FT-IR, FT-raman and UV spectra and ab initio HF and DFT study of conformational analysis, molecular structure and properties of ortho- meta- and para-chlorophenylboronic acid isomers

In this study, the FT-IR, FT-Raman, and UV-Vis spectroscopic properties of three monosubstituted phenylboronic acid derivatives: ortho-chlorophenylboronic acid (o-ClPhBA), meta-chlorophenylboronic acid (m-ClPhBA) and para-chlorophenylboronic acid (p-ClPhBA) molecules are investigated both experimentally and theoretically using Density Functional Theory (B3LYP) and Hartree Fock (HF). In order to find the stable possible conformations of the compounds, the conformational analysis was carried out by running potential energy surface (PES) scan by means of rotation of two structural parameters, the dihedral angles indicated as φ2 (C6-B-O1-H1A) and φ3 (C6-B-O2-H2A), varying from -180° to 180° with an increment of 10° using B3LYP/6-31G level of theory. Also, to determinate the most stable conformer for all the molecules, potential energy curve (PEC) the stable possible conformations on PES scan were investigated as a function of φ1 (C1-C6-B-O1) dihedral angle from 0° up to 180° with an increment of 10° using B3LYP/6-311++G(d,p) and HF/6-311++G(d,p) level of theory. For all the studied compounds, two conformational structures (conformer anti-anti, syn-syn) that did not have imaginary frequency values outside the equilibrium state (conformer anti-syn) were detected theoretically at the both methods. Due to their conformational flexibility, the relative stabilities of the anti-syn, anti-anti, and syn-syn conformers of o-ClPhBA, m-ClPhBA, and p-ClPhBA are 0.0, 4.66, and 6.76 kcal/mol, respectively, at the B3LYP/6-311++G(d,p) level of theory. For the HF/6-311++G(d,p) level of theory, the relative stabilities are 0.00, 4.54, and 6.11 kcal/mol for o-ClPhBA; 0.00, 3.98, and 1.51 kcal/mol for m-ClPhBA; and 0.00, 4.10, and 1.44 kcal/mol for p-ClPhBA, respectively. Some of the determined stable conformations of these molecules are different in symmetry groups. It was observed that the increase in the symmetry was effective in the of molecular properties, especially for vibrational frequencies. The structural parameter, dipole moments (μ), vibrational frequencies, polarizability (α), hyperpolarizability (β), the highest occupied molecular orbital (HOMO), and the lowest unoccupied molecular orbital (LUMO) of the stable conformers were calculated by using Ab initio HF/6-311++G(d,p) and DFT/B3LYP/6-311++G(d,p) level of theory. The assignments of fundamental vibrational modes of the studied molecule were performed based on total energy distribution (TED) analysis.

Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design

Inter-residue interactions in protein structures provide valuable insights into protein folding and stability. Understanding these interactions can be helpful in many crucial applications, including rational design of therapeutic small molecules and biologics, locating functional protein sites, and predicting protein-protein and protein-ligand interactions. The process of developing machine learning models incorporating inter-residue interactions has been improved recently. This review highlights the theoretical models incorporating inter-residue interactions in predicting folding and unfolding rates of proteins. Utilizing contact maps to depict inter-residue interactions aids researchers in developing computer models for detecting remote homologs and interface residues within protein-protein complexes which, in turn, enhances our knowledge of the relationship between sequence and structure of proteins. Further, the application of contact maps derived from inter-residue interactions is highlighted in the field of drug discovery. Overall, this review presents an extensive assessment of the significant models that use inter-residue interactions to investigate folding rates, unfolding rates, remote homology, and drug development, providing potential future advancements in constructing efficient computational models in structural biology.

The mutual and dynamic role of TSPO and ligands in their binding process: An example with PK-11195

Translocator protein (TSPO) is an 18 kDa transmembrane protein, localized primarily on the outer mitochondrial membrane. It has been found to be involved in various physiological processes and pathophysiological conditions. Though studies on its structure have been performed only recently, there is little information on the nature of dynamics and doubts about some structures referenced in the literature, especially the NMR structure of mouse TSPO. In the present work, we thoroughly study the dynamics of mouse TSPO protein by means of atomistic molecular dynamics simulations, in presence as well as in absence of the diagnostic ligand PKA. We considered two starting structures: the NMR structure and a homology model (HM) generated on the basis of X-ray structures from bacterial TSPO. We examine the conformational landscape in both the modes for both starting points, in presence and absence of the ligand, in order to measure its impact for both structures. The analysis highlights high flexibility of the protein globally, but NMR simulations show a surprisingly flexibility even in the presence of the ligand. Interestingly, this is not the case for HM calculations, to the point that the ligand seems not so stable as in the NMR system and an unbinding event process is partially sampled. All those results tend to show that the NMR structure of mTSPO seems not deficient but is just in another portion of the global conformation space of TSPO.

Structure prediction of physiological bis(amino acidato)copper(II) species in aqueous solution: The copper(II) compounds with l-glutamine and l-histidine

Neutral (l-histidinato)(l-glutaminato)copper(II) [Cu(His)(Gln)] has been established as the most abundant ternary copper(II) amino acid compound of the exchangeable copper(II) pool in blood plasma. The experimental studies of Cu(His)(Gln) and bis(glutaminato)copper(II) [Cu(Gln)2] in solutions did not specify their complete geometries. To determine the geometries, this paper investigates the conformers, energy landscapes, and a structure-magnetic parameters relation of Cu(Gln)2 and Cu(His)(Gln) by the density functional theory (DFT) calculations. We assume a glycine-like coordination of Gln (other coordination patterns are dismissed because of steric reasons), and three His in-plane copper(II) binding modes. The conformational analyses are performed in the gas phase and implicitly modeled aqueous solution. The reliability of the DFT relative electronic and Gibbs free energies of the Cu(His)(Gln) conformers is confirmed by benchmarking against the corresponding energies obtained by the domain-based local pair natural orbital coupled-cluster method with singles, doubles, and perturbative triples [DLPNO-CCSD(T)]. Several cis- and trans-Cu(His)(Gln) conformers with His in the histaminate-like and glycine-like modes have low Gibbs free energies, and the greatest estimated metal-binding affinities. The DFT-calculated magnetic parameters of the low-energy conformers reproduce best the experimental electron paramagnetic resonance parameters measured in aqueous solutions for trans- and cis-Cu(Gln)2 conformers having two oxygen atoms (either from Gln or water molecules) at the apical positions, and Cu(His)(Gln) conformers having His in the histaminate-like mode with an apically placed carboxylato oxygen atom. The predicted conformational flexibility of His‑copper(II)-amino acid compounds may be connected with their physiological abundance, and the role in copper(II) exchange reactions in blood plasma.

Introduction of constrained Trp analogs in RW9 modulates structure and partition in membrane models

Over the past decades, many cell-penetrating peptides (CPP) have been studied for their capacity to cross cellular membranes, mostly in order to improve cellular uptake of therapeutic agents. Even though hydrophobic and anionic CPPs have been described, many of them are polycationic, due to the presence of several arginine (Arg) residues. Noteworthy, however, the presence of aromatic amino acids such as tryptophan (Trp) within CPPs seems to play an important role to reach high membranotropic activity. RW9 (RRWWRRWRR) is a designed CPP derived from the polyarginine R9 presenting both features. In general, when interacting with membranes, CPPs adopt an optimal conformation for membrane interactions - an amphipathic helical secondary structure in the case of RW9. Herein, we assumed that the incorporation of a locally constrained amino acid in the peptide sequence could improve the membranotropic activity of RW9, by facilitating its structuration upon contact with a membrane, while leaving a certain plasticity. Therefore, two cyclized Trp derivatives (Tcc and Aia) were synthesized to be incorporated in RW9 as surrogates of Trp residues. Thus, a series of peptides containing these building blocks has been synthesized by varying the type, position, and number of modifications. The membranotropic activity of the RW9 analogs was studied by spectrofluorescence titration of the peptides in presence of liposomes (DMPG), allowing to calculate partition coefficients (Kp). Our results indicate that the partitioning of the modified peptides depends on the type, the number and the position of the modification, with the best sequence being [Aia4]RW9. Interestingly, both NMR analysis and molecular dynamic (MD) simulations indicate that this analog presents an extended conformation similar to the native RW9, but with a much-reduced structural flexibility. Finally, cell internalization properties were also confirmed by confocal microscopy.

Conformations and non-covalent interactions of cyclohexyl isothiocyanate and its water complex

The conformational equilibria of cyclohexyl isothiocyanate and its complex with water were studied by microwave spectroscopy combined with theoretical calculations. For the bare cyclohexyl isothiocyanate, the rotational spectra of the two conformers, namely a-trans and e-trans, were measured and analyzed. Additional mono-substituted isotopologues of two ¹³C and one ³⁴S of a-trans and e-trans were also measured, which result in an accurate structural determination of the two conformers. For the binary complex with water, the rotational spectra were measured for the monohydrates of both a-trans and e-trans conformers. Water isotopologues were also detected for the monohydrates. All the measured rotational spectra show ¹⁴N quadrupole coupling hyperfine structures. Water molecule prefers linking to the isothiocyanate group through a O_wH⋯S hydrogen bond and forming two CH⋯O_w hydrogen bonds with the oxygen atom of water acting as a proton acceptor. The non-covalent bonding features of the monohydrates were revealed by natural bond orbital analysis and symmetry-adapted perturbation theory analysis.

The conformational behavior of N‑ethylformamide as observed by rotational spectroscopy and quantum chemistry

A peptide linkage (CO)NH containing molecule, N-ethylformamide, was investigated by rotational spectroscopy in order to determine the molecular constants of its highest-energy conformer, cis-ac. Its rotational spectrum was observed in two different frequency ranges, in the 4-26 GHz frequency region using a Fourier transform microwave spectrometer and at millimeter wave frequencies between 75 and 116 GHz, employing a broadband high-resolution rotational spectrometer. The measurements at low frequencies allowed to resolve the hyperfine structure components due to nitrogen nuclear quadrupole coupling while the data at higher frequencies provided spectroscopic information about high order centrifugal effects. From a merged fit using all the observational data we have determined a total of thirteen molecular constants that provide a more accurate spectral modelling of the cis-ac conformer and serves a basis for their astronomical search. We have also observed spectra of five singly substituted isotopologues for the cis-ac conformer, three ¹³C and one for each of ¹⁵N and the deuterated species on the N-D position, from which we derived a partial r₀ structure, in fair agreement with an ab initio result. In addition, the rotational transitions of the deuterated species of the most stable trans-sc conformer were observed and assigned and three rotational, five centrifugal distortion constants and nuclear quadrupole coupling constants of the nitrogen and deuterium nuclei were determined.

DFT and Molecular Docking Study of 1-(2´-Thiophen)-2-propen-1-one-3-(2,3,5-trichlorophenyl) (TTCP) Molecule as Antiviral to Covid-19 Main Protease

Thiophene-containing compounds have antiviral properties and may be among the drugs tested for the treatment of COVID-19 diseases. In order to better understand the molecular definition of the 1-(2´-Thiophen)-2-propen-1-one-3-(2,3,5-trichlorophenyl) molecule from thiophene-containing compounds, the physico-chemical (molecular structure analysis, spectroscopic properties, boundary orbital analysis) mechanisms underlying the protein-ligand interaction should be examined in detail. For this reason, geometric parameters, IR and UV-vis spectra, conformational analysis, electronic, NBO and NLO properties, molecular electrostatic potential map and Mulliken charge distributions of the TTCP molecule were investigated theoretically using DFT theory in the Gaussian program. Accordingly, molecular docking calculations with COVID-19 main protease (PDB 5R7Y) were performed to determine the pharmaceutical activities of the TTCP molecule against coronavirus diseases.

Imidazole-amino acids. Conformational switch under tautomer and pH change

Replacement of the main chain peptide bond by imidazole ring seems to be a promising tool for the peptide-based drug design, due to the specific prototropic tautomeric as well as amphoteric properties. In this study, we present that both tautomer and pH change can cause a conformational switch of the studied residues of alanine (1-4) and dehydroalanine (5-8) with the C-terminal peptide group replaced by imidazole. The DFT methods are applied and an environment of increasing polarity is simulated. The conformational maps (Ramachandram diagrams) are presented and the stability of possible conformations is discussed. The neutral forms, tautomers τ (1) and π (2), adapt the conformations αRτ (φ, ψ = - 75°, - 114°) and C7eq (φ, ψ = - 75°, 66°), respectively. Their torsion angles ψ differ by about 180°, which results in a considerable impact on the peptide chain conformation. The cation form (3) adapts both these conformations, whereas the anion analogue (4) prefers the conformations C5 (φ, ψ = - 165°, - 178°) and β2 (φ, ψ ~ - 165°, - 3°). Dehydroamino acid analogues, the tautomers τ (5) and π (6) as well as the anion form (8), have a strong tendency toward the conformations β2 (φ, ψ = - 179°, 0°) and C5 (φ, ψ = - 180°, 180°). The preferences of the protonated imidazolium form (7) depend on the environment. The imidazole ring, acting as a donor or acceptor of the hydrogen bonds created within the studied residues, has a profound effect on the type of conformation.

Pseudo-glycoconjugates with a C-glycoside linkage

Work by the author and colleagues has been focused on the development of pseudo-glycans (pseudo-glycoconjugates), in which the O-glycosidic linkage of the natural-type glycan structure is replaced by a C-glycosidic linkage. These analogs are not degraded by cellular glycoside hydrolases and are thus expected to be useful molecular tools that may maintain the original biological activity for a long period in the cell. However, their biological potential is not yet well understood because only a few pseudo glycans have so far been synthesized. This article aims to provide a bird's-eye view of our recent studies on the creation of C-glycoside analogs of ganglioside GM3 based on the CHF-sialoside linkage, and summarizes the chemical insights acquired during our stereoselective synthesis of the C-sialoside bond, ultimately leading to pseudo-GM3. Conformational analysis of the synthesized CHF-sialoside disaccharides confirmed that the anticipated conformational control by F-atom introduction was successful, and furthermore, enhanced the biological activity. In order to improve access to C-glycoside analogs based on pseudo-GM3, it is still important to streamline the synthesis process. With this in mind, we designed and developed a direct C-glycosylation method using atom-transfer radical coupling, and employed it in syntheses of pseudo-isomaltose and pseudo-KRN7000.

A computational study of metal ions interaction with amyloid-β 1-42 peptide structure in hyperpyrexia: Implications for Alzheimer disease

Given the current context of the SARS-CoV-19 pandemic, among the interfering risky factors with the Aβ peptide aggregation in the brains of Alzheimer's disease (AD) patients can be hyperpyrexia and increased intracranial pressure (ICP). According to our hypothesis on the relationship between hyperpyrexia and cognitive decline in AD, two models of Aβ peptides were used in this study: the structure of AD amyloid beta-peptide and near-atomic resolution fibril structures of the Aβ peptide. Therefore, the binding templates were constructed for Aβ peptide regions able to bind 9 different metal ions. The fragment transformation method was used for the structural comparison between Aβ chains. Molecular dynamics simulation (MDS) was applied using the Nose-Poincare-Anderson equation to generate a theoretically correct NPT (isothermal-isobaric ensemble). The smallest dissimilarities were observed in the case of Cu⁺ binding potential followed by Co²⁺, both with similar variation. Structural changes have also occurred as a result of the dynamic simulation. All these changes suggest an aggravating factor in both hyperpyretic and AD conditions. Our findings suggest that elevated temperature and increased intracranial pressure rise the effect of peptide aggregation, by converting α-helix motif to β-sheet and random coil conformation, which are related to the formation of senile plaques in AD brains.

Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis

Heparin (HP) belongs to glycosaminoglycans (GAGs), anionic linear polysaccharides composed of repetitive disaccharide units. They are key players in many biological processes occurring in the extracellular matrix and at the cell surface. GAGs are challenging molecules for computational research due to their high chemical heterogeneity, flexibility, periodicity, pseudosymmetry, predominantly electrostatics-driven nature of interactions with their protein partners and potential multipose binding. The molecular mechanisms underlying GAG interactions mediated by divalent ions, which are important for GAG binding to several proteins, are not well understood. The goal of this study was to characterize the binding of Ca²⁺ to two HP oligosaccharides of different lengths (dp10 and dp18, dp: degree of polymerization) and their impact on HP conformational space and their dynamic behavior with the use of molecular dynamics (MD)-based approaches with two Ca²⁺ parameter sets. MD data suggested that the flexibility of the monosaccharides, the glycosidic linkages and ring puckering were not affected by the presence of Ca²⁺, in contrast to H-bond propensities and the calculated R_g for a fraction of the oligosaccharide populations in both dp10 and dp18. Moreover, the essential differences in the data obtained by using two Ca²⁺ parameter sets were reported.

Molecular dynamics of fibric acids

¹H- and ¹³C-NMR chemical shifts were measured for four fibric acids (bezafibrate, clofibric acid, fenofibric acid, and gemfibrozil), which are lipid-lowering drugs. Correlation is found with DFT-computed chemical shifts from the conformational analysis. Equilibrium populations of optimized conformers at 298 K are very different when based on computed Gibbs energies rather than on potential energies. This is due to the significant entropic advantages of extended rather than bent conformational shapes. Abundant conformers with intramolecular hydrogen bonding via five-member rings are computed for three fibric acids, but not gemfibrozil, which lacks suitable connectivity of carboxyl and phenoxy groups. Trends in computed atom-positional deviations, molecular volumes, surface areas, and dipole moments among the fibric acids and their constituent conformations indicate that bezafibrate has the greatest hydrophilicity and fenofibric acid has the greatest flexibility. Theoretical and experimental comparison of chemical shifts of standards with sufficient overlap of fragments containing common atoms, groups, and connectivity may provide a reliable minimal set to benchmark and generate leads.

Novel ferrocene imide derivatives: synthesis, conformational analysis and X-ray structure

The synthesis and structural characterization of the ferrocene imide derivatives Fc−CO−NH−CO−Me (4), Fc−CO−NH−CO−Fc (7) and Fc−CO−NH−CO−Fn−CO−NH−CO−Fc (8) have been reported. The mononuclear, dinuclear and trinuclear ferrocene imides were prepared by the reaction of ferrocenecarboxamide (3), with acetyl chloride, ferrocenecarbonyl chloride (2) and ferrocene-1,1’-(dicarbonyl chloride) (6), respectively. IR spectroscopic analysis revealed the absence of intramolecular hydrogen bonds in solutions of imides 4, 7 and 8. The crystal packing of N-acetylferrocenecarboxamide (4) is characterized by N−H⋯O hydrogen bonds forming centrosymmetric dimers, while the molecules of its homologue N-methylferrocenecarboxamide (5) are self-assembled by intermolecular N−H⋯O bonds into infinite chains. A detailed conformational analysis (DFT study) suggests the cis-trans configuration of ferrocene imide derivative 7 in solution. The effect of different substituents attached to bridged imide nitrogen on conformational properties of bis-ferrocenyl imides was further investigated and results compared to the existing experimental data.

Rotational spectroscopy of the large saturated dinitriles hexanedinitrile and heptanedinitrile

Dinitriles with a saturated hydrocarbon skeleton and a -C≡N group at each end can have large electric dipole moments. Their formation can be related to highly reactive radicals such as CH₂CN, C₂N, or CN. Thus, these saturated dinitriles are potential candidates to be observed in the interstellar medium. In this work, two members of this family, hexanedinitrile and heptanedinitrile, have been investigated through their rotational spectra. The jet-cooled broadband chirped-pulse Fourier transform microwave spectra of both molecules were measured in the 2-8 GHz frequency region. Three and six conformers of hexanedinitrile and heptanedinitrile, respectively, were detected and assigned based on the rotational and quadrupole coupling constants.

Conformations and structures of 1,4-pentadien-3-ol and its water complex characterized by rotational spectroscopy

The 1,4-pentadien-3-ol and its monohydrate have been characterized by microwave spectroscopy in combination with theoretical computations. Experiments and ab initio calculations revealed that the 1,4-pentadien-3-ol monomer prefers a configuration with one vinyl being syn to the hydroxyl oxygen and the hydroxyl hydrogen toward the skew arranged vinyl, which therefore makes possible simultaneous CH···O and OH···π interactions. The observed monohydrate corresponds to the global minimum predicted theoretically, which is stabilized through a primary OH···O_w hydrogen bond together with a much weaker O_wH···π hydrogen bond. The NCI analyses, NBO calculation and SAPT method were applied to further elucidate the characteristics of hydrogen bonds in the 1,4-pentadien-3-ol···water complex.

Extracting the Dynamic Motion of Proteins Using Normal Mode Analysis

Normal mode analysis (NMA) is a technique for describing the conformational states accessible to a protein in a minimum energy conformation. NMA gives results similar to those produced by principal components analysis of a molecular dynamics simulation, but with only a fraction of the computational effort. Here, we provide a brief overview of the theory and describe three methods for carrying out NMA, including the use of one of the on-line services, the use of off-line software for calculating the projection of the modes calculated from one conformation onto another, and an all-atom NMA calculated using GROMACS. For all three methods, we will use the E1·2Ca²⁺ form of the Ca²⁺-ATPase as a concrete example.

Unusual C-C bond cleavage of an α-trifloxy Sialic acid hemiacetal under Lattrell-Dax conditions

We describe the novel oxidative fragmentation of methyl (5-acetamido-4,7,8,9-tetra-O-acetyl-5-deoxy-3-O-trifluoromethanesulfonyl-β-D-erythro-L-gluco-2-nonulopyranos)onate 2 on stirring with sodium nitrite in DMF to give the novel 3-acetamido-2,5,6,7-tetra-O-acetyl-d-glycero-d-galacto-heptono-1,4-lactone 3 in excellent yield. Stirring of the same triflate with sodium carbonate on the other hand affords the novel methyl (5-acetamido-7,8,9-tri-O-acetyl-3,6-anhydro-5-deoxy-d-manno-3-ene-2-nonulos)onate 19 also in excellent yield. Reduction of the heptono lactone with sodium borohydride followed by acetylation gives a peracetylated aminodeoxyheptitol 6 that adopts the zig zag conformation of its carbon backbone.

Conformational analysis and concentration detection of linuron: Spectroscopic NMR and SERS study

Linuron is a commonly used organic herbicide which is used in plant growth control. Due to its potential health concerns, the characterization and monitoring of linuron have been a subject of several studies. In this work, we employed nuclear magnetic resonance (NMR) and Raman spectroscopic techniques supported with the density functional theory (DFT) to investigate the conformational behavior and electronic aspects of linuron. The selective nuclear Overhauser effect (SelNOE) spectra confirmed that linuron exists predominantly in the anti configuration and is facilitated with a weak intramolecular hydrogen bonding between the acidic amide proton and oxygen of methoxy moiety. Quantum chemical results showed that the corresponding syn form of the molecule is 8.5 kcal/mol less stable. Further, the surface enhanced Raman scattering (SERS) technique using gold nanoparticles (AuNPs) was implemented as a potential spectroscopic protocol for the concentration monitoring of trace linuron. The Raman responses of four vibrational modes, namely CC stretching, CN stretching, N-H rocking and ring deformation, were successfully enhanced with an excellent linear concentration-intensity dependency. The aromatic CC stretching vibration at 1595 cm^-1 in the Raman spectra has demonstrated the highest enhancement factor (6.5 × 10⁴) and the lowest limit of detection (10^-7 M). The interaction of linuron with the gold nanocluster was simulated by establishing a simple DFT model which predicted that the most pronounced binding with the gold atom takes place at the benzene ring.

Comprehensive Characterization of the Self-Folding Cavitand Dynamics

The conformational equilibria and guest exchange process of a resorcin[4]arene derived self-folding cavitand receptor have been characterized in detail by molecular dynamics simulations (MD) and ¹ H EXSY NMR experiments. A multi-timescale strategy for exploring the fluxional behaviour of this system has been constructed, exploiting conventional MD and accelerated MD (aMD) techniques. The use of aMD allows the reconstruction of the folding/unfolding process of the receptor by sampling high-energy barrier processes unattainable by conventional MD simulations. We obtained MD trajectories sampling events occurring at different timescales from ns to s: 1) rearrangement of the directional hydrogen bond seam stabilizing the receptor, 2) folding/unfolding of the structure transiting partially open intermediates, and 3) guest departure from different folding stages. Most remarkably, reweighing of the biased aMD simulations provided kinetic barriers that are in very good agreement with those determined experimentally by ¹ H NMR. These results constitute the first comprehensive characterization of the complex dynamic features of cavitand receptors. Our approach emerges as a valuable rational design tool for synthetic host-guest systems.

Conformational epitope matching and prediction based on protein surface spiral features

Background

A conformational epitope (CE) is composed of neighboring amino acid residues located on an antigenic protein surface structure. CEs bind their complementary paratopes in B-cell receptors and/or antibodies. An effective and efficient prediction tool for CE analysis is critical for the development of immunology-related applications, such as vaccine design and disease diagnosis.

Results

We propose a novel method consisting of two sequential modules: matching and prediction. The matching module includes two main approaches. The first approach is a complete sequence search (CSS) that applies BLAST to align the sequence with all known antigen sequences. Fragments with high epitope sequence identities are identified and the predicted residues are annotated on the query structure. The second approach is a spiral vector search (SVS) that adopts a novel surface spiral feature vector for large-scale surface patch detection when queried against a comprehensive epitope database. The prediction module also contains two proposed subsystems. The first system is based on knowledge-based energy and geometrical neighboring residue contents, and the second system adopts combinatorial features, including amino acid contents and physicochemical characteristics, to formulate corresponding geometric spiral vectors and compare them with all spiral vectors from known CEs. An integrated testing dataset was generated for method evaluation, and our two searching methods effectively identified all epitope regions. The prediction results show that our proposed method outperforms previously published systems in terms of sensitivity, specificity, positive predictive value, and accuracy.

Conclusions

The proposed method significantly improves the performance of traditional epitope prediction. Matching followed by prediction is an efficient and effective approach compared to predicting directly on specific surfaces containing antigenic characteristics.

Thiazole-amino acids: influence of thiazole ring on conformational properties of amino acid residues

Post-translational modified thiazole-amino acid (Xaa-Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Conformational study of the series of model compounds containing this structural motif with alanine, dehydroalanine, dehydrobutyrine and dehydrophenylalanine were performed using DFT method in various environments. The solid-state crystal structure conformations of thiazole-amino acid residues retrieved from the Cambridge Structural Database were also analysed. The studied structural units tend to adopt the unique semi-extended β2 conformation; which is stabilised mainly by N-H⋯NTzl hydrogen bond, and for dehydroamino acids also by π-electron conjugation. The conformational preferences of amino acids with a thiazole ring were compared with oxazole analogues and the role of the sulfur atom in stabilising the conformations of studied peptides was discussed.

A general RNA force field: comprehensive analysis of energy minima of molecular fragments of RNA

Force fields are actively used to study RNA. Development of accurate force fields relies on a knowledge of how the variation of properties of molecules depends on their structure. Detailed scrutiny of RNA's conformational preferences is needed to guide such development. Towards this end, minimum energy structures for each of a set of 16 small RNA-derived molecules were obtained by geometry optimization at the HF/6-31G(d,p), B3LYP/apc-1, and MP2/cc-pVDZ levels of theory. The number of minima computed for a given fragment was found to be related to both its size and flexibility. Atomic electrostatic multipole moments of atoms occurring in the [HO-P(O₃)-CH₂-] fragment of 30 sugar-phosphate-sugar geometries were calculated at the HF/6-31G(d,p) and B3LYP/apc-1 levels of theory, and the transferability of these properties between different conformations was investigated. The atomic multipole moments were found to be highly transferable between different conformations with small standard deviations. These results indicate necessary elements of the development of accurate RNA force fields.

The effect of acidic pH on the adsorption and lytic activity of the peptides Polybia-MP1 and its histidine-containing analog in anionic lipid membrane: a biophysical study by molecular dynamics and spectroscopy

Antimicrobial peptides (AMPs) are part of the innate immune system of many species. AMPs are short sequences rich in charged and non-polar residues. They act on the lipid phase of the plasma membrane without requiring membrane receptors. Polybia-MP1 (MP1), extracted from a native wasp, is a broad-spectrum bactericide, an inhibitor of cancer cell proliferation being non-hemolytic and non-cytotoxic. MP1 mechanism of action and its adsorption mode is not yet completely known. Its adsorption to lipid bilayer and lytic activity is most likely dependent on the ionization state of its two acidic and three basic residues and consequently on the bulk pH. Here we investigated the effect of bulk acidic (pH 5.5) and neutral pH (7.4) solution on the adsorption, insertion, and lytic activity of MP1 and its analog H-MP1 to anionic (7POPC:3POPG) model membrane. H-MP1 is a synthetic analog of MP1 with lysines replaced by histidines. Bulk pH changes could modulate this peptide efficiency. The combination of different experimental techniques and molecular dynamics (MD) simulations showed that the adsorption, insertion, and lytic activity of H-MP1 are highly sensitive to bulk pH in opposition to MP1. The atomistic details, provided by MD simulations, showed peptides contact their N-termini to the bilayer before the insertion and then lay parallel to the bilayer. Their hydrophobic faces inserted into the acyl chain phase disturb the lipid-packing.

NMR analysis and molecular dynamics conformation of α-1,6-linear and α-1,3-branched isomaltose oligomers as mimetics of α-1,6-linked dextran

The conformational preferences of several α-1,6-linear and α-1,3-branched isomalto-oligosaccharides were investigated by NMR and MD-simulations. Right-handed helical structure contributed to the solution geometry in isomaltotriose and isomaltotetraose with one nearly complete helix turn and stabilizing intramolecular hydrogen bonds in the latter by MD-simulation. Decreased helix contribution was observed in α-1,3-glucopyranosyl- and α-1,3-isomaltosyl-branched saccharide chains. Especially the latter modification was predicted to cause a more compact structure consistent with literature rheology measurements as well as with published dextranase-resistant α-1,3-branched oligosaccharides. The findings presented here are significant because they shed further light on the conformational preference of isomalto-oligosaccharides and provide possible help for the design of dextran-based drug delivery systems or for the targeted degradation of capsular polysaccharides by dextranases in multi-drug resistant bacteria.

A novel β-hairpin peptide derived from the ARC repressor selectively interacts with the major groove of B-DNA

Transcription factors (TFs) have a remarkable role in the homeostasis of the organisms and there is a growing interest in how they recognize and interact with specific DNA sequences. TFs recognize DNA using a variety of structural motifs. Among those, the ribbon-helix-helix (RHH) proteins, exemplified by the MetJ and ARC repressors, form dimers that insert antiparallel β-sheets into the major groove of DNA. A great chemical challenge consists of using the principles of DNA recognition by TFs to design minimized peptides that maintain the DNA affinity and specificity characteristics of the natural counterparts. In this context, a peptide mimic of an antiparallel β-sheet is very attractive since it can be obtained by a single peptide chain folding in a β-hairpin structure and can be as short as 14 amino acids or less. Herein, we designed eight linear and two cyclic dodeca-peptides endowed with β-hairpins. Their DNA binding properties have been investigated using fluorescence spectroscopy together with the conformational analysis through circular dichroism and solution NMR. We found that one of our peptides, peptide 6, is able to bind DNA, albeit without sequence selectivity. Notably, it shows a topological selectivity for the major groove of the DNA which is the interaction site of ARC and many other DNA-binding proteins. Moreover, we found that a type I' β-hairpin folding pattern is a favorite peptide structure for interaction with the B-DNA major groove. Peptide 6 is a valuable lead compound for the development of novel analogs with sequence selectivity.

Piloty's acid and its hydrazide analogue: Insights from the density functional theory and vibrational spectroscopy on the conformational stability and chemical reactivity

N-hydroxybenzenesulfonamide (commonly known as Piloty's acid) is considered a major source for nitroxyl (HNO) species which has potential biological and medicinal applications. In the present study, the conformational preferences and chemical reactivity of Piloty's acid (PA) and its hydrazide analogue (benzenesulfonylhydrazide, BSH) were studied using spectroscopic and computational tools. Six stable conformations of each molecule were theoretically identified, and their structures were fully optimized at the DFT-B3LYP and MP2 levels. Both molecules in their most stable forms adopt the anti configuration with the NH bond of the secondary amine pointing away from the terminal hydroxyl and amine moieties in the acid and hydrazide molecules, respectively. Three stable gauche states facilitated by weak intramolecular interactions of the SO⋯HO and SO⋯HN types arise due to the internal rotation about the SN linkage. Reliable assignments of the vibrational modes and the calculated reaction coordinates support a two-step mechanistic pathway of the Piloty's acid dissociation leading to the production of the nitroxyl (HNO) intermediate with moderate transition state barriers. Frontier molecular orbitals distributions, molecular electrostatic potential maps and condensed Fukui functions analysis of the molecules were employed to elucidate the agility of PA to dissociate to produce HNO and the absence of such a dissociation of BSH that would produce diazene (N₂H₂).

Influence of substitution at the 5α-Position on the side chain conformation of glucopyranosides

We describe the preparation of methyl 5α-methyl-α-d-glucopyranoside and of 5α-fluoro-β-d-glucopyranose per acetate and the NMR-based conformational analysis of their side chains. Both the 5α-methyl and 5α-fluoro substituents increase the population of the gauche,gauche side chain conformer to the extent that it becomes the predominant conformation. In the 5α-methyl series this is attributed to steric effects, whereas in the 5α-fluoro series the optimization of attractive gauche effects is the more likely reason.

Artichoke pectic oligosaccharide characterisation and virtual screening of prebiotic properties using in silico colonic fermentation

The aim of this work was to develop a comprehensive workflow to elucidate molecular features of artichoke pectic oligosaccharides (POS) contributing to high potential prebiotic activity. First, obtainment of artichoke POS by Pectinex® Ultra-Olio was optimised using an artificial neural network. Under optimal conditions (pH 6.86; 1.5 h; enzyme dose 520.5 U/g pectin) POS yield was 624 mg/g pectin. Oligosaccharide structures (M_w < 1.3 kDa) were characterised by MALDI-TOF-MS. Then, conformational analysis of glycosidic bonds was performed by replica exchange molecular dynamics simulations and interaction mechanisms between POS and several microbial glycosidases were proposed by molecular modelling. Chemical information was integrated in virtual simulations of colonic fermentation. Highest hydrolysis rate was obtained for GalA-Rha-GalA trisaccharide, while the presence of partial negative charges and high radius of gyration enhance short chain fatty acid formation in distal colon. Established structure-activity relationships could help the rational design of prebiotics and clinical trials.

Structural, spectroscopic, and photochemical study of ethyl propiolate isolated in cryogenic argon and nitrogen matrices

Ethyl propiolate (HC ≡ CCOOCH₂CH₃, EP) was studied experimentally by infrared spectroscopy in argon and nitrogen cryomatrices (15 K) and by quantum chemical calculations (at the DFT(B3LYP) and MP2 levels of theory). Calculations predict the existence of four conformers: two low-energy conformers (I and II) possessing the carboxylic moiety in the cis configuration (O=C-O-C dihedral equal to ~0°) and two higher-energy trans forms (O=C-O-C dihedral equal to ~180°; III and IV). The conformation of the ethyl ester group within each pair of conformers is either anti (C-O-C-C equal to 180°; in conformers I and III) or gauche (C-O-C-C equal to ±86.6° in II, and ± 92.5° in IV). The two low-energy cis conformers (I and II) were predicted to differ in energy by less than 2.5 kJ mol^-1 and were shown to be present in the studied cryogenic matrices. Characteristic bands for each one of these conformers were identified in the infrared spectra of the matrix-isolated compound and assigned taking into account the results of normal coordinate analysis, which used the geometries and harmonic force constants obtained in the DFT calculations. The two trans conformers (III and IV) were estimated to be 17.5 kJ mol^-1 higher in energy than the conformational ground state (form I) and were not observed experimentally. The unimolecular photochemistry of matrix-isolated EP (in N₂ matrix) was also investigated. In situ irradiation with UV light (λ > 235 nm) leads mainly to decarbonylation of the compound, with generation of ethoxyethyne, which in a subsequent photoreaction generates ketene (plus ethene).

Revisiting biomolecular NMR spectroscopy for promoting small-molecule drug discovery

Recently, there has been increasing interest in new modalities such as therapeutic antibodies and gene therapy at a number of pharmaceutical companies. Moreover, in small-molecule drug discovery at such companies, efforts have focused on hard-to-drug targets such as inhibiting protein-protein interactions. Biomolecular NMR spectroscopy has been used in drug discovery in a variety of ways, such as for the reliable detection of binding and providing three-dimensional structural information for structure-based drug design. The advantages of using NMR spectroscopy have been known for decades (Jahnke in J Biomol NMR 39:87-90, (2007); Gossert and Jahnke in Prog Nucl Magn Reson Spectrosc 97:82-125, (2016)). For tackling hard-to-drug targets and increasing the success in discovering drug molecules, in-depth analysis of drug-target protein interactions performed by biophysical methods will be more and more essential. Here, we review the advantages of NMR spectroscopy as a key technology of biophysical methods and also discuss issues such as using cutting-edge NMR spectrometers and increasing the demand of utilizing conformational dynamics information for promoting small-molecule drug discovery.

Design, synthesis, and biological evaluation of spiroindolines as novel inducers of oligodendrocyte progenitor cell differentiation-Use of a conformation-based hypothesis to facilitate compound design

Inducing oligodendrocyte progenitor cell (OPC) differentiation is a novel therapeutic strategy for the treatment of demyelinating diseases such as multiple sclerosis (MS). In the preceding article, we detailed the discovery of compound 1, a potent inducer of OPC differentiation possessing a characteristic spiroindoline structure. Also, we found that N-methylation and des-carbonyl compound 1 (4) led to a loss in potency. Herein, we describe our investigations of a conformation-based hypothesis for OPC differentiation activity based on the preferred conformation of the spiro core, and further structure-activity relationship (SAR) exploration led to the identification of 6-CF₃ derivative 8, which was more potent compared to compound 1.

Isolation, structural elucidation, and immunoregulation properties of an arabinofuranan from the rinds of Garcinia mangostana

In our search for bioactive polysaccharides as immunomodulatory agents, an arabinofuranan (GMP90-1) was purified and characterized from the rinds of Garcinia mangostana L. GMP90-1 (absolute molecular weight: 5.30 × 10³ g/mol) was found to be composed of arabinose, galactose, and rhamnose. The backbone of GMP90-1 was determined as (1→5)-linked α-l-Araf, (1→2,3,5)-linked α-l-Araf, (1→3,5)-linked α-l-Araf, (1→6)-linked β-d-Galp, and (1→2)-linked α-l-Rhap. Conformational analysis revealed GMP90-1 to exist as a rigid rod structure in sodium chloride solution. To explore its potential as immunomodulatory agents, an in vitro cell screening was performed and GMP90-1 was found to significantly enhance the phagocytic uptake of neutral red and improve the secreted level of nitric oxide (NO), interleukin (IL)-6, IL-1β, and tumor necrosis factor-α (TNF-α) of macrophages. Furthermore, the cellular immunomodulatory activities were confirmed by the in vivo zebrafish experiment, which suggested that GMP90-1 with immunomodulatory effects could be considered as a potential immunomodulatory for immune diseases.

Short-Chained Anthracene Strapped Porphyrins and their Endoperoxides

The syntheses of short-chained anthracene-strapped porphyrins and their Zn(II)complexes are reported. The key synthetic step is a [2+2] condensation between a dipyrromethane and an anthracene bisaldehyde, 2,2'-((anthracene-9,10-diylbis(methylene))bis(oxy))dibenzaldehyde. Following exposure to white light, self-sensitized singlet oxygen and the anthracene moieties underwent [4+2] cycloaddition reactions to yield the corresponding endoperoxides. 1H NMR studies demonstrate that the endoperoxide readily formed in [D]chloroform and decayed at 85 °C. X-ray crystallography and absorption spectroscopy were used to confirm macrocyclic distortion in the parent strapped porphyrins and endoperoxides. Additionally, X-ray crystallography indicated that endoperoxide formation occurred exclusively on the outside face of the anthracene moiety.

Assessment of the conformational profile of bombesin by computational methods

In the present work, the results of a computational study aimed at assessing the conformational profile of bombesin are reported. The conformational space of the peptide was sampled by means of a 4 μs accelerated molecular dynamics simulation in water, using an explicit solvent model. The results were analyzed using Principal Component Analysis to get essential information on peptide fluctuations, along with cluster analysis to characterize different conformations in the sample. Analysis of the results suggests that the peptide adopts helical structures at the C-terminus that tend to unwind at the end of the peptide chain, since there are many structures exhibiting only two turns of a helix at the central segment of the peptide. In addition, the peptide also adopts hairpin turn structures at the N-terminus. Results of the simulation were confronted with available NMR results in a 2,2,2-trifluoroethanol/water (30% v/v) solution. Distances deduced form NOEs experiments only provide support to the presence of helical conformations that represent the most populated structures in the simulation. The absence of other conformations in the NMR experiments can be explained to be due to the α-helix enhancing nature of the solvent used in the experiments.

Vibrational dynamics of 1,3-propanediol in liquid, polycrystalline and glassy states: A Raman spectroscopic study

Vibrational transitions of 1,3-propanediol in liquid and crystal phases are assigned on the basis of Raman and infrared spectra of liquid and low temperature (295K-10K) Raman spectra which are presented here for the first time. In the crystal, there are four molecules per unit cell, each having a gGGg' conformation. The vibrations for the P2₁/n crystal phase having four molecules in the unit cell are obtained by an ab initio calculation using CRYSTAL09 program, and are in good agreement with the observed Raman bands. Observed bands in Raman spectrum of liquid are in proximity of those observed for crystal phase, and it is tempting to assign them as belonging mainly to gGGg' conformer. However, quantum chemical ab initio calculations provide basis to ascertain that tGG'g and tGGt are two conformers having lowest energy at the B3LYP/6-31++G(d,p) level of theory. Several bands that disappear from Raman spectrum of liquid on solidification (384, 872 and 1040 cm^-1) could give an insight into the nature of conformers present in liquid. Since the closest calculated vibrations are 386cm^-1 for tGG'g and 1043cm^-1 for tGG't conformer, we conclude that all three conformers: tGG'g, tGGt and gGGg', are present in the liquid.

Computational investigations and molecular dynamics simulations envisioned for potent antioxidant and anticancer drugs using indole-chalcone-triazole hybrids

Cancer, also called malignancy, is a disease which is closely related with the oxidative stress instigated by the overproduction of vulnerable oxygen and nitrogen species. Available drugs are relatively painful and toxic and so are trailing their captivation. Keeping this in mind, we have attempted to reach a novel anti-cancer drug by taking a set of nineteen ligands which are hybrids of Indole-chalcone and triazole. These ligands were allowed to interact with the DNA dodecamer 5'(CGCGAATTCGCG)3' one by one using various docking protocols of Glide. Better docked complexes screened through docking scores and reported activity data were selected and exposed to molecular dynamics run of 20 ns. The dynamical pathways were investigated for each complex comparing the pre- and post- dynamics run. The outcome of the work is discussed in this paper. Among the better hybrids of this series, one of the molecules has shown interesting features, confirming its non-toxic nature and working as intercalator as well minor groove binder, perhaps making it suitable as a potent drug for further pharmacological use.

Luminescent properties of new 2,2-, 2,3- and 3,3-CH2-bis(BODIPY)s dyes: Structural and solvation effects

In this paper the synthesis and spectral properties of three new dimeric bis(BODIPY)s with two indacene domains connected by a methylene (-CH₂-) spacer at 2,2-, 2,3- or 3,3- positions were reported. It was found bis(BODIPY)s exhibit a high sensitivity of fluorescence to the medium properties. To interpret solvatochromic effects of bis(BODIPY)s, a multilinear correlation analysis of bis(BODIPY)s fluorescence quantum yields with respect to solvent different parameters was carried out. To understand the features of the spectral properties of bis(BODIPY)s, we carried out a thorough quantum-chemical analysis of the structural, conformational, and spectral characteristics of bis(BODIPY)s. The obtained bis(BODIPY)s have a high potential for application as sensors of medium polarity.

Spectroscopic and theoretical studies of some 2‑(methoxy)‑2‑[(4‑substituted)‑phenylsulfanyl]‑(4'‑substituted) acetophenones

The conformational analysis of some 2‑(methoxy)‑2‑[(4‑substituted)‑phenylsulfanyl]‑(4'‑substituted) acetophenones was performed through infrared (IR) spectroscopic analysis of the carbonyl stretching band (ν_CO), supported by B3LYP/6-31+G(d,p) calculations and X-ray diffraction. Five (1-5) of the seven studied compounds (1-7) presented Fermi resonance (FR) on the ν_CO fundamental transition band. Deuteration of these compounds (1a-5a) precluded the occurrence of FR, revealing a ν_CO doublet for all compounds in all solvents used. The computational results indicated the existence of three conformers (c₁, c₂ and c₃) for the whole series whose relative abundances varied with solvent permittivity. The higher ν_CO frequency c₁ conformer was assigned to the higher frequency component of the carbonyl doublet, while both c₂ and c₃ were assigned to the lower frequency one. Anharmonic vibrational frequencies and Potential Energy Distribution (PED) calculations of compound 3 indicated that the combination band (cb) between the methyne δ_CH and one skeletal mode couples with the ν_CO mode giving rise to the FR on the c₂ conformer in vacuum and on the c₁ one in non-polar solvents. The experimental data indicated a progressive increase in c₁ conformer stability with the increase of the solvent dielectric constant, which is in good agreement with the polarizable continuum model (PCM) calculations. The higher ν_CO frequency and the stronger solvation of the c₁ conformer is a consequence of the repulsive field effect (RFE) originated by the alignment and closeness of the C^δ+O^δ- and C^δ+O^δ- dipoles. Finally, the balance between orbital and electrostatic interactions dictates the conformational preferences. X-ray single crystal analysis for compound 6 revealed the c₁ geometry in the solid state and its stabilization by CH…O hydrogen bonds.

Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis

Mycobacterium tuberculosis remains a persistent pathogen, partly due to its lipid rich cell wall, of which mycolic acids (MAs) are a major component. The fluidity and conformational flexibilities of different MAs in the bacterial cell wall significantly influence its properties, function, and observed pathogenicity; thus, a proper conformational description of different MAs in different environments (e.g., in vacuum, in solution, in monolayers) can inform about their potential role in the complex setup of the bacterial cell wall. Previously, we have shown that molecular dynamics (MD) simulations of MA folding in vacuo can be used to characterize MA conformers in seven groupings relating to bending at the functional groups (W, U and Z-conformations). Providing a new OPLS-based forcefield parameterization for the critical cyclopropyl group of MAs and extensive simulations in explicit solvents (TIP4P water, hexane), we now present a more complete picture of MA folding properties together with improved simulation analysis techniques. We show that the 'WUZ' distance-based analysis can be used to pinpoint conformers with hairpin bends at the functional groups, with these conformers constituting only a fraction of accessible conformations. Applying principle component analysis (PCA) and refinement using free energy landscapes (FELs), we are able to discriminate a complete and unique set of conformational preferences for representative alpha-, methoxy- and keto-MAs, with overall preference for folded conformations. A control backbone-MA without any mero-chain functional groups showed significantly less folding in the mero-chain, confirming the role of functionalization in directing folding. Keto-MA showed the highest percentage of WUZ-type conformations and, in particular, a tendency to fold at its alpha-methyl trans-cyclopropane group, in agreement with results from Villeneuve et al. MAs demonstrate similar folding in vacuum and water, with a majority of folded conformations around the W-conformation, although the molecules are more flexible in vacuum than in water. Exchange between conformations, with a disperse distribution that includes unfolded conformers, is common in hexane for all MAs, although with more organization for Keto-MA. Globular, folded conformations are newly defined and may be specifically relevant in biofilms. Graphical abstract Through advanced simulation analysis, including principle component analysis and free energy landscapes, we reveal detailed physical insights into the solvent-dependant folding behavior of mycolic acids from M. tb.

Modeling and Simulation of hGAT1: A Mechanistic Investigation of the GABA Transport Process

Human γ-Aminobutyric acid transporter 1 (hGAT1) is a Na+/Cl- dependent co-transporter that plays a key role in the inhibitory neurotransmission of GABA in the brain. Due to the lack of structural data, the exact co-transport mechanism of GABA reuptake by hGAT1 remains unclear. To examine the roles of the co-transport ions and the nature of their interactions with GABA, homology modeling and molecular dynamics simulations of the hGAT1 in the open-to-out conformation were carried out. Our study focused on the sequential preloading of Na+ and Cl- ions, followed by GABA binding. Our simulations showed pre-loading of ions maintains the transport ready state of hGAT1 in the open-to-out conformation essential for GABA binding. Of the four putative preloaded states, GABA binding to the fully loaded state is most favored. Binding of Na+ ion to the Na1 site helps to maintain the open-to-out conformation for GABA binding as compared to the Na2 site. GABA binding to the mono-sodium or the di-sodium loaded states leads to destabilization of Na+ ions within their binding sites. The two most prominent interactions required for GABA binding include interaction between carboxylate group of GABA with the bound Na+ ion in Na1 binding site and the hydroxyl group of Y140. Overall our results support the fully loaded state as the predominate state for GABA binding. Our study further illustrates that Na+ ion within the Na1 site is crucial for GABA recognition. Therefore, a revised mechanism is proposed for the initial step of hGAT1 translocation cycle.

Computational conformational analysis of α-thrombin inhibitors possessing distinct scaffolds in aqueous solution and on Ala-sheet

Recent computational simulations on protein-ligand binding/unbinding have precisely been uncovering the ligand-binding process at the atomic level. In the process, the non-specific binding of ligands to the target site is suggested to occur before binding to the target. We in this study analyzed the conformations of ligands under the non-specific binding on a protein surface to figure out the differences in the conformational characteristics in aqueous solution using the 55-ns molecular dynamic simulation. As for the protein surface, we constructed an artificial β-sheet, composed of poly-alanine residues (Ala-sheet). For the ligands, the four α-thrombin inhibitors possessing two scaffolds with distinct hydrophobicity profiles were used. During the simulation, all the inhibitors kept interaction with Ala-sheet and had the limited conformational fluctuations compared with in aqueous solution. The representative conformations obtained from the cluster analysis showed that two of hydrophobic inhibitors adopted the extended conformations in aqueous solution and also on Ala-sheet. For the other two hydrophilic inhibitors, the conformations in aqueous solution adopted the bent conformation with two terminal hydrophobic rings closely packed. On Ala-sheet, contrarily, the two hydrophobic rings were open and took the extended conformations, which were placed on the sheet as a foothold. The charged moieties in the hydrophilic inhibitors were protruded into aqueous environment with the extended conformation. The conformational characteristics of the inhibitors in aqueous solution and Ala-sheet varied likely by chemical features or structures of the inhibitors, but each was considered to be physicochemically reasonable.

O6C-20-nor-salvinorin A is a stable and potent KOR agonist

Salvinorin A (SalA) is a potent and selective agonist of the kappa-opioid receptor (KOR), but its instability has frustrated medicinal chemistry efforts. Treatment of SalA with weak bases like DBU leads to C8 epimerization with loss of receptor affinity and signaling potency. Here we show that replacement of C20 with H and replacement of O6 with CH2 stabilizes the SalA scaffold relative to its C8 epimer, so much so that epimerization is completely supressed. This new compound, O6C-20-nor-SalA, retains high potency for agonism of KOR.

Synthesis of unsymmetrical disulfanes bearing 1,2,4-triazine scaffold and their in vitro screening towards anti-breast cancer activity

ABSTRACT

A new series of 1,2,4-triazine unsymmetrical disulfanes were prepared and evaluated as anticancer activity compounds against MCF-7 human breast cancer cells with some of them acting as low micromolar inhibitors. Evaluation of the cytotoxicity using an MTT assay, the inhibition of [3H]-thymidine incorporation into DNA demonstrated that these products exhibit cytotoxic effects on breast cancer cells in vitro. The most effective compounds with 59 and 60 µM compared to chlorambucil with 47 µM were disulfanes bearing methyl and methoxy substituent in an aromatic ring. Furthermore, all new 14 compounds were obtained with 22-74% yield via mild and efficient synthesis of the sulfur-sulfur bond formation from thiols and symmetrical disulfanes using 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ). The molecular structure of the newly obtained compounds was confirmed by X-ray analysis. The conformational preferences of disulfide system were characterized using theoretical calculations at DFT level and statistical distributions of C-S-S-C torsion angle values based on the Cambridge Structural Database (CSD). The DFT calculations and CSD searching show two preferential conformations for C-S-S-C torsion angle close to ± 90° and relatively large freedom of rotation on S-S bond in physiological conditions. The molecular docking studies were performed using the human estrogen receptor alpha (ERα) as molecular target to find possible binding orientation and intermolecular interactions of investigated disulfanes within the active site of ERα. The S…H-S and S…H-C hydrogen bonds between sulfur atoms of bisulfide bridge and S-H and C-H groups of Cys530 and Ala350 as protein residues play crucial role in interaction with estrogen receptor for the most anticancer active disulfane.

GRAPHICAL ABSTRACT

Molecular Dynamics of Gangliosides

Computational methodologies have immense potential to delineate the dynamic conformations of glycoconjugates including gangliosides, thereby characterizing the conformational adaptability of their glycans upon interacting with various target proteins. Replica-exchange molecular dynamics simulations have been employed to effectively explore the vast conformational spaces of large, branched carbohydrate moieties. When experimentally validated using NMR, molecular simulations can provide dynamical views of molecular recognition events involving the ganglioside glycans.

Nuclear Magnetic Resonance of Gangliosides

Structure, conformation, and dynamics of sphingolipids can provide substantial help in better understanding sphingolipid-ligand interaction mechanisms. Both the oligosaccharide structure and the ceramide moiety of native glycosphingolipid can be established directly by NMR spectroscopic analysis without the necessity to resort to any other chemical or spectroscopic methods. NMR is a powerful technique to investigate interaction between small ligand, such as ganglioside, and membrane protein.

Modeling of a C-end rule peptide adsorbed onto gold nanoparticles

The RPAR peptide, a prototype C-end Rule (CendR) sequence that binds to neuropilin-1 (NRP-1), has potential therapeutic uses as internalization trigger in anticancer nanodevices. Recently, the functionalization of gold nanoparticles with CendR peptides has been proved to be a successful strategy to target the NRP-1 receptor in prostate cancer cells. In this work, we investigate the influence of two gold surface facets, (100) and (111), on the conformational preferences of RPAR using molecular dynamics simulations. Both clustering and conformational analyses revealed that the peptide backbone becomes very rigid upon adsorption onto gold, which is a very fast and favored process, the only flexibility being attributed to the side chains of the two Arg residues. Thus, the different components of RPAR tend to adopt an elongated shape, which is characterized by the pseudo-extended conformation of both the backbone and the Arg side chains. This conformation is very different from the already known bioactive conformation, indicating that RPAR is drastically affected by the substrate. Interestingly, the preferred conformations of the peptide adsorbed onto gold facets are not stabilized by salt bridges and/or specific intramolecular hydrogen bonds, which represent an important difference with respect to the conformations found in other environments (e.g. the peptide in solution and interacting with NRP-1 receptor). However, the conformational changes induced by the substrate are not detrimental for the use of gold nanoparticles as appropriate vehicles for the transport and targeted delivery of the RPAR. Thus, once their high affinity for the NRP-1 receptor induces the targeted delivery of the elongated peptide molecules from the gold nanoparticles, the lack of intramolecular interactions facilitates their evolution towards the bioactive conformation, increasing the therapeutic efficacy of the peptide.

Immunoproteasome inhibition and bioactivity of thiasyrbactins

A family of macrodilactam natural products, the syrbactins, are known proteasome inhibitors. A small group of syrbactin analogs was prepared with a sulfur-for-carbon substitution to enhance synthetic accessibility and facilitate modulation of their solubility. Two of these compounds surprisingly proved to be inhibitors of the trypsin-like catalytic site, including of the immunoproteasome. Their bound and free conformations suggest special properties of the thiasyrbactin ring are responsible for this unusual preference, which may be exploited to develop drug-like immunoproteasome inhibitors. These compounds show greater selectivity than earlier compounds used to infer phenotypes of immunoproteasome inhibition, like ONX-0914.

Pyranose ring puckering in aldopentoses, ketohexoses and deoxyaldohexoses. A molecular dynamics study

Conformation of monosaccharides, including the ring shape, has for years been the subject of intensive research. Although d-aldohexopyranoses are the most extensively studied pyranoses, there also exist other groups of saccharides that contain analogous chemical system of the six-membered ring. Here we describe in details the results of the molecular dynamics-based conformational analysis concerning a series of pyranoses, namely: d-aldopentoses, d-ketohexoses as well as deoxy- (d-quinovose, l-fucose, l-rhamnose) and dideoxy- (abequose, paratose, tyvelose, digitoxose) derivatives of aldohexoses. By using the carbohydrate-dedicated GROMOS 56a6_CARBO force field, we determined the conformational properties of both the lactol and hydroxymethyl groups as well as the anomeric populations for all considered compounds. The orientation of the lactol group follows the trend expected on the basis of the exo-anomeric effect for all compounds whereas the conformation of the hydroxymethyl group in d-ketohexoses is represented by the two gauche (with respect to the ring oxygen atom) rotamers. The special emphasis is put on the ring-inversion properties studied in the context of both the full chair-chair inversion and the chair-boat/skew-boat rearrangement. The calculated ring-distortion energies, compared with those obtained for regular d-aldohexopyranoses allowed for estimating the influence of particular substituents on the ring flexibility. Overall, such influence is correlated with the dimension of the substituent and its orientation but is limited to the case of the chair-chair inversion whereas the chair-to-boat/skew-boat rearrangement exhibits roughly the same properties for all pyranoses. For all d-aldopyranoses the α anomers exhibit lower ring-inversion free energies in comparison to the β anomers whereas this trend is inverted in the case of d-ketohexopyranoses.

The influence of solvent on conformational properties of peptides with Aib residue-a DFT study

The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe₂ (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N–H⋯O hydrogen bonds, i.e., C₅ and C₇ conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/−60°, +/−40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data.

Graphical abstract