A computational study to assess the pathogenicity of single or combinations of missense variants on respiratory complex I.

Variants found in the respiratory complex I (CI) subunit genes encoded by mitochondrial DNA can cause severe genetic diseases. However, it is difficult to establish a priori whether a single or a combination of CI variants may impact oxidative phosphorylation. Here we propose a computational approach based on coarse-grained molecular dynamics simulations aimed at investigating new CI variants. One of the primary CI variants associated with the Leber hereditary optic neuropathy (m.14484T>C/MT-ND6) was used as a test case and was investigated alone or in combination with two additional rare CI variants whose role remains uncertain. We found that the primary variant positioned in the E-channel region, which is fundamental for CI function, stiffens the enzyme dynamics. Moreover, a new mechanism for the transition between π- and α-conformation in the helix carrying the primary variant is proposed. This may have implications for the E-channel opening/closing mechanism. Finally, our findings show that one of the rare variants, located next to the primary one, further worsens the stiffening, while the other rare variant does not affect CI function. This approach may be extended to other variants candidate to exert a pathogenic impact on CI dynamics, or to investigate the interaction of multiple variants.

Identification of Potential Drug Targets of Calix[4]arene by Reverse Docking.

Calixarenes are displaying great potential for the development of new drug delivery systems, diagnostic imaging, biosensing devices and inhibitors of biological processes. In particular, calixarene derivatives are able to interact with many different enzymes and function as inhibitors. By screening of the potential drug target database (PDTD) with a reverse docking procedure, we identify and discuss a selection of 100 proteins that interact strongly with calix[4]arene. We also discover that leucine (23.5 %), isoleucine (11.3 %), phenylalanines (11.3 %) and valine (9.5 %) are the most frequent binding residues followed by hydrophobic cysteines and methionines and aromatic histidines, tyrosines and tryptophanes. Top binders are peroxisome proliferator-activated receptors that already are targeted by commercial drugs, demonstrating the practical interest in calix[4]arene. Nuclear receptors, potassium channel, several carrier proteins, a variety of cancer-related proteins and viral proteins are prominent in the list. It is concluded that calix[4]arene, which is characterized by facile access, well-defined conformational characteristics, and ease of functionalization at both the lower and higher rims, could be a potential lead compound for the development of enzyme inhibitors and theranostic platforms.

Interaction of Au(III) with amino acids: a vade mecum for medicinal chemistry and nanotechnology.

Au(III) is highly reactive. At odds with its reduced counterpart, Au(I), it is hardly present in structural databases. And yet, it is the starting reactant to form gold nanoclusters (AuNCs) and the constitutive component of a new class of drugs. Its reactivity is a world apart from that of the iso-electronic Pt(II) species. Rather than DNA, it targets proteins. Its interaction with amino acid residues is manifold. It can strongly interact with the residue backbones, amino acid side chains and protein ends, it can form appropriate complexes whose stabilization energy reaches up to more than 40 kcal mol-1, it can affect the pKa of amino acid residues, and it can promote charge transfer from the residues to the amount that it is reduced. Here, quantum chemical calculations provide quantitative information on all the processes where Au(III) can be involved. A myriad of structural arrangements are examined in order to determine the strongest interactions and quantify the amount of charge transfer between protonated and deprotonated residues and Au(III). The calculated interaction energies of the amino acid side chains with Au(III) quantitatively reproduce the experimental tendency of Au(III) to interact with selenocysteine, cysteine and histidine and negatively charged amino acids such as Glu and Asp. Also, aromatic residues such as tyrosine and tryptophan strongly interact with Au(III). In proteins, basic pH plays a role in the deprotonation of cysteine, lysine and tyrosine and strongly increases the binding affinity of Au(III) toward these amino acids. The amino acid residues in the protein can also trigger the reduction of Au(III) ions. Sulfur-containing amino acids (cysteine and methionine) and selenocysteine provide almost one electron to Au(III) upon binding. Tyrosine also shows a considerable tendency to act as a reductant. Other amino acids, commonly identified in Au-protein adducts, such as Ser, Trp, Thr, Gln, Glu, Asn, Asp, Lys, Arg and His, possess a notable reducing power toward Au(III). These results and their discussion form a vade mecum that can find application in medicinal chemistry and nanotech applications of Au(III).

Polaritonic Chemistry: Hindering and Easing Ground State Polyenic Isomerization via Breakdown of σ-π Separation.

The ground state conformational isomerization in polyenes is a symmetry allowed process. Its low energy barrier is governed by electron density transfer from the formal single bond that is rotated to the nearby formal double bonds. Along the reaction pathway, the transition state is therefore destabilized. The rules of polaritonic chemistry, i.e., chemistry in a nanocavity with reflecting windows, are barely beginning to be laid out. The standing electric field of the nanocavity couples strongly with the molecular wave function and modifies the potential energy curve in unexpected ways. A quantum electrodynamics approach, applied to the torsional degree of freedom of the central bond of butadiene, shows that formation of the polariton mixes the σ-π frameworks thereby stabilizing/destabilizing the planar, reactant-like conformations. The values of the fundamental mode of the cavity field used in the absence of the cavity do not trigger this mechanism.

Robust Biosensor Based on Carbon Nanotubes/Protein Hybrid Electrolyte Gated Transistors.

Semiconducting single walled carbon nanotubes (SWCNTs) are promising materials for biosensing applications with electrolyte-gated transistors (EGT). However, to be employed in EGT devices, SWCNTs often require lengthy solution-processing fabrication techniques. Here, we introduce a simple solution-based method that allows fabricating EGT devices from stable dispersions of SWCNTs/bovine serum albumin (BSA) hybrids in water. The dispersion is then deposited on a substrate allowing the formation of a SWCNTs random network as the semiconducting channel. We demonstrate that this methodology allows the fabrication of EGT devices with electric performances that allow their use in biosensing applications. We demonstrate their application for the detection of cortisol in solution, upon gate electrode functionalization with anti-cortisol antibodies. This is a robust and cost-effective methodology that sets the ground for a SWCNT/BSA-based biosensing platform that allows overcoming many limitations of standard SWCNTs biosensor fabrications.

Exploiting Blood Transport Proteins as Carborane Supramolecular Vehicles for Boron Neutron Capture Therapy.

Carboranes are promising agents for applications in boron neutron capture therapy (BNCT), but their hydrophobicity prevents their use in physiological environments. Here, by using reverse docking and molecular dynamics (MD) simulations, we identified blood transport proteins as candidate carriers of carboranes. Hemoglobin showed a higher binding affinity for carboranes than transthyretin and human serum albumin (HSA), which are well-known carborane-binding proteins. Myoglobin, ceruloplasmin, sex hormone-binding protein, lactoferrin, plasma retinol-binding protein, thyroxine-binding globulin, corticosteroid-binding globulin and afamin have a binding affinity comparable to transthyretin/HSA. The carborane@protein complexes are stable in water and characterized by favorable binding energy. The driving force in the carborane binding is represented by the formation of hydrophobic interactions with aliphatic amino acids and BH-π and CH-π interactions with aromatic amino acids. Dihydrogen bonds, classical hydrogen bonds and surfactant-like interactions also assist the binding. These results (i) identify the plasma proteins responsible for binding carborane upon their intravenous administration, and (ii) suggest an innovative formulation for carboranes based on the formation of a carborane@protein complex prior to the administration.

Identification of Blood Transport Proteins to Carry Temoporfin: A Domino Approach from Virtual Screening to Synthesis and In Vitro PDT Testing.

Temoporfin (mTHPC) is one of the most promising photosensitizers used in photodynamic therapy (PDT). Despite its clinical use, the lipophilic character of mTHPC still hampers the full exploitation of its potential. Low solubility in water, high tendency to aggregate, and low biocompatibility are the main limitations because they cause poor stability in physiological environments, dark toxicity, and ultimately reduce the generation of reactive oxygen species (ROS). Applying a reverse docking approach, here, we identified a number of blood transport proteins able to bind and disperse monomolecularly mTHPC, namely apohemoglobin, apomyoglobin, hemopexin, and afamin. We validated the computational results synthesizing the mTHPC-apomyoglobin complex (mTHPC@apoMb) and demonstrated that the protein monodisperses mTHPC in a physiological environment. The mTHPC@apoMb complex preserves the imaging properties of the molecule and improves its ability to produce ROS via both type I and type II mechanisms. The effectiveness of photodynamic treatment using the mTHPC@apoMb complex was then demonstrated in vitro. Blood transport proteins can be used as molecular "Trojan horses" in cancer cells by conferring mTHPC (i) water solubility, (ii) monodispersity, and (iii) biocompatibility, ultimately bypassing the current limitations of mTHPC.

Enhanced Uptake and Phototoxicity of C60@albumin Hybrids by Folate Bioconjugation.

Fullerenes are considered excellent photosensitizers, being highly suitable for photodynamic therapy (PDT). A lack of water solubility and low biocompatibility are, in many instances, still hampering the full exploitation of their potential in nanomedicine. Here, we used human serum albumin (HSA) to disperse fullerenes by binding up to five fullerene cages inside the hydrophobic cavities. Albumin was bioconjugated with folic acid to specifically address the folate receptors that are usually overexpressed in several solid tumors. Concurrently, tetramethylrhodamine isothiocyanate, TRITC, a tag for imaging, was conjugated to C60@HSA in order to build an effective phototheranostic platform. The in vitro experiments demonstrated that: (i) HSA disperses C60 molecules in a physiological environment, (ii) HSA, upon C60 binding, maintains its biological identity and biocompatibility, (iii) the C60@HSA complex shows a significant visible-light-induced production of reactive oxygen species, and (iv) folate bioconjugation improves both the internalization and the PDT-induced phototoxicity of the C60@HSA complex in HeLa cells.

Universal Markers Unveil Metastatic Cancerous Cross-Sections at Nanoscale.

The characterization of cancer histological sections as metastatic, M, or not-metastatic, NM, at the cellular size level is important for early diagnosis and treatment. We present timely warning markers of metastasis, not identified by existing protocols and used methods. Digitized atomic force microscopy images of human histological cross-sections of M and NM colorectal cancer cells were analyzed by multifractal detrended fluctuation analysis and the generalized moments method analysis. Findings emphasize the multifractal character of all samples and accentuate room for the differentiation of M from NM cross-sections. Two universal markers emphatically achieve this goal performing very well: (a) the ratio of the singularity parameters (left/right), which are defined relative to weak/strong fluctuations in the multifractal spectrum, is always greater than 0.8 for NM tissues; and (b) the index of multifractality, used to classify universal multifractals, points to log-normal distribution for NM and to log-Cauchy for M tissues. An immediate large-scale screening of cancerous sections is doable based on these findings.

High-resolution crystal structure of a 20 kDa superfluorinated gold nanocluster.

Crystallization of atomically precise nanoclusters is gaining increasing attention, due to the opportunity of elucidating both intracluster and intercluster packing modes, and exploiting the functionality of the resulting highly pure crystallized materials. Herein, we report the design and single-crystal X-ray structure of a superfluorinated 20 kDa gold nanocluster, with an Au25 core coated by a shell of multi-branched highly fluorinated thiols (SF27) resulting in almost 500 fluorine atoms, i.e., ([Au25(SF27)18]0). The cluster shows a switchable solubility in the fluorous phase. X-ray analysis and computational studies reveal the key role of both intracluster and intercluster F···F contacts in driving [Au25(SF27)18]0 crystal packing and stabilization, highlighting the ability of multi-branched fluorinated thiols to endow atomically precise nanoclusters with remarkable crystallogenic behavior.

Photothermal motion: effect of low-intensity irradiation on the thermal motion of organic nanoparticles.

The effect of local photo-triggered heat release on the motion of organic nanopartcles (NP), a process that is itself thermal, is largely unexplored under low-intensity irradiation. Here, we develop organic NP specifically tailored for this study and demonstrate, comparing three different irradiation intensity regimes, that indeed the NP undergo "acceleration" upon light absorption (Photothermal Motion). These NP have a well-defined chemical composition and extremely high molar absorbance coefficient, and upon excitation, they deactivate mostly non radiatively with localized heat dissipation. The residual fluorescence efficiency is high enough to allow the detection of their trajectory in a simple wide field fluorescence microscope under low-intensity irradiation, a typical condition for NP bio-applications. The NP were characterized in detail from the photophysical point of view using UV-VIS absorption, steady-state and time-resolved fluorescence spectroscopy and ultra-fast transient absorption (UF-TA). A detailed analysis of the trajectories of the NP reveals a strong dependency of the diffusion coefficient on the irradiation intensity even in a low power regime. This behavior demonstrates the inhomogeneity of the environment surrounding the NP as a result of local heat generation. Upon irradiation, the effective temperature increase, that emerges from the analysis, is much larger than that expected for plasmonic NP. Anomalous diffusion object-motion analysis (ADOMA) revealed that, in the more intense irradiation regime, the motion of the NP is a fractional Brownian motion, which is a simple generalization of Brownian motion where the steps are not independent of each other.

Fullerenes against COVID-19: Repurposing C60 and C70 to Clog the Active Site of SARS-CoV-2 Protease.

The persistency of COVID-19 in the world and the continuous rise of its variants demand new treatments to complement vaccines. Computational chemistry can assist in the identification of moieties able to lead to new drugs to fight the disease. Fullerenes and carbon nanomaterials can interact with proteins and are considered promising antiviral agents. Here, we propose the possibility to repurpose fullerenes to clog the active site of the SARS-CoV-2 protease, Mpro. Through the use of docking, molecular dynamics, and energy decomposition techniques, it is shown that C60 has a substantial binding energy to the main protease of the SARS-CoV-2 virus, Mpro, higher than masitinib, a known inhibitor of the protein. Furthermore, we suggest the use of C70 as an innovative scaffold for the inhibition of SARS-CoV-2 Mpro. At odds with masitinib, both C60 and C70 interact more strongly with SARS-CoV-2 Mpro when different protonation states of the catalytic dyad are considered. The binding of fullerenes to Mpro is due to shape complementarity, i.e., vdW interactions, and is aspecific. As such, it is not sensitive to mutations that can eliminate or invert the charges of the amino acids composing the binding pocket. Fullerenic cages should therefore be more effective against the SARS-CoV-2 virus than the available inhibitors such as masinitib, where the electrostatic term plays a crucial role in the binding.

Deciphering the Reactive Pathways of Competitive Reactions inside Carbon Nanotubes.

Nanoscale control of chemical reactivity, manipulation of reaction pathways, and ultimately driving the outcome of chemical reactions are quickly becoming reality. A variety of tools are concurring to establish such capability. The confinement of guest molecules inside nanoreactors, such as the hollow nanostructures of carbon nanotubes (CNTs), is a straightforward and highly fascinating approach. It mechanically hinders some molecular movements but also decreases the free energy of translation of the system with respect to that of a macroscopic solution. Here, we examined, at the quantum mechanics/molecular mechanics (QM/MM) level, the effect of confinement inside CNTs on nucleophilic substitution (SN2) and elimination (syn-E2 and anti-E2) using as a model system the reaction between ethyl chloride and chloride. Our results show that the three reaction mechanisms are kinetically and thermodynamically affected by the CNT host. The size of the nanoreactor, i.e., the CNT diameter, represents the key factor to control the energy profiles of the reactions. A careful analysis of the interactions between the CNTs and the reactive system allowed us to identify the driving force of the catalytic process. The electrostatic term controls the reaction kinetics in the SN2 and syn/anti-E2 reactions. The van der Waals interactions play an important role in the stabilization of the product of the elimination process.

Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60.

Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C60. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol-1, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol-1 for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π-π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C60 was not present. The amino acid backbone assumed a "tepee-like" geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C60 binding.

Viscoelasticity and Noise Properties Reveal the Formation of Biomemory in Cells.

Living cells are neither perfectly elastic nor liquid and return a viscoelastic response to external stimuli. Nanoindentation provides force-distance curves, allowing the investigation of cell mechanical properties, and yet, these curves can differ from point to point on the cell surface, revealing its inhomogeneous character. In the present work, we propose a mathematical method to estimate both viscoelastic and noise properties of cells as these are depicted on the values of the scaling exponents of relaxation function and power spectral density, respectively. The method uses as input the time derivative of the response force in a nanoindentation experiment. Generalized moments method and/or rescaled range analysis is used to study the resulting time series depending on their nonstationary or stationary nature. We conducted experiments in living Ulocladium chartarum spores. We found that spores in the approaching phase present a viscoelastic behavior with the corresponding scaling exponent in the range 0.25-0.52 and in the retracting phase present a liquid-like behavior with exponents in the range 0.67-0.85. This substantial difference of the scaling exponents in the two phases suggests the formation of biomemory as a response of the spores to the indenting AFM mechanical stimulus. The retracting phase may be described as a process driven by bluish noises, while the approaching one is driven by persistent noise.

Human Serum Albumin-Oligothiophene Bioconjugate: A Phototheranostic Platform for Localized Killing of Cancer Cells by Precise Light Activation.

The electronic, optical, and redox properties of thiophene-based materials have made them pivotal in nanoscience and nanotechnology. However, the exploitation of oligothiophenes in photodynamic therapy is hindered by their intrinsic hydrophobicity that lowers their biocompatibility and availability in water environments. Here, we developed human serum albumin (HSA)-oligothiophene bioconjugates that afford the use of insoluble oligothiophenes in physiological environments. UV-vis and electrophoresis proved the conjugation of the oligothiophene sensitizers to the protein. The bioconjugate is water-soluble and biocompatible, does not have any "dark toxicity", and preserves HSA in the physiological monomeric form, as confirmed by dynamic light scattering and circular dichroism measurements. In contrast, upon irradiation with ultralow light doses, the bioconjugate efficiently produces reactive oxygen species (ROS) and leads to the complete eradication of cancer cells. Real-time monitoring of the photokilling activity of the HSA-oligothiophene bioconjugate shows that living cells "explode" upon irradiation. Photodependent and dose-dependent apoptosis is one of the primary mechanisms of cell death activated by bioconjugate irradiation. The bioconjugate is a novel theranostic platform able to generate ROS intracellularly and provide imaging through the fluorescence of the oligothiophene. It is also a real-time self-reporting system able to monitor the apoptotic process. The induced phototoxicity is strongly confined to the irradiated region, showing localized killing of cancer cells by precise light activation of the bioconjugate.

Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site.

The preferred spatial orientation of single-wall carbon nanotubes (SWCNTs) in their interaction with enzymes determines their behavior either as nano-supports or as inhibitors. α -chymotrypsin (α-CT) is considered a serine protease model for studying nanomaterial/proteases interactions. The interaction of α-CT with pristine single-wall carbon nanotubes is still unknown. Here α-CT/SWCNT hybrids are synthesized and characterized. Spectroscopic, microscopic and kinetic measurements, coupled to molecular dynamics simulations, provide a detailed description of the interaction between α-CT and SWCNTs. The SWCNT binding pocket was unambiguously identified. A perfect match is observed with the crevice structure of the α-CT substrate binding pocket. The activity of α-CT, upon SWCNT binding, is dramatically reduced, as expected by the interaction of the SWCNT in the active site of the protein. π-π stacking between aromatic residues and the conjugated surface of SWCNT governs α-CT/SWCNT interactions. An important role in the bonding appears also for purely hydrophobic residues and with residues able to establish surfactant-like interactions. The secondary structure of α-CT and the catalytic triad structure are not perturbed by the complex formation, on the contrary the volume of the substrate binding pocket is strongly reduced by SWCNT binding because SWCNT occupies the α-CT substrate binding site, clogging the active site.

Electron Dynamics with Explicit-Time Density Functional Theory of the [4+2] Diels-Alder Reaction.

The prototype Diels-Alder (DA) reaction between butadiene and ethene (system 1) and the DA reaction involving 1-methoxy-butadiene and cyano-ethylene (system 2) are investigated with an explicit-time-dependent Density Functional Theory approach. Bond orders and atomic net charges obtained in the dynamics at the transition state geometry and along the reaction coordinate toward reactants are used to provide a picture of the process in terms of VB/Lewis resonance structures that contribute to a resonance hybrid. The entire dynamics can be divided into different domains (reactant-like, product-like, and transition state domains) where different Lewis resonance structures contribute with different weights. The relative importance of these three domains varies along the reaction coordinate. In addition to the usual reactant-like and product-like covalent Lewis structures, ionic Lewis structures have non-negligible weights. In system 2, the electron-donor OCH3 on the diene and the electron-acceptor CN on the dienophile make more important the contributions of ionic Lewis structures that stabilize the transition state and determine the decrease of the reaction barrier with respect to system 1.

Complex Nanoparticle Diffusional Motion in Liquid-Cell Transmission Electron Microscopy.

Liquid-cell transmission electron microscopy (LCTEM) is a powerful in situ videography technique that has the potential to allow us to observe solution-phase dynamic processes at the nanoscale, including imaging the diffusion and interaction of nanoparticles. Artefactual effects imposed by the irradiated and confined liquid-cell vessel alter the system from normal "bulk-like" behavior in multiple ways. These artefactual LCTEM effects will leave their fingerprints in the motion behavior of the diffusing objects, which can be revealed through careful analysis of the object-motion trajectories. Improper treatment of the motion data can lead to erroneous descriptions of the LCTEM system's conditions. Here, we advance our anomalous diffusion object-motion analysis (ADOMA) method to extract a detailed description of the liquid-cell system conditions during any LCTEM experiment by applying a multistep analysis of the data and treating the x/y vectors of motion independently and in correlation with each other and with the object's orientation/angle.

Photocatalytic activity of exfoliated graphite-TiO2 nanoparticle composites.

We investigate the photocatalytic performance of composites prepared in a one-step process by liquid-phase exfoliation of graphite in the presence of TiO2 nanoparticles (NPs) at atmospheric pressure and in water, without heating or adding any surfactant, and starting from low-cost commercial reagents. These show enhanced photocatalytic activity, degrading up to 40% more pollutants with respect to the starting TiO2-NPs, in the case of a model dye target, and up to 70% more pollutants in the case of nitrogen oxides. In order to understand the photo-physical mechanisms underlying this enhancement, we investigate the photo-generation of reactive species (trapped holes and electrons) by ultrafast transient absorption spectroscopy. We observe an electron transfer process from TiO2 to the graphite flakes within the first picoseconds of the relaxation dynamics, which causes the decrease of the charge recombination rate, and increases the efficiency of the reactive species photo-production.