Author: Christian Cobaugh, CEO, Genetic Medicine Division at Alloy Therapeutics
RNA therapeutics are moving from promise to reality. By operating upstream of protein targets and closer to the genetic root causes of many diseases, RNA medicines often offer treatment approaches that differ fundamentally from conventional small molecules or biologics. Antisense molecules have evolved from conceptual tools in the late 1970s into a clinically validated therapeutic class, with more than 25 approved oligonucleotide medicines spanning RNase H–mediated antisense, splice modulation, and RNA interference.
These advances have been driven primarily by medicinal chemistry innovations that improved nuclease stability, hybridization affinity, and pharmacokinetics. While transformative, these chemical advances also introduced new trade-offs, including extensive protein binding, immune activation linked to end accessibility, and potency that often requires relatively high systemic exposure. The next leap in RNA therapeutics will not come from chemistry alone. It will come from structural engineering.
Through our partnership with Dr. Sudhir Agrawal, Alloy’s AntiClastic™ Cyclic Oligonucleotide technology introduces conformationally constrained, transiently circular molecules designed to enhance potency while reducing inflammatory signaling compared to first-generation linear oligonucleotides. Because AntiClastics use the same clinically validated nucleotide chemistries as existing RNA medicines, manufacturing remains compatible with established processes and best practices. The Alloy AntiClastic platform of cyclic RNA medicines represents a step-change in functional performance, with the potential to unlock targets and mechanisms that have been difficult to address using legacy linear oligos, siRNA, and other nucleic acid modalities.
Why Are Linear ASO Therapies Limited?
ASO technology is a well-established drug platform, with approximately 15 product approvals across gapmers and morpholinos. The class is expected to grow substantially in the coming years. However, many preclinical programs and several clinical candidates have failed due to insufficient efficacy, off-target toxicities (including nephrotoxicity, hepatotoxicity, and neurotoxicity), and narrow therapeutic indices driven in part by limited potency and inflammatory responses.
These challenges are multifactorial. They can arise from extensive protein binding associated with certain backbone chemistries, immune activation linked to exposed 5′ ends and specific sequence motifs, susceptibility to nuclease-mediated degradation, and suboptimal target engagement. While medicinal chemistry has addressed many of these factors, architectural constraints remain.
How Do AntiClastic Cyclic Oligonucleotides Provide a Step Change in Performance?
Unlike conventional linear ASOs, AntiClastic molecules incorporate an optimized molecular architecture that works in concert with carefully selected sequence chemistry and delivery strategies. Intramolecular circularization through Watson–Crick base pairing transiently protects the oligonucleotide ends during delivery and cellular uptake. By reducing exposure of 5′ ends, innate immune recognition may be attenuated, and excessive protein interactions may be modulated.
AntiClastic structures are thermodynamically programmed to open intracellularly, combining structural protection with functional release. Once inside the cell, the cyclic structure is designed to open upon engagement with the target RNA sequence. The intramolecular cyclizing interactions are thermodynamically weaker than the duplex formed between the functional domain and its target, ensuring that cyclization does not interfere with productive target binding. In preclinical systems, AntiClastic ASOs have demonstrated enhanced potency, improved resistance to nuclease degradation, reduced off-target effects, and lower pro-inflammatory signaling compared to matched linear counterparts. Increased potency may be driven by improved functional availability and more efficient RNase H engagement. Importantly, these benefits are achieved using standard, clinically validated nucleic acid chemistries.
Expanding What Is Druggable
ASOs are already highly versatile, capable of mediating the degradation of pre-mRNA, mRNA, and regulatory RNAs, such as lncRNAs, in both the cytoplasm and the nucleus. They can modulate pre-mRNA splicing to drive exon skipping or inclusion and have been adapted for ADAR-mediated RNA editing. AntiClastic architecture is designed to support and potentially enhance performance across these applications, enabling more precise modulation of gene expression with an improved therapeutic index relative to conventional gapmers and morpholinos.
Alloy has extended the AntiClastic concept beyond antisense. By incorporating cyclizing domains in a prodrug-like format, the technology has been applied to siRNA and sgRNA for CRISPR/Cas gene editing, delivering benefits similar to those observed with cyclic ASOs. AntiClastic siRNAs are designed to reduce off-target effects and inflammatory signaling without introducing additional modifications, while preserving the potency and durability associated with RNA interference. In preclinical studies, cyclic siRNAs demonstrated enhanced cellular uptake and improved knockdown activity compared with linear siRNAs, both in vitro and in animal models. For gene editing applications, cyclic guide RNA architectures offer additional structural control, potentially improving the functional duration and specificity of RNA-guided nucleases.
How Drug Developers Benefit from the AntiClastic Platform
The AntiClastic™ Cyclic Oligonucleotide platform converts linear RNA medicines into IP-protected, configurable cyclic architectures designed to deliver nuclease-resistant therapeutics with greater potency, durability, specificity, and in vivo efficacy while reducing immunostimulation. These structures extend beyond traditional chemical modification strategies and introduce architectural differentiation into RNA drug design.
Proprietary AntiClastic architectures expand the genetic medicine toolbox across RNA degradation, splice modulation, gene editing, and related modalities. Development of clinic-ready oligonucleotide assets is accelerated by Alloy’s integrated capabilities, from AI/ML-driven sequence design using our Oligonucleotide Design Studio through preclinical validation. Partner programs are de-risked through technology licensing, platform access, and coordinated discovery and early development services. For partners, this means differentiated IP positioning, enhanced performance potential, and accelerated timelines to IND.
Alloy Genetic Medicines is committed to advancing breakthrough therapies with clinically meaningful target product profiles and improved therapeutic indices. By designing, building, testing, and refining discovery candidates in partnership with pharmaceutical innovators, biotechs, and academic laboratories, we aim to democratize access to advanced RNA medicines and accelerate the translation of transformational therapies to patients.
Learn more:
Agrawal, S. The Evolution of Antisense Oligonucleotide Chemistry—A Personal Journey. Biomedicines 2021, 9, 503.
Agrawal, S. Transient Cyclic Structured Oligonucleotide Designs for Therapeutic Applications. Current Protocols, 2026.
Antisense oligonucleotides
Antisense oligonucleotides (ASOs) are an exciting and growing therapeutic modality that provides precise
Antisense oligonucleotides (ASOs) are an exciting and growing therapeutic modality that provides precise on-target effects with showing remarkably versatililty towards a variety of druggable targets. The precise on-target effects are driven by the simplicity of programming or designing the molecules due to the basic rules that follow Watson-Crick base pairing.
The versatile nature is exemplified by the growing number of ASO mechansims, including cytoplasmic and nuclear RNase-H mediated decay of mRNA and pre-mRNA, splice modulation of pre-mRNA, and ADAR-mediated RNA editing. By operating upstream of protein targets and closer to the root cause of most diseases at the genetic level, RNA medicines better manage disease progression instead of targeting complex, cascading downstream pathways and symptoms.
However, traditional ASOs such as gapmers and morpholinos suffer from deficient potency, stability, and off-target profiles. Their therapeutic indices are affected by their stimulation of undesired inflammation through activation of pattern recognition receptor (PRRs). ASO medicines re-engineered or discovered de novo using Alloy’s AntiClastic™ Cyclic RNA platform deliver conformationally constrained, transiently circular ASOs that result in higher potency and lower inflammatory effects than first-generation linear oligonucleotides. Since AntiClastics use the same chemistry as all other RNA medicines, manufacturing is identical as with gapmers and morpholinos and they can be conjugated to targeting shuttles and other targeting domains to achieve programmable delivery to target-rich organs and cell types.
The Alloy AntiClastic platform of cyclic RNA medicines is a step-change in functional performance, unlocking targets and mechanisms that legacy linear oligos, siRNA, and other nucleic acid medicines cannot reach.
Why are linear ASO therapies limited?
The ASO technology is a well-established drug substance platform with approximately 15 product approvals spread across gapmers and morpholinos. This class of medicines is expected to grow substantially in the coming years in terms of approvals and market share. However, there have been many preclinical and several clinical failures due to insufficient efficacy, off-target toxicity (e.g. nephrotoxicity, hepatotoxicity, and even neurotoxicity), and a poor therapeutic index driven in part by weak potency and high levels of inflammation. (1)
The root causes of these failures is tied to the presence of 5’ ends within the molecules that are potent activators of PRRs, instability due to nuclease-mediated degradation, and poor on-target potency. (2) Alloy’s next-generation cyclic RNA structures (AntiClastics) improve upon first-generation ASOs by eliminating 5’ ends to reduce PRR activation and by base-pairing the 3’ ends to enhance stability and bioavailability.
How do AntiClastic cyclic provide a step change in ASO performance?
Unlike linear ASOs that contain a 5’ and 3’ end, AntiClastic ASOs are made using both standard and inverted phosphoroamidites in traditional linkage and sugar modifications and have either two 3’ ends or two 5’ ends. The functional domain (FD) contains an innovative arrangement of RNA and DNA that hybridizes the molecular target with higher potency than the typical 5-10-5 arrangement of gapmers.
The inverted cyclization domain (CD), which is complementary to the 3’ end of the FD, is connected to the FD through a 5’-5’ linkage so that the free end of the CD is 3’. The elimination of any 5’ end results in a molecule that has greatly reduced pro-inflammatory properties while the base pairing between the 3’ end of the CD and the 3’ end of the FD results in a transiently cyclic RNA molecule(1,2,7-9). The cyclizing interactions are relatively weak in comparison to the Tm between the functional domain and its molecular target, which means that the cyclization does not interfere with the target engagement and ultimately the functionality of the molecule.
Once an AntiClastic ASO is released into the cytoplasm or nucleoplasm, the base pairing between the CD and FD that holds the molecules in their cyclic structure is overcome by the base pairing between the FD and molecular target. The molecule opens up into a linear structure while the highly potent FD hybridizes with the target RNA to form a duplex that is more thermodynamically favored than the intramolecular cyclic structure (10).
AntiClastic ASO are more potent, more resistant to nuclease degradation, have lower off-target effects, and are less pro-inflammatory than their linear counterparts. The increase in potency results from enhanced endosomal escape and RNase H efficiency. This is all achieved with standard, clinically validated nucleic acid chemistry.
What are Anticlastic™ ASOs?
AntiClastic ASO are just the latest innovation from the mind of Sudhir Agrawal, Ph.D., also the inventor of gapmers ASOs. Dr. Agrawal recently shared more details of this innovation in an invited review in Current Protocols (10).
Key advantages of Alloy’s AntiClastic platform’s ASOs include:
- Precise AI designed functional domains incorporated into cyclic molecules that result in enhanced on-target effects and potency
- Functional domains with more precise RNaseH mediated cleavage due to the novel RNA and DNA arrangement
- Improvement of potency by up to 30-fold compared to standard gapmer ASOs against a wide variety of therapeutic targets
- Enhanced cellular uptake and endosomal escape due to the transiently cyclic shape
- 3’ ends with improved nuclease stability
- Minimal inflammatory responses and greater therapeutic index due to reduced engagement of off-target RNA and PRRs
- Ready for delivery as antibody oligonucleotide conjugates or through other shuttles
- Straightforward and scalable manufacturing using conventional oligonucleotide methods and the same building blocks as clinically validated and established ASOs
How can the AntiClastic cyclic oligonucleotides expand what is druggable?
ASOs are already remarkably versatile with the ability to mediate degradation of targeted RNAs including pre-mRNA, mRNA, and regulatory RNAs such as lncRNAs in the cytoplasm and nucleus. This class of molecules is also able to modulate the splicing of pre-mRNA resulting in exon skipping or exon inculsion (1,7). More recently, ASOs have also been used for adenosine deaminase acting on RNA (ADAR)-based RNA editing. The AntiClastic technology demonstrates benefits for all of these applications to finely tuning the expression of desired proteins and regulatory RNAs to take control of diseases with a better therapeutic index than with standard gapmers and morpholinos (10).
Alloy has applied the AntiClastic technology to more than just ASOs by adding CDs to siRNA for RNAi and to sgRNA for CRISPR/Cas gene-editing with benefits similar to those seen with cyclic ASOs (11). siRNA therapies bind to and silence target mRNAs that are involved in disease progression but are limited based on off-target effects and toxic chemical modifications.
The AntiClastic versions of siRNA show improved off-target effects and reduced pro-inflammatory effects without adding toxic sugar chemical modifications while maintaining the legendary potency and durability of effects of traditional siRNA (6,7). In a recent study, anticlastic siRNAs showed greater cellular uptake and improved knockdown activity compared to linear siRNA, both in vitro and in mice (6).
For gene editing therapies, adopting a cyclic structure for the guide RNA allows for optimized architectures for RNA-guided nucleases such as CRISPR/Cas nucleases and editors.10 The inherent properties of cyclic sgRNAs provide for improved functional period and control. It is also worth noting that cyclic ASOs with 3’-3’ linkages have the potential for use as immunostimulatory agents (e.g., act as PAMPs) with applications in immunotherapy(10).
How can drug developers benefit from Alloy’s AntiClastic platform?
The AntiClastic™ Cyclic RNA platform converts linear RNA medicines into IP-protected, configurable cyclic architectures, delivering nuclease-resistant therapeutics with greater potency, durability, specificity, and in vivo stability while reducing immunostimulation. These new structures go beyond traditional chemical modifications. Proprietary AntiClastic cyclic architectures unlock therapeutic applications with improved safety profiles for the genetic medicine’s toolbox, including targeted RNA degradation, splice modulation, gene editing and regulation, DNA modulation, ADAR editing, and gene expression modulation.
Development of novel, clinic-ready oligonucleotide assets is accelerated by leveraging Alloy’s services from sequence design (using the AI/ML-driven RNA Design Studio) all the way through preclincal testing. Partner programs are de-risked by combining technology licensing, platform access, and integrated discovery and early development services.
High-performing oligonucleotides enabled by the AntiClastic platform are translated into clinical candidates that sponsors can trust through:
- AI-driven sequence design across cyclic ASO, siRNA, and sgRNA modalities
- Discovery and screening of potent oligonucleotides and antibody-based shuttles using internal antibody discovery platforms to achieve programmable delivery to target-rich organs and specific cell types
- Process development using a quality-by-design (QbD) approach from the earliest stages
- Robust analytical method development and qualification
- Rapid, in-house research-grade material manufacturing
- Structure-function understanding to support IND-enabling packages
- Cellular model development and mechanistic validation
- Animal model development, screening, and candidate profiling
- Iterative design-make-test-learn cycles to accelerate lead optimization, with rapid identification of the top 50 candidates in just two months
- Technical transfer packages that de-risk downstream CMC
- Collaborative planning for clinical readiness
- Accelerated development timelines to IND filing of as little as 18 months for naked ASOs
Alloy Genetic Medicines aspires to improve the health of patients in need of breakthrough therapies with more convenient target product profiles and molecules with a better therapeutic index. By designing, building, testing, and refining discovery candidates in partnership with pharmaceutical innovators, biotechs, and academic laboratories, we are democratizing access to innovative RNA medicnes and helping bring transformational and promising RNA candidates to the clinic and patients in need.
References
- Sudhir Agrawal and Quiyan Zhao, Antisense Therapeutics, Current Opinion in Chemical Biology 1998, 2:519-528.
- Peter T. Rowlet, Barbara A. Kosciolek, and Eric T. Kool, “Circiular Antisense Oligonucloetides Inhibit Growth of Chronic Myeloid Leukemia Cells,” Molecular Medicine 5: 693-700 (1999).
- S. Agrawal, “Considerations for creating the next generation RNA therapeutics: Oligonucleotide chemistry and Innate immune responses to nucleic acids,” Nucleic Acid Therapeutics, 2024, 37-51
- Sudhir Agrawal and Ekambar R. Kandimalla, “Intratumoral immunotherapy: activation of nucleic acid sensing pattern recognition receptors,” Immunooncology Technol. 2019 Oct; 3: 15-23.
- S. Agrawal, O.K. Rustagi, and D. R. Shaw, “Novel enzymatic and immunological responses to oligonucleotides,” Toxico Lett. 1995 Dec; 82083:431-4
- Q. Zhao, J. Temsamani, P.L. Iadiarola, Z. Jiang, and S. Agrawal, “Effect of different chemically modified oligodeoxynucleotides on immune stimulation,” Biochem Pharmacol. 1996 Jan 26;51(2): 173-82
- Agrawal, S. The Evolution of Antisense Oligonucleotide Chemistry—A Personal Journey. Biomedicines 2021, 9, 503. https://doi.org/10.3390/biomedicines9050503
- Kenji Hagiwara et al., “Development of Prodrug Type Circular siRNA for In Vivo Knockdown by Systemic Administration,” Nucleic Acid Ther. 2020 Dec;30(6):346-364. doi: 10.1089/nat.2020.0894.
- Hartmut Jahns et al., “Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing, ”Nucleic Acids Research, 202. https://doi.org/10.1093/nar/gkab724
- Sudhir Agrawal, “Transient Cyclic Structured Oligonucleotide Designs for Therapeutic Applications,” Curr Protoc. 2026 Feb;6(2):e70319. doi: 10.1002/cpz1.70319.
- Sudhir Agrawal, CYCLIC STRUCTURED OLIGONUCLEOTIDES AS THERAPEUTIC AGENTS, WO/2023/049275, March 30, 2023.
- Sudhir Agrawal, DELIVERY OF RNA THERAPEUTICS USING CIRCULAR PRODRUG NUCLEIC ACIDS, WO/2024/197139, September 26, 2024.
- Sudhir Agrawal, DELIVERY OF RNA THERAPEUTICS USING RING-SHAPED NUCLEIC ACIDS, WO/2024/263891, December 26, 2024.