On the antibacterial photodynamic inactivation mechanism of Emodin and Dermocybin natural photosensitizers: A theoretical investigation.

A DFT and TDDFT study has been carried out on monomeric anthraquinones Emodin and Dermocybin (Em, Derm) recently proposed as natural antibacterial photosensitizers able to act also against gram-negative microbes. The computational study has been performed considering the relative amount of neutral and ionic forms of each compound in water, with the variation of pH. The occurrence of both Type I and Type II photoreactions has been explored computing the absorption properties of each species, the spin-orbit coupling constants (SOC), the vertical ionization potentials and the vertical electron affinities. The most plausible deactivation channels leading to the population of excited triplet states have been proposed. Our data indicate Emodin as more active than Dermocybin in antimicrobial photodynamic therapy throughout the Type II mechanism. Our data support a dual TypeI/II activity of the monomeric anthraquinones Emodin and Dermccybin in water, in all the considered protonation states.

Chalcogen atom effect on the intersystem crossing kinetic constant of oxygen- and sulfur disubstituted heteroporphyrins.

The modulation of the photophysical properties of di-substituted porphyrin rings upon the oxygen and sulfur-for-nitrogen replacement has been investigated at density functional theory (DFT) and its time-dependent formulation (TDDFT). The considered properties range from structural behaviors and excitation energies to spin-orbit coupling (SOC) and nonradiative intersystem kinetic constants. Results show that the SOC strongly increase upon chalcogen substitution and, accordingly, the computed nonradiative kinetic constant also indicate an efficient singlet-triplet intersystem crossing in the sulfur containing macrocycle. The presented results indicate an alternative way to properly modulate the porphyrin's crucial properties for their use in photodynamic therapy, without resorting to the use of heavy atoms.

On the Role of Temperature in the Depolymerization of PET by FAST-PETase: An Atomistic Point of View on Possible Active Site Pre-Organization and Substrate-Destabilization Effects.

Enzyme FAST-PETase, recently obtained by a machine learning approach, can depolymerize poly(ethylene terephthalate) (PET), a synthetic resin employed in plastics and in clothing fibers. Therefore it represents a promising solution for the recycling of PET-based materials. In this study, a model of PET was adopted to describe the substrate, and all-atoms classical molecular dynamics (MD) simulations on apo- and substrate-bound FAST-PETase were carried out at 30 and 50 °C to provide atomistic details on the binding step of the catalytic cycle. Comparative analysis shed light on the interactions occurring between the FAST-PETase and 4PET at 50 °C, the optimal working conditions of the enzyme. Pre-organization of the enzyme active and binding sites has been highlighted, while MD simulations of FAST-PETase:4PET pointed out the occurrence of solvent-inaccessible conformations of the substrate promoted by the enzyme. Indeed, neither of these conformations was observed during MD simulations of the substrate alone in solution performed at 30, 50 and 150 °C. The analysis led us to propose that, at 50 °C, the FAST-PETase is pre-organized to bind the PET and that the interactions occurring in the binding site can promote a more reactive conformation of PET substrate, thus enhancing the catalytic activity of the enzyme.

Sulphur- and Selenium-for-Oxygen Replacement as a Strategy to Obtain Dual Type I/Type II Photosensitizers for Photodynamic Therapy.

The effect on the photophysical properties of sulfur- and selenium-for-oxygen replacement in the skeleton of the oxo-4-dimethylaminonaphthalimide molecule (DMNP) has been explored at the density functional (DFT) level of theory. Structural parameters, excitation energies, singlet-triplet energy gaps (ΔES-T), and spin-orbit coupling constants (SOC) have been computed. The determined SOCs indicate an enhanced probability of intersystem crossing (ISC) in both the thio- and seleno-derivatives (SDMNP and SeDMNP, respectively) and, consequently, an enhancement of the singlet oxygen quantum yields. Inspection of Type I reactions reveals that the electron transfer mechanisms leading to the generation of superoxide is feasible for all the compounds, suggesting a dual Type I/Type II activity.

On the origin of photodynamic activity of hypericin and its iodine-containing derivatives.

The main photophysical properties, useful for establishing whether hypericin in anionic form and some of its derivatives containing heavy atoms such as iodine, can be proposed for their use in photodynamic therapy, were determined using density functional based computations. The results showed that in the anionic form and in the iodinated derivatives, the absorption wavelength undergoes a bathochromic shift, the singlet-triplet energy gap assumes values ​that allow to excite the oxygen molecule from its ground to the excited singlet state, and that the spin-orbit couplings between singlet and triplet states significantly increase.

Activation by Glutathione in Hypoxic Environment of an Azo-based Rhodamine Activatable Photosensitizer. A Computational Elucidation.

In the present paper, density functional theory (DFT) has been applied to the study of the activation mechanism of a new selenium azo-rhodamine (azoSeRho) in presence of the tripeptide thiol, glutathione (GSH), as potent activatable photosensitizer to be employed in photodynamic therapy. The introduction of the azo group into the conjugated system of the seleno-rhodamine dye and its reaction with GSH allow the selective formation of the active photosensitizer, SeRho. Furthermore, DFT calculations have allowed to shed light on the activation mechanism of the azoSeRho photosensitizer when molecular oxygen is present and hydrogen peroxide is formed. This study is the first theoretical investigation revealing how the reductive cleavage of the azo moiety by GSH occurs. Time-dependent DFT approach has been used to evaluate the chalcogen-substitution effect on the structures and photophysical properties of the azo derivatives and, then, on the activated photosensitizers.

Antioxidant and copper-chelating power of new molecules suggested as multiple target agents against Alzheimer's disease. A theoretical comparative study.

In this study, the scavenging activity against OOH radicals and the copper-chelating ability of two new synthesized molecules (named L1 and L2) that can act as multiple target agents against Alzheimer's disease have been investigated at the density functional theory level. The pKa and molar fractions at physiological pH have been predicted. The main antioxidant reaction mechanisms in lipid-like and water environments have been considered and the relative rate constants determined. The copper-chelating ability of the two compounds has also been explored at different coordination sites and computing the complexation kinetic constants. Results show the L1 compound is a more effective radical scavenging and copper-chelating agent than L2.

Chalcogen Effects in the Photophysical Properties of Dimethylamino-1,8-naphthalimide Dyes Revealed by DFT Investigation.

Thionation of carbonyl groups of known dyes is a rapidly emerging strategy to propose an advance toward heavy-atom-free photosensitizers to be used in photodynamic therapy (PDT). The sulfur-for-oxygen replacement has recently proved to enhance the singlet oxygen quantum yield of some existing fluorophores and to shift the absorption band at longer wavelengths. Drawing inspiration from this challenging evidence, the effect of both sulfur- and selenium-for-oxygen replacement in the skeleton of the oxo-4-dimethylamino-1,8-naphthalimide molecule (DMN) has been analyzed by means of a DFT study. The thio- and seleno-derivatives (SDMN and SeDMN, respectively) have been shown to offer the possibility to access a multitude of ISC (intersystem crossing) pathways involved in the triplet deactivation mechanisms with a consequent enhancement of the singlet oxygen production, also arising from the change of orbital type involved in the radiationless 1nπ* → 3ππ* transitions. Moreover, the change in nature from a 1ππ* to a 1nπ* observed in the SeDMN has been revealed to be crucial to reach more clinically useful regions of the spectrum suggesting that the selenium-for-oxygen replacement can be proposed as a strategy to achieve more suitable PDT agents while proposing an advance toward heavy-atom-free PSs.

Photophysical properties of heavy atom containing tetrasulfonyl phthalocyanines as possible photosensitizers in photodynamic therapy.

The excitation energies, singlet-triplet energy gap and spin-orbit coupling constants for Zn-, GaCl-, Pd-, and Pt- tetrasulfonyl phthalocyanines complexes (ZnPc, GaClPc, PdPc, and PtPc) have been computed by using the density functional theory and employing the M06 exchange-correlation functional. Results show that these systems possess interesting photophysical properties, which make them possible photosensitizers to be proposed in photodynamic therapy (PDT). Absorption energies of all the complexes examined have been found falling inside the so-called therapeutic window (550-800 nm). Singlet-triplet energy gap values are higher than those required for the production of cytotoxic molecular oxygen and the spin-orbit coupling constants are such as to ensure an efficient spin orbit intersystem crossing. The obtained data are consistent with the experimental oxygen singlet quantum yields. The platinum complex appears to be the most effective candidate to propose for PDT.

Anticancer Activity, DNA Binding, and Photodynamic Properties of a N∧C∧N-Coordinated Pt(II) Complex.

In the effort to discover new targets and improve the therapeutic efficacy of metal-containing anticancer compounds, transition metal complexes that can elicit cytotoxicity when irradiated with light of a proper wavelength and, then, candidates as potential photosensitizers for photodynamic therapy are actively being investigated. In this work, the cytotoxicity in the dark and the photophysical properties of the complex Pt(N∧C∧N)Cl, where the N∧C∧N ligand is 2,6-dipyrido-4-methyl-benzene chloride, are investigated in detail by means of a series of theoretical levels, that is density functional theory and its time-dependent extension together with molecular dynamics (MD) simulations. In the dark, cytotoxicity has been explored by simulating the steps of the mechanism of action of classical Pt(II) complexes. The suitability of the investigated complex to act as a photosensitizer has been verified by calculating spectroscopic properties for both the unperturbed complex and its aquated and guanine-bound forms. Furthermore, using MD simulation outcomes as a starting point, the photophysical properties of DNA-intercalated and -bound complexes have been evaluated with the goal of establishing how intercalation and binding affect sensitization activity.

Computational Study Reveals the Role of Water Molecules in the Inhibition Mechanism of LAT1 by 1,2,3-Dithiazoles.

The L-type amino acid transporter LAT1, involved in many biological processes including the overexpression of some tumors, is considered a potential pharmacological target. The 1,2,3-Dithiazole scaffold was predicted to inhibit LAT1 by the formation of an intermolecular disulfide bond with the thiolate group of cysteine(s). As a result of the identification of these irreversible covalent inhibitors, we decided to deeply investigate the recognition stage and the covalent interaction, characterizing the chemical structures of the selected ligands. With the aim to provide new insights into the access of the ligands to the binding pocket and to reveal the residues involved in the inhibition, we performed docking, molecular dynamics simulations, and density functional theory-based investigation of three 1,2,3-dithiazoles against LAT1. Our computational analysis further highlighted the crucial role played by water molecules in the inhibition mechanism. The results here presented are consistent with experimental observations and provide insights that can be helpful for the rational design of new-to-come LAT1's inhibitors.

A Boron-Containing Compound Acting on Multiple Targets Against Alzheimer's Disease. Insights from Ab Initio and Molecular Dynamics Simulations.

Given the multifactorial nature and pathogenesis of Alzheimer's disease, therapeutic strategies are addressed to combine the benefits of every single-target drug into a sole molecule. Quantum mechanics and molecular dynamics (MD) methods were employed here to investigate the multitarget action of a boron-containing compound against Alzheimer's disease. The antioxidant activity as a radical scavenger and metal chelator was explored by means of density functional theory. The most plausible radical scavenger mechanisms, which are hydrogen transfer, radical adduct formation, and single-electron transfer in aqueous and lipid environments, were fully examined. Metal chelation ability was investigated by considering the complexation of Cu(II) ion, one of the metals that in excess can even catalyze the ß-amyloid (Aß) aggregation. The most probable complexes in the physiological environment were identified by considering both the stabilization energy and the shift of the λmax induced by the complexation. The excellent capability to counteract Aß aggregation was explored by performing MD simulations on protein-ligand adducts, and the activity was compared with that of curcumin, chosen as a reference.

Theoretical investigation on bisarylselanylbenzo-2,1,3-selenadiazoles as potential photosensitizers in photodynamic therapy.

Density functional theory and time-dependent (TDDFT) calculations were carried out for recently reported bisarylselanylbenzo-2,1,3-selenadiazoles derivatives capable of producing singlet oxygen (1O2) under UV-Vis irradiation. Conformational behaviors, excitation energies, singlet-triplet energy gaps, and spin-orbit coupling constants were evaluated. The conformational analysis evidences that two different conformers have to be taken into consideration to completely describe the photophysical properties of this class of molecules. TDDFT results show that these compounds, though possessing absorption wavelengths that fall in the violet region, are characterized by singlet-triplet energy gaps greater than the energy required to excite the molecular oxygen, thus being able to produce the cytotoxic species, spin-orbit coupling constants large enough to ensure efficient singlet-triplet intersystem spin crossing, and even the highly reactive superoxide anion O2 •(-) by autoionization and subsequent electron transfer to molecular oxygen in its ground state.

The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study.

The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.

The Contribution of Density Functional Theory to the Atomistic Knowledge of Electrochromic Processes.

In this review, we provide a brief overview of the contribution that computational studies can offer to the elucidation of the electronic mechanisms responsible for the electrochromism phenomenon, through the use of the density functional theory (DFT) and its time-dependent formulation (TDDFT). Although computational studies on electrochromic systems are not as numerous as those for other physico-chemical processes, we will show their reliability and ability to predict structures, excitation energies, and redox potentials. The results confirm that these methods not only help in the interpretation of experimental data but can also be used for the rational design of molecules with interesting electrochromic properties to be initiated for synthesis and experimental characterization.

Iodine substituted phosphorus corrole complexes as possible photosensitizers in photodynamic therapy: Insights from theory.

The search for new dyes to be used as photosensitizers in photodynamic therapy (PDT) is a field of great interest from both experimental and theoretical viewpoints. In this study, the main photophysical properties (excitation energies, singlet-triplet energy gap, and spin orbit coupling matrix elements) of some unsubstituted and iodine substituted phosphorus corrole complexes have been determined by using density functional theory and its time-dependent formulation. Results show that these compounds can be proposed as photosensitizers in PDT. The heavy atom effects have been rationalized on the basis of El-Sayed rules.

How Lanthanide Ions Affect the Addition-Elimination Step of Methanol Dehydrogenases.

The recently discovered methanol dehydrogenase, XoxF, is a widespread enzyme used by methylotrophic bacteria to oxidize methanol for carbon and energy, and requires lanthanide ions for its activity. This enzyme represents an essential component of methanol utilization by both methanol- and methane-utilizing bacteria. The present investigation looks on the electronic, energetic and geometrical behavior of the methanol dehydrogenase from Methylacidiphilum fumariolicum SolV, which is strictly dependent on early lanthanide metals with +3 oxidation states, by examining enzyme-substrate complexes of all the lanthanides. We focus on the catalytic reaction mechanism of two methanol dehydrogenases having as cofactor europium and ytterbium belonging to the mid- and later- series of lanthanides, in comparison with the methanol dehydrogenase containing the cerium, one early lanthanide. Our results provide evidence for the influence of the lanthanide contraction effect in all the elementary steps of the catalytic reaction mechanism. This indication may prove useful for developing new catalytic machineries of enzymes that adopt new-to-nature transformations.

Rationalization of the Superior Anticancer Activity of Phenanthriplatin: An In-Depth Computational Exploration.

In the effort to overcome issues of toxicity and resistance inherent to treatment by the approved platinum anticancer agents, a large number of cisplatin variants continues today to be prepared and tested. One of the applied strategies is to use monofunctional platinum complexes that, unlike traditional bifunctional compounds, are able to form only a single covalent bond with nuclear DNA. Chirality, aquation reaction, interaction with guanine and N-acetyl methionine as well as, intercalation into, binding to and distortion of DNA have been investigated by using both quantum mechanical DFT and molecular dynamics computations aiming at contributing to the elucidation of the molecular mechanism underlying the significantly enhanced spectrum of activity of the monofunctional PtII drug phenanthriplatin. Analogous calculations have been performed in parallel for other two less potent monofunctional PtII drugs, pyriplatin and enpyriplatin, which show very different cytotoxic effects.

Spin-Orbit Charge-Transfer Intersystem Crossing (ISC) in Compact Electron Donor-Acceptor Dyads: ISC Mechanism and Application as Novel and Potent Photodynamic Therapy Reagents.

Spin-orbit charge-transfer intersystem crossing (SOCT-ISC) is useful for the preparation of heavy atom-free triplet photosensitisers (PSs). Herein, a series of perylene-Bodipy compact electron donor/acceptor dyads showing efficient SOCT-ISC is prepared. The photophysical properties of the dyads were studied with steady-state and time-resolved spectroscopies. Efficient triplet state formation (quantum yield ΦT =60 %) was observed, with a triplet state lifetime (τT =436 µs) much longer than that accessed with the conventional heavy atom effect (τT =62 µs). The SOCT-ISC mechanism was unambiguously confirmed by direct excitation of the charge transfer (CT) absorption band by using nanosecond transient absorption spectroscopy and time-resolved electron paramagnetic resonance (TREPR) spectroscopy. The factors affecting the SOCT-ISC efficiency include the geometry, the potential energy surface of the torsion, the spin density for the atoms of the linker, solvent polarity, and the energy matching of the 1 CT/3 LE states. Remarkably, these heavy atom-free triplet PSs were demonstrated as a new type of efficient photodynamic therapy (PDT) reagents (phototoxicity, EC50 =75 nm), with a negligible dark toxicity (EC50 =78.1 µm) compared with the conventional heavy atom PSs (dark toxicity, EC50 =6.0 µm, light toxicity, EC50 =4.0 nm). This study provides in-depth understanding of the SOCT-ISC, unveils the design principles of triplet PSs based on SOCT-ISC, and underlines their application as a new generation of potent PDT reagents.

Os(II) Oligothienyl Complexes as a Hypoxia-Active Photosensitizer Class for Photodynamic Therapy.

Hypoxia presents a challenge to anticancer therapy, reducing the efficacy of many available treatments. Photodynamic therapy is particularly susceptible to hypoxia, given that its mechanism relies on oxygen. Herein, we introduce two new osmium-based polypyridyl photosensitizers that are active in hypoxia. The lead compounds emerged from a systematic study of two Os(II) polypyridyl families derived from 2,2'-bipyridine (bpy) or 4,4'-dimethyl-2,2'-bipyridine (dmb) as coligands combined with imidazo[4,5-f][1,10]phenanthroline ligands tethered to n = 0-4 thiophenes (IP-nT). The compounds were characterized and investigated for their spectroscopic and (photo)biological activities. The two hypoxia-active Os(II) photosensitizers had n = 4 thiophenes, with the bpy analogue 1-4T being the most potent. In normoxia, 1-4T had low nanomolar activity (half-maximal effective concentration (EC50) = 1-13 nM) with phototherapeutic indices (PI) ranging from 5500 to 55 000 with red and visible light, respectively. A sub-micromolar potency was maintained even in hypoxia (1% O2), with light EC50 and PI values of 732-812 nM and 68-76, respectively -currently among the largest PIs for hypoxic photoactivity. This high degree of activity coincided with a low-energy, long-lived (0.98-3.6 µs) mixed-character intraligand charge-transfer (3ILCT)/ligand-to-ligand charge-transfer (3LLCT) state only accessible in quaterthiophene complexes 1-4T and 2-4T. The coligand identity strongly influenced the photophysical and photobiological results in this study, whereby the bpy coligand led to longer lifetimes (3.6 µs) and more potent photo-cytotoxicity relative to those of dmb. The unactivated compounds were relatively nontoxic both in vitro and in vivo. The maximum tolerated dose for 1-4T and 2-4T in mice was greater than or equal to 200 mg kg-1, an excellent starting point for future in vivo validation.