bims-drudre 2022-08-07 papers

bims-drudre

Biomed News

on Targeted drug delivery and programmed release mechanisms

Issue of 2022–08–07
fiveteen papers selected by
Ceren Kimna, Technical University of Munich

Artificial primary-miRNAs as a platform for simultaneous delivery of siRNA and antisense oligonucleotide for multimodal gene regulation.
Manipulating Offense and Defense Signaling to Fight Cold Tumors with Carrier-Free Nanoassembly of Fluorinated Prodrug and siRNA.
Ultrasound-Activated, Tumor-Specific In Situ Synthesis of a Chemotherapeutic Agent Using ZIF-8 Nanoreactors for Precision Cancer Therapy.
Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs.
Macrophage-Encapsulated Bioorthogonal Nanozymes for Targeting Cancer Cells.
Antibacterial Theranostic Agents with Negligible Living Cell Invasiveness: AIE-Active Cationic Amphiphiles Regulated by Alkyl Chain Engineering.
Cellulose-Based Cryogel Microspheres with Nanoporous and Controllable Wrinkled Morphologies for Rapid Hemostasis.
Multifunctional synthetic nano-chaperone for peptide folding and intracellular delivery.
Intrinsically fluorescent polyureas toward conformation-assisted metamorphosis, discoloration and intracellular drug delivery.
Bacterial Growth-Induced Tobramycin Smart Release Self-Healing Hydrogel for Pseudomonas aeruginosa-Infected Burn Wound Healing.
Spatiotemporal control of engineered bacteria to express interferon-γ by focused ultrasound for tumor immunotherapy.
Dynamic actuation enhances transport and extends therapeutic lifespan in an implantable drug delivery platform.
Programmable Bispecific Nano-immunoengager That Captures T Cells and Reprograms Tumor Microenvironment.
Protein Cages Engineered for Interaction-Driven Selective Encapsulation of Biomolecules.
Generating experimentally unrelated target molecule-binding highly functionalized nucleic-acid polymers using machine learning.

J Control Release. 2022 Aug 02. pii: S0168-3659(22)00479-5. [Epub ahead of print]

Artificial primary-miRNAs as a platform for simultaneous delivery of siRNA and antisense oligonucleotide for multimodal gene regulation.

Hyunsook Kim, Bora Jang, Dayoung Lee, S Chul Kwon, Hyukjin Lee.

  Self-assembled nucleic acid nanostructures have been widely explored for gene therapy applications due to their unique advantages. Their roles are not limited to offer intracellular delivery platforms but additionally provide a biological function to induce targeted gene regulation. Here, we report a self-assembled artificial primary-miRNA (pri-miRNA) for achieving simultaneous multimodal gene regulation. Artificial pri-miRNAs are designed to play a role as substrate RNAs to recruit and interact with Drosha/DGCR8 (Microprocessor). Incorporation of functional RNA motifs and site-specific chemical modification of the primary miRNA are utilized for the biogenesis of two individual gene-regulating oligonucleotides. Once they are cleaved by the endogenous Drosha/DGCR8 complex, basal strands and pre-miRNA can be generated inside of cells. In this study, we integrated basal strands with either SMN2 ASO or anti-miR21 to induce multimodal gene regulation. Microprocessing and subsequent gene regulation were first evaluated by measuring the activity of reporter pre-miRNA. Chemical modification on the primary miRNA was optimized through a series of in vitro Drosha cleavage tests and targeted gene silencing in cells. Primary miRNA with the basal ASO or anti-miR strands showed a successful in vitro activity and resulted in simultaneous multimodal gene regulation in cells. Artificial primary miRNA may offer synergistic therapeutic effects for treating various diseases, including spinal muscular atrophy and cancer.

Keywords:  Artificial primary miRNA; Multimodal gene regulation; Nucleic acid nanostructures; RNA motif

DOI:  https://doi.org/10.1016/j.jconrel.2022.07.043
Adv Mater. 2022 Aug 02. e2203019

Manipulating Offense and Defense Signaling to Fight Cold Tumors with Carrier-Free Nanoassembly of Fluorinated Prodrug and siRNA.

Pengkai Wu, Haitian Zhang, Meiling Sun, Shuai Mao, Qifeng He, Yuze Shi, Yexuan Deng, Zhongjun Dong, Qingxiang Xu, Chen Zhao, Wenjie Zhang, Beicheng Sun.

  Chemoimmunotherapy has shown great potential to activate immune response, but immunosuppressive microenvironment associated T cell exhaustion remains a challenge in cancer therapy. The proper immune-modulatory strategy to provoke a robust immune response is to simultaneously regulate T-cell exhaustion and infiltration. Here, a new kind of carrier-free nanoparticle (NP) was developed to simultaneously deliver chemotherapeutic drug (doxorubicin, DOX), cytolytic peptide (melittin, MPI), and anti-TOX small interfering RNA (thymocyte selection-associated high mobility group box protein, TOX) using a fluorinated prodrug strategy. In this way, the enhanced immunogenic cell death induced by the combination of DOX and MPI can act as "offense" signaling to increase CD8+ T-cell infiltration, while the decreased TOX expression interfered with siTOX can serve as "defense" signaling to mitigate CD8+ T-cell exhaustion. As a result, the integration of DOX, MPI, and siTOX in such a bifunctional system produced a potent antitumor immune response in liver cancer and metastasis, making it a promising delivery platform and effective strategy for converting "cold" tumors into "hot" ones. This article is protected by copyright. All rights reserved.

Keywords:  T-cell exhaustion; carrier-free; fluorinated prodrug; immunogenic cell death; immunotherapy

DOI:  https://doi.org/10.1002/adma.202203019
ACS Nano. 2022 Aug 03.

Ultrasound-Activated, Tumor-Specific In Situ Synthesis of a Chemotherapeutic Agent Using ZIF-8 Nanoreactors for Precision Cancer Therapy.

Putry Yosefa Siboro, Van Khanh Thi Nguyen, Yang-Bao Miao, Amit Kumar Sharma, Fwu-Long Mi, Hsin-Lung Chen, Kuan-Hung Chen, Yu-Tzu Yu, Yen Chang, Hsing-Wen Sung.

  The in situ transformation of low-toxicity precursors into a chemotherapeutic agent at a tumor site to enhance the efficacy of its treatment has long been an elusive goal. In this work, a zinc-based zeolitic imidazolate framework that incorporates pharmaceutically acceptable precursors is prepared as a nanoreactor (NR) system for the localized synthesis of an antitumor drug. The as-prepared NRs are administered intratumorally in a tumor-bearing mouse model and then irradiated with ultrasound (US) to activate the chemical synthesis. The US promotes the penetration of the administered NRs into the tumor tissue to cover the lesion entirely, although some NRs leak into the surrounding normal tissue. Nevertheless, only the tumor tissue, where the H2O2 concentration is high, is adequately exposed to the as-synthesized antitumor drug, which markedly impedes development of the tumor. No significant chemical synthesis is detected in the surrounding normal tissue, where the local H2O2 concentration is negligible and the US irradiation is not directly applied. The as-proposed tumor-specific in situ synthesis of therapeutic molecules induces hardly any significant in vivo toxicity and, thus, is potentially a potent biocompatible approach to precision chemotherapy.

Keywords:  in situ synthesis; precision chemotherapy; pyrimidine-based derivative; sonotherapy; therapeutic nanoreactor

DOI:  https://doi.org/10.1021/acsnano.2c03587
Nat Nanotechnol. 2022 Aug 04.

Nanozyme-catalysed CRISPR assay for preamplification-free detection of non-coding RNAs.

Marta Broto, Michael M Kaminski, Christopher Adrianus, Nayoung Kim, Robert Greensmith, Schan Dissanayake-Perera, Alexander J Schubert, Xiao Tan, Hyemin Kim, Anand S Dighe, James J Collins, Molly M Stevens.

CRISPR-based diagnostics enable specific sensing of DNA and RNA biomarkers associated with human diseases. This is achieved through the binding of guide RNAs to a complementary sequence that activates Cas enzymes to cleave reporter molecules. Currently, most CRISPR-based diagnostics rely on target preamplification to reach sufficient sensitivity for clinical applications. This limits quantification capability and adds complexity to the reaction chemistry. Here we show the combination of a CRISPR-Cas-based reaction with a nanozyme-linked immunosorbent assay, which allows for the quantitative and colorimetric readout of Cas13-mediated RNA detection through catalytic metallic nanoparticles at room temperature (CrisprZyme). We demonstrate that CrisprZyme is easily adaptable to a lateral-flow-based readout and different Cas enzymes and enables the sensing of non-coding RNAs including microRNAs, long non-coding RNAs and circular RNAs. We utilize this platform to identify patients with acute myocardial infarction and to monitor cellular differentiation in vitro and in tissue biopsies from prostate cancer patients. We anticipate that CrisprZyme will serve as a universally applicable signal catalyst for CRISPR-based diagnostics, which will expand the spectrum of targets for preamplification-free, quantitative detection.

DOI: https://doi.org/10.1038/s41565-022-01179-0
JACS Au. 2022 Jul 25. 2(7): 1679-1685

Macrophage-Encapsulated Bioorthogonal Nanozymes for Targeting Cancer Cells.

Riddha Das, Joseph Hardie, Bishnu P Joshi, Xianzhi Zhang, Aarohi Gupta, David C Luther, Stefano Fedeli, Michelle E Farkas, Vincent M Rotello.

Macrophages migrate to tumor sites by following chemoattractant gradients secreted by tumor cells, providing a truly active targeting strategy for cancer therapy. However, macrophage-based delivery faces challenges of cargo loading, control of release, and effects of the payload on the macrophage vehicle. We present a strategy that employs bioorthogonal "nanozymes" featuring transition metal catalysts (TMCs) to provide intracellular "factories" for the conversion of prodyes and prodrugs into imaging agents and chemotherapeutics. These nanozymes solubilize and stabilize the TMCs by embedding them into self-assembled monolayer coating gold nanoparticles. Nanozymes delivered into macrophages were intracellularly localized and retained activity even after prolonged (72 h) incubation. Significantly, nanozyme-loaded macrophages maintained their inherent migratory ability toward tumor cell chemoattractants, efficiently killing cancer cells in cocultures. This work establishes the potential of nanozyme-loaded macrophages for tumor site activation of prodrugs, providing readily tunable dosages and delivery rates while minimizing off-target toxicity of chemotherapeutics.

DOI: https://doi.org/10.1021/jacsau.2c00247
ACS Nano. 2022 Aug 02.

Antibacterial Theranostic Agents with Negligible Living Cell Invasiveness: AIE-Active Cationic Amphiphiles Regulated by Alkyl Chain Engineering.

Zeyan Zhuang, Zijuan Meng, Jianqing Li, Pingchuan Shen, Jun Dai, Xiaoding Lou, Fan Xia, Ben Zhong Tang, Zujin Zhao.

  To address the threat of bacterial infection in the following post-antibiotic era, developing effective antibacterial approaches is of utmost urgency. Theranostic medicine integrating diagnosis and therapy is a promising protocol to fight against pathogenic bacteria. But numerous reported antibacterial theranostic materials are disclosed to be trapped in the excessive invasiveness to living mammal cells, leading to false positives and possible biosafety risks. Herein, a series of cationic pyridinium-substituted phosphindole oxide derivatives featuring aggregation-induced emission are designed, and alkyl chain engineering is conducted to finely tune their hydrophobicity and investigate their bioaffinity preference for living mammal cells and pathogenic bacteria. Most importantly, an efficient theranostic agent (PyBu-PIO) is acquired that is free from living cell invasiveness with negligible cytotoxicity and yet holds a good affinity for Gram-positive bacteria, including drug-resistant strains, with a superior inactivating effect. Externally applying PyBu-PIO onto Gram-positive bacteria-infected skin wounds can achieve creditable imaging effects and successfully accelerate the healing processes with reliable biosafety. This work proposes living cell invasiveness as a criterion for antibacterial theranostic materials and provides important enlightenment for the design of antibacterial theranostic materials.

Keywords:  Gram-positive bacteria; aggregation-induced emission; alkyl chain engineering; antibacterial theranostic agent; drug-resistant bacteria; living cell invasiveness; phosphindole oxide

DOI:  https://doi.org/10.1021/acsnano.2c01721
Nano Lett. 2022 Jul 31.

Cellulose-Based Cryogel Microspheres with Nanoporous and Controllable Wrinkled Morphologies for Rapid Hemostasis.

Zhan Xu, Weiguo Tian, Chaojun Wen, Xin Ji, Huailing Diao, Yuzhen Hou, Jialiang Fan, Zongxi Liu, Tianjiao Ji, Feifei Sun, Decheng Wu, Jun Zhang.

  First-aid hemostatic agents for acute bleeding can save lives in emergency situations. However, rapid hemostasis remains challenging when uncontrolled hemorrhage occurs on lethal noncompressible and irregular wounds. Herein, cellulose-based cryogel microspheres with deliberately customized micromorphologies for ultrafast water transportation and diffusion, including the shark skin riblet-inspired wrinkled surface with low fluid drag and the hydrophilic nanoporous 3D networks, are developed to deal with the acute noncompressible bleeding within seconds. These cryogel microspheres can rapidly absorb a large amount of blood over 6 times their own weight in 10 s and form a robust barrier to seal a bleeding wound without applying pressure. Remarkably, massive bleeding from a cardiac penetrating hole is effectively stopped using the microspheres within 20 s and no blood leakage is observed after 30 min. Additionally, these microspheres could be readily removed without rebleeding and capillary thrombus, which is highly favorable to rapid hemostasis in emergency rescue.

Keywords:  cellulose; cryogel microspheres; noncompressible bleeding; rapid hemostasis

DOI:  https://doi.org/10.1021/acs.nanolett.2c02144
Nat Commun. 2022 Aug 05. 13(1): 4568

Multifunctional synthetic nano-chaperone for peptide folding and intracellular delivery.

Il-Soo Park, Seongchan Kim, Yeajee Yim, Ginam Park, Jinahn Choi, Cheolhee Won, Dal-Hee Min.

Artificial, synthetic chaperones have attracted much attention in biomedical research due to their ability to control the folding of proteins and peptides. Here, we report bio-inspired multifunctional porous nanoparticles to modulate proper folding and intracellular delivery of therapeutic α-helical peptide. The Synthetic Nano-Chaperone for Peptide (SNCP) based on porous nanoparticles provides an internal hydrophobic environment which contributes in stabilizing secondary structure of encapsulated α-helical peptides due to the hydrophobic internal environments. In addition, SNCP with optimized inner surface modification not only improves thermal stability for α-helical peptide but also supports the peptide stapling methods in situ, serving as a nanoreactor. Then, SNCP subsequently delivers the stabilized therapeutic α-helical peptides into cancer cells, resulting in high therapeutic efficacy. SNCP improves cellular uptake and bioavailability of the anti-cancer peptide, so the cancer growth is effectively inhibited in vivo. These data indicate that the bio-inspired SNCP system combining nanoreactor and delivery carrier could provide a strategy to expedite the development of peptide therapeutics by overcoming existing drawbacks of α-helical peptides as drug candidates.

DOI: https://doi.org/10.1038/s41467-022-32268-2
Nat Commun. 2022 Aug 05. 13(1): 4551

Intrinsically fluorescent polyureas toward conformation-assisted metamorphosis, discoloration and intracellular drug delivery.

Yeqiang Zhou, Fan Fan, Jinling Zhao, Zhaoding Wang, Rui Wang, Yi Zheng, Hang Liu, Chuan Peng, Jianshu Li, Hong Tan, Qiang Fu, Mingming Ding.

Peptidomimetic polymers have attracted increasing interest because of the advantages of facile synthesis, high molecular tunability, resistance to degradation, and low immunogenicity. However, the presence of non-native linkages compromises their ability to form higher ordered structures and protein-inspired functions. Here we report a class of amino acid-constructed polyureas with molecular weight- and solvent-dependent helical and sheet-like conformations as well as green fluorescent protein-mimic autofluorescence with aggregation-induced emission characteristics. The copolymers self-assemble into vesicles and nanotubes and exhibit H-bonding-mediated metamorphosis and discoloration behaviors. We show that these polymeric vehicles with ultrahigh stability, superfast responsivity and conformation-assisted cell internalization efficiency could act as an "on-off" switchable nanocarrier for specific intracellular drug delivery and effective cancer theranosis in vitro and in vivo. This work provides insights into the folding and hierarchical assembly of biomacromolecules, and a new generation of bioresponsive polymers and nonconventional luminescent aliphatic materials for diverse applications.

DOI: https://doi.org/10.1038/s41467-022-32053-1
ACS Nano. 2022 Aug 03.

Bacterial Growth-Induced Tobramycin Smart Release Self-Healing Hydrogel for Pseudomonas aeruginosa-Infected Burn Wound Healing.

Ying Huang, Lei Mu, Xin Zhao, Yong Han, Baolin Guo.

  Burns are a common health problem worldwide and are highly susceptible to bacterial infections that are difficult to handle with ordinary wound dressings. Therefore, burn wound repair is extremely challenging in clinical practice. Herein, a series of self-healing hydrogels (QCS/OD/TOB/PPY@PDA) with good electrical conductivity and antioxidant activity were prepared on the basis of quaternized chitosan (QCS), oxidized dextran (OD), tobramycin (TOB), and polydopamine-coated polypyrrole nanowires (PPY@PDA NWs). These Schiff base cross-links between the aminoglycoside antibiotic TOB and OD enable TOB to be slowly released and responsive to pH. Interestingly, the acidic substances during the bacteria growth process can induce the on-demand release of TOB, avoiding the abuse of antibiotics. The antibacterial results showed that the QCS/OD/TOB/PPY@PDA9 hydrogel could kill high concentrations of Pseudomonas aeruginosa (PA), Staphylococcus aureus, and Escherichia coli in a short time and showed a bactericidal effect for up to 11 days in an agar plate diffusion experiment, while showing good in vivo antibacterial activity. Excellent and long-lasting antibacterial properties make it suitable for severely infected wounds. Furthermore, the incorporation of PPY@PDA endowed the hydrogel with near-infrared (NIR) irradiation assisted bactericidal activity of drug-resistant bacteria, conductivity, and antioxidant activity. Most importantly, in the PA-infected burn wound model, the QCS/OD/TOB/PPY@PDA9 hydrogel more effectively controlled wound inflammation levels and promoted collagen deposition, vascular generation, and earlier wound closure compared to Tegaderm dressings. Therefore, the TOB smart release hydrogels with on-demand delivery are extremely advantageous for bacterial-infected burn wound healing.

Keywords:  antibacterial infection; antibiotic smart release hydrogel; bacterial growth response; burn wound healing; on-demand delivery

DOI:  https://doi.org/10.1021/acsnano.2c05557
Nat Commun. 2022 Aug 02. 13(1): 4468

Spatiotemporal control of engineered bacteria to express interferon-γ by focused ultrasound for tumor immunotherapy.

Yuhao Chen, Meng Du, Zhen Yuan, Zhiyi Chen, Fei Yan.

Bacteria-based tumor therapy has recently attracted wide attentions due to its unique capability in targeting tumors and preferentially colonizing the core area of the tumor. Various therapeutic genes are also harbored into these engineering bacteria to enhance their anti-tumor efficacy. However, it is difficult to spatiotemporally control the expression of these inserted genes in the tumor site. Here, we engineer an ultrasound-responsive bacterium (URB) which can induce the expression of exogenous genes in an ultrasound-controllable manner. Owing to the advantage of ultrasound in tissue penetration, an acoustic remote control of bacterial gene expression can be realized by designing a temperature-actuated genetic switch. Cytokine interferon-γ (IFN-γ), an important immune regulatory molecule that plays a significant role in tumor immunotherapy, is used to test the system. Our results show that brief hyperthermia induced by focused ultrasound promotes the expression of IFN-γ gene, improving anti-tumor efficacy of URB in vitro and in vivo. Our study provides an alternative strategy for bacteria-mediated tumor immunotherapy.

DOI: https://doi.org/10.1038/s41467-022-31932-x
Nat Commun. 2022 Aug 03. 13(1): 4496

Dynamic actuation enhances transport and extends therapeutic lifespan in an implantable drug delivery platform.

William Whyte, Debkalpa Goswami, Sophie X Wang, Yiling Fan, Niamh A Ward, Ruth E Levey, Rachel Beatty, Scott T Robinson, Declan Sheppard, Raymond O'Connor, David S Monahan, Lesley Trask, Keegan L Mendez, Claudia E Varela, Markus A Horvath, Robert Wylie, Joanne O'Dwyer, Daniel A Domingo-Lopez, Arielle S Rothman, Garry P Duffy, Eimear B Dolan, Ellen T Roche.

Fibrous capsule (FC) formation, secondary to the foreign body response (FBR), impedes molecular transport and is detrimental to the long-term efficacy of implantable drug delivery devices, especially when tunable, temporal control is necessary. We report the development of an implantable mechanotherapeutic drug delivery platform to mitigate and overcome this host immune response using two distinct, yet synergistic soft robotic strategies. Firstly, daily intermittent actuation (cycling at 1 Hz for 5 minutes every 12 hours) preserves long-term, rapid delivery of a model drug (insulin) over 8 weeks of implantation, by mediating local immunomodulation of the cellular FBR and inducing multiphasic temporal FC changes. Secondly, actuation-mediated rapid release of therapy can enhance mass transport and therapeutic effect with tunable, temporal control. In a step towards clinical translation, we utilise a minimally invasive percutaneous approach to implant a scaled-up device in a human cadaveric model. Our soft actuatable platform has potential clinical utility for a variety of indications where transport is affected by fibrosis, such as the management of type 1 diabetes.

DOI: https://doi.org/10.1038/s41467-022-32147-w
Nano Lett. 2022 Aug 04.

Programmable Bispecific Nano-immunoengager That Captures T Cells and Reprograms Tumor Microenvironment.

Lu Zhang, Ruonan Bo, Yi Wu, Longmeng Li, Zheng Zhu, Ai-Hong Ma, Wenwu Xiao, Yanyu Huang, Tatu Rojalin, Xingbin Yin, Chunping Mao, Fengyi Wang, Yongheng Wang, Hongyong Zhang, Kelmen E Low, Kiana Lee, Yousif Ajena, Di Jing, Dalin Zhang, Christopher M Baehr, Ruiwu Liu, Lei Wang, Yuanpei Li, Kit S Lam.

  Immune checkpoint blockade (ICB) therapy has revolutionized clinical oncology. However, the efficacy of ICB therapy is limited by the ineffective infiltration of T effector (Teff) cells to tumors and the immunosuppressive tumor microenvironment (TME). Here, we report a programmable tumor cells/Teff cells bispecific nano-immunoengager (NIE) that can circumvent these limitations to improve ICB therapy. The peptidic nanoparticles (NIE-NPs) bind tumor cell surface α3β1 integrin and undergo in situ transformation into nanofibrillar network nanofibers (NIE-NFs). The prolonged retained nanofibrillar network at the TME captures Teff cells via the activatable α4β1 integrin ligand and allows sustained release of resiquimod for immunomodulation. This bispecific NIE eliminates syngeneic 4T1 breast cancer and Lewis lung cancer models in mice, when given together with anti-PD-1 antibody. The in vivo structural transformation-based supramolecular bispecific NIE represents an innovative class of programmable receptor-mediated targeted immunotherapeutics to greatly enhance ICB therapy against cancers.

Keywords:  T cells capture; fibrillar transformation; immune checkpoint blockade (ICB) therapy; nano-immuno-engager

DOI:  https://doi.org/10.1021/acs.nanolett.2c00582
ACS Appl Mater Interfaces. 2022 Aug 02.

Protein Cages Engineered for Interaction-Driven Selective Encapsulation of Biomolecules.

Yeolin Lee, Minjae Kim, Jin Young Kang, Yongwon Jung.

  Hollow protein cages have become attractive drug delivery vehicles with high biocompatibility and precise functional/structural manipulability. However, difficulties in effective cargo loading inside the cages have been limiting further development of protein cage-based drug carriers. Here, we developed a specific interaction-driven encapsulation and cellular delivery strategy for various biomolecules by engineering a porous protein cage. The computationally designed hyperstable mi3 protein cage was circularly permuted to fuse the cancer targeting RGD tripeptide to the cage surface and SpyTag (ST), which forms a covalent bond with SpyCatcher (SC), to the cage inner cavity. SC-fused proteins with different sizes and charges could be stably and actively encapsulated in the engineered nanocage via the ST/SC reaction. Cargo protein encapsulation inside the cage was directly confirmed by cryo-electron microscopy (EM) structure determination. In addition, SC-fused monomeric avidin was added to the nanocage to encapsulate various biotinylated (nonprotein) cargos such as oligonucleotides and the anticancer drug doxorubicin. All cargo molecules loaded onto the engineered mi3 were effectively delivered to cells. This work introduces a highly versatile cargo loading/delivery strategy, where loading/delivery interactions, cargo molecules, and cell targeting moieties can be further varied for optimal cellular drug delivery.

Keywords:  biomolecule delivery; cage interface engineering; cargo encapsulation; cell targeting; protein cage

DOI:  https://doi.org/10.1021/acsami.2c06924
Nat Commun. 2022 Aug 04. 13(1): 4541

Generating experimentally unrelated target molecule-binding highly functionalized nucleic-acid polymers using machine learning.

Jonathan C Chen, Jonathan P Chen, Max W Shen, Michael Wornow, Minwoo Bae, Wei-Hsi Yeh, Alvin Hsu, David R Liu.

In vitro selection queries large combinatorial libraries for sequence-defined polymers with target binding and reaction catalysis activity. While the total sequence space of these libraries can extend beyond 1022 sequences, practical considerations limit starting sequences to ≤~1015 distinct molecules. Selection-induced sequence convergence and limited sequencing depth further constrain experimentally observable sequence space. To address these limitations, we integrate experimental and machine learning approaches to explore regions of sequence space unrelated to experimentally derived variants. We perform in vitro selections to discover highly side-chain-functionalized nucleic acid polymers (HFNAPs) with potent affinities for a target small molecule (daunomycin KD = 5-65 nM). We then use the selection data to train a conditional variational autoencoder (CVAE) machine learning model to generate diverse and unique HFNAP sequences with high daunomycin affinities (KD = 9-26 nM), even though they are unrelated in sequence to experimental polymers. Coupling in vitro selection with a machine learning model thus enables direct generation of active variants, demonstrating a new approach to the discovery of functional biopolymers.

DOI: https://doi.org/10.1038/s41467-022-31955-4