PepPre: Promote Peptide Identification Using Accurate and Comprehensive Precursors.

Accurate and comprehensive peptide precursor ions are crucial to tandem mass-spectrometry-based peptide identification. An identification engine can derive great advantages from the search space reduction enabled by credible and detailed precursors. Furthermore, by considering multiple precursors per spectrum, both the number of identifications and the spectrum explainability can be substantially improved. Here, we introduce PepPre, which detects precursors by decomposing peaks into multiple isotope clusters using linear programming methods. The detected precursors are scored and ranked, and the high-scoring ones are used for subsequent peptide identification. PepPre is evaluated both on regular and cross-linked peptide data sets and compared with 11 methods. The experimental results show that PepPre achieves a remarkable increase of 203% in PSM and 68% in peptide identifications compared to instrument software for regular peptides and 99% in PSM and 27% in peptide pair identifications for cross-linked peptides, surpassing the performance of all other evaluated methods. In addition to the increased identification numbers, further credibility evaluations evidence the reliability of the identified results. Moreover, by widening the isolation window of data acquisition from 2 to 8 Th, with PepPre, an engine is able to identify at least 64% more PSMs, thereby demonstrating the potential advantages of wide-window data acquisition. PepPre is open-source and available at http://peppre.ctarn.io.

[Advances in animal models of chronic heart failure and its applications in traditional Chinese medicine].

Chronic heart failure(CHF) is a series of clinical syndromes in which various heart diseases progress to their end stage. Its morbidity and mortality are increasing year by year, which seriously threatens people's life and health. The diseases causing CHF are complex and varied, such as coronary heart disease, hypertension, diabetes, cardiomyopathy and so on. It is of great significance to establish animal models of CHF according to different etiologies to explore the pathogenesis of CHF and develop drugs to prevent and treat CHF induced by different diseases. Therefore, based on the classification of the etiology of CHF, this paper summarizes the animal models of CHF widely used in recent 10 years, and the application of these animal models in traditional Chinese medicine(TCM) research, in order to provide ideas and strategies for studying the pathogenesis and treatment of CHF, and provide ideas for TCM modernization research.

Seco and Nor-seco Isodhilarane-Type Meroterpenoids from Penicillium purpurogenum and the Configuration Revisions of Related Compounds.

Seco and nor-seco isodhilarane-type meroterpenoids (SIMs and NSIMs) are mainly found in Penicillium fungi and have been characterized by highly congested polycyclic skeletons and a broad range of bioactivities. However, the literature reports inconsistent configuration assignments for some SIMs and NSIMs, due to their complex polycyclic systems and multichiral centers. Herein, we described eight SIMs and NSIMs isolated from the EtOAc extract of Penicillium purpurogenum, which led to the configuration revisions of purpurogenolide C (1a), berkeleyacetal B (2a), chrysogenolide F (3a), and berkeleyacetal C (4a) as compounds 1-4, respectively. Furthermore, extensive re-evaluation of the experimental and computational 13C NMR chemical shifts of the reported 39 SIMs and NSIMs provided an empirical approach for determining the C-9 relative configuration, according to the 13C NMR chemical shifts of C-9, which contributed to the configuration revisions of another three SIMs (5a and 6a) and NSIMs (7a), denoted as compounds 5-7, respectively. Biological assays indicated that compound 3 exhibited cytotoxic activity against HepG2 and A549 cell lines with IC50 values of 5.58 and 6.80 µM, respectively. Compounds 2-4, 8, 9, and 32 showed moderate hepatoprotective activity at 10 µM in the APAP-induced HepG2 cell injury model.

Two New Nor-seco-Isodhilarane-Type Meroterpenoids from the Endophytic Fungus Penicillium purpurogenum.

Two new nor-seco isodhilarane meroterpenoids (NSIMs), purpurogenolides F (1) and G (2), along with three known meroterpenoid analogs (3-5), were isolated from the cultures of an endophytic fungus, Penicillium purpurogenum. Structures and absolute configurations of the new NSIMs were determined based on extensive spectroscopic data analyses, including HR-ESI-MS, UV, IR, NMR chemical shift calculations together with DP4+ probability analysis, as well as ECD calculations. All the isolated meroterpenoids were assessed for their anti-inflammatory activities, and compound 4 exhibited moderate inhibitory activity against the nitric oxide (NO) production in lipopolysaccharide (LPS) induced RAW 264.7 cells with an IC50 value of 20.85±2.31 µM.

Penicipurate A, a new polyketide derivative from the endophytic fungus Penicillium purpurogenum.

A new polyketide derivative containing a 3-hydroxydecanoic acid ester moiety, penicipurate A (1), was purified from the solid cultures of the fungus Penicillium purpurogenum, a fungal strain endophytic in the leaves of Edgeworthia chrysantha. The structure of 1 was established by spectroscopic methods, including UV, IR, HRESIMS, 1D, and 2D NMR and 13C NMR chemical shifts calculations coupled with DP4+ analysis, as well as the chemical degradation method. Compound 1 showed moderate inhibitory activity against pancreatic lipase (PL) with an IC50 value of 9.61 ± 1.42 µM.

[Progress of target determination and mechanism of bioactive components of traditional Chinese medicine].

The pharmacodynamic substances of traditional Chinese medicine(TCM) are the basis for the research of TCM and the development of innovative drugs. However, the lack of clarity of targets and molecular mechanisms is the bottleneck problem that restricts the research of pharmacodynamic substances of TCM. Bioactive components are the material basis of the efficacy of TCM, which exert activity by regulating the corresponding targets. Therefore, it is very important to identify the targets of the bioactive components to elucidate the pharmacological mechanism of TCM. Proteins are the most important drug targets, and study of the interaction between the proteins and bioactive components of TCM plays a key role in the development of pharmacological mechanism of TCM. In recent years, the main techniques for detecting the interaction between the bioactive components and proteins include surface plasmon resonance, fluorescence resonance energy transfer, bio-layer interference, molecular docking, proteome chip, target fishing, target mutant, and protein crystallization techniques, etc. This review summarized the biological target detection techniques and their applications in locating the targets of the bioactive components in TCM in the last decade, and this paper will provide useful strategies to elucidate the pharmacological mechanisms of TCM.

[Concept and method of evidence-based toxicology of traditional Chinese medicine from origin and development of evidence-based toxicology].

Advances in science and technology promote the rapid development of toxicological detection technologies. However, there is still a lack of decision-making tools for toxicological risk assessment, such as the lack of transparent schemes to evaluate current toxicological research and practice and the lag of toxicological testing tools to evaluate toxicity, resulting in difficulties in toxicity verification and hindering the transformation of toxicological research paradigm. Some scholars have proposed to integrate the concept of evidence-based medicine with the toxicological practice to improve the technical methods of toxicological research concept and risk assessment decision-making. With the promotion of relevant scholars and academic organizations, the concept and connotation of evidence-based toxicology have gradually become clear and a framework for research and practice has been initially formed. Although there are still many challenges, it also provides a new idea for the toxicity risk assessment and safe medication decision-making of traditional Chinese medicine(TCM). The era of digital intelligence has brought new opportunities and broad space for the development of TCM evidence-based toxicology. The exploration of TCM evidence-based toxicology from concept to method is an important embodiment of the development of TCM evidence-based toxicology, and will also promote the continuous enrichment and improvement of the research and practice system of TCM evidence-based toxicology.

[Trace therapeutic substances of traditional Chinese medicine: great resources of innovative drugs derived from traditional Chinese medicine].

The traditional Chinese medicine(TCM) contains very complex constituents. Besides the major constituents, there are a large number of unclear trace constituents with novel skeletons and potent bioactivities, which have been regarded as one of the important therapeutic substances and the great resources of innovative drugs derived from TCM. The present review highlighted that the development of the trace therapeutic substances of TCM is closely depends on the advanced technologies for their identification, isolation, structure elucidation, and bioactivity evaluation. Additionally, this paper reviewed the novel trace compounds derived from Chinese herbal medicines which have been published in Organic Letters during 2001-2021, and summarized the important licensed drugs originated from the trace therapeutic substances and the discovery and development of trace therapeutic substances of 8 kinds of Chinese herbal medicines. This review provides references for the research and development of TCM therapeutic substances and innovative drugs.

Denudatine-type diterpenoid alkaloids from an aqueous extract of the lateral root of Aconitum carmichaelii.

Five new denudatine-type diterpenoid alkaloids (1-5), along with the known analogue aconicarmine (6), were isolated from an aqueous decoction of the lateral roots of Aconitum carmichaelii (fu-zi). Their structures were determined by spectroscopic data analysis and electronic circular dichroism (ECD) calculations. Compound 5 is the first denudatine-type diterpenoid alcohol iminium alkaloid, which could be partially transformed into the aza acetal form in pyridine-d5. Compound 5 inhibited mice writhing in an acetic acid-induced writhing assay.

[A new phenolic acid ester from solid culture of Colletotrichum capsici, an endophytic fungus from Paeonia lactiflora].

A new phenolic acid ester, 4'-hydroxyphenylethyl 4,8(R)-dihydroxyphenylpropionate(1), was isolated from an endophytic fungus Colletotrichum capsici of Paeonia lactiflora roots, along with eight known phenolic derivatives, tyrosol(2), 2-(4-hydroxyphenyl) ethyl acetate(3), methyl p-hydroxyphenylacetate(4), methyl m-hydroxyphenylacetate(5), 4-(4-hydroxyphene-thoxy)-4-oxobutanoic acid(6), 4-hydroxyphenethyl methyl succinate(7), trichodenol B(8) and 4-hydroxyphenethyl 2-(4-hydroxyphenyl) acetate(9). Their structures were identified by a combination of high-resolution electrospray ionization mass spectrometry(HR-ESI-MS), nuclear magnetic resonance(NMR) spectroscopy, ultraviolet(UV) spectroscopy and electronic circular dichroism(ECD) spectroscopy. Compounds 2-9 were isolated from this fungus for the first time.

Three new polyketides from the endophytic fungus Penicillium purpurogenum.

Three new polyketides including two benzophenone derivatives, penibenzones A and B (1 and 2), and a new phthalide derivative, penibenzone C (3), along with six known compounds, were isolated from the solid-substrate cultures of the endophytic fungus Penicillium purpurogenum IMM003. Their structures were elucidated on the basis of spectroscopic data (UV, IR, HRESIMS, 1D and 2D NMR). All compounds were evaluated for inhibitory activity against pancreatic lipase, but none of them displayed activity.[Formula: see text].

Structures and Biological Evaluation of Monoterpenoid Glycosides from the Roots of Paeonia lactiflora.

Fractionation of an aqueous extract of the air-dried roots of a traditional Chinese medicinal plant, Paeonia lactiflora, yielded the new monoterpenoid glycosides 1-10. Their structures were assigned via spectroscopic techniques, and the absolute configurations of 1, 4-6, and 8 were verified via chemical methods, specific rotation, and electronic circular dichroism data. Compounds 1-4 are rare compared to the reported cage-like paeoniflorin derivatives; that is, they comprised two monoterpenoidal moieties. In the in vitro assay, compounds 5, 8, and 9 showed weak inhibitions against lipopolysaccharide-induced nitric oxide production in RAW264.7 macrophages, with IC50 values of 64.8, 60.1, and 97.5 µM, respectively.

Polyketides from the fungus Penicillium decumbens.

Two new polyketides, 3,11-dihydroxy-6,8-dimethyldodecanoic acid (1) and trichopyrone B (2), together with two known polyketides, sorbicillin (3) and penicillone A (4), have been isolated from the cultures broth of the fungus Penicillium decumbens. Their structures were elucidated by extensive spectroscopic analysis. All isolated compounds were evaluated for their antibacterial and cytotoxic activities. Of these, compound 3 showed antifungal activity toward Candida albicans Y0109 with a MIC value of 50 µM. Moreover, compounds 3 and 4 exhibited selective cytotoxicity against the human hepatocellular carcinoma (QGY-7703) cell line with the IC50 values of 32.5 and 22.8 µM, respectively.

A new cytotoxic 12-membered macrolactone from the endophytic fungus Exserohilum rostratum LPC-001.

A new oxacyclododecindione-type macrolactone, (13R,14S,15R)-13-hydroxy-14-deoxyoxacyclododecindione (1), has been obtained from the solid cultures of the fungus Exserohilum rostratum, a fungal strain endophytic in Gymnadenia conopsea. Its structure, including the absolute configuration, was extensively established by 1D and 2D NMR data, the modified Mosher method, and a combination of experimental and theoretically calculated electronic circular dichroism (ECD) spectra. Compound 1 showed weak selective cytotoxicity against the A549 lung cell line with an IC50 value of 9.2 µM.

Two new terpenoid ester glycosides from the twigs of Litsea cubeba.

A new sesquiterpenoid ester glycoside (1) and a new monoterpenoid ester glycoside (2) have been isolated from an ethanol extract of the twigs of Litsea cubeba. Their structures were elucidated by extensive 1D- and 2D-NMR experiments, and the absolute configurations were determined by chemical methods, specific rotation, and a combination of experimental and theoretically calculated electronic circular dichroism spectra. Compound 1 exhibited selective cytotoxicity against A549 and HCT-8 cell lines with the IC50 values of 8.9 and 9.6 µM, respectively.

[Chemical constituents from water-soluble extract of dry roots of Paeonia lactiflora].

Nineteen compounds were isolated from the water-soluble extract of the dry roots of Paeonia lactiflora by using various chromatographic techniques. Their structures were identified by MS， NMR and other spectroscopic analysis as paeoniflorin(1)， 4-O-ethylpaeoniflorin(2)， 2'-O-benzoylpaeoniflorin(3)， benzoylpaeoniflorin(4)， 4"-hydroxy-benzoyloxypaeoniflorin(5)， moudanpioside C(6)， 6'-O-benzoyl-4"-hydroxy-3"-methoxy-paeoniflorin(7)， paeoniflorin B(8)， 6-O-benzoylalbiflorin(9)， secoisolariciresinol (10)， (+)-lyoniresinol(11)， dihyrodehydrodiconiferyl alcohol(12)， (7S，8S)-threo-7，9，9'-trihydroxy-3，3'-dimethoxy-8-O-4'-neolignan(13)， (+)-neo-olivil (14)， [(3S)-5-methyl-2，3-dihydro-1-benzofuran-3-yl]methanol(15)， 5-hydroxy-3S-hydroxymethyl-6-methyl-2，3-dihydrobenzofuran(16)， (+)-(R)-2-hydroxy-1-(4-methoxyphenyl)-1-propan-1-one(17)， (+)-(2R)-1-(4-hydroxy-3-methoxyphenyl)-2-propanol(18)， (+)-(4S)-(2E)-4-hydroxy-2-nonenoic acid(19). Compounds 15 and 18 are new natural products， while compounds 10， 11， 13， 14， 17 and 19 are isolated from the genus Paeonia for the first time.

[Study on structural conversion of dihydrochelerythrine in different solvents].

Dihydrochelerythrine was isolated from the ethanol extract of Corydalis yanhusuo by chromatographic and recrystallization techniques. To our knowledge, this is the first report that dihydrochelerythrine was found to be unstable. The NMR, HPLC, and LC-MS were applied to monitor the structural conversion process of dihydrochelerythrine. The results showed that when dissolved in polar deuteration solvent (e.g., DMSO-d6 & MeOD), dihydrochelerythrine is directly converted to chelerythrine gradually. However, if used non-polar reagent (e.g.,CD2Cl2), the sample of dihydrochelerythrine undergoes the formation of pseudobase, chelerythrine, and bimolecular ether then followed by oxidation to oxychelerythrine as the major final product. Which leads to this phenomenon maybe is that the C-6 in dihydrochelerythrine is highly reactive to nucleophiles, and is easily converted to different derivatives in different solvents attributed to the solvent effect. This finding will contribute to the extraction and isolation, bioactivity screening, and quality evaluation of medicinal materials containing dihydrochelerythrine and other similar derivatives.

Bioactive Glycosides from the Twigs of Litsea cubeba.

The air-dried twigs of Litsea cubeba, a traditional Chinese medicinal tree, afforded 10 new aromatic glycosides (1-10) and 26 known analogues. Their structures were assigned by extensive 1D and 2D NMR experiments, and the absolute configurations were resolved by chemical methods, electronic circular dichroism, specific rotation, and X-ray crystallographic analysis. Compound 4 is the first example of a naturally occurring homoneolignan glucoside. Compounds 4, 6-8, and the known neolignan glucosides (11, 12, and 14) at respective 10 µM concentrations were found to reduce acetaminophen-induced HepG2 cell injury with 30.5-46.0% inhibitions. Furthermore, compounds 12 and 15 demonstrated moderate inhibitory activities against HDAC1, with IC50 values of 3.6 and 4.6 µM, respectively.

[Water soluble constituents from the twigs of Litsea cubeba].

Twenty five known aromatic glycosides (1-25) and three known sesquiterpene glycosides (26-28) have been isolated from the twigs of Litsea cubeba by using various chromatographic techniques. Their structures were identified by spectroscopic data analysis (MS, IR, 1D and 2D NMR) as (7S,8R)-dehydrodiconiferyl alcohol 4,9'-di-O-ß-D-glucopyranoside(1),(7S,8R)-5-methoxydihydrodehydrodiconiferyl alcohol 4-O-ß-D-glucopyranoside(2), (7S,8R)-urolignoside(3), (7R,8S)-dihydrodehydrodiconiferyl alcohol 4-O-ß-D-glucopyranoside(4), saposide B(5), lanicepside A(6), matairesinol-4-O-ß-D-glucopyranoside (7), tyraxjaponoside B(8), (+)-lyoniresinol-9'-O-ß-D-glucopyranoside (9), alaschanisoside A (10), syringin (11), psoralenoside (12), isopsoralenoside (13), scopolin(14), 2,6-dimethoxy-4-hydroxyphenol-1-O-ß-D-glucopyranoside (15), 3-hydroxy-4,5-dimethoxyphenyl-ß-D-glucopyranoside (16), 2-(3,4-dihydroxyphenyl)ethyl-ß-D-glucopyrnoside (17), 2-(4-dihydroxyphenyl)ethyl-ß-D-glucopyranoside (18), (+)-catechin-7-O-ß-D-glucopyranoside (19), 3'-O-methylepicatechin-7-O-ß-D-glucopyranoside (20), kaempferitrin (21), quercetin-3-O-α-L-rhamnopyranside (22), kaempferol-3-O-ß-D-glucopyranoside (23), kaempferol 3-O-ß-D-glucopyranosyl(1→2)-O-ß-D-galactopyr anoside-7-O-α-L-rhamnopyranoside (24), quercetin 3-O-α-L-rhamnopyranosyl(1→6)-O-ß-D-glucopyranosyl(1→3)-O-α-L-rhamnopyranosyl(1→2)-O-ß-D-glucopyranoside (25), staphylionoside D(26), vomifoliol 9-O-ß-D-glucopyranoside (27), dihydrovomifoliol-O-ß-D-glucopyranoside (28). Compounds 1-21 and 24-28 were obtained from this genus for the first time.

[A new styrene dimer derivative from Litsea greenmaniana].

A new styrene dimer derivative has been isolated from the branch of Litsea greenmaniana by column chromatography over silica gel and Sephadex LH-20, as well as semi-preparative HPLC. Its structure was identified by spectroscopic data analysis (MS, UV, IR, 1D and 2D NMR) as (E)-2,4-bis(p-hydroxyphenyl)-2-butenol, named as listeanol. At a concentration of 1×10-5 mol•L⁻¹, compound 1 was inactive in the assays, including cytotoxicity against human tumor cell lines (HCT-8, Bel-7402, BGC-823, A549 and A2780), antioxidant activity in Fe²âº-cystine-induced rat liver microsomal lipid peroxidation, neuroprotective activity against serum deprivation or glutamate induced neurotoxicity in cultures of PC12 cells, and the inhibitory activity against protein tyrosine phosphatase 1B (PTP1B).