Peng Nan

Fudan University, Shanghai, Shanghai Shi, China

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Publications (40)47.98 Total impact

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    ABSTRACT: In the field of drug discovery, it is particularly important to discover bioactive compounds through high-throughput virtual screening. The maximum common substructure-based (MCS) algorithm is a promising method for the virtual screening of drug candidates. However, in practical applications, there is always a trade-off between efficiency and accuracy. In this paper, we optimized this method by running time evaluation using essential drugs defined by WHO and FDA-approved small-molecule drugs. The amount of running time allocated to the MCS-based virtual screening was varied, and statistical analysis was conducted to study the impact of computation running time on the screening results. It was determined that the running time efficiency can be improved without compromising accuracy by setting proper running time thresholds. In addition, the similarity of compound structures and its relevance to biological activity are analyzed quantitatively, which highlight the applicability of the MCS-based methods in predicting functions of small molecules. 15-30s was established as a reasonable range for selecting a candidate running time threshold. The effect of CPU speed is considered and the conclusion is generalized. The potential biological activity of small molecules with unknown functions can be predicted by the MCS-based methods.
    Computational biology and chemistry 11/2013; 48C:14-20. · 1.37 Impact Factor
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    ABSTRACT: A chalcone reductase (CHR) gene was isolated from Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao (A. mongholicus). The full-length cDNA of A. mongholicus CHR, designated as Amchr (GenBank accession No. HM357239), was 1196 bp long. It had a 957 bp open reading frame encoding a 318-amino acid protein of 35 kDa, a 67 bp 5' non-coding region and a 172 bp 3'-untranslated region. The putative AmCHR protein showed striking similarity to CHR from other leguminous species. Two-dimensional structure modeling showed that AmCHR consisted of 45.28% α-helix, 10.38% extended strand and 44.34% random coil. Prediction showed that three-dimensional AmCHR was a global protein containing an aldo-ket-red domain, with a putative Asp-Tyr-Lys-His catalytic tetrad in the center. The AmCHR gene was 1251 bp long, consisting of three exons and two introns. Intron I was 125 bp and intron II was 169 bp long. Southern blot analysis indicated that Amchr belonged to a small multigene family. Under natural conditions, Amchr was expressed differentially in the root, stem and leaf tissues of A. mongholicus, with a preferential expression in the root. The recombinant AmCHR protein was successfully expressed in Escherichia coli strain BL21 with pET42a vector. The result showed that the expressed AmCHR protein had molecular weight of about 35 kDa, which matched the size of the predicted protein by bioinformatic analysis. This study opened avenues towards understanding of the function of AmCHR protein and the role of the Amchr gene in the calycosin-7-O-β-D: -glucoside branch pathway in A. mongholicus.
    Molecular Biology Reports 06/2011; 39(3):2275-83. · 2.51 Impact Factor
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    ABSTRACT: Glucose-6-phosphate dehydrogenase (G6PD) is an essential enzyme that protects human red blood cells from premature destruction caused by oxidative damage. People suffering from G6PD deficiency would be vulnerable to various oxidative substances, such as fava beans and oxidant drugs. Until now, many institutes, organizations or domain experts have compiled low-risk or high-risk drugs collection for patients with G6PD deficiency, mainly from the case report or clinical trails. Recently, we have explored a classification system to predict drug-induced hemolytic potential. In this paper, we screen the normally used over-the-counter (OTC) drugs for "high-risk" and "low-risk" ones to G6PD deficient patients by this system.
    Computational biology and chemistry 06/2011; 35(3):189-92. · 1.37 Impact Factor
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    ABSTRACT: Hereditary non-polyposis Colorectal Cancer (HNPCC) is an autosomal dominant inheritance syndrome. HNPCC is the most common hereditary variant of colorectal cancer (CRC), which accounts for 2-5% CRCs, mainly due to hMLH1 and hMSH2 mutations that impair DNA repair functions. Our study aimed to identify the patterns of hMSH2 and hMLH1 mutations in Chinese HNPCC patients. Ninety-eight unrelated families from China meeting Amsterdam or Bethesda criteria were included in our study. Germline mutations in MLH1 and MSH2 genes, located in the exons and the splice-site junctions, were screened in the 98 probands by direct sequencing. Eleven mutations were found in ten patients (11%), with six in MLH1 (54.5%) and five in MSH2 (45.5%) genes. One patient had mutations in both MLH1 and MSH2 genes. Three novel mutations in MLH1 gene (c.157_160delGAGG, c.2157dupT and c.-64G>T) were found for the first time, and one suspected hotspot in MSH2 (c.1168C>T) was revealed.
    BMB reports 05/2011; 44(5):317-22. · 1.63 Impact Factor
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    ABSTRACT: Isoflavonoids are a group of phenolic secondary metabolites found almost exclusively in leguminous plants. Formononetin, calycosin and calycosin-7-O-β-d-glucoside (CG) are isoflavonoid products in the CG pathway. Accumulation of the three isoflavonoids plus daidzein and expression of six genes of enzymes involved in the CG pathway were studied in Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao with ultraviolet (UV) irradiation. Our results showed that (1) main isoflavonoids in roots, stems and leaves were CG, daidzein and calycosin, respectively; they accumulated significantly under the induction of UV irradiation during 8 days but their content declined later; (2) expression of six genes of enzymes involved in the CG pathway was inhibited slightly at early stage but the expression was increased greatly afterward; (3) chalcone synthase, chalcone reductase and chalcone isomerase were expressed to their individual maximum level within shorter hours than were cinnamate 4-hydroxylase, isoflavone synthase (IFS) and isoflavone 3'-hydroxylase and (4) more calycosin but less daidzein accumulated in leaves. IFS was highly expressed in leaves, which might lead to high accumulation of the common precursor of daidzein and 2,7-dihydroxy-4'-O-methoxy-isoflavanone, the latter of which would be converted to formononetin, calycosin and CG via a series of reactions. Little daidzein accumulated in leaves, which suggested that rather than be converted to daidzein, the 2,7,4'-trihydroxyisoflavanone was probably more easily caught by 2-hydroxyisoflavanone 4'-O-methyltransferase and hence provided more precursors for formononetin. The findings were discussed in terms of the influence of UV irradiation in the accumulation of isoflavonoids.
    Physiologia Plantarum 03/2011; 142(3):265-73. · 3.66 Impact Factor
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    ABSTRACT: MLH1 and MSH2 mutations underlie 90% of hereditary nonpolyposis colorectal cancer (HNPCC) mutations. The International Society of Gastrointestinal Hereditary Tumors (InSiGHT) has established an international database of mutations associated with HNPCC. Based on the InSiGHT database and the original references that reported the mutations, we analyzed the distributions of MLH1 and MSH2 mutations in yellow race and white race respectively and compared them subsequently. We found: (1) the distributions of mutation individuals in exon 1, 17 and 19 of MLH1 gene and in exon 2 of MSH2 gene showed significant differences between the two race groups (p < 0.05); (2) the distributions of mutation types in exon 2, 7 and 18 of MLH1 and exon 10 and 16 of MSH2 showed significant differences (p < 0.05); and (3) three mutations (c.649C > T, c.1625A > T and c.1721T > C) in MLH1 and five mutations (c.23C > T, c.187dupG, c.505A > G, c.1168C > T and c.2211-6T > C) in MSH2 have much higher frequency in yellow race than those in white race. Furthermore, three mutations (c.1453G > C, c.1742C > T and c.1758dupC) in MLH1 and two mutations (c.1255C > A and c.1886A > G) in MSH2 were only found in yellow race, which implies that specific mutations in yellow race need more attention when screening mutations in these two genes.
    Journal of Bioinformatics and Computational Biology 12/2010; 8 Suppl 1:111-25.
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    ABSTRACT: Essential oils of two Tibetan Junipers Juniperus saltuaria and J. squamata var. fargesii (Cupressaceae) were obtained by distilling dried leaves and branches using a Clevenger apparatus. Sixty-seven compounds from J. saltuaria and 58 from J. squamata var. fargesii were identified by gas chromatography-mass spectrometry (GC-MS). Both essential oils contained similar ratios of four abundant monoterpenoids: 44 and 35% sabinene, 13 and 9% elemol, 8 and 7% terpinen-4-ol, and 4 and 17% alpha-pinene, respectively. These oils had antifungal activity based on a direct bioautography assay of Colletotrichum acutatum, C. fragariae, and C. gloeosporioides, and insecticidal activity based on serial-time mortality bioassay of azalea lace bugs, Stephanitis pyrioides. Antifungal activity of Juniperus oils was weak when compared with commercial fungicides such as benomyl and captan. Whole Juniperus oils at quarter the dosage used against Colletotrichum species were more insecticidal than 10 mg/mL malathion, killing > or =70-90% adult lace bugs after 4 hours of exposure. Rf values of 0.18 for J. saltuaria oil and 0.19 for J. squamata oil indicated lipophilic monoterpenes which were the putative sources of biological activity.
    Natural product communications 01/2009; 4(1):123-7. · 0.96 Impact Factor
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    ABSTRACT: Previously it had been shown that calycosin and calycosin-7-O-beta-D-glucoside (CGs) accumulate in whole plants, mainly in leaves, of Astragalus membranaceus Bge. var. mongholicus (Bge.) Hsiao (A. mongholicus) plants in response to low temperature. In this work, it was demonstrated that the influences of different conditions on CGs biosynthesis, by examining the changes in CGs content, as well as the expression of related genes, including phenylalanine ammonia lyase (PAL1), cinnamic acid 4-hydroxylase (C4H), chalcone synthase (CHS), chalcone reductase (CHR), chalcone isomerase (CHI), isoflavone synthase (IFS), and isoflavone 3'-hydroxylase (I3'H). The seven gene mRNAs accumulated in leaves of A. mongholicus upon exposure to low temperature in a light-dependent manner, though they exhibited different expression patterns. Transcriptions of CHS, CHR, CHI, IFS, and I3'H of the calycosin-7-O-beta-D-glucoside pathway were all up-regulated when plants were transferred from 16 degrees C to 2 degrees C or 25 degrees C or from 2 degrees C (kept for 24 h) to 25 degrees C. However, fluctuations in temperature influenced differently the transcriptions of PAL1 and C4H of the general phenylpropanoid pathway in leaves. Moreover, the amount of PAL1 expression changed sharply up and down, consistent with the variation of the content of CGs. PAL enzyme activity appears to be the limiting factor in determining the CGs levels. The inhibitor of PAL enzyme, L-alpha-aminooxy-beta-phenylpropionic acid, almost entirely shut down CGs accumulation at low temperature. All these results confirmed that PAL1, as a smart gene switch, directly controls the accumulation of CGs in A. mongholicus plants, in a light-dependent manner, during low temperature treatment.
    Journal of Experimental Botany 07/2008; 59(11):3027-37. · 5.24 Impact Factor
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    ABSTRACT: The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics, since many computational methods for solving various biological problems critically rely on bona fide orthologs as input. While it is usually done using sequence similarity search, we recently proposed a new combinatorial approach that combines sequence similarity and genome rearrangement. This paper continues the development of the approach and unites genome rearrangement events and (post-speciation) duplication events in a single framework under the parsimony principle. In this framework, orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangement and (post-speciation) gene duplication. Besides several original algorithmic contributions, the enhanced method allows for the detection of inparalogs. Following this approach, we have implemented a high-throughput system for ortholog assignment on a genome scale, called MSOAR, and applied it to human and mouse genomes. As the result will show, MSOAR is able to find 99 more true orthologs than the INPARANOID program did. In comparison to the iterated exemplar algorithm on simulated data, MSOAR performed favorably in terms of assignment accuracy. We also validated our predicted main ortholog pairs between human and mouse using public ortholog assignment datasets, synteny information, and gene function classification. These test results indicate that our approach is very promising for genome-wide ortholog assignment. Supplemental material and MSOAR program are available at http://msoar.cs.ucr.edu.
    Journal of Computational Biology 12/2007; 14(9):1160-75. · 1.56 Impact Factor
  • Chemistry of Natural Compounds 10/2007; 43(6):741-743. · 0.60 Impact Factor
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    Chemistry of Natural Compounds 10/2007; 43(6):716-718. · 0.60 Impact Factor
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    ABSTRACT: As a critical adaptive mechanism, amino acid replacements on the severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein could alter the receptor-binding specificity of this envelope glycoprotein and in turn lead to the emergence or reemergence of this viral zoonosis. Based on the X-ray structures of SARS-CoV spike receptor-binding domain (RBD) in complex with its functional receptor (angiotensin-converting enzyme 2, ACE2), we perform computational simulations of interactions between three representative RBD mutants and four host species-specific receptors. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics approaches. And the predictions further indicate that some viral prototypes might utilize the rat ACE2 while rats might serve as a vector or reservoir of SARS-CoV.
    Computational Biology and Chemistry 05/2007; 31(2):134-7. · 1.79 Impact Factor
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    ABSTRACT: The composition of the volatile oils obtained from the leaves and flowers of Salvia przewalskii Maxim. grown in Tibet was analysed by gas chromatography–mass spectrometry (GC–MS) for the first time. Totals of 43 compounds were identified in the leaf oil and 69 compounds in the flower oil. A comparative study of the oil composition from the leaves and flowers found 22 common constituents of these oils, viz. α-thujene, β-phellandrene, linalool, terpinene-4-ol, diisopropenyl methyl vinyl cyclohexane, caryophyllene, germacrene D, borneol, caryophyllene oxide, spathulenol, germacrene B, δ-cadinene, humulene, farnesane, α-cadinol, β-caryophyllene, elemene, sabinene hydrate, γ-terpinene, p-cymene, camphene and α-pinene. The percentages of the most components were higher in the leaf oil than in the flower oil, especially those of β-phellandrene and caryophyllene (26.08% and 11.11%, respectively). Farnesene, chamigrene, n-hexadecane, epicedrol, cyclotetradecane, n-octadecane, 9-octadecen-1-ol, 1-heneicosyl formate, Z-8-hexadecen-1-ol acetate, n-heneicosane and n-pentacosane were the specific constituents found only in the flower oil, while β-cadinol was the specific constituent found only in the leaf oil. Copyright © 2006 John Wiley & Sons, Ltd.
    Flavour and Fragrance Journal 02/2006; 21(3):435 - 438. · 1.82 Impact Factor
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    ABSTRACT: Hydrodistilled leaf oils of Pistacia chinensis Bunge from five locations in China were analyzed using GC/MS. A total of 58 compounds was identified in the oils, and a relatively high variation in their contents was found. The major compounds include β-phellandrene (0.54–53.86%), α-pinene (4.74–54.44%), β-pinene (0.49–42.90%), caryophyllene (5.64–20.01%), cis-ocimene (tr−43.93%), eudesmadiene (0–15.06%), and camphene (tr−20.57%). Cluster analysis classified the leaf oils into two chemotypes: one rich in α-pinene and β-pinene, and the other rich in β-phellandrene.
    Chemistry of Natural Compounds 01/2006; 42(4):422-425. · 0.60 Impact Factor
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    ABSTRACT: Hydro-distillated volatile oils of Ephedra sinica Stapf. from six populations of Inner Mongolia in Northeastern China were analyzed by using GC/MS. Ninety-nine compounds were identified in the oils and a relatively high variation in their contents was found. The main constituents of the essential oils were α-terpineol (19.28–52.23%), p-vinylanisole (0.59–11.64%), 3-methyl-2-buten-1-ol (0–5.44%), tetramethylpyrazine (0.63–8.99%), terpine-4-ol (1.17–4.37%), α-linalool (1.62–5.15%), phytol (1.24–15.73%), γ-eudesmol (0–7.77%), and eudesm-7(11)-en-4-ol (0.41–6.13). Six populations were divided into two chemotypes based on cluster analysis and principal component analysis (PCA); one rich in α-terpineol and p-vinylanisole, and the other rich in phytol, γ-eudesmol, and eudesm-7(11)-en-4-ol.
    Food Chemistry. 01/2006; 98(1):52-58.
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    ABSTRACT: Lipophilic extracts from flowers, leaves, and roots of Lamiophlomis rotata (Benth.) were analyzed using GC-MS. A total of 67 compounds were identified.
    Chemistry of Natural Compounds 01/2006; 42(5):525-528. · 0.60 Impact Factor
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    ABSTRACT: Physiological functions and characteristic structures of the serpin gene superfamily have been studied extensively, yet the evolution of the serpin genes remains unclear. Gene duplication in this superfamily may shed light on this issue. Two models are used to predict the preservation of duplicated genes: the classical model and the duplication-degeneration-complementation (DDC) model. In this study, we analyzed the phylogenetic relationships of 33 human serpin genes and the expression data of some members of the serpin superfamily from a DNA microarray of human leukemia U937 cells with stably inducible expression of the leukemia-related AML1-ETO gene. We then determined the utility of the DDC model by mapping serpin superfamily expression data to the phylogenetic tree. The correlation between sequence and expression divergences as measured by the Pearson correlation coefficient indicated that human serpin genes evolved under the DDC model. Our study provides a new strategy for comparative analysis of gene sequences and microarray data.
    Biosystems 01/2006; 82(3):226-34. · 1.58 Impact Factor
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    ABSTRACT: Volatiles were distilled from leaves of three Bergenia species collected from Yunnan, Xinjiang and Tibet in western China and analyzed using GC/MS instrumentation. The contents of extractable volatiles varied substantially among the three species with B. crassifolia having approximately 0.05% dry wt (v/w), B. purpurscens 0.01% (v/w) and B. stracheyi 0.13% (v/w), respectively. In B. crassifolia, the main components were present as 3-methyl-2-buten-1-ol (26.56%), hexadecanoic acid (16.06%), dodecanoic acid (9.99%), linalool (5.63%) and octadecadienoic acid (4.10%). In B. purpurascens, the main components were β-eudesmol (18.63%), phytol (14.50%), hexadecanoic acid (13.05%), n-nonacosane (9.19%) and 3-methyl-2-buten-1-ol (7.52%). In B. stracheyi, 3-methyl-2-buten-1-ol was the dominant sort of volatile (52.71%), whereas detected major constituents included β-eudesmol (7.44%), damascenone (3.22%), caryophyllene (2.75%) and phytol (2.57%). Copyright © 2006 John Wiley & Sons, Ltd.
    Flavour and Fragrance Journal 01/2006; 21(3):431-434. · 1.82 Impact Factor
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    ABSTRACT: The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative ge- nomics, since many computational methods for solving various biological problems critically rely on bona fide orthologs as input. While it is usu- ally done using sequence similarity search, we recently proposed a new combinatorial approach that combines sequence similarity and genome rearrangement. This paper continues the development of the approach and unites genome rearrangement events and (post-speciation) duplica- tion events in a single framework under the parsimony principle. In this framework, orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangement and (post-speciation) gene duplication. Besides several original algorithmic contributions, the enhanced method allows for the detection of inparalogs. Following this approach, we have implemented a high-throughput system for ortholog assignment on a genome scale, called MSOAR, and applied it to the genomes of human and mouse. As the result will show, MSOAR is able to find 99 more true orthologs than the INPARANOID program did. We have also compared MSOAR with the iterated exemplar algorithm on simulated data and found that MSOAR performed very well in terms of assignment accuracy. These test results indiate that our approach is very promising for genome-wide ortholog assignment.
    Research in Computational Molecular Biology, 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 2-5, 2006, Proceedings; 01/2006
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    ABSTRACT: The chemical constituents of leaf oils of Elephantopus scaber L. from 12 locations in Southern China, including three provinces and Hong Kong, were investigated using GC/MS. A total of 24 compounds were detected, of which 20 were identified by their mass spectra fragmentation patterns. The major compounds include hexadecanoic acid (8.19–39.22%), octadecadienoic acid (trace - 29.22%), five alkane homologues, i.e., n-tetradecane (1.19–5.26%), n-pentadecane (3.22–12.05%), n-hexadecane (2.38–16.26%), n-heptadecane (2.48–15.32%), and n-octadecane (1.39–9.59%), as well as tetramethylhexadecenol (2.06–4.31%). Hierarchical cluster analysis classified the leaf oils into two groups. Two main chemotypes of leaf oils in E. scaber were thus identified, one rich in hexadecanoic acid and octadecadienoic acid, and the other rich in the five alkane homologues.
    Chemistry of Natural Compounds 08/2005; 41(5):491-493. · 0.60 Impact Factor

Publication Stats

312 Citations
47.98 Total Impact Points

Institutions

  • 2004–2013
    • Fudan University
      • • School of Life Sciences
      • • Institute of Biodiversity Science
      • • Key Laboratory for Biodiversity Science and Ecological Engineering
      Shanghai, Shanghai Shi, China
  • 2005–2007
    • University of California, Riverside
      • Department of Computer Science and Engineering
      Riverside, CA, United States
  • 2006
    • Aarhus University
      Aarhus, Central Jutland, Denmark
  • 2005–2006
    • Yunnan Academy of Agricultural Sciences
      Yün-nan, Yunnan, China
  • 2004–2006
    • Shanghai Center for Bioinformation Technology
      Shanghai, Shanghai Shi, China
  • 2003
    • Zhongshan University
      Shengcheng, Guangdong, China