Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

A Computational Approach to Investigate TDP-43 RNA-Recognition Motif 2 C-Terminal Fragments Aggregation in Amyotrophic Lateral Sclerosis

Many of the molecular mechanisms underlying the pathological aggregation of proteins observed in neurodegenerative diseases are still not fully understood. Among the aggregate-associated diseases, Amyotrophic Lateral Sclerosis (ALS) is of relevant importance. In fact, although understanding the processes that cause the disease is still an open challenge, its relationship with protein aggregation is widely known. In particular, human TDP-43, an RNA/DNA binding protein, is a major component of the pathological cytoplasmic inclusions observed in ALS patients. Indeed, the deposition of the phosphorylated full-length TDP-43 in spinal cord cells has been widely studied. Moreover, it has also been shown that the brain cortex presents an accumulation of phosphorylated C-terminal fragments (CTFs). Even if it is debated whether the aggregation of CTFs represents a primary cause of ALS, it is a hallmark of TDP-43 related neurodegeneration in the brain. Here, we investigate the CTFs aggregation process, providing a computational model of interaction based on the evaluation of shape complementarity at the molecular interfaces. To this end, extensive Molecular Dynamics (MD) simulations were conducted for different types of protein fragments, with the aim of exploring the equilibrium conformations. Adopting a newly developed approach based on Zernike polynomials, able to find complementary regions in the molecular surface, we sampled a large set of solvent-exposed portions of CTFs structures as obtained from MD simulations. Our analysis proposes and assesses a set of possible association mechanisms between the CTFs, which could drive the aggregation process of the CTFs. To further evaluate the structural details of such associations, we perform molecular docking and additional MD simulations to propose possible complexes and assess their stability, focusing on complexes whose interacting regions are both characterized by a high shape complementarity and involve β3 and β5 strands at their interfaces.

Assessment of Globularity of Protein Structures via Minimum Volume Ellipsoids and Voxel-Based Atom Representation

A computer algorithm for assessment of globularity of protein structures is presented. By enclosing the input protein in a minimum volume ellipsoid (MVEE) and calculating a profile measuring how voxelized space within this shape (cubes on a uniform grid) is occupied by atoms, it is possible to estimate how well the molecule resembles a globule. For any protein to satisfy the proposed globularity criterion, its ellipsoid profile (EP) should first confirm that atoms adequately fill the ellipsoid’s center. This property should then propagate towards the surface of the ellipsoid, although with diminishing importance. It is not required to compute the molecular surface. Globular status (full or partial) is assigned to proteins with values of their ellipsoid profiles, called here the ellipsoid indexes (EI), above certain levels. Due to structural outliers which may considerably distort the measurements, a companion method for their detection and reduction of their influence is also introduced. It is based on kernel density estimation and is shown to work well as an optional input preparation step for MVEE. Finally, the complete workflow is applied to over two thousand representatives of SCOP 2.08 domain superfamilies, surveying the landscape of tertiary structure of proteins from the Protein Data Bank.

Delafloxacin, Finafloxacin, and Zabofloxacin: Novel Fluoroquinolones in the Antibiotic Pipeline

Novel antimicrobial agents, approved for clinical use in past years, represent potential treatment options for various infections. In this review, we summarize the most important medical and microbiological features of three recently approved fluoroquinolones, namely delafloxacin, finafloxacin, and zabofloxacin. Delafloxacin possesses an anionic chemical structure, and represents broad-spectrum activity, as it targets both bacterial DNA gyrase and topoisomerase IV enzymes of gram-positive and gram-negative bacteria with equal affinity. Its molecular surface is larger than that of other fluoroquinolones, and it has enhanced antibacterial efficacy in acidic environments. Delafloxacin has been approved to treat acute bacterial skin and skin-structure infections, as well as community-acquired bacterial pneumonia. Finafloxacin has a zwitterionic chemical structure, and targets both DNA gyrase and topoisomerase IV enzymes. This enables a broad antibacterial spectrum; however, finafloxacin has so far only been approved in ear-drops to treat bacterial otitis externa. Zabofloxacin is also a broad-spectrum fluoroquinolone agent, and was first approved in South Korea to treat acute bacterial exacerbation of chronic obstructive pulmonary disease. The introduction of these novel fluoroquinolones into daily practice extends the possible indications of antibiotics into different bacterial infections, and provides treatment options in difficult-to-treat infections. However, some reports of delafloxacin resistance have already appeared, thus underlining the importance of the prudent use of antibiotics.

Subzero Nonfreezing Hypothermia with Insect Antifreeze Protein Dramatically Improves Survival Rate of Mammalian Cells

Cells for therapeutic use are often preserved at +4 °C, and the storage period is generally limited to 2–3 days. Here, we report that the survival rate (%) of mammalian cells is improved to 10–20 days when they are preserved with a subzero supercooled solution containing the antifreeze protein (AFP), for which an ability to stabilize both supercooled water and cell membrane integrity has been postulated. We chose adherent rat insulinoma (RIN-5F) cells as the preservation target, which were immersed into −5 °C-, −2 °C-, or +4 °C-chilled “unfrozen” solution of Euro-Collins or University of Washington (UW) containing the AFP sample obtained from insect or fish. Our results show that the survival rate of the cells preserved with the solution containing insect AFP was always higher than that of the fish AFP solution. A combination of the −5 °C-supercooling and insect AFP gave the best preservation result, namely, UW solution containing insect AFP kept 53% of the cells alive, even after 20 days of preservation at −5 °C. The insect AFP locates highly organized ice-like waters on its molecular surface. Such waters may bind to semiclathrate waters constructing both embryonic ice crystals and a membrane–water interface in the supercooled solution, thereby protecting the cells from damage due to chilling.

Application of the Zimm-Bragg Model to the Removal of Azo Dyes with Pectin

In this work, the ability of pectin (Pec) to remove direct red 80 (DR80), Congo red (CR), methyl orange (MO), and methyl red (MR) was studied. The removal percentages under adequate pH and ionic strength conditions were as follows: DR80 (99.5%), CR (99.8%), MO (88.6%), and MR (68%), showing that this methodology is efficient to remove azo dyes. The proposed method included the addition of native Pec to the dye aqueous solution and the formation of a gel that occurred when a calcium salt solution was added. This gel retains the molecules adsorbed onto the molecular surface of Pec through hydrogen bonds and electrostatic and hydrophobic interactions. To our knowledge, it is the first time that the Zimm-Bragg model is used to describe the removal of azo dyes with native Pec. This model includes two parameters: K u (nucleation constant), which is related to the tendency exerted by a dye molecule attached to the Pec to bind to other molecules present in the aqueous phase, and U (cooperativity parameter), which determines the aggregation capacity of the dye molecules already attached to the Pec. This model fits the experimental isotherms very well, suggesting that Pec binds single molecules and dye aggregates. The obtained results in the values of K u ranged from 922 mol/kg (MR) to 1,157,462 mol/kg (CR), and U varied from 2.51 (MR) to 169.19 (MO). These results suggest that the use of Pec is a viable option to remove azo dyes from aqueous effluents and that the Zimm-Bragg model fits adequately the isotherms of dyes that have a high tendency to form aggregates.

Synthesis and Crystal Structure of Benzyl 4-(2-fluoro-4-(trifluoromethyl)phenyl)- 2,6,6-trimethyl-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate and Its DFT Analysis Combined with Bond Order Modeling in Terms of The Bond Critical Point Quantities

Inflammation is the underlying cause of many diseases such as cardiovascular diseases, cancer and autoimmune diseases. Recently 1,4-dihydropyridine (1,4-DHP) compounds were found effective to reduce inflammation which contributes to development of inflammation associated diseases. Based on these data we synthesized to investigate this type of action of annulated 1,4-DHP molecule, benzyl 4-(2-fluoro-4-(trifluoromethyl)phenyl)-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate and proved the structure of this molecule by IR, 1H-NMR, 13C-NMR, HMRS and X-ray crystallography.X-ray analyses were conducted to find out the exact 3D structure of the mentioned molecule. The molecular structure crystallizes in triclinic space group, P-1, with a = 7.0889(11) Å, b = 12.4861(18) Å, c = 14.338(2) Å, α = 66.899(4)°, β = 89.025(4)°, γ = 85.101(4)° and V = 1162.9(3) Å3. In the title molecule, C27H25F4NO3, the cyclohexene ring is in a sofa conformation and the 1,4-dihydropyridine ring is in a slight boat conformation. In the 2-fluoro phenyl and benzyl rings form a dihedral angle of 13.6(1)°. In the crystal structure stabilized by the intra- and intermolecular N—H···O, C—H···O and C—H···F interactions. The molecules are linked together to form a dimer by N(1)—H(1N) ···O(1)i and C(2)—H(2A) ···O(1)i hydrogen bonds [symmetry code: (i) x+1,y,z ], producing two R12(6) rings.Natural charge, QTAIM, bond order, molecular planarity and molecular surface analyses have been performed on the optimized geometry by DFT. Considering the quantities obtained at the bond critical poins, the chemical bonds are discussed for classification. The correlation between bond critical point quantities and the bond orders based on different definitions have been explored considering different bond order models from the literature. The Laplacian Bond Order (LBO) gives best correlation for four of five bond order models. All the bond order models with an exception of the model with parameter G have approximately same correlation degree for C-C bonds. For C-H bonds, only bond model with parameters of electron density and the principle curvatures for LBO gives relatively good correlation with R2 value of 0.943. The two phenyl rings of the structure have aromaticity comparable to benzene as deduced from QTAIM quantities and molecular planarity metrics. As a result of molecular surface analysis, the mass density, molecular polarity index, v (the measure of charge balance), σ2tot .v (measure of intermolecular interactions) were calculated and compared with literature values.

Production and Characterization of Paper Board Mill ETP Sludge Derived Hydrochar

Hydrothermal Carbonization an emerging technology for the conversion of biomass into carbon rich materials called as hydrochar. In this study, the paper board mill ETP sludge has been used for the production of hydrochar. The characterization of point of zero charge, Heavy metals, proximate and ultimate constituents, structural morphology (SEM), and molecular surface functionalities (FTIR) were also analysed. The results of Hydrochar showed slightly acidic pH (6.40), EC (1.33), and the pHPZC (point of zero charge) of 7.8 and the heavy metals content were found to be below detectable limit. FTIR analysis revealed that, the produced hydrochar have oxygen containing functional groups (-OH, C-O-C, -C=O). SEM analysis has the morphological features such as spongy, fuzzy and fluffy porous network on surfaces. These results of hydrochar can be act as an active adsorbent with further activation.

Real-Time Structure Search and Structure Classification for AlphaFold Protein Models

AlphaFold2 showed a substantial improvement in the accuracy of protein structure prediction. Following the release of the software, whole-proteome protein structure predictions by AlphaFold2 for 21 organisms were made publicly available. Here, we developed the infrastructure, 3D-AF-Surfer, to enable real-time structure-based search for the AlphaFold2 models by combining molecular surface representation with 3D Zernike descriptors and deep neural networks.

Simulation atomic force microscopy to predict correlated conformational dynamics in proteins from topographic imaging

Atomic force microscopy (AFM) of proteins can detect only changes within the scanned molecular surface, missing all motions in other regions and thus information about functionally relevant conformational couplings. We show that simulation AFM can overcome this drawback by reconstruction of 3D molecular structures from topographic AFM images. A proof of principle demonstration is provided for an in-silico AFM experiment visualizing the conformational dynamics of a membrane transporter. The application shows that the alternating access mechanism underlying its operation can be retrieved from only AFM imaging of one membrane side. Simulation AFM is implemented in the freely available BioAFMviewer software platform, providing the convenient applicability to better understand experimental AFM observations.