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Yang Q, Ji H, Xu Z, Li Y, Wang P, Sun J, Fan X, Zhang H, Lu H, Zhang Z. Ultra-fast and accurate electron ionization mass spectrum matching for compound identification with million-scale in-silico library. Nat Commun 2023; 14:3722. [PMID: 37349295 DOI: 10.1038/s41467-023-39279-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
Spectrum matching is the most common method for compound identification in mass spectrometry (MS). However, some challenges limit its efficiency, including the coverage of spectral libraries, the accuracy, and the speed of matching. In this study, a million-scale in-silico EI-MS library is established. Furthermore, an ultra-fast and accurate spectrum matching (FastEI) method is proposed to substantially improve accuracy using Word2vec spectral embedding and boost the speed using the hierarchical navigable small-world graph (HNSW). It achieves 80.4% recall@10 accuracy (88.3% with 5 Da mass filter) with a speedup of two orders of magnitude compared with the weighted cosine similarity method (WCS). When FastEI is applied to identify the molecules beyond NIST 2017 library, it achieves 50% recall@1 accuracy. FastEI is packaged as a standalone and user-friendly software for common users with limited computational backgrounds. Overall, FastEI combined with a million-scale in-silico library facilitates compound identification as an accurate and ultra-fast tool.
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Affiliation(s)
- Qiong Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR, China
| | - Hongchao Ji
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, PR, China
| | - Zhenbo Xu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR, China
| | - Yiming Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR, China
| | - Pingshan Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR, China
| | - Jinyu Sun
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR, China
| | - Xiaqiong Fan
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR, China
| | - Hailiang Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR, China
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR, China.
| | - Zhimin Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR, China.
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Kurtzhals P, Østergaard S, Nishimura E, Kjeldsen T. Derivatization with fatty acids in peptide and protein drug discovery. Nat Rev Drug Discov 2023; 22:59-80. [PMID: 36002588 DOI: 10.1038/s41573-022-00529-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2022] [Indexed: 01/28/2023]
Abstract
Peptides and proteins are widely used to treat a range of medical conditions; however, they often have to be injected and their effects are short-lived. These shortcomings of the native structure can be addressed by molecular engineering, but this is a complex undertaking. A molecular engineering technology initially applied to insulin - and which has now been successfully applied to several biopharmaceuticals - entails the derivatization of peptides and proteins with fatty acids. Various protraction mechanisms are enabled by the specific characteristics and positions of the attached fatty acid. Furthermore, the technology can ensure a long half-life following oral administration of peptide drugs, can alter the distribution of peptides and may hold potential for tissue targeting. Due to the inherent safety and well-defined chemical nature of the fatty acids, this technology provides a versatile approach to peptide and protein drug discovery.
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Zhang X, Gao S, Liu M, Wei N, Zhang Q, Li X, Niu X. Novel XTENylated AWRK6 analog with hypoglycemic activity, and anti-HSV-2 potential in combination with double shRNA. Life Sci 2021; 274:119313. [PMID: 33667511 DOI: 10.1016/j.lfs.2021.119313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 12/17/2022]
Abstract
AIMS To design and evaluate a novel AWRK6 peptide-based long-acting GLP-1 receptor agonist (GLP-1RA) conjugated a recombinant polyethylene glycol mimetic (XTEN protein) with significant therapeutic potential on type 2 diabetes mellitus (T2DM) alone as well as Herpes simplex virus type 2 (HSV-2) infection in combination with double shRNA. MAIN METHODS First, four AWRK6 analogs (termed XA-1 to XA-4) were designed and produced by solid phase synthesis strategy. Further surface plasmon resonance (SPR) measurement and in vitro cAMP accumulation assay were performed to detect the GLP-1R binding affinities and GLP-1R activation, respectively. The in vivo efficacy evaluation including pharmacokinetic test, oral glucose tolerance test (OGTT), hypoglycemic duration test and chronic pharmacodynamics study in rodent animals were all carefully performed. KEY FINDINGS Four XA peptides were synthesized with purity >99%. High binding affinity as well as activation potency of XA-4 for GLP-1R were demonstrated by SPR and cell-based luciferase reporter assay, respectively. Additionally, XA-4 exhibited the long-lasting antidiabetic effects in the multiple OGTTs, hypoglycemic duration test and chronic study in mice. Furthermore, combined treatment of XA-4 and double shRNA (D-shRNA) achieved potent antiviral effects in HSV-2 infected HEK293 cells. SIGNIFICANCE XA-4 exhibited promising pharmaceutical potential to be a therapeutic drug for treating T2D, and also held potential to against the HSV-2 infection, which is really an accidental discovery. The strategy of recombinant XTENylation can also be applied to other peptides or small molecules for the development of long-acting therapeutic drugs.
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Affiliation(s)
- Xiaomin Zhang
- Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai 519100, Guangdong, PR China
| | - Shuying Gao
- Department of Biochemistry and Molecular Biology, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, Guangdong, PR China
| | - Maosheng Liu
- Department of Biochemistry and Molecular Biology, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, Guangdong, PR China
| | - Nina Wei
- Department of Biochemistry and Molecular Biology, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, Guangdong, PR China
| | - Qingfeng Zhang
- Department of Biochemistry and Molecular Biology, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, Guangdong, PR China
| | - Xiangyang Li
- Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai 519100, Guangdong, PR China
| | - Xianli Niu
- Department of Biochemistry and Molecular Biology, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, Guangdong, PR China.
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Wei XQ, Ba K. Construction a Long-Circulating Delivery System of Liposomal Curcumin by Coating Albumin. ACS OMEGA 2020; 5:16502-16509. [PMID: 32685814 PMCID: PMC7364587 DOI: 10.1021/acsomega.0c00930] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/02/2020] [Indexed: 05/11/2023]
Abstract
Although the bioavailability and stability of curcumin can be greatly improved by liposomes encapsulation, its application is still limited due to the short circulating time. In this present work, we aim to construct a long-circulating delivery system of liposomal curcumin (Cur-Lips) by coating bovine serum albumin (BSA), namely, BSA-coated liposomal curcumin (BSA-Cur-Lips). The effects of coating albumin on the physicochemical properties of Cur-Lips were investigated. It was found that BSA-Cur-Lips was more spherical, more homogeneous in size, and significantly larger than Cur-Lips. Combining sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), Coomassie bright blue staining, and X-ray photoelectron spectroscopy analysis (XPS), we confirmed that albumin molecules were stably located on the surface of BSA-Cur-Lips. In addition, the impacts of the coating albumin on the Cur-Lips release and phagocytosis by mouse macrophages Raw264.7 in vitro were investigated. We found that no significant initial burst drug release effect was observed for both Cur-Lips and BSA-Cur-Lips and the presence of albumin can enhance the liposome structure stability and slow down the release of Cur. More importantly, the macrophage phagocytosis of Cur-Lips was significantly reduced after coating albumin. In conclusion, coating albumin is a promising approach for developing a long-circulating delivery system of liposomal curcumin, and its properties including low phagocytosis, slow drug release, enhanced stability, and nontoxicity give this system great prospects for practical use.
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Niu X, Nong S, Zhang X, Li X, Wang C, Li W, Zhou T. Design and evaluation of novel thrombin-based GLP-1 analogs with peptidic albumin binding domain for the controlled release of GLP-1. RSC Adv 2020; 10:4725-4732. [PMID: 35495226 PMCID: PMC9049141 DOI: 10.1039/d0ra00104j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 01/22/2020] [Indexed: 11/21/2022] Open
Abstract
Currently, the curative effects of polypeptide drugs are often restricted due to the short in vivo duration of action.
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Affiliation(s)
- Xianli Niu
- Key Laboratory of Genetic Engineering and Medicine
- Key Laboratory of Viral Biology
- Jinan University
- Guangzhou
- P. R. China
| | - Shirong Nong
- Key Laboratory of Genetic Engineering and Medicine
- Key Laboratory of Viral Biology
- Jinan University
- Guangzhou
- P. R. China
| | - Xiaomin Zhang
- Department of Biochemistry and Molecular Biology
- Zunyi Medical University
- Zhuhai
- P. R. China
- Fifth Affiliated Hospital of Zunyi Medical University
| | - Xiangyang Li
- Department of Biochemistry and Molecular Biology
- Zunyi Medical University
- Zhuhai
- P. R. China
- Fifth Affiliated Hospital of Zunyi Medical University
| | - Cheng Wang
- Department of Biochemistry and Molecular Biology
- Zunyi Medical University
- Zhuhai
- P. R. China
- Fifth Affiliated Hospital of Zunyi Medical University
| | - Wei Li
- Key Laboratory of Genetic Engineering and Medicine
- Key Laboratory of Viral Biology
- Jinan University
- Guangzhou
- P. R. China
| | - Tianhong Zhou
- Key Laboratory of Genetic Engineering and Medicine
- Key Laboratory of Viral Biology
- Jinan University
- Guangzhou
- P. R. China
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Li SW, Kang Q. Catalytic asymmetric synthesis of diphenylbutazone analogues. Chem Commun (Camb) 2018; 54:10479-10482. [DOI: 10.1039/c8cc06426a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The asymmetric Michael addition of diphenylbutazone and its analogues to α,β-unsaturated 2-acyl imidazoles has been developed with a chiral-at-metal Rh(iii) complex as a catalyst.
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Affiliation(s)
- Shi-Wu Li
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou
- P. R. China
| | - Qiang Kang
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences
- Fuzhou
- P. R. China
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Synthesis and biological evaluation of novel aliphatic acid-conjugated antimicrobial peptides as potential agents with anti-tumor, multidrug resistance-reversing activity and enhanced stability. Amino Acids 2017; 49:1831-1841. [PMID: 28831625 DOI: 10.1007/s00726-017-2482-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/16/2017] [Indexed: 02/02/2023]
Abstract
Compared with traditional anti-tumor drugs, antimicrobial peptides as novel anti-tumor agents have prominent advantages of higher specificity and circumvention of multi-drug resistance. BP100 is a multifunctional membrane-active peptide with high antimicrobial activity. Taking BP100 as a lead peptide, we designed and synthesized a series of aliphatic chain-conjugated peptides through solid-phase synthesis. Biological evaluation revealed that these peptides exhibited better anti-cancer activity than BP100. Further investigations revealed that these peptides could disrupt the cell membrane and trigger the cytochrome C release into cytoplasm, which ultimately resulted in apoptosis. Meanwhile, these peptides also exhibited effective anti-tumor activity against multidrug resistant cells and had multidrug resistance-reversing effect. Additionally, conjugation of aliphatic acid to those peptides could enhance their stability in plasma. In conclusion, aliphatic acid-modified peptides might be promising anti-tumor agents for cancer therapy.
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