molecular chains, size of the simulation box and simulation time, have been evaluated. This protocol has been used to study the chain mobility and also the self-healing capacity, which depends on the probability to generate radicals ( ρ ), the barrier of the exchange reaction ( Δ G ) and the mobility of the chains ( ω ). The first two parameters have been obtained in previous quantum chemical calculations on the systems under study in this work. After analyzing the self-healing capacity, it is concluded that aromatic diselenides (PD-SeSe) are the best candidates among those studied to show self-healing, due to lower reaction barriers and larger ω values.

Oxidation of organic diselenides and ditellurides by H2O2 for bioinspired catalyst design

The reactivity of diselenides and ditellurides of general formula (RX)2 (X = Se, Te; R = H, CH3, Ph) toward hydrogen peroxide was studied through a computational approach based on accurate Density Functional Theory (DFT) calculations. The aliphatic and aromatic dichalcogenides have been chosen in light of their activity in glutathione peroxidase (GPx)-like catalytic cycles and their promising features as efficient antioxidant compounds. The reaction products, the energetics and the mechanistic details of these oxidations are discussed. Analogous disulfides are included in our analysis for completeness. We find that the barrier for oxidation of dichalcogenides decreases from disulfides to diselenides to ditellurides. On the other hand, variation of the substituents at the chalcogen nucleus has relatively little effect on the reactivity.

The 125Te Chemical Shift of Diphenyl Ditelluride: Chasing Conformers over a Flat Energy Surface

The interest in diphenyl ditelluride (Ph₂Te₂) is related to its strict analogy to diphenyl diselenide (Ph₂Se₂), whose capacity to reduce organic peroxides is largely exploited in catalysis and green chemistry. Since the latter is also a promising candidate as an antioxidant drug and mimic of the ubiquitous enzyme glutathione peroxidase (GPx), the use of organotellurides in medicinal chemistry is gaining importance, despite the fact that tellurium has no recognized biological role and its toxicity must be cautiously pondered. Both Ph₂Se₂ and Ph₂Te₂ exhibit significant conformational freedom due to the softness of the inter-chalcogen and carbon–chalcogen bonds, preventing the existence of a unique structure in solution. Therefore, the accurate calculation of the NMR chemical shifts of these flexible molecules is not trivial. In this study, a detailed structural analysis of Ph₂Te₂ is carried out using a computational approach combining classical molecular dynamics and relativistic density functional theory methods. The goal is to establish how structural changes affect the electronic structure of diphenyl ditelluride, particularly the ¹²⁵Te chemical shift.

Mechanistic Insight into the Oxidation of Organic Phenylselenides by H2 O2

The oxidation of organic phenylselenides by H₂ O₂ is investigated in model compounds, namely, n-butyl phenyl selenide (PhSe(nBu)), bis(phenylselanyl)methane (PhSeMeSePh), diphenyl diselenide (PhSeSePh), and 1,2-bis(phenylselanyl)ethane (PhSeEtSePh). Through a combined experimental (¹ H and ⁷⁷ Se NMR) and computational approach, we characterize the direct oxidation of monoselenide to selenoxide, the stepwise double oxidation of PhSeMeSePh that leads to different diastereomeric diselenoxides, the complete oxidation of the diphenyldiselenide that leads to selenium-selenium bond cleavage, and the subsequent formation of the phenylseleninic product. The oxidation of PhSeEtSePh also results in the formation of phenylseleninic acid along with 1-(vinylseleninyl)benzene, which is derived from a side elimination reaction. The evidence of a direct mechanism, in addition to an autocatalytic mechanism that emerges from kinetic studies, is discussed. By considering our observations of diselenides with chalcogen atoms that are separated by alkyl spacers of different length, a rationale for the advantage of diselenide versus monoselenide catalysts is presented.