Si Zhang

California University of Pennsylvania

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Vincent A. Voelz

Temple College

Qingxin Li

Chinese Academy of Sciences

Jun Wu

New Generation University College

Zhihui Xiao

Shaoxing University

Shu‐Hua Qi

South China Sea Institute Of Oceanology

Yonghong Liu

Chinese Academy of Sciences

Qiang Xiao

Jiangxi Science and Technology Normal University

Fa‐Zuo Wang

South China Sea Institute Of Oceanology

Ge Yunhui

Alkermes (United States)

Jie Li

Institute of Microbiology

Cooperative Institutions

Chinese Academy of Sciences

121

University of Chinese Academy of Sciences

South China Sea Institute Of Oceanology

Institute of Oceanology

Temple University

Institute of Physics

National Laboratory for Superconductivity

Fudan University

Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)

Nanjing University

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Chemical Constituents of the Bark of Thespesia populnea

Lishizhen Medicine and Materia Medica Research (2007)

Zhang Dao-jing Si Zhang Wu Jun

Objective To study the chemical constituents from the stem bark of Thespesia populnea.Methods The compounds were isolated by silica gel column chromatography,and their structures were elucidated by means of spectral analysis.Re- sults Seven compounds were identified asβ-sitosterol-3-O-β-D-glucopyranoside-6'-O-stearate (Ⅰ),β-sitosterol (Ⅱ),dan- costerol (Ⅲ),kaempferol (Ⅳ),1-hentriacontanol (Ⅴ),stearic acid (Ⅵ),betulin(Ⅶ).Conclusion CompoundsⅠ-Ⅵare isolated from this plant for the first time.

Betulin

Stearic acid

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Heterocyclic Terpenes: Linear Furano‐ and Pyrroloterpenoids

ChemInform (2006)

Yonghong Liu Si Zhang Pedro Abreu

Terpene

10.1002/chin.200642235

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Citations (1)

Three new flavonol triglycosides from Derris trifoliata

Journal of Asian Natural Products Research (2009)

Lurong Xu Pei Zhou Yuee Zhi Jun Wu Si Zhang

Three new flavonol triglycosides, kaempferol-3-O-α-l-rhamnopyranosyl-(1 → 6)-β-d-glucopyranosyl-(1 → 3)-β-d-glucopyranoside (1), quercetin-3-O-α-l-rhamnopyranosyl-(1 → 6)-β-d-glucopyranosyl-(1 → 3)-β-d-glucopyranoside (2), quercetin-3-O-α-l-rhamnopyranosyl-(1 → 6)-β-d-glucopyranosyl-(1 → 2)-β-d-glucopyranoside (3), together with the two known flavonol glycosides, kaempferol-3-O-α-l-rhamnopyranosyl-(1 → 6)-β-d-glucopyranoside and kaempferol-3-O-α-l-rhamnopyranosyl-(1 → 6)-β-d-glucopyranosyl-(1 → 2)-β-d-glucopyranoside, were isolated from the aerial parts of Derris trifoliata. Their structures were determined on the basis of chemical and spectroscopic analyses.

10.1080/10286020802514598

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Magnetotransport properties of the type-II Weyl semimetal candidateTa3S2

Physical review. B./Physical review. B (2016)

D. Chen Lingxiao Zhao J. B. He H. Liang Si Zhang

We have investigated the magnetoresistance (MR) and Hall resistivity properties of the single crystals of tantalum sulfide, ${\mathrm{Ta}}_{3}{\mathrm{S}}_{2}$, which was recently predicted to be a new type-II Weyl semimetal. Large MR (up to $\ensuremath{\sim}8000%$ at 2 K and 16 T), field-induced metal-insulator-like transition, and nonlinear Hall resistivity are observed at low temperatures. The large MR shows a strong dependence on the field orientation, leading to a giant anisotropic magnetoresistance effect. For the field applied along the $b$ axis $(B\ensuremath{\parallel}b)$, MR exhibits quadratic field dependence at low fields and tends towards saturation at high fields; while for $B\ensuremath{\parallel}a$, MR presents quadratic field dependence at low fields and becomes linear at high fields without any trend towards saturation. The analysis of the Hall resistivity data indicates the coexistence of a large number of electrons with low mobility and a small number of holes with high mobility. Shubnikov-de Haas oscillation analysis reveals three fundamental frequencies originated from the three-dimensional Fermi surface pockets. We find that the semiclassical multiband model is sufficient to account for the experimentally observed MR in ${\mathrm{Ta}}_{3}{\mathrm{S}}_{2}$.

Weyl semimetal

Saturation (graph theory)

10.1103/physrevb.94.174411

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Two New Mexicanolides from the Fruit of the Chinese Mangrove Xylocarpus granatum

Zeitschrift für Naturforschung B (2005)

Jun Wu Si Zhang Yang Song Zhihui Xiao Qiang Xiao

Two new mexicanolides, 3-deacetyl xyloccensin M and 3-deacetyl xyloccensin N were isolated from the fruit of the Chinese mangrove Xylocarpus granatum. Their structures were elucidated on the basis of modern spectroscopic techniques.

10.1515/znb-2005-1213

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Citations (23)

Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2

Ge Yunhui Si Zhang Máté Erdélyi Vincent A. Voelz

Understanding mechanisms of protein folding and binding is crucial to designing their molecular function. Molecular dynamics (MD) simulations and Markov State Model (MSM) approaches provide a powerful way to understand complex conformational change that occurs over long timescales. Consideration of such dynamics are important for the design of therapeutic peptidomimetic ligands, whose affinity and binding mechanism are dictated by a combination of folding and binding. To examine the role of preorganization in peptide binding to protein targets, we performed massively parallel explicit-solvent MD simulations of cyclic β-hairpin ligands designed to disrupt the MDM2-p53 interaction. MSM analysis of over 3 ms of aggregate trajectory data enabled us to build a detailed mechanistic model of coupled folding and binding of four cyclic peptides which we compare to experimental binding affinities and rates. The results show a striking relationship between the relative preorganization of each ligand in solution and its affinity for MDM2. Specifically, changes in peptide conformational populations predicted by the MSMs suggest that entropy loss upon binding is the main factor influencing affinity. The MSMs also enable detailed examination of non-native interactions which lead to misfolded states, and comparison of structural ensembles with experimental NMR measurements. In contrast to an MSM study of p53 TAD binding to MDM2, MSMs of cyclic β-hairpin binding show a conformational selection mechanism. Finally, we make progress towards predicting accurate off-rates of cyclic peptides using multiensemble Markov models (MEMMs) constructed from unbiased and biased simulated trajectories.

Binding affinities

Affinities

Conformational entropy

Conformational change

Cyclic peptide

Conformational ensembles

10.26434/chemrxiv.13500765.v1

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Citations (1)

Triterpenoid saponins from the stem bark of Catunaregam spinosa

Canadian Journal of Chemistry (2011)

Guangchun Gao Zhongxian Lü Shu‐Hong Tao Si Zhang Fa‐Zuo Wang

Four new triterpenoid saponins, Catunaroside E (1; 3-O-{β-D-glucopyranosyl-(1→2)-[β-D-glucopyranosyl-(1→3)]-β-D-glucopyranosyl}-siaresinolic acid), Catunaroside F (2; 3-O-{α-L-rhamnopyranosyl-(1→2)-[β-D-glucopyranosyl-(1→3)]-β-D-glucopyranosyl}-28-O-(β-D-glucopyranosyl)-oleanolic acid), Catunaroside G (3; 3-O-[α-L-rhamnopyranosyl-(1→2)-β-D-glucopyranosyl]- 28-O-(β-D-glucopyranosyl)-siaresinolic acid), and Catunaroside H (4; 3-O-{β-D-glucopyranosyl-(1→2)-[β-D-glucopyranosyl-(1→3)]-β-D-glucopyranosyl}-28-O-(β-D-glucopyranosyl)-siaresinolic acid), and the known triterpenoid saponin Mussaendoside J (5), were isolated from the stem bark of Catunaregam spinosa . Their structures were elucidated on the basis of their spectral data and chemical evidence.

Triterpenoid saponin

10.1139/v11-090

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Citations (8)

ChemInform Abstract: Scyphiphorins C and D, Two New Iridoid Glycosides from the Chinese Mangrove Scyphiphora hydrophyllacea.

ChemInform (2009)

Shu‐Hong Tao Shu‐Hua Qi Si Zhang Zhihui Xiao Qingxin Li

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

10.1002/chin.200943213

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New Briaranes from the South China Sea GorgonianJunceella fragilis

Helvetica Chimica Acta (2005)

Shu‐Hua Qi Si Zhang Yanmei Wen Zhihui Xiao Qingxin Li

Three new briarane diterpenes, junceellonoids C–E (1–3), along with six known briaranes, junceellin A (4), praelolide (5), and junceellolides A-D (6–9), were isolated from the EtOH/CH2Cl2 extracts of the South China Sea gorgonian coral Junceella fragilis. The structures of 1–3 were established by extensive spectroscopic analysis, including 1D- and 2D-NMR data. Compounds 1 and 2 exhibited mild cytotoxicity against human galactophore carcinoma (MDA-mB-231 and MCF-7) cells at the concentration of 100 μM.

Gorgonian

Carcinoma Cell

10.1002/hlca.200590170

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Citations (22)

A simple method to optimize the spacing and number of alchemical intermediates in expanded ensemble free energy calculations

Dylan Novack Robert M. Raddi Si Zhang Matthew F. D. Hurley Vincent A. Voelz

Alchemical free energy calculations are essential to modern structure-based drug design. Such calculations are usually performed at a series of discrete intermediates along a nonphysical thermodynamic pathway to estimate the free energy difference between two endpoints of an alchemical transformation. The efficiency and accuracy of the free energy estimate depends critically on the choice of alchemical intermediates. In this paper, we review the concept of thermodynamic length, and how it can be used as a principle to choose alchemical paths in free energy simulations. We then present an algorithm for optimizing the choice of alchemical intermediates in free energy simulations. Our method is similar to the thermodynamic trailblazing algorithm of Rizzi et al. (2020) but with several improvements for use with expanded ensemble (EE) simulations. Our method only requires a single initial round of EE simulation, and includes a method for optimizing the number of alchemical intermediates in an EE simulation, based on the predicted mixing time. We first show how the method performs in a simple toy model, and then demonstrate its use in a realistic example for an alchemical relative binding free energy calculation. We also show how our method can be used to optimize free energy estimates in other contexts, namely, calculating a score for model selection in the Bayesian Inference of Conformational Populations (BICePs) approach. We have implemented our optimization algorithm in a freely available Python package called pylambdaopt (https://github.com/vvoelz/pylambdaopt)

10.26434/chemrxiv-2025-7fdpf

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