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Duan H, Hu K, Zheng D, Cheng Y, Zhang Z, Wang Y, Liang L, Hu J, Luo T. Recognition and release of uridine and hCNT3: From multivariate interactions to molecular design. Int J Biol Macromol 2022; 223:1562-1577. [PMID: 36402394 DOI: 10.1016/j.ijbiomac.2022.11.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
As a vital target for the development of novel anti-cancer drugs, human concentrative nucleoside transporter 3 (hCNT3) has been widely concerned. Nevertheless, the lack of a comprehensive understanding of molecular interactions and motion mechanism has greatly hindered the development of novel inhibitors against hCNT3. In this paper, molecular recognition of hCNT3 with uridine was investigated with molecular docking, conventional molecular dynamics (CMD) simulations and adaptive steered molecular dynamics (ASMD) simulations; and then, the uridine derivatives with possibly highly inhibitory activity were designed. The result of CMD showed that more water-mediated H-bonds and lower binding free energy both explained higher recognition ability and transported efficiency of hCNT3. While during the ASMD simulation, nucleoside transport process involved the significant side-chain flip of residues F321 and Q142, a typical substrate-induced conformational change. By considering electronegativity, atomic radius, functional group and key H-bonds factors, 25 novel uridine derivatives were constructed. Subsequently, the receptor-ligand binding free energy was predicted by solvated interaction energy (SIE) method to determine the inhibitor c8 with the best potential performance. This work not only revealed molecular recognition and release mechanism of uridine with hCNT3, but also designed a series of uridine derivatives to obtain lead compounds with potential high activity.
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Affiliation(s)
- Huaichuan Duan
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Kaixuan Hu
- School of Pharmaceutical Sciences, Jishou University, Jishou, China
| | - Dan Zheng
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Cheng
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Zelan Zhang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Yueteng Wang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Ting Luo
- Department of Head, Neck and Mammary Gland Oncology, Cancer Center, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China.
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Martín-Nieves V, Fàbrega C, Guasch M, Fernández S, Sanghvi YS, Ferrero M, Eritja R. Oligonucleotides Containing 1-Aminomethyl or 1-Mercaptomethyl-2-deoxy-d-ribofuranoses: Synthesis, Purification, Characterization, and Conjugation with Fluorophores and Lipids. Bioconjug Chem 2021; 32:350-366. [PMID: 33543930 PMCID: PMC9122261 DOI: 10.1021/acs.bioconjchem.0c00717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Oligonucleotide conjugates are widely used as therapeutic drugs, gene analysis, and diagnostic tools. A critical step in the biologically relevant oligonucleotide conjugates is the design and synthesis of functional molecules that connect oligonucleotide with ligands. Here, we report the synthesis and application for oligonucleotide functionalization of novel tethers based on aminomethyl and mercaptomethyl sugar derivatives. Starting from a common cyano sugar precursor, three novel phosphoramidites have been prepared in the two α- and β-anomeric forms. The mercaptomethyl sugar was protected with the S-acetyl group, while two different protecting groups have been developed for the aminomethyl sugar. These two protecting groups are orthogonal, as they can be removed independently using photolysis or ammonolysis. This combination allowed the introduction of two different ligands in a single oligonucleotide.
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Affiliation(s)
- Virginia Martín-Nieves
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
| | - Carme Fàbrega
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), 08034-Barcelona, Spain.,CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08034-Barcelona, Spain
| | - Marc Guasch
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), 08034-Barcelona, Spain.,CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08034-Barcelona, Spain
| | - Susana Fernández
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, California 92024-6615, United States
| | - Miguel Ferrero
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
| | - Ramon Eritja
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), 08034-Barcelona, Spain.,CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08034-Barcelona, Spain
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Salunke RV, Mishra PK, Sanghvi YS, Ramesh NG. Synthesis of novel homoazanucleosides and their peptidyl analogs. Org Biomol Chem 2020; 18:5639-5651. [PMID: 32724966 DOI: 10.1039/d0ob01046d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthesis of novel homoazanucleosides and their peptidyl analogs as hybrid molecules comprised of amino acids, an iminosugar and natural nucleobases is reported for the first time. A pluripotent amino-substituted chiral polyhydroxypyrrolidine, possessing orthogonally different functional groups on either arm of the pyrrolidine ring, served as an ideal substrate for the synthesis of the proposed peptidyl homoazanucleosides. The acid sensitive primary benzyloxy group, on one arm of the pyrrolidine ring, after selective deprotection, was utilized for the introduction of nucleobases to obtain the homoazanucleosides. The amino group on the other side offered the opportunity to be coupled with amino acids to deliver the desired peptidyl homoazanucleosides. Glycosidase inhibition studies revealed that the acetamido derivatives of homoazanucleosides were found to be sub-millimolar inhibitors of β-N-acetyl-glucosaminidase.
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Affiliation(s)
- Rahul Vilas Salunke
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi - 110016, India.
| | - Pawan Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi - 110016, India.
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, CA 92024-6615, USA
| | - Namakkal G Ramesh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi - 110016, India.
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