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Yun-Dong Wu

Publications and source records attributed to Yun-Dong Wu.

At least 19 recordsLinked to original sources
PubMed2026

TCRspec: A Recognition Interface-Informed Multimodal Method for TCR-pMHC Specificity Prediction.

Specific recognition between T-cell receptors (TCRs) and peptide-major histocompatibility complexes (pMHCs) is central to adaptive immunity, yet accurate prediction of TCR-pMHC specificity remains challenging. Existing models mainly rely on sequence features or isolated molecular structures, limiting their ability to capture interface-level determinants within the ternary recognition complex. Here, we constructed the multimodal TCR-pMHC ternary complex (MM-TCR) data set, integrating paired TCR-pMHC sequences, V/J gene annotations, and modeled TCR-pMHC complex structures refined by short molecular dynamics-based relaxation. Based on MM-TCR, we developed TCRspec, an interpretable multimodal framework combining sequence embeddings, gene-usage features, and complex-level structural representations. Under a stringent CD-HIT TCR-cluster-disjoint split, TCRspec achieved an average AUROC of 0.896 and AUPRC of 0.882 across seven antigen-specific test data sets, outperforming representative baseline models. Cross-validation and ablation analyses confirmed the contribution of ternary complex structural information and MD-refined structures. In independent OOD peptide-TCR systems, TCRspec retained discriminative performance and identified model-inferred peptide positions associated with TCR recognition, providing a structure-informed framework for TCR specificity prediction.

Receptors, Antigen, T-Cell↗
PubMed2007

Molecular dynamics studies of hexamers of amyloid-beta peptide (16-35) and its mutants: influence of charge states on amyloid formation.

To study the early stage of amyloid-beta peptide (Abeta) aggregation, hexamers of the wild-type (WT) Abeta(16-35) and its mutants with amyloid-like conformations have been studied by molecular dynamics simulations in explicit water for a total time of 1.7 micros. We found that the amyloid-like structures in the WT oligomers are destabilized by the solvation of ionic D23/K28 residues, which are buried in the fibrils. This means that the desolvation of D23/K28 residues may contribute to the kinetic barrier of aggregation in the early stage. In the E22Q/D23N, D23N/K28Q, and E22Q/D23N/K28Q mutants, hydration becomes much less significant because the mutated residues have neutral amide side-chains. These amide side-chains can form linear cross-strand hydrogen bond chains, or "polar zippers", if dehydrated. These "polar zippers" increase the stability of the amyloid-like conformation, reducing the barrier for the early-stage oligomerization. This is in accord with experimental observations that both the D23/K28 lactamization and the E22Q/D23N mutation promote aggregation. We also found that the E22Q/D23N mutant prefers an amyloid-like conformation that differs from the one found for WT Abeta. This suggests that different amyloid structures may be formed under different conditions.

Alzheimer Disease↗
PubMed2006

Synthetic study of 1,3-butadiene-based IMDA approach to construct a [5-7-6] tricyclic core and its application to the total synthesis of C8-epi-guanacastepene O.

An efficient intramolecular Diels-Alder (IMDA) strategy for the construction of the [5-7-6] tricyclic core (18) of guanacastepenes has been developed from cis- and trans-1,3-butadiene-tethered 4-oxopent-2-ynoic acid ethyl esters 10 and 11. This method facilitates the synthesis of C8-epi-guanacastepene O (36) in a very efficient manner.

Butadienes↗
PubMed2006

Computational study on the reaction mechanism of hydrosilylation of carbonyls catalyzed by high-valent rhenium(V)-di-oxo complexes.

Density functional theory (DFT) calculations have been performed to elucidate the reaction mechanism of hydrosilylation of carbonyl compounds catalyzed by high-valent rhenium(V)-di-oxo complexes ReO2I(PR3)2 (R = Me, Ph). The calculations suggest that the most favorable mechanism involves the rate-determining dissociative [2 + 2] addition of the Si-H bond across a Re=O bond to form a Re(V) hydrido siloxy intermediate; this is followed by carbonyl coordination, reduction of the carbonyl, rearrangement, and final intramolecular nucleophilic attack from the alkoxy group to the silyl center (dissociative retro-[2 + 2] addition). It was also found that the additional oxo ligand in the ReO2I(PR3)2 complexes promotes the [2 + 2] addition across the rhenium-oxo bond both kinetically and thermodynamically, as compared to the neutral rhenium(V)-mono-oxo complex ReOCl3(PMe3)2. The effect of different silanes on the [2 + 2] addition barriers is also studied.

Catalysis↗
PubMed2006

Enantioselective synthesis of vinylcyclopropanes and vinylepoxides mediated by camphor-derived sulfur ylides: rationale of enantioselectivity, scope, and limitation.

By a sidearm approach, camphor-derived sulfur ylides 1 were designed and synthesized for the cyclopropanation of electron-deficient alkenes and epoxidation of aldehydes. Under the optimal conditions, the exo-type sulfonium salts 4a and 4b reacted with beta-aryl-alpha,beta-unsaturated esters, amides, ketones, and nitriles to give 1,3-disubstituted-2-vinylcyclopropanes with high diastereoselectivities and enantioselectivities. When the endo-type sulfonium salts 5a and 5b were used, the diastereoselectivities were not changed, whereas the absolute configurations of the products became the opposite to those of the reactions of 4a and 4b. An ylide cyclopropanation of chalcone derivatives with phenylvinyl bromide in the presence of catalytic amount of chiral sulfonium salts 4b and 5b has been developed. The sidearmed hydroxyl group was found to play a key role in the control of enantioselectivity and diastereoselectivity. The origins of the high diastereoselectivity and enantioselectivity were also studied by density functional theory calculations, which reveal the importance of the hydrogen-bonding between the sidearmed hydroxyl group and the substrate in determining the diastereoselectivity and enantioselectivity. The ylides 1 were also successfully applied for the epoxidation of aromatic aldehydes.

Journal Article↗
PubMed2006

Effect of M(CO)3 (M = Cr, Mn+) on aromatic C-Cl BDE in (eta6-ArCl)M(CO)3 complexes.

The coordination of Cr(CO)3 to chlorobenzenes significantly reduces the C-Cl bond dissociation energy. Treatment of chloroarene-Cr(CO)3 complexes with SmI2/HMPA at room temperature led to complete dechlorination. Reaction of o-allyloxychlorobenzene-Cr(CO)3 complexes with SmI2 at room temperature resulted in the corresponding dechlorinative cyclization products in good to excellent yields. Competition experiments indicated the following relative reactivities of dehalogenation by SmI2: PhI/PhCl-Cr(CO)3/PhBr/PhCl = 50:1:0.3:<0.001. On the other hand, the coordination of Mn(CO)3(+) to chlorobenzene showed a much smaller activation effect. Density functional theory calculations revealed that the spin delocalization effect of the metal center plays an important role in the C-Cl bond activation.

Journal Article↗
PubMed2006

Experimental and theoretical studies on the hydrogen-bond-promoted enantioselective hetero-Diels-Alder reaction of Danishefsky's diene with benzaldehyde.

The enantioselective hetero-Diels-Alder (HDA) reaction of Danishefsky's diene with benzaldehyde has been achieved catalytically by a series of alpha,alpha,alpha',alpha'-tetraaryl-1,3-dioxolane-4,5-dimethanol (TADDOL) derivatives through hydrogen-bonding activation, affording 2-phenyl-2,3-dihydro-4H-pyran-4-one after trifluoroacetic acid workup in moderate yield and good enantioselectivity. The alpha,alpha'-aryl substituents in the TADDOL molecules are found to exert a significant impact on both the activity and the enantioselectivity of the catalysis. In combination with the experimental investigations, the mechanism of the present reaction has also been studied theoretically using the ONIOM (B3LYP/6-31G:PM3) method with trans-1,3-dimethoxy-1,3-butadiene as the model for Danishefsky's diene. In agreement with the experimental findings, the calculation results indicate that this TADDOL-catalyzed HDA reaction proceeds via a concerted mechanism through an asynchronous and zwitterionic transition structure (TS). The carbonyl group of benzaldehyde is activated by forming an intermolecular hydrogen bond with one of the hydroxy groups of TADDOL. Meanwhile, the intramolecular hydrogen bond between the two hydroxy groups in TADDOL is found to facilitate the intermolecular hydrogen bonding with benzaldehyde. The sense of asymmetric induction is well-rationalized by the analysis of the relative energies of TADDOL-complexed TSs, while the different stereocontrol capabilities exhibited by TADDOLs in the reaction can be qualitatively established on the basis of the structural features of their corresponding TSs.

Alkenes↗
PubMed2005

A strand-loop-strand structure is a possible intermediate in fibril elongation: long time simulations of amyloid-beta peptide (10-35).

A total of 6.2 micros molecular dynamics simulations of amyloid-beta (10-35) (Abeta) were performed in explicit water solvent. The results reveal that the collapsed-coil (cc) structure determined by experiments is stable at pH 5.6 for hundreds of nanoseconds, but it can exchange with a strand-loop-strand (SLS) structure on the microsecond time scale. The SLS structure has D23-K28 as a reverse loop and the central hydrophobic core and the C-terminal in hydrophobic contact. This SLS structure topologically resembles the proposed monomer conformation in fibrils. Since it has been suggested that a special conformation of Abeta is needed when the monomer binds to fibril ends to elongate fibrils, we propose that the SLS structure may be an important intermediate binding structure for Abeta fibril growth. Simulations at pH 2.0, which is used to mimic the mutation of E22Q and D23N, and at high temperature (400 K) indicate that the SLS structure is considerably populated under these conditions while the cc structure is disrupted. These results imply that the SLS structures may also be a binding intermediate in other conditions such as E22Q and/or D23N mutations and high temperature, which have been proved to promote fibril formation previously.

Amyloid beta-Peptides↗
PubMed2005

Exploring an expedient IMDA reaction approach to construct the guanacastepene core.

Construction of the [5-7-6] tricyclic core of guanacastepenes was attempted by using the intramolecular Diels-Alder (IMDA) reaction and Me(3)Al-mediated ring opening of the oxabridge as key synthetic steps. The illustrated chemistry demonstrated a synthetic feasibility to build up the framework of guanacastepenes by the IMDA reaction. [reaction: see text]

Catalysis↗
PubMed2005

A cyclic hexapeptide comprising alternating alpha-aminoxy and alpha-amino acids is a selective chloride ion receptor.

In nonpolar solvents, the cyclic hexapeptide 2, which comprises alternating D-alpha-amino and D-alpha-aminoxy acids, adopts a C3-symmetric conformation with alternating eight (N--O turns)- and seven (gamma turns)-membered-ring hydrogen bonds. A series of anion-binding studies has suggested that 2 can function as an effective anion receptor that not only displays a high selectivity for chloride ions, but also the capability to extract chloride ions from aqueous solutions into organic phases.

Amination↗
PubMed2005

Reactions of d0 group 4 amides with dioxygen. Preparation of unusual oxo aminoxy complexes and theoretical studies of their formation.

Reactions of d0 amides M(NMe2)4 (M = Zr, 1; Hf, 2) with O2 have been found to yield unusual trinuclear oxo aminoxide complexes M3(NMe2)6(mu-NMe2)3(mu3-O)(mu3-ONMe2) (M = Zr, 3; Hf, 4) in high yields. Tetramethylhydrazine Me2N-NMe2 was also observed in the reaction mixtures. Crystal structures of 3 and 4 have been determined. Density functional theory calculations have been performed to explore the mechanistic pathways in the reactions of model complexes Zr(NR2)4 (R = H, 5; Me, 1) and [Zr(NR2)4]2 (R = H, 5a; Me, 1a) with triplet O2. Monomeric and dimeric reaction pathways in the formation of the Zr complex 3 are proposed.

Journal Article↗
PubMed2005

A theoretical study on the mechanism of the reductive half-reaction of xanthine oxidase.

On the basis of the crystal structure of an aldehyde oxidoreductase, Huber et al. proposed a catalytic mechanism for the reductive half-reaction of xanthine oxidase which involves nucleophilic addition of Mo-bound hydroxide (Moco 1) to the substrate and hydride transfer from the substrate to sulfido group (Mo=S). Density functional theory calculations have been carried out for the oxidation of formaldehyde, acetaldehyde, formamide, and formamidine with Moco 2 to understand more detailed catalytic pathways. Our calculation results indicate that the anionic catalyst model acts as a nucleophile and is reactive for the oxidation of aldehyde substrates, which are reactive for nucleophilic addition. In these cases, a concerted mechanism is found to be more favorable than a stepwise mechanism. The concerted mechanism is further shown to be promoted by the presence of a nearby water molecule, in the active site, which serves as a Lewis acid for the nucleophilic addition of hydroxide. For less reactive formamide and formamidine (a model for xanthine) substrates, the calculated activation energies with the above mechanisms are high. These reactions also do not benefit from the presence of the water molecule. The results indicate that different catalyst forms might be responsible for the oxidation of different substrates, which could be regulated by the enzyme active site environment.

Coenzymes↗
PubMed2005

8-endo versus 7-exo cyclization of alpha-carbamoyl radicals. A combination of experimental and theoretical studies.

Atom transfer radical cyclization reactions of N-(4-pentenyl)iodoacetamides were investigated. The reactions were efficiently promoted by BF3.OEt2. For N-alkenyl-substituted iodoamides, excellent regioselectivity in favor of 8-endo cyclization was observed, while both 7-exo and 8-endo cyclization products were formed with the 8-endo cyclization preferred in the cases of N-(2-allylphenyl)-substituted iodoamides. Density functional theory calculations at the B3LYP/6-31G level revealed that both the s-trans and the s-cis conformational transition structures were feasible for the 8-endo cyclization of N-alkenyl-substituted alpha-carbamoyl radicals while 7-exo transition structures were much less stable. For the cyclization of N-(2-allylphenyl)-substituted alpha-carbamoyl radicals, the transition structures for 8-endo and 7-exo cyclizations were of comparable energy. These results were in excellent agreement with the experimental observations.

Cyclization↗
PubMed2005

Clarification of the mechanism of the cascade reactions between amino-substituted heterocycles and 1,3,5-triazines.

The mechanisms of the cascade reactions of amino-substituted imidazoles, pyrroles, and pyrazoles with 1,3,5-triazines have been studied using first principle MP2/6-311++G**//B3LYP/6-31G* calculations in both the gas phase and solution. Calculations indicate that these cascade reactions start with stepwise inverse-electron demand Diels-Alder (IDA) reactions, followed by elimination of ammonia from the IDA adducts, and retro Diels-Alder (RDA) reactions (referred as to the IER path). An alternative IRE path involving a reaction sequence of IDA, RDA, and elimination of ammonia is ruled out since the RDA transition states in this pathway are higher in energy than the reactants by as much as 50 kcal/mol. The preference of the IER over the IRE path is discussed.

Journal Article↗
PubMed2004

Experimental and theoretical studies of the propargyl-allenylindium system.

The transient organoindium intermediates formed in the reaction of propargyl bromide with indium in aqueous media and tetrahydrofuran were investigated by NMR spectroscopy and found to be allenylindium(I) and allenylindium(III) dibromide. The influence of solvent and methyl substitution on the propargyl-allenylindium system was also studied. The experimental observations were supported by theoretical calculations using the B3LYP/6-311+G* method.

Journal Article↗