A diversity-oriented synthesis of bioactive benzanilides via a regioselective C(sp2)-H hydroxylation strategy

A diversity-oriented synthesis of bioactive benzanilides via C(sp2)-H hydroxylation has been studied. Different regioselectivity was observed with Ru(ii) and Pd(ii) catalysts. The reaction demonstrates excellent regioselectivity, good tolerance of functional groups, and high yields. A wide range of ortho-hydroxylated-benzanilides can be readily synthesized with excellent regioselectivity via this new synthetic strategy. Computational investigations revealed that the regioselectivity was controlled mainly by both steric and electronic factors. Steric effects determine the regioselective outcomes in the Ru-catalyzed reaction, while electronic effects are dominant in the Pd-catalyzed reaction.

Why does Togni's reagent I exist in the high-energy hypervalent iodine form? Re-evaluation of benziodoxole based hypervalent iodine reagents

For Togni's reagent I, the high energy barrier could prevent it from converting to its ether isomer. This might be one reason why it exists in the high-energy hypervalent iodine form.

Folding Simulations of an α-Helical Hairpin Motif αtα with Residue-Specific Force Fields

α-Helical hairpin (two-helix bundle) is a structure motif composed of two interacting helices connected by a turn or a short loop. It is an important model for protein folding studies, filling the gap between isolated α-helix and larger all-α domains. Here, we present, for the first time, successful folding simulations of an α-helical hairpin. Our RSFF1 and RSFF2 force fields give very similar predicted structures of this αtα peptide, which is in good agreement with its NMR structure. Our simulations also give site-specific stability of α-helix formation in good agreement with amide hydrogen exchange experiments. Combining the folding free energy landscapes and analyses of structures sampled in five different ranges of the fraction of native contacts (Q), a folding mechanism of αtα is proposed. The most stable sites of Q9-E15 in helix-1 and E24-A30 in helix-2 close to the loop region act as the folding initiation sites. The formation of interhelix side-chain contacts also initiates near the loop region, but some residues in the central parts of the two helices also form contacts quite early. The two termini fold at a final stage, and the loop region remains flexible during the whole folding process. This mechanism is similar to the "zipping out" pathway of β-hairpin folding.

Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides

The coupling of a coarse-grained (CG) protein model with the CG water model developed by Marrink et al. (J. Phys. Chem. B 2004, 108, 750) is presented. The model was used in the molecular dynamics studies of Ac-(Ala)6-Xaa-(Ala)7-NHMe, Xaa = Ala, Leu, Val, and Gly. A Gly mutation in the middle of polyalanine is found to destabilize the helix and stabilize the hairpin by favoring a type-II' turn and probably to speed up hairpin folding. The simulations allow us to derive thermodynamic parameters of, in particular, the helical propensities (s) of amino acids in these polyalanine-based peptides. The calculated s values are 1.18 (Ala), 0.84 (Leu), 0.30 (Val), and <0.02 (Gly) at 291 K, in excellent agreement with experimental values (R(2)=0.970). Analyses using a structural approach method show that the helical propensity difference of these amino acids mainly comes from solvation effect. Leu and Val have lower helical propensities than Ala mainly because the larger side chains shield the solvation of helical structures, while Gly has a much poorer helical propensity mainly due to the much better solvation for the coil structures than for the helical structures. Overall, the model is at least about 10(2) times faster than current all-atom MD methods with explicit solvent.

Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains

Recently, we reported that molecular dynamics (MD) simulations using a coarse-grained (CG) peptide model coupled with a CG water model are able to reproduce many of the structural and thermodynamic features of short peptides with nonpolar side chains at 10(3) times the normal speed (JCTC, 2007, 3, 2146-2161). To further develop a CG protein model for MD simulations, we systematically parametrized the side chains of all 20 naturally occurring amino acids. We developed the parameters by fitting the dihedral potentials of 13 small molecules, the densities and self-solvation free energies of liquids of eight organic molecules, and the hydration free energies of 35 small organic molecules. In a set of 11 classes of compounds (105 in total) including alkanes, alcohols, ethers, ketones/aldehydes, amines, amides, aromatics, carboxylic acids, sulfides/thiols, alkyl ammoniums, and carboxylate ions, the average error in the calculated hydration free energies compared with experimental results is about 1.4 kJ/mol. The average error in the calculated transfer free energies of the 19 side-chain analogues of amino acids from cyclohexane to water is about 2.2 kJ/mol. These results are comparable to the results of all-atom models.

PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides

We present the application of our recently developed PACE force field to the folding of peptides. These peptides include α-helical (AK17 and Fs), β-sheet (GB1m2 and Trpzip2), and mixed helical/coil (Trp-cage) peptides. With replica exchange molecular dynamics (REMD), our force field can fold the five peptides into their native structures while maintaining their stabilities reasonably well. Our force field is also able to capture important thermodynamic features of the five peptides that have been observed in previous experimental and computational studies, such as different preferences for a helix-turn-helix topology for AK17 and Fs, the relative contribution of four hydrophobic side chains of GB1p to the stability of β-hairpin, and the distinct role of a hydrogen bond involving Trp-Hε and a D9/R16 salt bridge in stabilizing the Trp-cage native structure. Furthermore, multiple folding and unfolding events are observed in our microsecond-long normal MD simulations of AK17, Trpzip2, and Trp-cage. These simulations provide mechanistic information such as a "zip-out" pathway of the folding mechanism of Trpzip2 and the folding times of AK17 and Trp-cage, which are estimated to be about 51 ± 43 ns and 270 ± 110 ns, respectively. A 600 ns simulation of the peptides can be completed within one day. These features of our force field are potentially applicable to the study of thermodynamics and kinetics of real protein systems.

Folding Thermodynamics and Mechanism of Five Trp-Cage Variants from Replica-Exchange MD Simulations with RSFF2 Force Field

To test whether our recently developed residue-specific force field RSFF2 can reproduce the mutational effect on the thermal stability of Trp-cage mini-protein and decipher its detailed folding mechanism, we carried out long-time replica-exchange molecular dynamics (REMD) simulations on five Trp-cage variants, including TC5b and TC10b. Initiated from their unfolded structures, the simulations not only well-reproduce their experimental structures but also their melting temperatures and folding enthalpies reasonably well. For each Trp-cage variant, the overall folding free energy landscape is apparently two-state, but some intermediate states can be observed when projected on more detailed coordinates. We also found different variants have the same major folding pathway, including the well formed PII-helix in the unfolded state, the formation of W6-P12/P18/P19 contacts and the α-helix before the transition state, the following formation of most native contacts, and the final native loop formation. The folding mechanism derived here is consistent with many previous simulations and experiments.

A combined IM-MS/DFT study on [Pd(MPAA)]-catalyzed enantioselective C-H activation: relay of chirality through a rigid framework

A combined ion-mobility mass spectrometry (IM-MS) and DFT study has been employed to investigate the mechanism and the origin of selectivity of palladium/mono-N-protected amino acid (MPAA)-catalyzed enantioselective CH activation reactions of several prochiral substrates. We captured the [Pd(MPAA)(substrate)] complex at different stages, and demonstrated that the CH bond can be activated in the absence of an external base. DFT studies lead to the establishment of a significantly modified relay mechanism invoking a key conformational effect to account for the origin of enantioselectivity. This relay mechanism successfully accounts for the enantioselectivity for all the relevant reactions reported. The enantioselectivity originates from the rigid square-planar Pd coordination in the CH activation transition state: Bidentate MPAA and substrate coordination.

Significant Refinement of Protein Structure Models Using a Residue-Specific Force Field

An important application of all-atom explicit-solvent molecular dynamics (MD) simulations is the refinement of protein structures from low-resolution experiments or template-based modeling. A critical requirement is that the native structure is stable with the force field. We have applied a recently developed residue-specific force field, RSFF1, to a set of 30 refinement targets from recent CASP experiments. Starting from their experimental structures, 1.0 μs unrestrained simulations at 298 K retain most of the native structures quite well except for a few flexible terminals and long internal loops. Starting from each homology model, a 150 ns MD simulation at 380 K generates the best RMSD improvement of 0.85 Å on average. The structural improvements roughly correlate with the RMSD of the initial homology models, indicating possible consistent structure refinement. Finally, targets TR614 and TR624 have been subjected to long-time replica-exchange MD simulations. Significant structural improvements are generated, with RMSD of 1.91 and 1.36 Å with respect to their crystal structures. Thus, it is possible to achieve realistic refinement of protein structure models to near-experimental accuracy, using accurate force field with sufficient conformational sampling.

Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions

Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.

Non-manifesting AHI1 truncations indicate localized loss-of-function tolerance in a severe Mendelian disease gene

Determination of variant pathogenicity represents a major challenge in the era of high-throughput sequencing. Erroneous categorization may result if variants affect genes that are in fact dispensable. We demonstrate that this also applies to rare, apparently unambiguous truncating mutations of an established disease gene. By whole-exome sequencing (WES) in a consanguineous family with congenital non-syndromic deafness, we unexpectedly identified a homozygous nonsense variant, p.Arg1066*, in AHI1, a gene associated with Joubert syndrome (JBTS), a severe recessive ciliopathy. None of four homozygotes expressed any signs of JBTS, and one of them had normal hearing, which also ruled out p.Arg1066* as the cause of deafness. Homozygosity mapping and WES in the only other reported JBTS family with a homozygous C-terminal truncation (p.Trp1088Leufs*16) confirmed AHI1 as disease gene, but based on a more N-terminal missense mutation impairing WD40-repeat formation. Morpholinos against N-terminal zebrafish Ahi1, orthologous to where human mutations cluster, produced a ciliopathy, but targeting near human p.Arg1066 and p.Trp1088 did not. Most AHI1 mutations in JBTS patients result in truncated protein lacking WD40-repeats and the SH3 domain; disease was hitherto attributed to loss of these protein interaction modules. Our findings indicate that normal development does not require the C-terminal SH3 domain. This has far-reaching implications, considering that variants like p.Glu984* identified by preconception screening ('Kingsmore panel') do not necessarily indicate JBTS carriership. Genomes of individuals with consanguineous background are enriched for homozygous variants that may unmask dispensable regions of disease genes and unrecognized false positives in diagnostic large-scale sequencing and preconception carrier screening.

Toward electron-deficient pyrene derivatives: construction of pyrene tetracarboxylic diimide containing five-membered imide rings

Electron-deficient pyrene-1,2,6,7-tetracarboxylic diimide (PyrDI) and pyrene-4,9-dicyano-1,2,6,7-tetracarboxylic diimide (PyrDI-CN) containing five-membered imide rings have been designed and synthesized as a new family of aromatic diimides.

WDSPdb: a database for WD40-repeat proteins

WD40-repeat proteins, as one of the largest protein families, often serve as platforms to assemble functional complexes through the hotspot residues on their domain surfaces, and thus play vital roles in many biological processes. Consequently, it is highly required for researchers who study WD40 proteins and protein-protein interactions to obtain structural information of WD40 domains. Systematic identification of WD40-repeat proteins, including prediction of their secondary structures, tertiary structures and potential hotspot residues responsible for protein-protein interactions, may constitute a valuable resource upon this request. To achieve this goal, we developed a specialized database WDSPdb (http://wu.scbb.pkusz.edu.cn/wdsp/) to provide these details of WD40-repeat proteins based on our recently published method WDSP. The WDSPdb contains 63,211 WD40-repeat proteins identified from 3383 species, including most well-known model organisms. To better serve the community, we implemented a user-friendly interactive web interface to browse, search and download the secondary structures, 3D structure models and potential hotspot residues provided by WDSPdb.

Investigating the nature of palladium chain-walking in the enantioselective redox-relay Heck reaction of alkenyl alcohols

The mechanism of the redox-relay Heck reaction was investigated using deuterium-labeled substrates. Results support a pathway through a low energy palladium-alkyl intermediate that immediately precedes product formation, ruling out a tautomerization mechanism. DFT calculations of the relevant transition structures at the M06/LAN2DZ+f/6-31+G* level of theory show that the former pathway is favored by 5.8 kcal/mol. Palladium chain-walking toward the alcohol, following successive β-hydride eliminations and migratory insertions, is also supported in this study. The stereochemistry of deuterium labels is determined, lending support that the catalyst remains bound to the substrate during the relay process and that both cis- and trans-alkenes form from β-hydride elimination.

Inhibition and mechanism of HDAC8 revisited

Histone deacetylases (HDACs) have found intense interest as drug targets for a variety of diseases, but there is disagreement about basic aspects of the inhibition and mechanism of HDACs. QM/MM calculations of HDAC8 including a large QM region provide a model that is consistent with the available crystal structures and structure-activity relationships of different HDAC inhibitors. The calculations support a spontaneous proton transfer from a hydroxamic acid to an active site histidine upon binding to the zinc. The role of the H142/D176 catalytic dyad as the general base of the reaction is elucidated. The reasons for the disagreements between previous proposals are discussed. The results provide detailed insights into the unique mechanism of HDACs, including the role of the two catalytic dyads and function of the potassium near the active site. They also have important implications for the design of novel inhibitors for a number of HDACs such as the class IIa HDACs.

Enantioselective formation of cyano-bearing all-carbon quaternary stereocenters: desymmetrization by copper-catalyzed N-arylation

The enantioselective construction of all-carbon quaternary stereocenters is one of the most challenging fields in asymmetric synthesis. An asymmetric desymmetrization strategy offers an indirect and efficient method for the formation of all-carbon stereocenters. An enantioselective formation of cyano-bearing all-carbon quaternary stereocenters in 1,2,3,4,-tetrahydroquinolines and 2,3,4,5-tetrahydro-1H-benzo[b]azepines by copper-catalyzed desymmetric N-arylation is demonstrated. The cyano group at the prochiral center plays a key role for the high enantioselectivity and works as an important functional group for further transformations. DFT studies provide a model which successfully accounts for the origin of enantioselectivity.

Folding of fourteen small proteins with a residue-specific force field and replica-exchange molecular dynamics

Ab initio protein folding via physical-based all-atom simulation is still quite challenging. Using a recently developed residue-specific force field (RSFF1) in explicit solvent, we are able to fold a diverse set of 14 model proteins. The obtained structural features of unfolded state are in good agreement with previous observations. The replica-exchange molecular dynamics simulation is found to be efficient, resulting in multiple folding events for each protein. Transition path time is found to be significantly reduced under elevated temperature.