Direct Amination of α-Triaryl Alcohols via Vanadium Catalysis.

α-Triaryl amines have been used as pharmaceuticals and pharmaceutical intermediates for antifungal and anticancer applications. Current methods to synthesize such compounds require at least two steps, and no direct amination of tertiary alcohols has been reported. Herein, we disclose efficient catalytic conditions for the direct amination of α-triaryl alcohols to access α-triaryl amines. VO(OiPr)3, a commercially available reagent, has been identified as an effective catalyst for the direct amination of several α-triaryl alcohols. This process is scalable, as demonstrated by a gram-scale synthesis, and the reaction still works at as low as a 0.01 mol % catalyst loading with the turnover number reaching 3900. Moreover, commercial pharmaceuticals including clotrimazole and flutrimazole have been successfully prepared rapidly and efficiently using this newly developed method.

Nickel-Catalyzed Enantioselective Reductive Arylation and Heteroarylation of Aldimines via an Elementary 1,4-Addition.

Nickel catalysts of chiral pyrox ligands promoted enantioselective reductive arylation and heteroarylation of aldimines, using directly (hetero)aryl halides and sulfonates. The catalytic arylation can also be conducted with crude aldimines generated from condensation of aldehydes and azaaryl amines. Mechanistically, density functional theory (DFT) calculations and experiments pointed to an elementary step of 1,4-addition of aryl nickel(I) complexes to N-azaaryl aldimines.

Nickel-Catalyzed Enantioselective Reductive Conjugate Arylation and Heteroarylation via an Elementary Mechanism of 1,4-Addition.

A nickel complex of isoquinox promoted enantioselective conjugate arylation and heteroarylation of enones using aryl and heteroaryl halides directly. The reaction was successfully applied to stereoselective syntheses of ar-turmerone, chiral fragments of (+)-tolterodine and AZD5672. Mechanistically, experiments and calculations supported that an arylnickel(I) complex inserted to enones via an elementary 1,4-addition.

Accurate Prediction for Protein-Peptide Binding Based on High-Temperature Molecular Dynamics Simulations.

The structural characterization of protein-peptide interactions is fundamental to elucidating biological processes and designing peptide drugs. Molecular dynamics (MD) simulations are extensively used to study biomolecular systems. However, simulating the protein-peptide binding process is usually quite expensive. Based on our previous studies, herein, we propose a simple and effective method to predict the binding site and pose of the peptide simultaneously using high-temperature (high-T) MD simulations with the RSFF2C force field. Thousands of binding events (nonspecific or specific) can be sampled during microseconds of high-T MD. From density-based clustering analysis, the structures of all of the 12 complexes (nine with linear peptides and three with cyclic peptides) can be successfully predicted with root-mean-square deviation (RMSD) < 2.5 Å. By directly simulating the process of the ligand binding onto the receptor, our method approaches experimental precision for the first time, significantly surpassing previous protein-peptide docking methods in terms of accuracy.

Systematic investigation of the aza-Cope reaction for fluorescence imaging of formaldehyde in vitro and in vivo.

Increasing evidence has highlighted the endogenous production of formaldehyde (FA) in a variety of fundamental biological processes and its involvement in many disease conditions ranging from cancer to neurodegeneration. To examine the physiological and pathological relevance and functions of FA, fluorescent probes for FA imaging in live biological samples are of great significance. Herein we report a systematic investigation of 2-aza-Cope reactions between homoallylamines and FA for identification of a highly efficient 2-aza-Cope reaction moiety and development of fluorescent probes for imaging FA in living systems. By screening a set of N-substituted homoallylamines and comparing them to previously reported homoallylamine structures for reaction with FA, we found that N-p-methoxybenzyl homoallylamine exhibited an optimal 2-aza-Cope reactivity to FA. Theoretical calculations were then performed to demonstrate that the N-substituent on homoallylamine greatly affects the condensation with FA, which is more likely the rate-determining step. Moreover, the newly identified optimal N-p-methoxybenzyl homoallylamine moiety with a self-immolative ß-elimination linker was generally utilized to construct a series of fluorescent probes with varying excitation/emission wavelengths for sensitive and selective detection of FA in aqueous solutions and live cells. Among these probes, the near-infrared probe FFP706 has been well demonstrated to enable direct fluorescence visualization of steady-state endogenous FA in live mouse brain tissues and elevated FA levels in a mouse model of breast cancer. This study provides the optimal aza-Cope reaction moiety for FA probe development and new chemical tools for fluorescence imaging and biological investigation of FA in living systems.

Iron-Catalyzed Enantioselective Radical Carboazidation and Diazidation of α,ß-Unsaturated Carbonyl Compounds.

Azidation of alkenes is an efficient protocol to synthesize organic azides which are important structural motifs in organic synthesis. Enantioselective radical azidation, as a useful strategy to install a C-N3 bond, remains challenging due to the inherently instability and unique structure of radicals. Here, we disclose an efficient enantioselective radical carboazidation and diazidation of α,ß-unsaturated ketones and amides catalyzed by chiral N,N'-dioxide/Fe(OTf)2 complexes. An array of substituted alkenes was transformed to the corresponding α-azido carbonyl derivatives in good to excellent enantioselectivities, benefiting the preparation of chiral α-amino ketones, vicinal amino alcohols, and vicinal diamines. Control experiments and mechanistic studies proved the radical pathway in the reaction process. The DFT calculations showed that the azido transferred to the radical intermediate via an intramolecular five-membered transition state with the internal nitrogen of the Fe-N3 species.

Enantioselective Intermolecular Heck and Reductive Heck Reactions of Aryl Triflates, Mesylates, and Tosylates Catalyzed by Nickel.

Nickel-catalyzed intermolecular Heck reaction of cycloalkenes proceeds well with aryl triflates, mesylates and tosylates in excellent enantiomeric ratios. The asymmetric reductive Heck reaction also works with a 2-cyclopentenone ketal, which is equivalent to conjugate arylation of the enone itself.

Prevention of underfeeding during enteral nutrition after gastrectomy in adult patients with gastric cancer: an evidence utilization project.

BACKGROUND: Enteral nutrition is commonly used in patients with gastric cancer after a partial or full gastrectomy since it is safe to use and nutrient delivery is in line with human physiological characteristics. However, enteral feeding often leads to deficiency, when the actual intake of the patient is lower than the target demand, which seriously affects the recovery of patients. OBJECTIVE: To implement the best practice for preventing and managing underfeeding during enteral nutrition, and to improve the nutritional status of patients with gastric cancer. METHODS: The current study was conducted following the Joanna Briggs Institute Practical Application of Clinical Evidence System program. Phase one referred to the development of the project, consisting of the generation of the best evidence, mainly based on literature review and discussions within a panel of experts. Phase two was the implementation of the project, including baseline audit, training of enteral nutrition and change of clinical practice. Phase three was a postimplementation reaudit. The intake of enteral nutrition was observed in the first 3 days, and feeding intolerance of enteral nutrition was observed within the first week of enteral nutrition. Data were collected using self-designed questionnaires. The nutritional status of patients was measured using Patient-Generated Subjective Global Assessment (PG-SGA) at admission, and 1 week after surgery. RESULTS: A total of 60 patients with gastric cancer and 10 registered nurses were enrolled in this study. The compliance rate for all audit criteria increased postimplementation. The feeding rate of enteral nutrition postimplementation was higher than the baseline audit on the third day, 54.29% (±12.01) vs. 42.89% (±10.63), and the incidence of underfeeding was lower (30%, n = 30) than the baseline audit (76.67%, n = 30). Furthermore, the feeding intolerance postimplementation (26.67%, n = 30) was lower than the baseline audit (76.67%, n = 30) within 1 week of enteral nutrition. The PG-SGA scores were not significantly different between the baseline audit and postimplementation on the day of admission, while the scores were lower postimplementation (12.90 ±â€Š1.47) compared with the baseline audit (14.00 ±â€Š1.82). CONCLUSION: In this study, we performed an audit of the clinical nursing quality, which can guide nurses to accurately identify obstacles to the implementation of enteral nutrition, and standardize the implementation and management process, thereby improving the quality of nursing and the nutritional status of patients. RELEVANCE TO CLINICAL PRACTICE: The evidence-based practice might optimize the enteral nutrition process, enhance the efficacy of enteral nutrition, and improve the nutritional status of patients. Medical staff should develop an individualized nutritional support protocol for patients based on the results of nutritional status assessments.

CRiSP: accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning.

MOTIVATION: High-throughput sequencing discovers many naturally occurring disulfide-rich peptides or cystine-rich peptides (CRPs) with diversified bioactivities. However, their structure information, which is very important to peptide drug discovery, is still very limited. RESULTS: We have developed a CRP-specific structure prediction method called Cystine-Rich peptide Structure Prediction (CRiSP), based on a customized template database with cystine-specific sequence alignment and three machine-learning predictors. The modeling accuracy is significantly better than several popular general-purpose structure modeling methods, and our CRiSP can provide useful model quality estimations. AVAILABILITY AND IMPLEMENTATION: The CRiSP server is freely available on the website at http://wulab.com.cn/CRISP. CONTACT: wuyd@pkusz.edu.cn or jiangfan@pku.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Developments and Applications of Coil-Library-Based Residue-Specific Force Fields for Molecular Dynamics Simulations of Peptides and Proteins.

Molecular dynamics (MD) simulation has become a powerful tool for studying the structures and functional mechanisms of biomolecules, and its reliability crucially depends on the accuracy of underlying force fields. This perspective describes our recent efforts to develop more accurate protein force fields by improving the description of intrinsic conformational preferences of amino acid residues using residue-specific dihedral-angle-related parameters. Both backbone and side-chain conformational distributions and their coupling were optimized to fit those from a protein coil library. The resulting force fields RSFF1 and RSFF2 have been found to be more accurate than popular protein force fields, in reproducing experimental structural data of various peptides and proteins. They have also been successfully used in studying folding mechanisms and refinement of structure models. Further methodology developments related to intrinsically disordered proteins (RSFF2+) and a more universal implementation (RSFF2C) based on CMAP potentials are also described.

The reaction of alkyl hydropersulfides (RSSH, R = CH3 and tBu) with H2S in the gas phase and in aqueous solution.

The RSSH + H2S → RSH + HSSH reaction has been suggested by numerous labs to be important in H2S-mediated biological processes. Seven different mechanisms for this reaction (R = CH3, as a model) have been studied using the DFT methods (M06-2X and ωB97X-D) with the Dunning aug-cc-pV(T+d)Z basis sets. The reaction of CH3SSH with gas phase H2S has a very high energy barrier (>45 kcal mol-1), consistent with the available experimental observations. A series of substitution reactions R1-S-S-H + -S-R2 (R1 = Me, tBu, Ad, R2 = H, S-Me, S-tBu, S-Ad) have been studied. The regioselectivity is largely affected by the steric bulkiness of R1, but is much less sensitive to R2. Thus, when R1 is Me, all -S-R2 favorably attack the internal S atom, leading to R1-S-S-R2. While for R1 = tBu, Ad, all -S-R2 significantly prefer to attack the external S atom to form -S-S-R2. These results are in good agreement with the experimental observations.

Nickel-catalyzed asymmetric hydrogenation of ß-acylamino nitroolefins: an efficient approach to chiral amines.

An efficient approach for synthesizing chiral ß-amino nitroalkanes has been developed via the Ni-catalyzed asymmetric hydrogenation of challenging ß-amino nitroolefins under mild conditions, affording the desired products in excellent yields and with high enantioselectivities. This protocol had good compatibility with the wide substrate scope and a range of functional groups. The synthesis of chiral ß-amino nitroalkanes on a gram scale has also been achieved. In addition, the reaction mechanism was elucidated using a combined experimental and computational study, and it involved acetate-assisted heterolytic H2 cleavage followed by 1,4-hydride addition and protonation to achieve the nitroalkanes.

Chiral Sulfoxide-Induced Single Turn Peptide α-Helicity.

Inducing α-helicity through side-chain cross-linking is a strategy that has been pursued to improve peptide conformational rigidity and bio-availability. Here we describe the preparation of small peptides tethered to chiral sulfoxide-containing macrocyclic rings. Furthermore, a study of structure-activity relationships (SARs) disclosed properties with respect to ring size, sulfur position, oxidation state, and stereochemistry that show a propensity to induce α-helicity. Supporting data include circular dichroism spectroscopy (CD), NMR spectroscopy, and a single crystal X-ray structure for one such stabilized peptide. Finally, theoretical studies are presented to elucidate the effect of chiral sulfoxides in inducing backbone α-helicity.

Crosslinked Aspartic Acids as Helix-Nucleating Templates.

Described is a facile helix-nucleating template based on a tethered aspartic acid at the N-terminus [terminal aspartic acid (TD)]. The nucleating effect of the template is subtly influenced by the substituent at the end of the side-chain-end tether as indicated by circular dichroism, nuclear magnetic resonance, and molecular dynamics simulations. Unlike most nucleating strategies, the N-terminal amine is preserved, thus enabling further modification. Peptidomimetic estrogen receptor modulators (PERMs) constructed using this strategy show improved therapeutic properties. The current strategy can be regarded as a good complement to existing helix-stabilizing methods.

An In-tether Chiral Center Modulates the Helicity, Cell Permeability, and Target Binding Affinity of a Peptide.

The addition of a precisely positioned chiral center in the tether of a constrained peptide is reported, yielding two separable peptide diastereomers with significantly different helicity, as supported by circular dichroism (CD) and NMR spectroscopy. Single crystal X-ray diffraction analysis suggests that the absolute configuration of the in-tether chiral center in helical form is R, which is in agreement with theoretical simulations. The relationship between the secondary structure of the short peptides and their biochemical/biophysical properties remains elusive, largely because of the lack of proper controls. The present strategy provides the only method for investigating the influence of solely conformational differences upon the biochemical/biophysical properties of peptides. The significant differences in permeability and target binding affinity between the peptide diastereomers demonstrate the importance of helical conformation.

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.

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.

Residue-specific force field based on protein coil library. RSFF2: modification of AMBER ff99SB.

Recently, we developed a residue-specific force field (RSFF1) based on conformational free-energy distributions of the 20 amino acid residues from a protein coil library. Most parameters in RSFF1 were adopted from the OPLS-AA/L force field, but some van der Waals and torsional parameters that effectively affect local conformational preferences were introduced specifically for individual residues to fit the coil library distributions. Here a similar strategy has been applied to modify the Amber ff99SB force field, and a new force field named RSFF2 is developed. It can successfully fold α-helical structures such as polyalanine peptides, Trp-cage miniprotein, and villin headpiece subdomain and ß-sheet structures such as Trpzip-2, GB1 ß-hairpins, and the WW domain, simultaneously. The properties of various popular force fields in balancing between α-helix and ß-sheet are analyzed based on their descriptions of local conformational features of various residues, and the analysis reveals the importance of accurate local free-energy distributions. Unlike the RSFF1, which overestimates the stability of both α-helix and ß-sheet, RSFF2 gives melting curves of α-helical peptides and Trp-cage in good agreement with experimental data. Fitting to the two-state model, RSFF2 gives folding enthalpies and entropies in reasonably good agreement with available experimental results.

Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L.

Traditional protein force fields use one set of parameters for most of the 20 amino acids (AAs), allowing transferability of the parameters. However, a significant shortcoming is the difficulty to fit the Ramachandran plots of all AA residues simultaneously, affecting the accuracy of the force field. In this Feature Article, we report a new strategy for protein force field parametrization. Backbone and side-chain conformational distributions of all 20 AA residues obtained from protein coil library were used as the target data. The dihedral angle (torsion) potentials and some local nonbonded (1-4/1-5/1-6) interactions in OPLS-AA/L force field were modified such that the target data can be excellently reproduced by molecular dynamics simulations of dipeptides (blocked AAs) in explicit water, resulting in a new force field with AA-specific parameters, RSFF1. An efficient free energy decomposition approach was developed to separate the corrections on ϕ and ψ from the two-dimensional Ramachandran plots. RSFF1 is shown to reproduce the experimental NMR (3)J-coupling constants of AA dipeptides better than other force fields. It has a good balance between α-helical and ß-sheet secondary structures. It can successfully fold a set of α-helix proteins (Trp-cage and Homeodomain) and ß-hairpins (Trpzip-2, GB1 hairpin), which cannot be consistently stabilized by other state-of-the-art force fields. Interestingly, the RSFF1 force field systematically overestimates the melting temperature (and the stability of native state) of these peptides/proteins. It has a potential application in the simulation of protein folding and protein structure refinement.

A method for WD40 repeat detection and secondary structure prediction.

WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar ß-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction.