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Tao L, Byrnes J, Varshney V, Li Y. Machine learning strategies for the structure-property relationship of copolymers. iScience 2022; 25:104585. [PMID: 35789847 PMCID: PMC9249671 DOI: 10.1016/j.isci.2022.104585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 11/15/2022] Open
Abstract
Establishing the structure-property relationship is extremely valuable for the molecular design of copolymers. However, machine learning (ML) models can incorporate both chemical composition and sequence distribution of monomers, and have the generalization ability to process various copolymer types (e.g., alternating, random, block, and gradient copolymers) with a unified approach are missing. To address this challenge, we formulate four different ML models for investigation, including a feedforward neural network (FFNN) model, a convolutional neural network (CNN) model, a recurrent neural network (RNN) model, and a combined FFNN/RNN (Fusion) model. We use various copolymer types to systematically validate the performance and generalizability of different models. We find that the RNN architecture that processes the monomer sequence information both forward and backward is a more suitable ML model for copolymers with better generalizability. As a supplement to polymer informatics, our proposed approach provides an efficient way for the evaluation of copolymers.
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Affiliation(s)
- Lei Tao
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | | | - Vikas Varshney
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Ying Li
- Department of Mechanical Engineering, University of Connecticut, Storrs, CT 06269, USA
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT 06269, USA
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2
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Patil NA. Conjugation Approaches for Peptide-Mediated Delivery of Oligonucleotides Therapeutics. Aust J Chem 2021. [DOI: 10.1071/ch21131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Jose A, Nanjan P, Porel M. Sequence-defined oligomer as a modular platform for selective sub-picomolar detection and removal of Hg 2+. Polym Chem 2021. [DOI: 10.1039/d1py00642h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A modular synthetic platform for selective sensing and removal of Hg2+ was developed.
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Affiliation(s)
- Anna Jose
- Discipline of Chemistry, Indian Institute of Technology Palakkad, Kerala-678577, India
| | - Pandurangan Nanjan
- Discipline of Chemistry, Indian Institute of Technology Palakkad, Kerala-678577, India
| | - Mintu Porel
- Discipline of Chemistry, Indian Institute of Technology Palakkad, Kerala-678577, India
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4
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Abstract
Sequence-defined polymer: A promising gateway for the next generation polymeric materials and vast opportunities for new synthetic strategies, functional diversity and its material and biomedical applications.
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Affiliation(s)
| | - Mintu Porel
- Discipline of Chemistry
- Indian Institute of Technology Palakkad
- India
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5
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Nanomaterial-Enabled Cancer Therapy. Mol Ther 2017; 25:1501-1513. [PMID: 28532763 DOI: 10.1016/j.ymthe.2017.04.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/19/2017] [Accepted: 04/27/2017] [Indexed: 01/02/2023] Open
Abstract
While cancer remains the major cause of death worldwide, nanomaterial (NM)-based diagnosis and treatment modalities are showing remarkable potential to better tackle clinical oncology by effectively targeting therapeutic agents to tumors. NMs can selectively accumulate in solid tumors, and they can improve the bioavailability and reduce the toxicity of encapsulated cytotoxic agents. Additional noteworthy functions of NMs in cancer treatment include the delivery of contrast agents to image tumor sites, delivery of genetic materials for gene therapy, and co-delivery of multiple agents to achieve combination therapy or simultaneous diagnostic and therapeutic outcomes. Although several NM therapeutics have been successfully translated to clinical applications, the gap between the bench and the bedside remains ominously wide. Tumor heterogeneity and the disparity between pre-clinical and clinical studies have been identified as two of the major translational challenges of NM-based cancer therapies. Herein, we review a handful of recent research studies on the use of NMs in cancer therapy and imaging, with a limited discussion on the consequences of tumor heterogeneity and pre-clinical studies on translational research of NM-based delivery systems and propositions in the literature to overcome these challenges.
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Lee DJ, He D, Kessel E, Padari K, Kempter S, Lächelt U, Rädler JO, Pooga M, Wagner E. Tumoral gene silencing by receptor-targeted combinatorial siRNA polyplexes. J Control Release 2016; 244:280-291. [DOI: 10.1016/j.jconrel.2016.06.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 02/06/2023]
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7
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Lehto T, Ezzat K, Wood MJA, El Andaloussi S. Peptides for nucleic acid delivery. Adv Drug Deliv Rev 2016; 106:172-182. [PMID: 27349594 DOI: 10.1016/j.addr.2016.06.008] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/08/2016] [Accepted: 06/15/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acids and their synthetic oligonucleotide (ON) analogs are a group of gene therapeutic compounds which hold enormous clinical potential. Despite their undoubted potential, clinical translation of these molecules, however, has been largely held back by their limited bioavailability in the target tissues/cells. To overcome this, many different drug delivery systems have been devised. Among others, short delivery peptides, called cell-penetrating peptides (CPPs), have been demonstrated to allow for efficient delivery of nucleic acids and their ON analogs, in both cell culture and animal models. In this review, we provide brief overview of the latest advances in nucleic acid delivery with CPPs, covering the two main vectorization strategies, covalent conjugation and nanoparticle formation-based approach. In conclusion, CPP-based drug delivery systems have the capacity to overcome the hurdle of delivery and thus have the potential to facilitate the clinical translation of nucleic acid-based therapeutics.
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Affiliation(s)
- Taavi Lehto
- Department of Laboratory Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden; Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia.
| | - Kariem Ezzat
- Department of Laboratory Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden
| | - Matthew J A Wood
- Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX Oxford, United Kingdom
| | - Samir El Andaloussi
- Department of Laboratory Medicine, Karolinska Institute, Stockholm SE-171 77, Sweden; Department of Physiology, Anatomy, and Genetics, University of Oxford, OX13QX Oxford, United Kingdom
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8
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Krivitsky A, Polyak D, Scomparin A, Eliyahu S, Ori A, Avkin-Nachum S, Krivitsky V, Satchi-Fainaro R. Structure–Function Correlation of Aminated Poly(α)glutamate as siRNA Nanocarriers. Biomacromolecules 2016; 17:2787-800. [DOI: 10.1021/acs.biomac.6b00555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Adva Krivitsky
- Department
of Physiology and Pharmacology, Sackler Faculty of Medicine, Room 607, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dina Polyak
- Department
of Physiology and Pharmacology, Sackler Faculty of Medicine, Room 607, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anna Scomparin
- Department
of Physiology and Pharmacology, Sackler Faculty of Medicine, Room 607, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shay Eliyahu
- Department
of Physiology and Pharmacology, Sackler Faculty of Medicine, Room 607, Tel Aviv University, Tel Aviv 69978, Israel
| | - Asaf Ori
- QBI Enterprise, Ltd., Ness-Ziona 70400, Israel
| | | | - Vadim Krivitsky
- School of Chemistry, the Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ronit Satchi-Fainaro
- Department
of Physiology and Pharmacology, Sackler Faculty of Medicine, Room 607, Tel Aviv University, Tel Aviv 69978, Israel
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Dual antitumoral potency of EG5 siRNA nanoplexes armed with cytotoxic bifunctional glutamyl-methotrexate targeting ligand. Biomaterials 2016; 77:98-110. [DOI: 10.1016/j.biomaterials.2015.11.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 10/29/2015] [Accepted: 11/03/2015] [Indexed: 12/19/2022]
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10
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Wagner E. Tumorspezifischer Transfer von Anti-microRNA zur Krebstherapie - pHLIP ist der Schlüssel. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Wagner E. Tumor-targeted Delivery of Anti-microRNA for Cancer Therapy: pHLIP is Key. Angew Chem Int Ed Engl 2015; 54:5824-6. [PMID: 25892205 DOI: 10.1002/anie.201502146] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Indexed: 01/22/2023]
Abstract
pHLIP opens the door to the cell: An improved cytosolic transfer of anti-microRNAs (anti-miRs) against onco-miRs paves the way for future cancer therapies. The employed anti-miR-peptide conjugates are based on peptide nucleic acids (PNAs), which are connected with the membrane translocation peptide pHLIP through a disulfide bond. The PNAs are thus transferred into the cell and released by the cleavage of the S-S bond.
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Affiliation(s)
- Ernst Wagner
- Department for Pharmacy and Center for NanoScience (CeNS), University of Munich (LMU), Butenandtstrasse 5-13, 81377 Munich (Germany); Nanosystems Initiative Munich (NIM), Schellingstrasse 4, 80799 Munich (Germany).
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