Structure-Based Rational and General Strategy for Stabilizing Single-Chain T-Cell Receptors to Enhance Affinity

The T-cell receptor (TCR) is a crucial molecule in cellular immunity. The single-chain T-cell receptor (scTCR) is a potential format in TCR therapeutics because it eliminates the possibility of αβ-TCR mispairing. However, its poor stability and solubility impede the in vitro study and manufacturing of therapeutic applications. In this study, some conserved structural motifs are identified in variable domains regardless of germlines and species. Theoretical analysis helps to identify those unfavored factors and leads to a general strategy for stabilizing scTCRs by substituting residues at exact IMGT positions with beneficial propensities on the consensus sequence of germlines. Several representative scTCRs are displayed to achieve stability optimization and retain comparable binding affinities with the corresponding αβ-TCRs in the range of μM to pM. These results demonstrate that our strategies for scTCR engineering are capable of providing the affinity-enhanced and specificity-retained format, which are of great value in facilitating the development of TCR-related therapeutics.

Mechanistic Insights into Sc(III)-Catalyzed Asymmetric Homologation of Ketones with Diazo Compounds: How Trans Influence Assists in Controlling Stereochemistry

Asymmetric one-carbon homologation or ring expansion of ketones with formal insertion of carbene intermediate, is a challenging but useful strategy to construct a complex skeleton. Sc(III) and chiral ligands have been employed in this regard. However, due to flexible conformations and a variety of stereo models, the origin of stereochemistry remains ambiguous. Density functional theory (DFT) calculations were carried out to explore the interactions that control the stereoselectivity of a Sc(III)-catalyzed asymmetric homologation. The trans influence of counterions was found to affect the coordination mode of ketone to Sc(III), and consequently affect the stereoselectivity.

Mild Stereoselective Synthesis of Densely Substituted [3]Dendralenes via Ru-Catalyzed Intermolecular Dimerization of 1,1-Disubstituted Allenes

Described here is a mild and stereoselective protocol for the synthesis of [3]dendralenes via the intermolecular dimerization of allenes. With the proper choice of a ruthenium catalyst, a range of unactivated 1,1-disubstituted allenes, without prefunctionalization in the allylic position, reacted efficiently to provide rapid access to densely substituted [3]dendralenes. An intermolecular C-C bond and three different types of C═C double bonds (di-, tri-, and tetrasubstituted) embedded in an acyclic structure were constructed with good to high E/Z stereocontrol. This is in contrast to the known catalytic protocols that focus on allenes with prefunctionalization at the allylic position and/or monosubstituted allenes, which would proceed by a different mechanism or require less stereocontrol. The silyl-substituted dendralene products are precursors of other useful dendralene molecules. Density functional theory (DFT) studies and control experiments supported a mechanism involving oxidative cyclometalation, β-H elimination (the rate-determining step), and reductive elimination.

[Association of sleep duration and physical exercise with dyslipidemia in older adults aged 80 years and over in China]

Objective: To explore the impact of sleep duration, physical exercise, and their interactions on the risk of dyslipidemia in older adults aged ≥80 (the oldest old) in China. Methods: The study subjects were the oldest old from four rounds of Healthy Aging and Biomarkers Cohort Study (2008-2009, 2011-2012, 2014 and 2017-2018). The information about their demographic characteristics, lifestyles, physical examination results and others were collected, and fasting venous blood samples were collected from them for blood lipid testing. Competing risk model was used to analyze the causal associations of sleep duration and physical exercise with the risk for dyslipidemia. Restricted cubic spline (RCS) function was used to explore the dose-response relationship between sleep duration and the risk for dyslipidemia. Additive and multiplicative interaction model were used to explore the interaction of sleep duration and physical exercise on the risk for dyslipidemia. Results: The average age of 1 809 subjects was (93.1±7.7) years, 65.1% of them were women. The average sleep duration of the subjects was (8.0±2.5) hours/day, 28.1% of them had sleep duration for less than 7 hours/day, and 27.2% had sleep for duration more than 9 hours/day at baseline survey. During the 9-year cumulative follow-up of 6 150.6 person years (follow-up of average 3.4 years for one person), there were 304 new cases of dyslipidemia, with an incidence density of 4 942.6/100 000 person years. The results of competitive risk model analysis showed that compared with those who slept for 7-9 hours/day, the risk for dyslipidemia in oldest old with sleep duration >9 hours/day increased by 22% (HR=1.22, 95%CI: 1.07-1.39). Compared with the oldest old having no physical exercise, the risk for dyslipidemia in the oldest old having physical exercise decreased by 33% (HR=0.67, 95%CI: 0.57-0.78). The RCS function showed a linear positive dose-response relationship between sleep duration and the risk for hyperlipidemia. The interaction analysis showed that physical exercise and sleep duration had an antagonistic effect on the risk for hyperlipidemia. Conclusion: Physical exercise could reduce the adverse effects of prolonged sleep on blood lipids in the oldest old.

[From treatment to whole course management: envisioning comprehensive management of Talaromycosis marneffei]

Talaromycosis marneffei has been increasing in recent years. Our understanding of this disease has gradually deepened through extensive basic and clinical research, but there are still many limitations. In this article, by incorporating the latest research advancements, we discuss important issues in managing Talaromycosis marneffei trends, aiming to guide effective prevention and control of the disease, improving public health, and reducing the healthcare burden.

New Insights into the Cooperativity and Dynamics of Dimeric Enzymes

A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.

Propeptide-Mediated Allosteric Regulation of Xylanase Xyl-1: An Integrated Experimental and Computational Analysis

Most GH11 family endo-β-1,4-xylanases contain a propeptide region linked to the N-terminal region. The mechanistic basis of this region harboring key regulation information for enzyme function, however, remains poorly understood. We reported an investigation on the allosteric regulation mechanism of the propeptide based on biochemical characterization, molecular dynamics simulations, and evolutionary analysis. We discovered that the mutant of truncated propeptide shows a remarkably increased thermal stability (melting temperature increased by 11.5 °C) and catalytic efficiency (1.7-fold k_cat/K_m value of wild type). Molecular dynamics simulations reveal that long-range fluctuations in the propeptide lead to a conformational perturbation in the catalytic pocket and the thumb region. The probability of sampling the active conformation during the glycosylation step is reduced (i.e., catalytic efficiency). In-depth sequence analysis indicates that the propeptide has a strong plasticity and degeneration trend, and propeptide truncation experiments of the homologous enzyme XynB validated the feasibility of the truncation strategy. This work reveals the role of GH11 family propeptides in functional regulation and provides a straightforward and practical method to increase the robustness of GH11 family xylanases.

Cobalt-Catalyzed Enantioselective Cross-Electrophile Couplings: Stereoselective Syntheses of 5-7-Membered Azacycles

Cobalt complexes of chiral pyrox ligands catalyzed enantioselective reductive couplings of nonconjugated iododienes with aryl iodides or alkenyl bromides. The reaction enabled stereoselective syntheses of 5-7-membered azacycles carrying quaternary stereocenters. Mechanistically, cross-electrophile selectivity originated from selective coupling of alkylcobalt(I) complexes generated after cyclization with aryl iodides.

[Clinical efficacy of the treatment of bilateral gluteal muscle contracture by inside-out iliotibial band release under arthroscopy in the supine position]

Objective: To investigate the clinical efficacy of bilateral gluteal muscle contracture treated with inside-out iliotibial band release under arthroscopy in the supine position. Methods: A prospective non-randomized controlled trial. Forty-six patients admitted to the Department of Sports Medicine, Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital from April 2021 to August 2022 for bilateral gluteal muscle contracture and proposed surgical treatment were enrolled. The subjects were divided into two groups according to the preferred surgical protocols of the patients: the supine position group was treated with inside-out iliotibial band release under arthroscopy in the supine position, and the operation in lateral position group was carried out with outside-in iliotibial band release under arthroscopy in the lateral position. The total duration of non-surgical operations and the total duration of surgical operations were recorded for all patients. The gluteal muscle contracture disability scale within 3 days before surgery and at least 2 months after surgery were compared between the two groups, and the occurrence of complications between the two groups was compared too. Results: There were 26 cases in the supine position group, 11 males and 15 females with a mean age of (31.8±7.3) years; and there were 20 cases in the lateral position group, 7 males and 13 females with a mean age of (30.6±6.3) years. The differences in gender, age, body mass index (BMI) and postoperative follow-up time between the two groups were not statistically significant (all P>0.05). The total duration of non-surgical operations was shorter in the supine position group than in the lateral position group [(47.9±10.4) min vs (63.9±7.5) min, P<0.001]. There was no statistically significant difference in the total duration of surgical operations between the supine position group and the lateral position group [31.0(27.0, 43.5) min vs 33.0(24.8, 38.0) min, P>0.05]. The postoperative gluteal muscle contracture disability scales were significantly improved in both the supine position and lateral position groups when compared with those before the operation [93.0 (85.0, 98.0) vs 61.0 (50.5, 66.8), P<0.001 and 88.5±6.9 vs 63.6±9.6, P<0.001, respectively]. There was no statistically significant difference in the gluteal muscle contracture disability scale between the supine position and lateral position groups before and 2 months after surgery [59.3±11.9 vs 63.6±9.6 and 93.0 (85.0, 98.0) vs 89.5(84.0, 94.8), both P>0.05, respectively]. Two patients in each group developed subcutaneous hematoma after surgery, and all of them resolved within 2 weeks after surgery, the difference in complication incidence rate was not statistically significant (P>0.05). No postoperative complications such as fat liquefaction in the operated area, infection, decreased hip abductor muscle strength or nerve injury in the lower extremity were observed in both groups. Conclusion: The treatment of bilateral gluteal muscle contracture by inside-out iliotibial band release under arthroscopy in the supine position can effectively improve clinical efficiency, with definite efficacy, and it is an operative program worth promoting.

[Predictive value of ultrasound-guided anesthesia injection in arthroscopy for borderline developmental dysplasia of the hip]

Objective: To evaluate the value of ultrasound-guided intra-articular anesthetic injection in predicting postoperative outcomes for borderline developmental hip dysplasia (BDDH). Methods: A follow-up study. The clinical data of 37 BDDH patients who received ultrasound-guided intra-articular anesthetic injection and arthroscopic examination in the Department of Sports Medicine, Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital from May 2018 to February 2021 were retrospectively analyzed. Among them, there were 17 males and 20 females with a mean age of (37.9±12.8) years. All patients underwent ultrasound-guided intra-articular anesthetic injection prior to arthroscopy, and were evaluated with hip physical examination before and after injection, as well as before and after arthroscopy, in order to obtain the visual analog score (VAS) of pain for seven assessments. The total VAS score was calculated based on these evaluations. Follow-up was conducted for at least 12 months. The effective rate of injection referred to the ratio of the improvement of VAS score after anesthetic injection to the total VAS score before injection. Pearson correlation analysis and Bland-Altman analysis were used to test the correlation between modified Harris hip score (mHHS) after ultrasound-guided intra-articular anesthetic injection and mHHS score after arthroscopic surgery. A binary logistic regression model was established to analyze the substantial clinical benefit (SCB) for patients. Following the logistic regression analysis, a receiver operating characteristic (ROC) curve was constructed to evaluate the predictive power of ultrasound-guided intra-articular anesthetic injection in achieving SCB in those patients. The optimal cut-off value for injection efficacy was determined based on the ROC curve when SCB was achieved. Results: The follow-up time for all patients was (26.3±7.6) months. After anesthetic injection for 20 minutes, the total VAS score of pain [M(Q₁,Q₃)] decreased from 13(8,23) points before injection to 1(0,4) points; and the mHHS score [M(Q₁,Q₃)] increased from 60(46,70) points before arthroscopy to 90(84,96) points after, with statistically significant differences before and after injection and before and after arthroscopy (both P<0.001). Pearson correlation analysis showed that the mHHS score after intra-articular anesthetic injection was positively correlated with the mHHS score after surgery (r=0.961, P<0.001). The area under the ROC curve for predicting SCB after arthroscopy with ultrasound-guided intra-articular anesthetic injection was 0.769 (95%CI: 0.561-0.976), the Youden index was 0.663, the cut-off value was 0.569 2, the sensitivity was 96.3%, and the specificity was 70.0%. Conclusions: The results of ultrasound-guided intra-articular anesthetic injection before arthroscopy can indicate the presence of intra-articular lesions, and the degree of pain relief after injection is proportional to the functional recovery after arthroscopy. Patients with intra-articular anesthetic injection efficacy>56.92% have better results in hip arthroscopy.

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.

[Outcomes of fluoroscopy-free hip arthroscopy technique in the treatment of femoroacetabular impingement syndrome]

Objective: To evaluate the effect of fluoroscopy-free technique in the arthroscopic treatment of femoroacetabular impingement syndrome (FAIS). Methods: A retrospective cohort study. Clinical data of FAI patients treated with hip arthroscopy in the No.4 Medical Center, PLA General Hospital from October 2018 to December 2021 were retrospectively analyzed. The patients were divided into two groups according to the surgical procedure: the fluoroscopy group and the fluoroscopy-free group. The operation time and modified Harris hip score (mHHS), international hip outcome tool (iHOT12) and visual analogue scale (VAS) of hip joint pain before and after the operation were observed and compared between the two groups. And the incidence of surgical complications in the two groups were compared too. Results: A total of 460 patients (213 males and 247 females) [aged (32.6±8.3) years (15-67 years)] with valid follow-up were included in this study. There were 275 cases in the fluoroscopy-free group and 185 cases in the fluoroscopy group. The operation time was shorter in the fluoroscopy-free group when compared with that in the fluoroscopy group, and the difference was statistically significant [(93.36±12.54) min vs (115.62±6.03) min, P<0.001]. In both groups, the VAS scores decreased and the mHHS scores and iHOT12 scores improved significantly at the last follow-up when compared with those before the operation (all P<0.001); however, there was no significant difference in the scores between the two groups (all P>0.05). The complication rate in the fluoroscopy-free group was 10.18% (28/275), and it was 10.81%(20/185) in the fluoroscopy group (P=0.829). Conclusion: Fluoroscopy-free hip arthroscopy technique for FAI can avoid radiation and shorten the operation time, but it does not increase the incidence of complications with reliable clinical outcomes.

Enantioselective anti-Dihalogenation of Electron-Deficient Olefin: A Triplet Halo-Radical Pylon Intermediate

The textbook alkene halogenation reaction establishes straightforward access to vicinal dihaloalkanes. However, a robust catalytic method for dihalogenizing electron-deficient olefins in an enantioselective manner is still under development, and its mechanism remains controversial. Herein, we disclose efficient regio-, anti-diastereo-, and enantioselective dibromination, bromochlorination, and dichlorination reactions of enones catalyzed by a chiral N,N'-dioxide/Yb(OTf)₃ complex. With the combination of electrophilic halogen and halide salts as halogenating agents, an array of homo- and heterodihalogenated derivatives is achieved in moderate to good enantioselectivities. Moreover, DFT calculations reveal that a novel triplet halo-radical pylon intermediate is probable in accounting for the exclusive regio- and anti-diastereoselectivity.

Selective Formal Carbene Insertion into Carbon-Boron Bonds of Diboronates by N-Trisylhydrazones

Bisborylalkanes play important roles in organic synthesis as versatile bifunctional reagents. The two boron moieties in these compounds can be selectively converted into other functional groups through cross-coupling, oxidation or radical reactions. Thus, the development of efficient methods for synthesizing bisborylalkanes is highly demanded. Herein we report a new strategy to access bisborylalkanes through the reaction of N-trisylhydrazones with diboronate, in which the bis(boryl) methane is transformed into 1,2-bis(boronates) via formal carbene insertion. Since the N-trisylhydrazones can be readily derived from the corresponding aldehydes, this strategy represents a practical synthesis of 1,2-diboronates with broad substrate scope. Mechanistic studies reveal an unusual neighboring group effect of 1,1-bis(boronates), which accounts for the observed regioselectivity when unsymmetric 1,1-diboronates are applied.

Inverse Electron-Demanding Diels-Alder Reactions in the Chemical Synthesis of Prenylated Indole Alkaloids Containing a Bicycle[2.2.2]diazaoctane Moiety: A Theoretical Study

The Diels-Alder reaction is believed to be a key step in the biosynthesis of prenylated indole alkaloids containing a bicycle[2.2.2]diazaoctane moiety. Many chemical syntheses of bicyclic structures by Diels-Alder reactions have been reported, but the reaction mechanism remains underexplored. We have carried out DFT calculations on both acid- and base-promoted Diels-Alder reactions in these syntheses and reveal that the reactions occur through an inverse-electron demand mechanism. We hope that the new mechanism is helpful for the mechanistic understanding of the biosynthesis of this class of important natural products.

Ir-Catalyzed Regioselective Dihydroboration of Thioalkynes toward Gem-Diboryl Thioethers

While 1,1-diboryl (gem-diboryl) compounds are valuable synthetic building blocks, currently, related studies have mainly focused on those 1,1-diboryl alkanes without a hetero functional group in the α-position. gem-Diboryl compounds with an α-hetero substituent, though highly versatile, have been limitedly accessible and thus rarely utilized. Herein, we have developed the first α-dihydroboration of heteroalkynes leading to the efficient construction of gem-diboryl, hetero-, and tetra-substituted carbon centers. This straightforward, practical, mild, and atom-economic reaction is an attractive complement to the conventional multistep synthetic strategy relying on deprotonation of gem-diborylmethane by a strong base. Specifically, [Ir(cod)(OMe)]₂ was found to be uniquely effective for this process of thioalkynes, leading to excellent α-regioselectivity when delivering the two boryl groups, which is remarkable in view of the many competitive paths including monohydroboration, 1,2-dihydroboration, dehydrodiboration, triboration, tetraboration, etc. Control experiments combined with DFT calculations suggested that this process involves two sequential hydroboration events. The second hydroboration requires a higher energy barrier due to severe steric repulsion in generating the highly congested α-sulfenyl gem-diboryl carbon center, a structural motif that was almost unknown before.

[Risk factors and chemoprophylaxis of ulcerative colitis-colorectal cancer]

Ulcerative colitis-colorectal cancer (UC-CRC) is one of the most serious complications in patients with ulcerative colitis (UC), with worse prognosis and higher mortality than sporadic colorectal cancer (CRC). Since most UC-CRC developed through the "inflammation-dysplasia-carcinoma" approach, early detection of dysplasia through identification of high-risk groups reasonable monitoring and active prevention are extremely important. However, there is no consensus on the risk factors of UC carcinogenesis and the drugs that can be used for chemoprevention currently. This article combined with relevant literature at home and abroad, reviewed the current risk factors and chemopreventive drugs for UC carcinogenesis, in order to provide reference for early prevention, early detection and early diagnosis of UC-CRC.

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.

Ruthenium-Catalyzed Geminal Hydroborative Cyclization of Enynes

Disclosed here is the first geminal (gem-) hydroborative cyclization of enynes. Different from known hydroborative cyclizations, this process adds hydrogen and boron to the same position, leading to a new reaction mode. With [Cp*RuCl]₄ as catalyst, a range of gem-hydroborated bicyclic products bearing a cyclopropane unit could be rapidly assembled from simple enyne substrates. Control experiments and density functional theory (DFT) calculations provided important insights into the reaction mechanism. Notably, two major competing pathways may operate with substrate-dependence. 1,6-Enynes favor initial oxidative cyclometalation to form a ruthenacyclopentene intermediate prior to engaging hydroborane, while other enynes (e.g., 1,7-enynes) that lack strong propensity toward cyclization prefer initial alkyne gem-(H,B)-addition to form an α-boryl ruthenium carbene followed by intramolecular olefin cyclopropanation. This process also represents the first ruthenium-catalyzed enyne hydroborative cyclization.

Ru-Catalyzed Hydroboration of Ynones Leads to a Nontraditional Mode of Reactivity

Although hydroboration of simple ketones and alkynes have been well-established, little is known about the unique hydroboration reactivity for ynones, a family of important building blocks. Herein we report a new reaction mode of ynones leading to structurally novel and synthetically useful but previously inaccessible products, vinyl α-hydroxylboronates, under mild ruthenium-catalyzed hydroboration conditions. This reaction features high efficiency, a broad scope, and complete chemo-, regio-, and stereoselectivity, in spite of many possible competitive pathways. Both control experiments and detailed DFT studies suggested a two-step mechanism, involving initial rate-determining conjugate addition of hydroborane to form the key boryl allenolate intermediate followed by a fast second hydroboration of the enolate motif of the allenolate. Notably, direct 1,4-addition of hydroborane to carbonyl-conjugated alkynes also represents a new mode of reactivity. Despite the overwhelming complexity of this process, which involves selectivity control in almost every step, a thorough and detailed computation on a large set of possible transition states explained the unusual reactivity and intrinsic origin of selectivity.

Study of Pd-catalyzed Selective Mono- and Di-C(sp3)-H Bond Activation: A Bi-ligand Model

Controlling the number of C-H bond activation is a long-standing challenge in organic synthesis. Recently, Yu's group demonstrated that in Pd-catalyzed alanine's arylation, pyridine-type ligands favor a mono-C-H bond activation, while quinoline-type ligands favor a di-C-H bond activation. To disclose the underlying principles, a theoretical study (density functional theory (DFT)) has been carried out. Our study indicates that a mono-ligand model, which is generally adopted in the community, does not reproduce the experimentally observed mono-/di-selectivity, while a bi-ligand model can rationalize the experimental observations well, including the observed diastereoselectivity in diarylation. The electron-rich pyridine-type ligands with less steric congestion can promote the C-H bond activation reaction of alanine derivatives. The quinoline-type ligands have a better π back-donation interaction with the metal, which makes a more active C-H bond activation than the pyridine-type ligands for this reaction. This bi-ligand model, which is a necessity, allows the understanding and future design of a dual ligand effect in C-H bond activation.

Asymmetric Catalytic (2+1) Cycloaddition of Thioketones to Synthesize Tetrasubstituted Thiiranes

Herein, we report the first example of enantioselective (2+1) cycloaddition of thioketones with α-diazo pyrazoleamides for the direct synthesis of tetrasubstituted thiiranes. In the presence of chiral N,N'-dioxide/cobalt(ΙΙ) complexes (2-5 mol%), excellent efficiency (up to 99 % yield within 15 mins) and high stereoselectivity (up to >19 : 1 dr and 97 % ee) are available. Elaborations of thiiranes via desulfuration have also been conducted to deliver tetrasubstituted olefins. Density functional theory calculations reveal that the reaction initiates from a doublet state cobalt(ΙΙ) carbenoid, which is followed by a quartet cobalt(ΙΙ)-bound thiocarbonyl ylide pathway. This work provides a route for the selective construction of tetrasubstituted thiiranes and olefins that are otherwise difficult to access.

Rh-Catalyzed [4 + 2] Annulation with a Removable Monodentate Structure toward Iminopyranes and Pyranones by C-H Annulation

The Rh-catalyzed reactions of N-pyridinyl enaminones with internal alkynes leading to the synthesis of iminopyranes via a key C-H bond activation and subsequent tautomeric O-H bond cleavage are reported. Moreover, the pyridine ring in the amino group acts as an auxiliary monodentate site for this annulation and can be easily removed by a simple hydrolysis to afford pyranones.

Total synthesis of monoterpenoid indole alkaloid (–)-arbophyllidine

The first asymmetric total synthesis of (–)-arbophyllidine, an unusual pentacyclic monoterpenoid indole alkaloid, has been achieved.

Incorporating structural features to improve the prediction and understanding of pathogenic amino acid substitutions

BACKGROUND

The wide application of gene sequencing has accumulated numerous amino acid substitutions (AAS) with unknown significance, posing significant challenges to predicting and understanding their pathogenicity. While various prediction methods have been proposed, most are sequence-based and lack insights for molecular mechanisms from the perspective of protein structures. Moreover, prediction performance must be improved.

METHODS

Herein, we trained a random forest (RF) prediction model, namely AAS3D-RF, underscoring sequence and three-dimensional (3D) structure-based features to explore the relationship between diseases and AASs.

RESULTS

AAS3D-RF was trained on more than 14,000 AASs with 21 selected features, and obtained accuracy (ACC) between 0.811 and 0.839 and Matthews correlation coefficient (MCC) between 0.591 and 0.684 on two independent testing datasets, superior to seven existing tools. In addition, AAS3D-RF possesses unique structure-based features, context-dependent substitution score (CDSS) and environment-dependent residue contact energy (ERCE), which could be applied to interpret whether pathogenic AASs would introduce incompatibilities to the protein structural microenvironments.

CONCLUSION

AAS3D-RF serves as a valuable tool for both predicting and understanding pathogenic AASs.

Enantioselective Synthesis of Nitriles Containing a Quaternary Carbon Center by Michael Reactions of Silyl Ketene Imines with 1-Acrylpyrazoles

The enantioselective construction of quaternary carbon centers is a marked challenge in asymmetric catalysis research. It is extremely difficult when a chiral catalyst can not distinguish the facial selectivity of the substrate through bond interactions. Here we realized an enantioselective Michael reaction of silyl ketene imines to 1-acrylpyrazoles using a chiral N,N'-dioxide-Co(II) complex. The protocol is highly efficient for the construction of nitrile-, aryl-, and dialkyl-bearing carbon centers and has been successful applied in the divergent synthesis of pharmaceuticals and natural products. The through-space dispersion interactions between unbound silyl ketene imines and the 1-acrylpyrazole-bonded catalyst play a key role in facilitating the reactivity and the enantioselectivity of this process.

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 β-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.

Asymmetric Domino Heck Arylation and Alkylation of Nonconjugated Dienes: Double C-F···Sodium Attractive Noncovalent Interaction

Palladium catalyzes a domino Heck arylation and alkylation of nonconjugated cyclodienes to produce trans isomers of disubstituted cyclohexenes in exceptionally high enantiomeric ratios, reaching 100:1 to 200:1 in many cases. Importantly, the interactions of the two CF bonds of Josiphos and the sodium ion of malonates facilitates stereoselective allylic attack through DFT calculations and experiments. This is a new type of attractive noncovalent interactions found in organometallic catalysis.

Precise Introduction of the -CHnX3-n (X = F, Cl, Br, I) Moiety to Target Molecules by a Radical Strategy: A Theoretical and Experimental Study

Addition of halomethyl radicals to form bioactive molecules has recently become an efficient strategy. The reaction has a bottleneck, however, which is the effective and selective generation of the proper halomethyl ^•CH_nX_3-n radical by combining CH_nX_4-n with a carbon radical. Understanding the reactivity and selectivity of carbon radicals in the hydrogen atom transfer (HAT) and halogen atom transfer (XAT) reactions of CH_nX_4-n is key to the development of such an attractive method. With the help of the emerging data-driven strategy, DFT calculations were used to explore various correlations. For selectivity, the relative energy barriers between HAT and XAT reactions (ΔG^⧧_H - ΔG^⧧_X) correlate reasonably well with the three parameters ΔG_H, ΔG_X, and IP, and the correlation studies reveal that the calculated IP_inver and the experimental ΔBDE can be used to conveniently predict the selectivity. Predicted selectivities are consistent with experimental determinations. This work not only provides a possibility for selecting carbon radicals with the known or easily obtained physicochemical data but also demonstrates that the informatic workflow such as generating data and identifying correlations has potential applications in mining reaction rules.

Iron-Catalyzed Enantioselective Radical Carboazidation and Diazidation of α,β-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,β-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.

Phosphate binding sites prediction in phosphorylation-dependent protein-protein interactions

MOTIVATION

Phosphate binding plays an important role in modulating protein-protein interactions, which are ubiquitous in various biological processes. Accurate prediction of phosphate binding sites is an important but challenging task. Small size and diversity of phosphate binding sites lead to a substantial challenge for developing accurate prediction methods.

RESULTS

Here we present the phosphate binding site predictor (PBSP), a novel and accurate approach to identifying phosphate binding sites from protein structures. PBSP combines an energy-based ligand-binding sites identification method with reverse focused docking using a phosphate probe. We show that PBSP outperforms not only general ligand binding sites predictors but also other existing phospholigand-specific binding sites predictors. It achieves ∼95% success rate for top 10 predicted sites with an average Matthews correlation coefficient (MCC) value of 0.84 for successful predictions. PBSP can accurately predict phosphate binding modes, with average position error of 1.4 Å and 2.4 Å in bound and unbound datasets, respectively. Lastly, visual inspection of the predictions is conducted. Reasons for failed predictions are further analyzed and possible ways to improve the performance are provided. These results demonstrate a novel and accurate approach to phosphate binding sites identification in protein structures.

AVAILABILITY

The software and benchmark datasets are freely available at http://web.pkusz.edu.cn/wu/PBSP/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Enantioselective Formal Vinylogous N-H Insertion of Secondary Aliphatic Amines Catalyzed by a High-Spin Cobalt(II) Complex

Vinylcarbene insertion into the nitrogen-hydrogen (N-H) bond of amines allows direct access to α,β-unsaturated γ-amino acid derivatives, meeting a marked challenge in the control of regio- and enantioselectivities. Here, we report a highly γ-selective and enantioselective insertion into N-H bonds of aliphatic or aromatic secondary amines with vinyl substituted α-diazo pyrazoleamides using a high-spin chiral N,N'-dioxide/cobalt(II) complex catalyst. The method affords a wide variety of valuable optically active Z- and E-type vinyl γ-amino amides. Calculation reveals a spin state change from the quartet cobalt(II) complex to a doublet Co(II)-carbene species for facile Z-selective and enantioselective nucleophilic addition.

Accurate Structure Prediction for Protein Loops Based on Molecular Dynamics Simulations with RSFF2C

Protein loops, connecting the α-helices and β-strands, are involved in many important biological processes. However, due to their conformational flexibility, it is still challenging to accurately determine three-dimensional (3D) structures of long loops experimentally and computationally. Herein, we present a systematic study of the protein loop structure prediction via a total of ∼850 μs molecular dynamics (MD) simulations. For a set of 15 long (10-16 residues) and solvent-exposed loops, we first evaluated the performance of four state-of-the-art loop modeling algorithms, DaReUS-Loop, Sphinx, Rosetta-NGK, and MODELLER, on each loop, and none of them could accurately predict the structures for most loops. Then, temperature replica exchange molecular dynamics (REMD) simulations were conducted with three recent force fields, RSFF2C with TIP3P water model, CHARMM36m with CHARMM-modified TIP3P, and AMBER ff19SB with OPC. We found that our recently developed residue-specific force field RSFF2C performed the best and successfully predicted 12 out of 15 loops with a root-mean-square deviation (RMSD) < 1.5 Å. As an alternative with lower computational cost, normal MD simulations at high temperatures (380, 500, and 620 K) were investigated. Temperature-dependent performance was observed for each force field, and, for RSFF2C+TIP3P, we found that three independent 100-ns MD simulations at 500 K gave comparable results with REMD simulations. These results suggest that MD simulations, especially with enhanced sampling techniques such as replica exchange, with the RSFF2C force field could be useful for accurate loop structure prediction.

Computational Studies of the Structural Basis of Human RPS19 Mutations Associated With Diamond-Blackfan Anemia

Diamond-Blackfan Anemia (DBA) is an inherited rare disease characterized with severe pure red cell aplasia, and it is caused by the defective ribosome biogenesis stemming from the impairment of ribosomal proteins. Among all DBA-associated ribosomal proteins, RPS19 affects most patients and carries most DBA mutations. Revealing how these mutations lead to the impairment of RPS19 is highly demanded for understanding the pathogenesis of DBA, but a systematic study is currently lacking. In this work, based on the complex structure of human ribosome, we comprehensively studied the structural basis of DBA mutations of RPS19 by using computational methods. Main structure elements and five conserved surface patches involved in RPS19-18S rRNA interaction were identified. We further revealed that DBA mutations would destabilize RPS19 through disrupting the hydrophobic core or breaking the helix, or perturb the RPS19-18S rRNA interaction through destroying hydrogen bonds, introducing steric hindrance effect, or altering surface electrostatic property at the interface. Moreover, we trained a machine-learning model to predict the pathogenicity of all possible RPS19 mutations. Our work has laid a foundation for revealing the pathogenesis of DBA from the structural perspective.

IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions

Motivation

Despite of the lack of folded structure, intrinsically disordered regions (IDRs) of proteins play versatile roles in various biological processes, and many nonsynonymous single nucleotide variants (nsSNVs) in IDRs are associated with human diseases. The continuous accumulation of nsSNVs resulted from the wide application of NGS has driven the development of disease-association prediction methods for decades. However, their performance on nsSNVs in IDRs remains inferior, possibly due to the domination of nsSNVs from structured regions in training data. Therefore, it is highly demanding to build a disease-association predictor specifically for nsSNVs in IDRs with better performance.

Results

We present IDRMutPred, a machine learning-based tool specifically for predicting disease-associated germline nsSNVs in IDRs. Based on 17 selected optimal features that are extracted from sequence alignments, protein annotations, hydrophobicity indices and disorder scores, IDRMutPred was trained using three ensemble learning algorithms on the training dataset containing only IDR nsSNVs. The evaluation on the two testing datasets shows that all the three prediction models outperform 17 other popular general predictors significantly, achieving the ACC between 0.856 and 0.868 and MCC between 0.713 and 0.737. IDRMutPred will prioritize disease-associated IDR germline nsSNVs more reliably than general predictors.

Availability and implementation

The software is freely available at http://www.wdspdb.com/IDRMutPred.

Supplementary information

Supplementary data are available at Bioinformatics online.

A Combined Computational and Experimental Study of Rh-Catalyzed C-H Silylation with Silacyclobutanes: Insights Leading to a More Efficient Catalyst System

The study of new C-H silylation reagents and reactions remains an important topic. We reported that under Rh catalysis, silacyclobutanes (SCBs) for the first time were able to react with C(sp²)-H and C(sp³)-H bonds, however the underlying reasons for such a new reactivity were not understood. Through this combined computational and experimental study on C-H silylation with SCBs, we not only depict a reaction pathway that fully accounts for the reactivity and all the experimental findings but also streamline a more efficient catalyst that significantly improves the reaction rates and yields. Our key findings include: (1) the active catalytic species is a [Rh]-H as opposed to the previously proposed [Rh]-Cl; (2) the [Rh]-H is generated via a reductive elimination/β-hydride (β-H) elimination sequence, as opposed to previously proposed endocyclic β-H elimination; (3) the regio- and enantio-determining steps are identified; (4) and of the same importance, the discretely synthesized [Rh]-H is shown to be a more efficient catalyst. This work suggests that the [Rh]-H/diphosphine system should find further applications in C-H silylations involving SCBs.

Catalytic Asymmetric Homologation of Ketones with α-Alkyl α-Diazo Esters

The homologation of ketones with diazo compounds is a useful strategy to synthesize one-carbon chain-extended acyclic ketones or ring-expanded cyclic ketones. However, the asymmetric homologation of acyclic ketones with α-diazo esters remains a challenge due to the lower reactivity and complicated selectivity. Herein, we report the enantioselective catalytic homologation of acetophenone and related derivatives with α-alkyl α-diazo esters utilizing a chiral scandium(III) N,N'-dioxide as the Lewis acid catalyst. This reaction supplies a highly chemo-, regio-, and enantioselective pathway for the synthesis of optically active β-keto esters with an all-carbon quaternary center through highly selective alkyl-group migration of the ketones. Moreover, the ring expansion of cyclic ketones was accomplished under slightly modified conditions, affording a series of enantioenriched cyclic β-keto esters. Density functional theory calculations have been carried out to elucidate the reaction pathway and possible working models that can explain the observed regio- and enantioselectivity.

Computational Study on the Fate of Oxidative Directing Groups in Ru(II), Rh(III), and Pd(II) Catalyzed C-H Functionalization

Activation of C-H bonds assisted by a directing group is indispensable in organic synthesis. Among them, utilizing oxidative directing groups that can serve as an internal oxidant to drive the Mⁿ/Mⁿ⁺² catalytic cycle has recently become a promising strategy. A survey of published reactions involving N-alkoxyamides or N-acyloxyamides reveals that not all N-O bonds act as an internal oxidant. We have therefore systematically investigated the effect of the oxidative groups on a model reaction catalyzed by Ru(II), Rh(III), and Pd(II) complexes. DFT calculations show that N-methoxy and N-acyloxy groups oxidize Ru(II) to Ru(IV) and Rh(III) to Rh(V), but cannot oxidize a cyclo-Pd(II) intermediate to Pd(IV). The stability of the metal imido intermediate 7-M (M = Ru, Rh, and Pd) controls whether the oxidation occurs or not. N-Acyloxy groups show a more pronounced selectivity than N-methoxy to oxidize Ru(II) and Rh(III) species, while no distinctive effect is observed for Pd(II).

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 ± 1.47) compared with the baseline audit (14.00 ± 1.82).

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.

WDSPdb: an updated resource for WD40 proteins

Summary

The WD40-repeat proteins are a large family of scaffold molecules that assemble complexes in various cellular processes. Obtaining their structures is the key to understanding their interaction details. We present WDSPdb 2.0, a significantly updated resource providing accurately predicted secondary and tertiary structures and featured sites annotations. Based on an optimized pipeline, WDSPdb 2.0 contains about 600 thousand entries, an increase of 10-fold, and integrates more than 37 000 variants from sources of ClinVar, Cosmic, 1000 Genomes, ExAC, IntOGen, cBioPortal and IntAct. In addition, the web site is largely improved for visualization, exploring and data downloading.

Availability and implementation

http://www.wdspdb.com/wdsp/ or http://wu.scbb.pkusz.edu.cn/wdsp/.

Supplementary information

Supplementary data are available at Bioinformatics online.