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Chahkandi B, Chahkandi M. An accurate DFT study within conformational survey of the D-form serine-alanine protected dipeptide. BMC Chem 2023; 17:138. [PMID: 37828563 PMCID: PMC10571400 DOI: 10.1186/s13065-023-01051-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
The conformational analysis of N-formyl-D-serine-D-alanine-NH2 dipeptide was studied using density functional theory methods at B3LYP, B3LYP‒D3, and M06‒2X levels using 6‒311 + G (d,p) basis set in the gas and water phases. 87 conformers of 243 stable ones were located and the rest of them were migrated to the more stable geometries. Migration pattern suggests the more stable dipeptide model bears serine in βL, γD, γL and the alanine in γL and γD configurations. The investigation of side‒chain‒backbone interactions revealed that the most stable conformer, γD-γL, is in the β‒turn region of Ramachandran map; therefore, serine-alanine dipeptide model should be adopted with a β‒turn conformation. Intramolecular hydrogen bonding in β‒turns consideration by QTAIM disclosed γD-γL includes three hydrogen bonds. The computed UV‒Vis spectrum alongside of NBO calculation showed the five main electronic transition bands derived of n → n* of intra‒ligand alanine moiety of dipeptide structure.
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Affiliation(s)
- Behzad Chahkandi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
| | - Mohammad Chahkandi
- Department of Chemistry, Hakim Sabzevari University, Sabzevar, 96179-76487, Iran
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Zheng S, Ye Z, Ji Y, Li N, Zhang L. Development of the Antithrombotic Peptide LEKNSTY Targeting the Collagen Surface: II. Improvement of Plasma Stability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7114-7120. [PMID: 35623058 DOI: 10.1021/acs.langmuir.2c00587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of antithrombotic peptides targeting collagen was proven effective, and an effective antithrombotic peptide LEKNSTY was obtained in part I. However, the plasma stability of LEKNSTY was found to be not good enough. In this part, the LEKNSTY was further optimized for improvement in plasma stability by substitution using d-amino acid residues. Two novel antithrombotic peptides LekNStY and lEKnsTy were designed, where lowercase letters represent d-amino acid residues. Improvements in plasma stability of both LekNStY and lEKnsTy were experimentally confirmed. Moreover, good binding of these antithrombotic peptides on the collagen surface was confirmed by molecular dynamics simulation and experimental validation. For example, a Kd of only 0.75 ± 0.10 μM was observed for lEKnsTy. Moreover, LekNStY and lEKnsTy were found to inhibit platelet adhesion on the collagen surface more effectively than LEKNSTY, and the IC50 of lEKnsTy was only 2/5 of that of LEKNSTY. These results confirmed the successful design of LekNStY and lEKnsTy that had good plasma stability and could effectively inhibit arterial thrombosis, which would be helpful for the research into interfaces involved in thrombus formation and the development of antithrombotic nanomedicine.
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Affiliation(s)
- Si Zheng
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Zhao Ye
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Yufan Ji
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Nanxing Li
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Lin Zhang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
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Watanabe T, Terada K, Takemura S, Masunaga H, Tsuchiya K, Lamprou A, Numata K. Chemoenzymatic Polymerization of l-Serine Ethyl Ester in Aqueous Media without Side-Group Protection. ACS POLYMERS AU 2022; 2:147-156. [PMID: 36855524 PMCID: PMC9954318 DOI: 10.1021/acspolymersau.1c00052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Poly(l-serine) (polySer) has tremendous potential as a polypeptide-based functional material due to the utility of the hydroxyl group on its side chain; however, tedious protection/deprotection of the hydroxyl groups is required for its synthesis. In this study, polySer was synthesized by the chemoenzymatic polymerization (CEP) of l-serine ethyl ester (Ser-OEt) or l-serine methyl ester (Ser-OMe) using papain as a catalyst in an aqueous medium. The CEP of Ser-OEt proceeded at basic pH ranging from 7.5 to 9.5 and resulted in the maximum precipitate yield of polySer at an optimized pH of 8.5. A series of peaks detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry revealed that the formed precipitate consisted of polySer with a degree of polymerization ranging from 5 to 22. Moreover, infrared spectroscopy, circular dichroism spectroscopy, and synchrotron wide-angle X-ray diffraction measurements indicated that the obtained polySer formed a β-sheet/strand structure. This is the first time the synthesis of polySer was realized by CEP in aqueous solution without protecting the hydroxyl group of the Ser monomer.
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Affiliation(s)
- Takumi Watanabe
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kayo Terada
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shogo Takemura
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hiroyasu Masunaga
- Japan
Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kousuke Tsuchiya
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan,Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan,
| | - Alexandros Lamprou
- Innovation
Campus Asia Pacific (Shanghai), BASF Advanced
Chemicals Co., Ltd., No 300, Jiangxinsha Road, Pudong, Shanghai 200137, P.R. China
| | - Keiji Numata
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan,Biomacromolecules
Research Team, RIKEN Center for Sustainable
Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan,
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