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Bian T, Pei Y, Gao S, Zhou S, Sun X, Dong M, Song J. Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application. Adv Healthc Mater 2024:e2401207. [PMID: 39036821 DOI: 10.1002/adhm.202401207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/14/2024] [Indexed: 07/23/2024]
Abstract
Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.
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Affiliation(s)
- Tianyuan Bian
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin, 300072, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yufeng Pei
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Shitao Gao
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- College of Materials Science and Engineering, Zhejiang University of Technology, ChaoWang Road 18, HangZhou, 310014, China
| | - Songtao Zhou
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinyu Sun
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Aarhus, DK-8000, Denmark
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310022, China
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Rihon J, Mattelaer CA, Montalvão RW, Froeyen M, Pinheiro VB, Lescrinier E. Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline. Nucleic Acids Res 2024; 52:2836-2847. [PMID: 38412249 PMCID: PMC11014352 DOI: 10.1093/nar/gkae135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
The field of synthetic nucleic acids with novel backbone structures [xenobiotic nucleic acids (XNAs)] has flourished due to the increased importance of XNA antisense oligonucleotides and aptamers in medicine, as well as the development of XNA processing enzymes and new XNA genetic materials. Molecular modeling on XNA structures can accelerate rational design in the field of XNAs as it contributes in understanding and predicting how changes in the sugar-phosphate backbone impact on the complementation properties of the nucleic acids. To support the development of novel XNA polymers, we present a first-in-class open-source program (Ducque) to build duplexes of nucleic acid analogs with customizable chemistry. A detailed procedure is described to extend the Ducque library with new user-defined XNA fragments using quantum mechanics (QM) and to generate QM-based force field parameters for molecular dynamics simulations within standard packages such as AMBER. The tool was used within a molecular modeling workflow to accurately reproduce a selection of experimental structures for nucleic acid duplexes with ribose-based as well as non-ribose-based nucleosides. Additionally, it was challenged to build duplexes of morpholino nucleic acids bound to complementary RNA sequences.
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Affiliation(s)
- Jérôme Rihon
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
| | - Charles-Alexandre Mattelaer
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
- Quantum Chemistry and Physical Chemistry, Celestijnenlaan 200f, Box 2404, B-3001, Leuven, Belgium
| | - Rinaldo Wander Montalvão
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
- Gain Therapeutics sucursal en España, Barcelona Science Park, Baldiri Reixac 4-10, 08028 Barcelona, Spain
| | - Mathy Froeyen
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
| | - Vitor Bernardes Pinheiro
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
| | - Eveline Lescrinier
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, Box 1030, B-3000 Leuven, Belgium
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Chandy SK, Raghavachari K. MIM-ML: A Novel Quantum Chemical Fragment-Based Random Forest Model for Accurate Prediction of NMR Chemical Shifts of Nucleic Acids. J Chem Theory Comput 2023; 19:6632-6642. [PMID: 37703522 DOI: 10.1021/acs.jctc.3c00563] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
We developed a random forest machine learning (ML) model for the prediction of 1H and 13C NMR chemical shifts of nucleic acids. Our ML model is trained entirely on reproducing computed chemical shifts obtained previously on 10 nucleic acids using a Molecules-in-Molecules (MIM) fragment-based density functional theory (DFT) protocol including microsolvation effects. Our ML model includes structural descriptors as well as electronic descriptors from an inexpensive low-level semiempirical calculation (GFN2-xTB) and trained on a relatively small number of DFT chemical shifts (2080 1H chemical shifts and 1780 13C chemical shifts on the 10 nucleic acids). The ML model is then used to make chemical shift predictions on 8 new nucleic acids ranging in size from 600 to 900 atoms and compared directly to experimental data. Though no experimental data was used in the training, the performance of our model is excellent (mean absolute deviation of 0.34 ppm for 1H chemical shifts and 2.52 ppm for 13C chemical shifts for the test set), despite having some nonstandard structures. A simple analysis suggests that both structural and electronic descriptors are critical for achieving reliable predictions. This is the first attempt to combine ML from fragment-based DFT calculations to predict experimental chemical shifts accurately, making the MIM-ML model a valuable tool for NMR predictions of nucleic acids.
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Affiliation(s)
- Sruthy K Chandy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [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: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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Mattelaer CA, Mattelaer HP, Rihon J, Froeyen M, Lescrinier E. Efficient and Accurate Potential Energy Surfaces of Puckering in Sugar-Modified Nucleosides. J Chem Theory Comput 2021; 17:3814-3823. [PMID: 34000809 DOI: 10.1021/acs.jctc.1c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Puckering of the sugar unit in nucleosides and nucleotides is an important structural aspect that directly influences the helical structure of nucleic acids. The preference for specific puckering modes in nucleic acids can be analyzed via in silico conformational analysis, but the large amount of conformations and the accuracy of the analysis leads to an extensive amount of computational time. In this paper, we show that the combination of geometry optimizations with the HF-3c method with single point energies at the RI-MP2 level results in accurate results for the puckering potential energy surface (PES) of DNA and RNA nucleosides while significantly reducing the necessary computational time. Applying this method to a series of known xeno nucleic acids (XNAs) allowed us to rapidly explore the puckering PES of each of the respective nucleosides and to explore the puckering PES of six-membered modified XNA (HNA and β-homo-DNA) for the first time.
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Affiliation(s)
- Charles-Alexandre Mattelaer
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Henri-Philippe Mattelaer
- Campus Drie Eiken, Laboratory of Medicinal Chemistry, UAntwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Jérôme Rihon
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
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