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1.
Beijing Da Xue Xue Bao Yi Xue Ban ; 56(2): 332-337, 2024 Apr 18.
Article in Chinese | MEDLINE | ID: mdl-38595254

ABSTRACT

OBJECTIVE: To analyze the concentration of formic acid, propionic acid and butyric acid in gingival crevicular fluid (GCF) of patients with stages Ⅲ and Ⅳ periodontitis, and their relationship with periodontitis. METHODS: The study enrolled 37 systemically healthy patients with periodontitis and 19 healthy controls who visited Department of Periodontology, Peking University School and Hospital of Stomatology from February 2008 to May 2011. Their GCFs were collected from the mesial-buccal site of one molar or incisor in each quadrant. Periodontal clinical parameters, including plaque index(PLI), probing depth(PD), bleeding index(BI), and attachment loss(AL). Concentrations of formic acid, propionic acid and butyric acid in the supernatant of the GCFs were analyzed by high-performance capillary electrophoresis (HPCE). The prediction ability of formic acid, propionic acid and butyric acid with the risk of periodontitis and the differences between grade B and grade C periodontitis were analyzed. RESULTS: In this study, 32 patients with stage Ⅲ and 5 patients with stage Ⅳ were enrolled, including 9 patients with grade B and 28 patients with grade C. Clinical periodontal variables in the patients with periodontitis were significantly higher than those in the control group (P<0.001). Formic acid was significantly lower in periodontitis than that in the control group [5.37 (3.39, 8.49) mmol/L vs. 12.29 (8.35, 16.57) mmol/L, P<0.001]. Propionic acid and butyric acid in periodontitis were significantly higher than those in the control group: Propionic acid, 10.23 (4.28, 14.90) mmol/L vs. 2.71 (0.00, 4.25) mmol/L, P < 0.001; butyric acid, 2.63 (0.47, 3.81) mmol/L vs. 0.00 (0.00, 0.24) mmol/L, P<0.001. There was no significant difference in formic acid, propionic acid and butyric acid concentrations between grade B and grade C periodontitis (P>0.05). Propionic acid and butyric acid in the deep pocket were significantly higher than in the shallow pocket, while the concentration of formic acid decreased with the increase of PD. Propionic acid (OR=1.51, 95%CI: 1.29-1.75) and butyric acid (OR=3.72, 95%CI: 1.93-7.17) were risk factors for periodontitis, while formic acid (OR=0.87, 95%CI: 0.81-0.93) might be a protective factor for periodontitis. Propionic acid (AUC=0.852, 95%CI: 0.805-0.900), butyric acid (AUC=0.889, 95%CI: 0.841-0.937), f (formic acid, AUC=0.844, 95%CI: 0.793-0.895) demonstrated a good predictive capacity for the risk of periodontitis. CONCLUSION: The concentration of formic acid decrease in the GCF of periodontitis patients, which is a protective factor for periodontitis, its reciprocal have good predictive capacity. However, propionic acid and butyric acid increase, which are risk factors for periodontitis and have good predictive capacity. The concentration of formic acid, propionic acid, and butyric acid vary with probing depth, but there is no significant difference between grade B and grade C periodontitis.


Subject(s)
Formates , Gingival Crevicular Fluid , Periodontitis , Propionates , Humans , Butyric Acid/analysis , Gingival Crevicular Fluid/chemistry , Fatty Acids, Volatile/analysis , Periodontal Attachment Loss
2.
BMC Plant Biol ; 24(1): 188, 2024 Mar 15.
Article in English | MEDLINE | ID: mdl-38486139

ABSTRACT

BACKGROUND: Proper flowering time is important for the growth and development of plants, and both too early and too late flowering impose strong negative influences on plant adaptation and seed yield. Thus, it is vitally important to study the mechanism underlying flowering time control in plants. In a previous study by the authors, genome-wide association analysis was used to screen the candidate gene SISTER OF FCA (SSF) that regulates FLOWERING LOCUS C (FLC), a central gene encoding a flowering suppressor in Arabidopsis thaliana. RESULTS: SSF physically interacts with Protein arginine methyltransferase 5 (PRMT5, SKB1). Subcellular co-localization analysis showed that SSF and SKB1 interact in the nucleus. Genetically, SSF and SKB1 exist in the same regulatory pathway that controls FLC expression. Furthermore, RNA-sequencing analysis showed that both SSF and SKB1 regulate certain common pathways. CONCLUSIONS: This study shows that PRMT5 interacts with SSF, thus controlling FLC expression and facilitating flowering time control.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Flowers/metabolism , Gene Expression Regulation, Plant , Genome-Wide Association Study , MADS Domain Proteins/genetics , MADS Domain Proteins/metabolism
3.
Nat Commun ; 15(1): 1013, 2024 Feb 03.
Article in English | MEDLINE | ID: mdl-38307850

ABSTRACT

Through pumping a spin current from ferromagnet into heavy metal (HM) via magnetization precession, parts of the injected spins are in-plane rotated by the lattice vibration, namely acoustic spin rotation (ASR), which manifests itself as an inverse spin Hall voltage in HM with an additional 90° difference in angular dependency. When reversing the stacking order of bilayer with a counter-propagating spin current or using HMs with an opposite spin Hall angle, such ASR voltage shows the same sign, strongly suggesting that ASR changes the rotation direction due to interface spin-orbit interaction. With the drift-diffusion model of spin transport, we quantify the efficiency of ASR up to 30%. The finding of ASR endows the acoustic device with an ability to manipulate spin, and further reveals a new spin-orbit coupling between spin current and lattice vibration.

4.
Lasers Med Sci ; 38(1): 243, 2023 Oct 26.
Article in English | MEDLINE | ID: mdl-37882915

ABSTRACT

The immune effect induced by photodynamic therapy (PDT) has a limited effect on breast tumor. This study hypothesized that suppressive immune checkpoints on T cells might upregulate after PDT, which may reduce the antitumor effect of PDT for treating breast tumor. This study explored the alteration of immune checkpoint for the first time. A bilateral subcutaneous transplanted breast tumor mice model was established, and right tumors imitated primary tumors, and left tumors imitated distant tumors. Primary tumors were treated with PDT mediated by hematoporphyrin derivatives (HpD-PDT). Costimulatory molecules (ICOS, OX40, and 4-1BB) and immune checkpoints (PD1, LAG-3, CTLA-4, TIM-3, TIGIT) on tumor infiltrating T cells after HpD-PDT were analyzed by flow cytometry. Antitumor and immune effects were also assessed after HpD-PDT combined with anti-PD1 and LAG-3 antibodies. Primary tumors were suppressed, but distant tumors could not be inhibited after HpD-PDT. The number of T cells was increased, but function did not enhance after HpD-PDT. Additionally, costimulatory molecules (ICOS, OX40, and 4-1BB) were not elevated, but the suppressive immune checkpoints on tumor infiltrating T cells were upregulated after HpD-PDT. Notably, PD1+ LAG-3+ CD4+ T and PD1+ LAG-3+ CD8+ T cells were significantly increased. When PD1 and LAG-3 blockade combined with HpD-PDT, both primary and distant tumors were significantly suppressed, and antitumor immune effects were significantly enhanced. HpD-PDT could upregulate the PD1+ LAG-3+ CD4+ T and PD1+ LAG-3+ CD8+ T cells. Dual blockade of PD1 and LAG-3 immune checkpoints can enhance the antitumor effect of HpD-PDT.


Subject(s)
Breast Neoplasms , Photochemotherapy , Animals , Mice , Humans , Female , Up-Regulation , CD8-Positive T-Lymphocytes , Hematoporphyrin Derivative , Breast Neoplasms/drug therapy
5.
Chem Sci ; 14(13): 3668-3675, 2023 Mar 29.
Article in English | MEDLINE | ID: mdl-37006698

ABSTRACT

Disulfide-rich peptides (DRPs) are an interesting and promising molecular format for drug discovery and development. However, the engineering and application of DRPs rely on the foldability of the peptides into specific structures with correct disulfide pairing, which strongly hinders the development of designed DRPs with randomly encoded sequences. Design or discovery of new DRPs with robust foldability would provide valuable scaffolds for developing peptide-based probes or therapeutics. Herein we report a cell-based selection system leveraging cellular protein quality control (termed PQC-select) to select DRPs with robust foldability from random sequences. By correlating the foldability of DRPs with their expression levels on the cell surface, thousands of sequences that can fold properly have been successfully identified. We anticipated that PQC-select will be applicable to many other designed DRP scaffolds in which the disulfide frameworks and/or the disulfide-directing motifs can be varied, enabling the generation of a variety of foldable DRPs with new structures and superior potential for further developments.

6.
J Exp Bot ; 74(12): 3749-3764, 2023 06 27.
Article in English | MEDLINE | ID: mdl-36964900

ABSTRACT

The corn leaf aphid (Rhopalosiphum maidis) is a major maize pest that frequently causes substantial yield losses. Exploring the genetic basis of resistance to aphids is important for improving maize yield and quality. Here, we used a maize recombinant inbred line population derived from two parents with different susceptibility to aphids, B73 (susceptible) and Abe2 (resistant), and performed quantitative trait locus (QTL) mapping using aphid resistance scores as an indicator. We mapped a stable QTL, qRTA6, to chromosome 6 using data from 2 years of field trials, which explained 40.12-55.17% of the phenotypic variation. To further investigate the mechanism of aphid resistance in Abe2, we constructed transcriptome and metabolome libraries from Abe2 and B73 leaves with or without aphid infestation at different time points. Integrating QTL mapping and transcriptome data revealed three aphid resistance candidate genes (Zm00001d035736, Zm00001d035751, and Zm00001d035767) associated with the hypersensitive response, the jasmonic acid pathway, and protein ubiquitination. Integrated transcriptomic and metabolomic analysis revealed that the differentially expressed genes and metabolites were enriched in flavonoid biosynthesis. These findings extend our understanding of the molecular mechanisms controlling aphid resistance in maize, and the QTL and candidate genes are valuable resources for increasing this resistance.


Subject(s)
Aphids , Animals , Aphids/physiology , Zea mays/genetics , Zea mays/metabolism , Quantitative Trait Loci , Multiomics , Plant Leaves/genetics
7.
BMC Musculoskelet Disord ; 24(1): 144, 2023 Feb 23.
Article in English | MEDLINE | ID: mdl-36823608

ABSTRACT

BACKGROUND: The purpose of our study was to explore the sonographic characteristics of fibromas of the tendon sheath of the hand and wrist and to evaluate the value of high frequency ultrasound in the diagnosis of FTS. METHODS: We retrospectively reviewed the sonography of 42 patients with surgically proven FTS, including one with a relapsing tumor (43 lesions in total). The location, size, distribution, relationship with the surrounding tissue, two-dimensional gray-scale sonographic appearance and internal color blood flow of all lesions were analysed. RESULTS: The maximum diameter ranged from 0.4 to 2.8 cm, with an average of 1.5 ± 0.6 cm. Twenty-eight lesions (65%) were associated with an adjacent tendon, while the other 15 lesions (35%) were next to the joint. Spindle or oval lesions were common, followed by irregular shape. The nodules with clear boundaries were hypoechoic and had posterior echo enhancement. Thirty-seven lesions (86%) were homogeneous, while 6 lesions (14%) had cystic components with no echo inside. Seventeen lesions (40%) had a large amount of blood flow. Nine lesions (20%) had a small amount of blood flow. The other 17 lesions (40%) had no significant blood flow. CONCLUSIONS: The diagnosis of fibroma of the tendon sheath can be considered when ultrasound examination reveals a focal nodular mass adjacent to a tendon sheath with homogeneous hypoechogenicity and no or small or large amounts of blood flow.


Subject(s)
Fibroma , Wrist , Humans , Wrist/diagnostic imaging , Wrist/pathology , Retrospective Studies , Neoplasm Recurrence, Local/pathology , Tendons/diagnostic imaging , Tendons/pathology , Fibroma/diagnostic imaging , Fibroma/surgery , Ultrasonography
8.
J Am Chem Soc ; 145(3): 1964-1972, 2023 01 25.
Article in English | MEDLINE | ID: mdl-36633218

ABSTRACT

Multicyclic peptides with stable 3D structures are a kind of novel and promising peptide formats for drug design and discovery as they have the potential to combine the best characteristics of small molecules and proteins. However, the development of multicyclic peptides is largely limited to naturally occurring products. It remains a big challenge to develop multicyclic peptides with new structures and functions without recourse to the existing natural scaffolds. Here, we report a general and robust method relying on the utility of new disulfide-directing motifs for designing and discovering diverse multicyclic peptides with potent protein-binding capability. These peptides, referred to as disulfide-directed multicyclic peptides (DDMPs), are tolerant to extensive sequence manipulations and variations of disulfide-pairing frameworks, enabling the development of de novo DDMP libraries useful for ligand and drug discovery. This study opens a new avenue for creating a new generation of multicyclic peptides in sequence and structure space inaccessible by natural scaffolds, thus would greatly benefit the field of peptide drug discovery.


Subject(s)
Disulfides , Peptide Library , Ligands , Peptides/chemistry , Drug Design
9.
Chem Sci ; 13(26): 7780-7789, 2022 Jul 06.
Article in English | MEDLINE | ID: mdl-35865895

ABSTRACT

Peptides constrained through multiple disulfides (or disulfide-rich peptides, DRPs) have been an emerging frontier for ligand and drug discovery. Such peptides have the potential to combine the binding capability of biologics with the stability and bioavailability of smaller molecules. However, DRPs with stable three-dimensional (3D) structures are usually of natural origin or engineered from natural ones. Here, we report the discovery and identification of CPPC (cysteine-proline-proline-cysteine) motif-directed DRPs with stable 3D structures (i.e., CPPC-DRPs). A range of new CPPC-DRPs were designed or selected from either random or structure-convergent peptide libraries. Thus, for the first time we revealed that the CPPC-DRPs can maintain diverse 3D structures by taking advantage of constraints from unique dimeric CPPC mini-loops, including irregular structures and regular α-helix and ß-sheet folds. New CPPC-DRPs that can specifically bind the receptors (CD28) on the cell surface were also successfully discovered and identified using our DRP-discovery platform. Overall, this study provides the basis for accessing an unconventional peptide structure space previously inaccessible by natural DRPs and computational designs, inspiring the development of new peptide ligands and therapeutics.

10.
Exp Biol Med (Maywood) ; 247(17): 1548-1557, 2022 09.
Article in English | MEDLINE | ID: mdl-35665630

ABSTRACT

Sepsis-induced inflammatory lung injury is a key factor causing failure of the lungs and other organs, as well as death, during sepsis. In the present study, a caecal ligation and puncture (CLP)-induced sepsis model was established to investigate the effect of ß-catenin on sepsis-induced inflammatory lung injury and the corresponding underlying mechanisms. C57BL/6 mice were randomly divided into five groups, namely, the sham, CLP, ß-catenin knockout (KO) + CLP, XAV-939 + CLP, and ICG-001 + CLP groups; the XAV-939 + CLP and ICG-001 + CLP groups were separately subjected to intraperitoneal injections of the ß-catenin inhibitors XAV-939 and ICG-001 for 1 week preoperatively and 2 days postoperatively, respectively. Forty-eight hours after CLP, we measured ß-catenin expression in lung tissues and evaluated mouse mortality, histopathological characteristics of hematoxylin and eosin (H&E)-stained lung tissues, serum cytokine (tumor necrosis factor [TNF]-α, interleukin [IL]-10, and IL-1ß) levels, lung myeloperoxidase (MPO) activity, and the number of apoptotic cells in the lung tissues. Our results indicated that both the inhibition of ß-catenin expression and blockage of ß-catenin/CREB-binding protein (CBP) interactions by ICG-001 effectively decreased mouse mortality, alleviated pathological lung injury, and reduced the serum TNF-α, IL-10, and IL-1ß levels, in addition to reducing the lung MPO activity and the number of apoptotic cells in lung tissues of the sepsis model mice. Therefore, it can be deduced that the ß-catenin/CBP signaling axis participates in regulating sepsis-induced inflammatory lung injury.


Subject(s)
Lung Injury , Sepsis , Animals , CREB-Binding Protein/metabolism , Cytokines/metabolism , Disease Models, Animal , Eosine Yellowish-(YS)/metabolism , Hematoxylin/metabolism , Interleukin-10/metabolism , Lung/pathology , Lung Injury/pathology , Mice , Mice, Inbred C57BL , Peroxidase/metabolism , Sepsis/pathology , Tumor Necrosis Factor-alpha/metabolism , beta Catenin/metabolism
11.
Front Genet ; 13: 831611, 2022.
Article in English | MEDLINE | ID: mdl-35432456

ABSTRACT

Modern research has proved that the main medicinal component of Rhodiola crenulata, which has a wide range of medicinal value, is its secondary metabolite salidroside. The MYB transcription factor family is widely involved in biosynthesis of second metabolism and other roles in the stress response in plants, so a genome-wide identification and analysis for this family in R. crenulata is worth conducting. In this research, genome-wide analysis identified 139 MYB genes based on conserved domains in the R. crenulata genome, and 137 genes were used to construct a phylogenetic tree and modified with expression files to reveal evolutionary characteristics. Physical and chemical characteristics, gene structure, and conserved motif analysis were also used to further analyze RcMYBs. Additionally, cis-acting elements related to transcription, hormone, and MYB binding were found in the promoter region of the selected RcMYBs. Four RcMYBs were cloned, sequenced, and their gene expression pattern was analyzed for further analysis of their functions. The research results lay the foundation for further research on the function of RcMYB and R. crenulata.

12.
J Clin Ultrasound ; 50(5): 639-645, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35285518

ABSTRACT

PURPOSE: An automatic evaluation technology based on artificial intelligence and three-dimensional ultrasonography (3D US) is proposed for hip US inspection plane selection. This study aimed to evaluate the consistency of the α angle as measured using 3D US to select the section plane and two-dimensional ultrasonography (2D US) to manually select the Graf image, as well as to explore the feasibility of diagnosing developmental dysplasia of the hip (DDH) using 3D US and reconstruction technology. METHODS: A total of 216 infant hips were included and assessed by doctors using 3D US layer-by-layer. The researchers used a computer to identify the coronal images that met the Graf standard and then compared the αX values obtained with the αG values measured artificially by 2D US. RESULTS: Compared with 2D US, 3D US more clearly showed the relative positions of the ilium, ischia, and pubis. The measured α value of the optimal section obtained by 3D US showed good agreement with the measured α value of the standard Graf section. CONCLUSION: The artificial intelligence and 3D US-based automatic evaluation technology for section selection and inspection for DDH showed good agreement with the Graf method based on standard sections.


Subject(s)
Artificial Intelligence , Humans , Infant , Ultrasonography/methods
13.
Nat Commun ; 13(1): 1539, 2022 03 22.
Article in English | MEDLINE | ID: mdl-35318337

ABSTRACT

Peptide heterodimers are prevalent in nature, which are not only functional macromolecules but molecular tools for chemical and synthetic biology. Computational methods have also been developed to design heterodimers of advanced functions. However, these peptide heterodimers are usually formed through noncovalent interactions, which are prone to dissociate and subject to concentration-dependent nonspecific aggregation. Heterodimers crosslinked with interchain disulfide bonds are more stable, but it represents a formidable challenge for both the computational design of heterodimers and the manipulation of disulfide pairing for heterodimer synthesis and applications. Here, we report the design, synthesis and application of interchain disulfide-bridged peptide heterodimers with mutual orthogonality by combining computational de novo designs with a directed disulfide pairing strategy. These heterodimers can be used as not only scaffolds for generating functional molecules but chemical tools or building blocks for protein labeling and construction of crosslinking hybrids. This study thus opens the door for using this unexplored dimeric structure space for many biological applications.


Subject(s)
Disulfides , Peptides , Disulfides/chemistry , Macromolecular Substances , Peptides/chemistry , Protein Folding , Proteins
14.
J Am Chem Soc ; 144(11): 5116-5125, 2022 03 23.
Article in English | MEDLINE | ID: mdl-35289603

ABSTRACT

The engineering of naturally occurring disulfide-rich peptides (DRPs) has been significantly hampered by the difficulty of manipulating disulfide pairing. New DRPs that take advantage of fold-directing motifs and noncanonical thiol-bearing amino acids are easy-to-fold with expected disulfide connectivities, representing a new class of scaffolds for the development of peptide ligands and therapeutics. However, the limited diversity of the scaffolds and particularly the use of noncanonical amino acids [e.g., penicillamine (Pen)] that are difficult to be translated by ribosomes greatly hamper the further development and application of these DRPs. Here, we designed and synthesized noncanonical bisthiol motifs bearing sterically obstructed thiol groups analogous to the Pen thiol to direct the folding of peptides into specific bicyclic and tricyclic structures. These bisthiol motifs can be ribosomally incorporated into peptides through a commercially available PURE system integrated with genetic code reprograming, which enables, for the first time, the in vitro expression of bicyclic peptides with two noncanonical and orthogonal disulfide bonds. We further constructed a bicyclic peptide library encoded by mRNA, with which new bicyclic peptide ligands with nanomolar affinity to proteins were successfully selected. Therefore, this study provides a new, general, and robust method for discovering de novo DRPs with new structures and functions not derived from natural peptides, which would greatly benefit the field of peptide drug discovery.


Subject(s)
Disulfides , Peptide Library , Amino Acids , Disulfides/chemistry , Ligands , Peptides/chemistry , Ribosomes , Sulfhydryl Compounds
15.
Chem Sci ; 12(34): 11464-11472, 2021 Sep 01.
Article in English | MEDLINE | ID: mdl-34567500

ABSTRACT

Natural disulfide-rich peptides (DRPs) are valuable scaffolds for the development of new bioactive molecules and therapeutics. However, there are only a limited number of topologically distinct DRP folds in nature, and most of them suffer from the problem of in vitro oxidative folding. Thus, strategies to design DRPs with new constrained topologies beyond the scope of natural folds are desired. Herein we report a general evolution-inspired strategy to design new DRPs with diverse disulfide frameworks, which relies on the incorporation of two cysteine residues and a random peptide sequence into a precursor disulfide-stabilized fold. These peptides can spontaneously fold in redox buffers to the expected tricyclic topologies with high yields. Moreover, we demonstrated that these DRPs can be used as templates for the construction of phage-displayed peptide libraries, enabling the discovery of new DRP ligands from fully randomized sequences. This study thus paves the way for the development of new DRP ligands and therapeutics with structures not derived from natural DRPs.

16.
Bioconjug Chem ; 32(9): 2065-2072, 2021 09 15.
Article in English | MEDLINE | ID: mdl-34405993

ABSTRACT

N-terminal cysteine (Cys)-specific reactions have been exploited for protein and peptide modifications. However, existing reactions for N-terminal Cys suffer from low reaction rate, unavoidable side reactions, or poor stability for reagents or products. Herein we report a fast, efficient, and selective conjugation between 2-benzylacrylaldehyde (BAA) and 1,2-aminothiol, which involves multistep reactions including aldimine condensation, Michael addition, and reduction of imine by NaBH3CN. This conjugation proceeds with a rate constant of ∼2700 M-1 s-1 under neutral condition at room temperature to produce a pair of seven-membered ring diastereoisomers, which are stable under neutral and acidic conditions. This method enables the selective modifications of the N-terminal Cys residue without interference from the internal Cys and lysine residues, providing a useful alternative to existing approaches for site-specific peptide or protein modifications and synthesis of cyclic peptides.


Subject(s)
Peptides, Cyclic , Sulfhydryl Compounds , Cyclization , Cysteine
17.
J Am Chem Soc ; 142(38): 16285-16291, 2020 09 23.
Article in English | MEDLINE | ID: mdl-32914969

ABSTRACT

Disulfide-rich peptides (DRPs) have been an emerging frontier for drug discovery. There have been two DRPs approved as drugs (i.e., Ziconotide and Linaclotide), and many others are undergoing preclinical studies or in clinical trials. All of these DRPs are of nature origin or derived from natural peptides. It is still a challenge to design new DRPs without recourse to natural scaffolds due to the difficulty in handling the disulfide pairing. Here we developed a simple and robust strategy for directing the disulfide pairing and folding of peptides with up to six cysteine residues. Our strategy exploits the dimeric pairing of CPPC (cysteine-proline-proline-cysteine) motifs for directing disulfide formation, and DRPs with different multicyclic topologies were designed and synthesized by regulating the patterns of CPPC motifs and cysteine residues in peptides. As neither sequence manipulations nor unnatural amino acids are involved, the designed DRPs can be used as templates for the de novo development of biosynthetic multicyclic peptide libraries, enabling selection of DRPs with new functions directly from fully randomized sequences. We believe that this work represents as an important step toward the discovery and design of new multicyclic peptide ligands and therapeutics with structures not derived from natural scaffolds.


Subject(s)
Disulfides/chemistry , Peptide Library , Peptides/chemistry , Protein Conformation , Protein Folding
18.
J Org Chem ; 85(17): 11475-11481, 2020 09 04.
Article in English | MEDLINE | ID: mdl-32786636

ABSTRACT

Disulfide-rich peptides (DRPs) are a class of peptides that are constrained through two or more disulfide bonds. Though natural DRPs have been extensively exploited for developing protein binders or potential therapeutics, their synthesis and re-engineering to bind new targets are not straightforward due to difficulties in handling the disulfide pairing problem. Rationally designed DRPs with an intrinsically orthogonal disulfide pairing propensity provide an alternative to the natural scaffolds for developing functional DRPs. Herein we report the use of tandem CXPen/PenXC motifs ((C) cysteine; (Pen) penicillamine; (X) any residue) for directing the oxidative folding of peptides. Diverse tricyclic peptides were designed and synthesized by varying the pattern of C/Pen residues and incorporating a tandem CXPen/PenXC motif into peptides. The folding of these peptides was determined primarily by C/Pen patterns and tolerated to sequence manipulations. The applicability of the designed C/Pen-DRPs was demonstrated by designing protein binders using an epitope grafting strategy. This study thus demonstrates the potential of using orthogonal disulfide pairing to design DRP scaffolds with new structures and functions, which would greatly benefit the development of multicyclic peptide ligands and therapeutics.

19.
Bioconjug Chem ; 31(9): 2085-2091, 2020 09 16.
Article in English | MEDLINE | ID: mdl-32794769

ABSTRACT

We report a biocompatible and rapid reaction between cysteine thiols and 2,4-difluoro-6-hydroxy-1,3,5-benzenetricarbonitrile (DFB), which enables the efficient cyclization of peptides in neutral aqueous solutions. The reaction was further applied to cyclize peptides displayed on the phage surface without reducing phage infectivity, thus affording high-quality cyclic peptide libraries useful for screening of cyclic peptide ligands. Using the DFB-cyclic peptide library, we identified ligands that can distinguish the pro-survival protein Bcl-xl from its close relative Bcl-2. Therefore, this study on one hand reports a useful reaction for the construction of cyclic peptide libraries, and on the other hand presents valuable hits for further design of selective Bcl-xl ligands.


Subject(s)
Benzene Derivatives/chemistry , Cycloaddition Reaction , Nitriles/chemistry , Peptides, Cyclic/chemistry , Benzene Derivatives/chemical synthesis , Cycloaddition Reaction/economics , Cycloaddition Reaction/methods , Halogenation , Ligands , Models, Molecular , Nitriles/chemical synthesis , Peptide Library , Peptides, Cyclic/chemical synthesis
20.
J Periodontol ; 91(12): 1584-1594, 2020 12.
Article in English | MEDLINE | ID: mdl-32490546

ABSTRACT

BACKGROUND: It remains unclear whether well-maintained subjects, with periodontitis in the past, effectively treated, and maintained for a long time, have the same subgingival microbiome as healthy subjects. Therefore, the objective of this study was to investigate the characteristics of the subgingival microbiome in well-maintained patients with a history of periodontitis compared with healthy subjects. METHODS: We recruited in 17 well-maintained individuals (no evidence of clinical inflammation and progress of periodontitis) and 21 healthy individuals. Periodontal clinical parameters, consisting of missing teeth, plaque index (PLI), periodontal depth (PD), and bleeding index (BI), were recorded and analyzed. The pooled subgingival samples from mesiobuccal sites of two maxillary first molars were collected. The V3-V4 region of 16S rRNA gene from 38 subgingival samples was sequenced and analyzed. Alpha diversity, microbial composition, types of bacteria, functional pathways between well-maintained group and health group were compared using Mann-Whitney U test. Spearman correlation was used in analyzing the symbiotic relationship among taxa. A classification model was constructed to distinguish two ecological types. RESULTS: The maintained individuals demonstrated a different microbiome from healthy subjects, with higher diversity, more disordered structure, more pathogenic microbiota, and more host-destructive metabolism pathways. The genera Actinomyces, Streptococcus, Leptotrichia, Capnocytophaga, Lautropia, and Fusobacterium were predominant components with relative abundance >5% in the subgingival microbiome of well-maintained patients. The classification model by microbiota got a remarkable accuracy of 83.33%. CONCLUSIONS: Individuals with well-maintained periodontitis showed a more dysbiotic microbial community than healthy individuals. Therefore, close monitoring and scheduled maintenance treatment are necessary for them to maintain a healthy periodontal condition.


Subject(s)
Microbiota , Periodontitis , Bacteria , Humans , Inflammation , RNA, Ribosomal, 16S/genetics
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