Conformational Interconversions of Amino Acid Derivatives

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.

Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness

Computational techniques applied to drug discovery have gained considerable popularity for their ability to filter potentially active drugs from inactive ones, reducing the time scale and costs of preclinical investigations. The main focus of these studies has historically been the search for compounds endowed with high affinity for a specific molecular target to ensure the formation of stable and long-lasting complexes. Recent evidence has also correlated the in vivo drug efficacy with its binding kinetics, thus opening new fascinating scenarios for ligand/protein binding kinetic simulations in drug discovery. The present article examines the state of the art in the field, providing a brief summary of the most popular and advanced ligand/protein binding kinetics techniques and evaluating their current limitations and the potential solutions to reach more accurate kinetic models. Particular emphasis is put on the need for a paradigm change in the present methodologies toward ligand and protein parametrization, the force field problem, characterization of the transition states, the sampling issue, and algorithms' performance, user-friendliness, and data openness.

Coupling and decoupling CH stretching vibration of methylene and methine in serine conformers

In the molecules of the early Earth, as a building block of proteins, serine has enormous chemical and biological significance. The vibrational spectroscopy of CH bonds plays an important role in probing biomolecules. Whether the CH stretching vibration bands can be accurately assigned will affect the accuracy of the detection results. In this study, we employed the MP2/cc-pVTZ method to calculate the Raman spectra of 85 serine conformers and the corresponding species with deuterium in the CH stretching region from 2800 cm^-1 to 3050 cm^-1 and then recorded the movement of each atom and the dihedral angles, CH bond lengths, and Raman shifts before and after deuterium for each conformer. We directly observed that the stretching vibration of two CH bonds in the methylene group decoupled to vibrate independently in some conformers, and the stretching vibrations of methylene and methine could be strongly coupled in some conformers. Those results are inconsistent with the traditional understanding, which is generally believed that the CH stretching vibrations are mutually coupled in a single methyl or methylene group to generate symmetric and antisymmetric stretching vibrations, while for different methyl, methylene or methine groups, the CH stretching vibrations cannot be mutually coupled. Through the statistical analysis between several factors, we found that the level of local coupling in serine methylene was correlated with the bond length difference between two CH bonds. Our work provides a new understanding of the vibrational modes of hydrocarbon bonds and the coupling between different hydrocarbon groups.

Inhibitory Effect and Mechanism of Action of Quercetin and Quercetin Diels-Alder anti-Dimer on Erastin-Induced Ferroptosis in Bone Marrow-Derived Mesenchymal Stem Cells

In this study, the anti-ferroptosis effects of catecholic flavonol quercetin and its metabolite quercetin Diels-Alder anti-dimer (QDAD) were studied using an erastin-treated bone marrow-derived mesenchymal stem cell (bmMSCs) model. Quercetin exhibited higher anti-ferroptosis levels than QDAD, as indicated by 4,4-difluoro-5-(4-phenyl-1,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-undecanoic acid (C11-BODIPY), 2',7'-dichlorodihydrofluoroscein diacetate (H2DCFDA), lactate dehydrogenase (LDH) release, cell counting kit-8 (CCK-8), and flow cytometric assays. To understand the possible pathways involved, the reaction product of quercetin with the 1,1-diphenyl-2-picrylhydrazyl radical (DPPH^●) was measured using ultra-performance liquid-chromatography coupled with electrospray-ionization quadrupole time-of-flight tandem mass spectrometry (UHPLC-ESI-Q-TOF-MS). Quercetin was found to produce the same clusters of molecular ion peaks and fragments as standard QDAD. Furthermore, the antioxidant effects of quercetin and QDAD were compared by determining their 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide radical-scavenging, Cu²⁺-reducing, Fe³⁺-reducing, lipid peroxidation-scavenging, and DPPH^●-scavenging activities. Quercetin consistently showed lower IC₅₀ values than QDAD. These findings indicate that quercetin and QDAD can protect bmMSCs from erastin-induced ferroptosis, possibly through the antioxidant pathway. The antioxidant pathway can convert quercetin into QDAD-an inferior ferroptosis-inhibitor and antioxidant. The weakening has highlighted a rule for predicting the relative anti-ferroptosis and antioxidant effects of catecholic flavonols and their Diels-Alder dimer metabolites.

Simultaneous Study of Anti-Ferroptosis and Antioxidant Mechanisms of Butein and (S)-Butin

To elucidate the mechanism of anti-ferroptosis and examine structural optimization in natural phenolics, cellular and chemical assays were performed with 2'-hydroxy chalcone butein and dihydroflavone (S)-butin. C11-BODIPY staining and flow cytometric assays suggest that butein more effectively inhibits ferroptosis in erastin-treated bone marrow-derived mesenchymal stem cells than (S)-butin. Butein also exhibited higher antioxidant percentages than (S)-butin in five antioxidant assays: linoleic acid emulsion assay, Fe3+-reducing antioxidant power assay, Cu2+-reducing antioxidant power assay, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide radical (PTIO•)-trapping assay, and α,α-diphenyl-β-picrylhydrazyl radical (DPPH•)-trapping assay. Their reaction products with DPPH• were further analyzed using ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-Q-TOF-MS). Butein and (S)-butin produced a butein 5,5-dimer (m/z 542, 271, 253, 225, 135, and 91) and a (S)-butin 5',5'-dimer (m/z 542, 389, 269, 253, and 151), respectively. Interestingly, butein forms a cross dimer with (S)-butin (m/z 542, 523, 433, 419, 415, 406, and 375). Therefore, we conclude that butein and (S)-butin exert anti-ferroptotic action via an antioxidant pathway (especially the hydrogen atom transfer pathway). Following this pathway, butein and (S)-butin yield both self-dimers and cross dimers. Butein displays superior antioxidant or anti-ferroptosis action to (S)-butin. This can be attributed the decrease in π-π conjugation in butein due to saturation of its α,β-double bond and loss of its 2'-hydroxy group upon biocatalytical isomerization.

Comparative Analysis of Radical Adduct Formation (RAF) Products and Antioxidant Pathways between Myricetin-3-O-Galactoside and Myricetin Aglycone

The biological process, 3-O-galactosylation, is important in plant cells. To understand the mechanism of the reduction of flavonol antioxidative activity by 3-O-galactosylation, myricetin-3-O-galactoside (M3OGa) and myricetin aglycone were each incubated with 2 mol α,α-diphenyl-β-picrylhydrazyl radical (DPPH^•) and subsequently comparatively analyzed for radical adduct formation (RAF) products using ultra-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-Q-TOF-MS) technology. The analyses revealed that M3OGa afforded an M3OGa–DPPH adduct (m/z 873.1573) and an M3OGa–M3OGa dimer (m/z 958.1620). Similarly, myricetin yielded a myricetin–DPPH adduct (m/z 711.1039) and a myricetin–myricetin dimer (m/z 634.0544). Subsequently, M3OGa and myricetin were compared using three redox-dependent antioxidant analyses, including DPPH^•-trapping analysis, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide radical (PTIO^•)-trapping analysis, and ^•O₂ inhibition analysis. In the three analyses, M3OGa always possessed higher IC₅₀ values than those of myricetin. Conclusively, M3OGa and its myricetin aglycone could trap the free radical via a chain reaction comprising of a propagation step and a termination step. At the propagation step, both M3OGa and myricetin could trap radicals through redox-dependent antioxidant pathways. The 3-O-galactosylation process, however, could limit these pathways; thus, M3OGa is an inferior antioxidant compared to its myricetin aglycone. Nevertheless, 3-O-galactosylation has a negligible effect on the termination step. This 3-O-galactosylation effect has provided novel evidence that the difference in the antioxidative activities of phytophenols exists at the propagation step rather than the termination step.

Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications

Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.

Experimental conformational energy maps of proteins and peptides

We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F. M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ, ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions. Further, we have identified low energy pathways for transitions between various minima in the (ϕ,ψ) plots. We have compared and presented the experimental plots with published theoretical plots obtained from both molecular mechanics and quantum mechanical approaches. In addition, we have developed and employed a root mean square deviation (RMSD) metric for isoenergy contours in various ranges, as a measure (in kcal.mol^-1 ) to compare any two plots and determine the extent of correlation and similarity between their isoenergy contours. In general, we observe a greater degree of compatibility with experimental plots for energy maps obtained from molecular mechanics methods compared to most quantum mechanical methods. The experimental energy plots we have investigated could be helpful in refining protein structures obtained from X-ray, NMR, and electron microscopy and in refining force field parameters to enable simulations of peptide and protein structures that have higher degree of consistency with experiments. Proteins 2017; 85:979-1001. © 2017 Wiley Periodicals, Inc.