Α-carbon Research Articles

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations.

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. We present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

Application of artificial intelligence and machine learning techniques to the analysis of dynamic protein sequences.

We apply methods of Artificial Intelligence and Machine Learning to protein dynamic bioinformatics. We rewrite the sequences of a large protein data set, containing both folded and intrinsically disordered molecules, using a representation developed previously, which encodes the intrinsic dynamic properties of the naturally occurring amino acids. We Fourier analyze the resulting sequences. It is demonstrated that classification models built using several different supervised learning methods are able to successfully distinguish folded from intrinsically disordered proteins from sequence alone. It is further shown that the most important sequence property for this discrimination is the sequence mobility, which is the sequence averaged value of the residue-specific average alpha carbon B factor. This is in agreement with previous work, in which we have demonstrated the central role played by the sequence mobility in protein dynamic bioinformatics and biophysics. This finding opens a path to the application of dynamic bioinformatics, in combination with machine learning algorithms, to a range of significant biomedical problems.

Mathematical topology and geometry-based classification of tauopathies

Neurodegenerative diseases, like Alzheimer’s, are associated with the presence of neurofibrillary lesions formed by tau protein filaments in the cerebral cortex. While it is known that different morphologies of tau filaments characterize different neurodegenerative diseases, there are few metrics of global and local structure complexity that enable to quantify their structural diversity rigorously. In this manuscript, we employ for the first time mathematical topology and geometry to classify neurodegenerative diseases by using cryo-electron microscopy structures of tau filaments that are available in the Protein Data Bank. By employing mathematical topology metrics (Gauss linking integral, writhe and second Vassiliev measure) we achieve a consistent, but more refined classification of tauopathies, than what was previously observed through visual inspection. Our results reveal a hierarchy of classification from global to local topology and geometry characteristics. In particular, we find that tauopathies can be classified with respect to the handedness of their global conformations and the handedness of the relative orientations of their repeats. Progressive supranuclear palsy is identified as an outlier, with a more complex structure than the rest, reflected by a small, but observable knotoid structure (a diagrammatic structure representing non-trivial topology). This topological characteristic can be attributed to a pattern in the beginning of the R3 repeat that is present in all tauopathies but at different extent. Moreover, by comparing single filament to paired filament structures within tauopathies we find a consistent change in the side-chain orientations with respect to the alpha carbon atoms at the area of interaction.

Selective Generation of Aldimine and Ketimine Tautomers of the Schiff Base Condensates of Amino Acids with Imidazole Aldehydes or of Imidazole Methanamines with Pyruvates-Isomeric Control with 2- vs. 4-Substituted Imidazoles.

The Schiff base condensation of 5-methyl-4-imidazole carboxaldehyde, 5Me4ImCHO, and the anion of an amino acid, H2N-CH(R)CO2- (R = -CH3, -CH(CH3)2 and -CH2CH(CH3)2), gives the aldimine tautomer, Im-CH=N-CH(R)CO2-, while that of 5-methylimidazole-4-methanamine, 5MeIm-4-CH2NH2, with a 2-oxocarboxylate anion, R-C(O)-CO2-, gives the isomeric ketimine tautomer, Im-CH2-N=C(R)CO2-. All are isolated as the neutral nickel(II) complexes, NiL2, and are characterized by single crystal structure determination, IR, and positive ion ESI MS. In the cases of the 4 substituted imidazoles, either 5MeIm-4-CHO or 5MeIm-4-CH2NH2, both the aldimine and ketimine complexes are isolated cleanly with no evidence of an equilibrium between the two tautomers under the experimental conditions. The aldimines are blue while the tautomeric ketimines are green. In contrast, for the 2-substituted imidazoles, with either Im-2-CHO or Im-2-CH2NH2, the isolated product from the Schiff base condensation is the ketimine, which in the solid is green, as observed for the 4-isomer. These results suggest that for the 2-substituted imidazoles, there is a facile equilibrium between the aldimine and ketimine tautomers, and that the ketimine form is the thermodynamically favored tautomer. The aldimine tautomers of the 4-substituted imidazoles have three stereogenic centers, the nickel (Δ or Ʌ) and the two alpha carbon atoms (R or S). The observed pair of enantiomers is the ɅRR/ΔSS enantiomeric pair, suggesting that this pair is lower in energy than the others and that this is in general the preferred chiral correlation in these complexes.

Synergizing structure and function: Cinnamoyl hydroxamic acids as potent urease inhibitors

The current investigation encompasses the structural planning, synthesis, and evaluation of the urease inhibitory activity of a series of molecular hybrids of hydroxamic acids and Michael acceptors, delineated from the structure of cinnamic acids. The synthesized compounds exhibited potent urease inhibitory effects, with IC50 values ranging from 3.8 to 12.8 µM. Kinetic experiments unveiled that the majority of the synthesized hybrids display characteristics of mixed inhibitors. Generally, derivatives containing electron-withdrawing groups on the aromatic ring demonstrate heightened activity, indicating that the increased electrophilicity of the beta carbon in the Michael Acceptor moiety positively influences the antiureolytic properties of this compounds class. Biophysical and theoretical investigations further corroborated the findings obtained from kinetic assays. These studies suggest that the hydroxamic acid core interacts with the urease active site, while the Michael acceptor moiety binds to one or more allosteric sites adjacent to the active site.

Determination of pKa values and deprotonation order of methotrexate using a combined experimental-theoretical study and binding constants of the methotrexate-Laponite complex at different pH values

The pKa values of the cancer drug methotrexate (MTX) were calculated, using experimental UV–Vis spectroscopic data and with the aid of the Stability Quotients from Absorbance Data (SQUAD) in addition to its deprotonation pathway from theoretical calculations using Gaussian 09 package (M062X functional and 6–311++g** basis set), since there is a discrepancy in the order of deprotonation. Also, the binding constants (K) of the complex formed between MTX and the nano clay called Laponite (Lap) were calculated at two pH values. From the log β values obtained with SQUAD, three pKa values for MTX were calculated: 2.68 ± 0.07, 4.11 ± 0.05 and 5.48 ± 0.01 associating the first pKa value to the carboxyl group attached to the alpha carbon and the second pKa value to the carboxyl group of the gamma carbon. The interaction between the chemical species of this drug (MTXH3+ and MTX2−) and Lap was studied with UV–Vis spectrophotometry and SQUAD at pH values 2.0, and 7.5, resulting in a single equilibrium for the formation of the MTX-Lap complex with log K 4.36 ± 0.01 (1:1) and 1.99 ± 0.04 M−1 (1:1) respectively. Lastly, the free and encapsulated MTX percentage was calculated from the chemical-species distribution diagram of the MTX-Lap system at pH 1.4, which agrees with those determined experimentally.

A Method for Calculating the Sign and Degree of Chirality of Supercoiled Protein Structures

Chirality plays an important role in studies of natural protein structures. Therefore, much attention is paid to solving the problems associated with the development of criteria and methods for assessing the chirality of biomolecules. In this paper, a new method for calculating the sign and degree of chirality of superhelices is proposed. The method makes it possible to characterize the chirality sign and to quantify coiled-coils and collagen superhelices. The degree of chirality is understood as a value indicating the intensity of twisting of individual helices around the axis of the superhelix. The calculation requires information about the relative spatial arrangement of the alpha carbon of the amino acid residues of the helices that make up the superhelix. The use of a small amount of raw data makes the method easy to apply, and the validity of the results of this study is confirmed through the analysis of real protein structures.

Efficient preparation of polyethylene glycol (PEG)-modified lignin from steam exploded hardwood biomass

The structures and characteristics of lignin derivatives prepared from steam exploded beech under alkali delignification and acid catalyzed polyethylene glycol (PEG) solvolysis were studied in detail. An efficient method for directly isolating PEG-modified lignin from wood was proposed to improve its thermal stability. The effects of steam explosion (SE) parameters and delignification process on lignin structure were studied by high performance anion exchange chromatograph, fourier transform infrared spectroscopy (FTIR), heteronuclear single quantum coherence (HSQC) NMR spectroscopies, ultraviolet and visible spectrophotometry, size exclusion chromatography (SEC) and thermogravimetric analysis (TGA). The results showed that SE pretreatment can greatly promote the yield of PEG-modified lignin. The PEG-modified lignin, isolated from steam exploded wood at 210 °C for 2.5 min, was ∼14% yield. The PEG moiety was located at the alpha carbon position of the β-O-4 linkage. The PEG-modified lignin exhibited improved thermal properties with a maximum weight loss temperature (Tdmax) greater than 380 ℃, and a degradation starting temperature (Tdst) in the range of 258–277 °C, met the temperature for polymer processing and contribute to improve the added value of lignin.

Molecular Mechanisms Involved in the Chemical Instability of ONC201 and Methods to Counter Its Degradation in Solution.

Glioblastoma is one of the most common and aggressive forms of brain tumor, a rare disease for which there is a great need for innovative therapies. ONC201, a new drug substance, has been used in a compassionate treatment program where the choice of dosage form and regimen have yet to be justified. The prior knowledge needed to anticipate ONC201 stability problems has recently been partially addressed, by (i) showing that ONC201 is sensitive to light and oxidation and (ii) identifying the molecular structures of the main degradation products formed. The aim of the work presented here was to improve our understanding of the degradation pathways of ONC201 using data from ab initio calculations and experimental work to supplement the structural information we already published. The C-H bonds located αto the amine of the tetrahydropyridine group and those located alpha to the imine function of the dihydroimidazole group exhibit the lowest bond dissociation energies (BDEs) within the ONC201 molecule. Moreover, these values drop well below 90 kcal.mol-1 when ONC201 is in an excited state (S1; T1). The structures of the photoproducts we had previously identified are consistent with these data, showing that they would have resulted from radical processes following the abstraction of alpha hydrogens. Concerning ONC201's sensitivity to oxidation, the structures of the oxidation products matched the critical points revealed through mapped electrostatic potential (MEP) and average local ionization energy (ALIE). The data obtained from ab initio calculations and experimental work showed that the reactivity of ONC201 to light and oxidation conditions is highly dependent on pH. While an acidic environment (pH < 6) contributes to making ONC201 quantitatively more stable in solution in the face of oxidation and photo-oxidation, it nevertheless seems that certain chemical groups in the molecule are more exposed to nucleophilic attacks, which explains the variation observed in the profile of degradation products formed in the presence of certain antioxidants tested. This information is crucial to better understand the stability results in the presence of antioxidant agents and to determine the right conditions for them to act.

Lipid biology of plasmalogen-derived halolipids: Signature molecules of myeloperoxidase and eosinophil peroxidase activity

Myeloperoxidase and eosinophil peroxidase exert their antimicrobial functions through the oxidative actions of their hypohalous acid products. Plasmalogen phospholipids are particularly susceptible to oxidation of their vinyl ether functional group by hypohalous acids. This produces a family of halogenated lipid products with pro-inflammatory roles and potential biomarker utility. The initial product of plasmalogen oxidation by HOCl is 2-chlorofatty aldehyde, which has been shown to play a key role at the blood-endothelium interface. In vitro and in vivo studies indicate increased endothelial barrier permeability, neutrophil chemotaxis, neutrophil and platelet adherence to endothelium, and promotion of erythrocyte lysis as some of its effects. These effects may be due to protein modification by 2-chlorofatty aldehyde. 2-Chlorofatty aldehyde is metabolized by host dehydrogenases to 2-chlorofatty acid. While it is less chemically reactive, 2-chlorofatty acid has partial overlap of pro-inflammatory effects with 2-chlorofatty aldehyde and unique actions such as induction of neutrophil extracellular trap formation. The stability of 2-chlorofatty acid in plasma also makes it well-suited as a biomarker of HOCl generation, and its plasma levels may be predictive of disease outcomes. 2-Bromofatty aldehydes and acids are produced analogously from HOBr reaction with plasmalogens. Their functions have yet to be well-elucidated, though similarities with chlorolipids have been observed, and increased reactivity with proteins is expected through enhanced electrophilicity of the alpha carbon. Altogether, these halogenated lipids represent underexplored mediators of diseases involving excess hypohalous acid production.

Gypenosides Synergistically Reduce the Extracellular Matrix of Hepatic Stellate Cells and Ameliorate Hepatic Fibrosis in Mice.

Liver fibrosis resulting from chronic liver damage is becoming one of the major threats to health worldwide. Active saponin constituents isolated from Gynostemma pentaphyllum were found to possess a protective effect in liver diseases. Here, we obtained a naturally abundant gypenoside, XLVI, and evaluated its liver protection activity in both animal and cellular models. The results showed that it ameliorated acute and chronic liver injuries and lightened the process of fibrogenesis in vivo. XLVI can inhibit TGF-β-induced activation of hepatic stellate cells and ECM deposition in vitro. The underlying mechanism study verified that it upregulated the protein expression of protein phosphatase 2C alpha and strengthened the vitality of the phosphatase together with a PP2Cα agonist gypenoside NPLC0393. These results shed new light on the molecular mechanisms and the potential therapeutic function of the traditional herb Gynostemma pentaphyllum in the treatment of liver fibrosis.

A detailed chemical kinetic mechanism of 1,1-diamino-2,2-dinitroethylene (FOX-7) initial decomposition in the gas phase

1,1-Diamino-2,2-dinitroethylene (FOX-7 or DADNE) is a promising ingredient of the low-vulnerability propellants. However, one of the major concerns in its further development and applications is the lack of detailed kinetic mechanism for its initial decomposition in the gas phase. In this study, a detailed chemical kinetic mechanism consisting of 38 species and 131 reactions was developed to describe the initial decomposition process of FOX-7. At first, a comprehensive reaction network was established with the aid of reactive molecular dynamics (MD) simulation. Then, the potential energy surfaces (PES) for both unimolecular and bimolecular reactions were identified at the QCISD(T)/CBS//M062X/6-311++G(d,p) level of theory. The rate coefficients were obtained by solving RRKM/ME, and the thermochemical properties of relevant species were calculated at CBS-APNO/G3/G4 levels with the atomization method. Finally, these kinetic and thermochemistry data were processed into a kinetic mechanism and used to simulate the initial decomposition process of FOX-7. The results demonstrated that the H-atom transfer to the beta carbon atom (enamino-imino isomerization) followed by the nitro group elimination dominates the initial decomposition, and the reaction FOX-7 = R3a + NO2 becomes the most significant one under high temperatures (Channel C3). Besides, bimolecular reactions also play a role as the decomposition goes on. Overall, this work provides quantitative predictions of the reaction pathways of gas-phase FOX-7 initial decomposition, and it would serve as a solid foundation for the development of a fully detailed combustion kinetic mechanism for FOX-7.

Review: Structure-Activity Relationship of Antimicrobial Peptoids.

Due to their broad-spectrum activity against Gram-negative and Gram-positive bacteria, natural antimicrobial peptides (AMPs) and their synthetic analogs have emerged as prospective therapies for treating illnesses brought on by multi-drug resistant pathogens. To overcome the limitations of AMPs, such as protease degradation, oligo-N-substituted glycines (peptoids) are a promising alternative. Despite having the same backbone atom sequence as natural peptides, peptoid structures are more stable because, unlike AMP, their functional side chains are attached to the backbone nitrogen (N)-atom rather than the alpha carbon atom. As a result, peptoid structures are less susceptible to proteolysis and enzymatic degradation. The advantages of AMPs, such as hydrophobicity, cationic character, and amphipathicity, are mimicked by peptoids. Furthermore, structure-activity relationship studies (SAR) have shown that tuning the structure of peptoids is a crucial step in developing effective antimicrobials.

Protein model quality assessment using rotation-equivariant transformations on point clouds.

Machine learning research concerning protein structure has seen a surge in popularity over the last years with promising advances for basic science and drug discovery. Working with macromolecular structure in a machine learning context requires an adequate numerical representation, and researchers have extensively studied representations such as graphs, discretized 3D grids, and distance maps. As part of CASP14, we explored a new and conceptually simple representation in a blind experiment: atoms as points in 3D, each with associated features. These features-initially just the basic element type of each atom-are updated through a series of neural network layers featuring rotation-equivariant convolutions. Starting from all atoms, we further aggregate information at the level of alpha carbons before making a prediction at the level of the entire protein structure. We find that this approach yields competitive results in protein model quality assessment despite its simplicity and despite the fact that it incorporates minimal prior information and is trained on relatively little data. Its performance and generality are particularly noteworthy in an era where highly complex, customized machine learning methods such as AlphaFold 2 have come to dominate protein structure prediction.

Increasing Linker Chain Length and Intestinal Stability Enhances Lymphatic Transport and Lymph Node Exposure of Triglyceride Mimetic Prodrugs of a Model Immunomodulator Mycophenolic Acid.

Targeted delivery of immunomodulators to the lymphatic system has the potential to enhance therapeutic efficacy by increasing colocalization of drugs with immune targets such as lymphocytes. A triglyceride (TG)-mimetic prodrug strategy has been recently shown to enhance the lymphatic delivery of a model immunomodulator, mycophenolic acid (MPA), via incorporation into the intestinal TG deacylation-reacylation and lymph lipoprotein transport pathways. In the current study, a series of structurally related TG prodrugs of MPA were examined to optimize structure-lymphatic transport relationships for lymph-directing lipid-mimetic prodrugs. MPA was conjugated to the sn-2 position of the glyceride backbone of the prodrugs using linkers of different chain length (5-21 carbons) and the effect of methyl substitutions at the alpha and/or beta carbons to the glyceride end of the linker was examined. Lymphatic transport was assessed in mesenteric lymph duct cannulated rats, and drug exposure in lymph nodes was examined following oral administration to mice. Prodrug stability in simulated intestinal digestive fluid was also evaluated. Prodrugs with straight chain linkers were relatively unstable in simulated intestinal fluid; however, co-administration of lipase inhibitors (JZL184 and orlistat) was able to reduce instability and increase lymphatic transport (2-fold for a prodrug with a 6-carbon spacer, i.e., MPA-C6-TG). Methyl substitutions to the chain resulted in similar trends in improving intestinal stability and lymphatic transport. Medium- to long-chain spacers (C12, C15) between MPA and the glyceride backbone were most effective in promoting lymphatic transport, consistent with increases in lipophilicity. In contrast, short-chain (C6-C10) linkers appeared to be too unstable in the intestine and insufficiently lipophilic to associate with lymph lipid transport pathways, while very long-chain (C18, C21) linkers were also not preferred, likely as a result of increases in molecular weight reducing solubility or permeability. In addition to more effectively promoting drug transport into mesenteric lymph, TG-mimetic prodrugs based on a C12 linker resulted in marked increases (>40 fold) in the exposure of MPA in the mesenteric lymph nodes in mice when compared to administration of MPA alone, suggesting that optimizing prodrug design has the potential to provide benefit in targeting and modulating immune cells.

A Systematic Degradation Kinetics Study of Dalbavancin Hydrochloride Injection Solutions

The degradation kinetics of the glycopeptide antibiotic dalbavancin in solution are systematically evaluated over the pH range 1–12 at 70°C. The decomposition rate of dalbavancin was measured as a function of pH, buffer composition, temperature, ionic strength, and drug concentration. A pH-rate profile was constructed using pseudo first-order kinetics at 70°C after correcting for buffer effects; the observed pH-rate profile could be fitted with standard pseudo first order rate laws. The degradation reactions of dalbavancin were found to be strongly dependent on pH and were catalyzed by protons or hydroxyl groups at extreme pH values. Dalbavancin shows maximum stability in the pH region 4–5. Based on the Arrhenius equation, dalbavancin solution at pH 4.5 is predicted to have a maximum stability of thirteen years under refrigerated conditions, eight months at room temperature and one month at 40°C. Mannosyl Aglycone (MAG), the major thermal and acid degradation product, and DB-R6, an additional acid degradation product, were formed in dalbavancin solutions at 70°C due to hydrolytic cleavage at the anomeric carbons of the sugars. Through deamination and hydrolytic cleavage of dalbavancin, a small amount of DB-Iso-DP2 (RRT-1.22) degradation product was also formed under thermal stress at 70°C. A greater amount of the base degradation product DB-R2 forms under basic conditions at 70°C due to epimerization of the alpha carbon of phenylglycine residue 3.

Fabrication and characterisation of proton exchange membrane from sulfonated natural rubber for possible use as an alternative separator in AGM battery

Proton Exchange Membrane was fabricated from sulfonated natural rubber (NR) as an alternative to absorptive glass mat (AGM) separator for AGM battery. The separator was fabricated using chlorosulphuric acid as the sulfonating agent at 0 °C under continuous stirring. Water uptake at 25 °C ranges from 0 to 58% while at 60 °C the range is from 4 to 38%, which suggest a strong attraction between the water molecules and sulfonate moiety. The acid uptake ranges from 18 to 83% for all three membranes (A, B and C) fabricated, which proves excellent electrolyte uptake, resistance to oxidation and acid attack. The FTIR analyses, water uptake, acid uptake and Carbon-Sulphur analysis confirm that the sulfonation occurred in NR through substitution reaction on the alpha carbons. The incorporation of ZnO and SiO2, caused increase in cell size, which indicate the porous and spongy structure throughout the surface area of each membrane, which indicate promising materials for application in AGM battery.

Evaluation of AlphaFold2 structures as docking targets.

AlphaFold2 is a promising new tool for researchers to predict protein structures and generate high-quality models, with low backbone and global root-mean-square deviation (RMSD) when compared with experimental structures. However, it is unclear if the structures predicted by AlphaFold2 will be valuable targets of docking. To address this question, we redocked ligands in the PDBbind datasets against the experimental co-crystallized receptor structures and against the AlphaFold2 structures using AutoDock-GPU. We find that the quality measure provided during structure prediction is not a good predictor of docking performance, despite accurately reflecting the quality of the alpha carbon alignment with experimental structures. Removing low-confidence regions of the predicted structure and making side chains flexible improves the docking outcomes. Overall, despite high-quality prediction of backbone conformation, fine structural details limit the naive application of AlphaFold2 models as docking targets.

MPAI-Ligand Accelerated Pd-Catalyzed C(sp3)-H Arylation of Free Aliphatic Acids.

Here, we report the development of a class of bifunctional monoprotected amino-imidazoline (MPAI) ligands and their applications in Pd-catalyzed C(sp3)-H arylation of free aliphatic acids. The newly developed MPAI ligand allows the use of 1.0 equiv of aliphatic acids containing an alpha hydrogen for the first time.

Molecular dynamics simulations of the SARS-CoV-2 Spike protein and variants of concern: structural evidence for convergent adaptive evolution

The Spike protein's structure of the SARS-CoV-2 provides a unique opportunity to consider perturbations at the atomic level. We used the cryo-electron microscopy structure of the open conformation of the Spike protein to assess the impact of the mutations observed in the variants of concern at the molecular level. Molecular dynamics were subsequently performed with both the wt and the mutated forms to compare the flexibility and variation data for each residue of the three-dimensional fluctuations in the region associated with each alpha carbon. Additionally, protein-protein docking was used to investigate the interaction of each mutated profile with the ACE-2 receptor. After the molecular dynamics, the results show that the mutations increased the stability of the trimeric protein, with greater stability observed in the Gamma variant harboring the 10 characteristic mutations. The results of molecular dynamics, as shown by RMSF demonstrated for the residues that comprise the binding domain receptor (RBD), exhibited a reduction in flexibility, which was more pronounced in the Gamma variant. Finally, protein-protein docking experiments revealed an increase in the number of hydrophobic interactions and hydrogen bonds in the Gamma variant against the ACE-2 receptor, as opposed to the other variants. Taken together, these in silico experiments suggest that the evolution of the mutations favored the increased stability of Spike protein while potentially improving its interaction with the ACE-2 receptor, which in turn may indicate putative structural outcomes of the selection of these mutations in the convergent adaptive evolution as it has been observed for SARS-CoV-2. Communicated by Ramaswamy H. Sarma